using Images folder by default\\\".format(\\n self.user[\\\"Video\\\"], self.savePathJoin(\\\"Images\\\")\\n )\\n )\\n elif not self.img_exist and not os.path.isfile(self.user[\\\"Video\\\"]):\\n stop_calculation = True\\n errors[\\\"Critical\\\"].append(\\n (\\n \\\"Images folder {0} and video file {1} don't exist -> Stopping run\\\".format(\\n self.savePathJoin(\\\"Images\\\"), self.user[\\\"Video\\\"]\\n )\\n )\\n )\\n\\n # Check video file\\n if self.user[\\\"Video\\\"] != \\\"\\\" and not os.path.isfile(self.user[\\\"Video\\\"]):\\n if os.path.exists(self.savePathJoin(\\\"Images\\\")):\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Video file {0} doesn't exist -> Using images in the Images folder instead\\\".format(\\n self.user[\\\"Video\\\"]\\n )\\n )\\n )\\n else:\\n stop_calculation = True\\n errors[\\\"Critical\\\"].append(\\n (\\n \\\"Images folder {0} and video file {1} don't exist -> Stopping run\\\".format(\\n self.savePathJoin(\\\"Images\\\"), self.user[\\\"Video\\\"]\\n )\\n )\\n )\\n elif os.path.isfile(self.user[\\\"Video\\\"]) and os.path.exists(\\n self.savePathJoin(\\\"Images\\\")\\n ):\\n pass\\n\\n # Check optical flow\\n if self.of_exist and not os.path.exists(self.savePathJoin(\\\"Of\\\")):\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Optical flow folder {0} doesn't exist -> Recalculating optical flow\\\".format(\\n self.savePathJoin(\\\"Of\\\")\\n )\\n )\\n )\\n error_types.append(\\\"NoOf\\\")\\n elif self.of_exist:\\n of_images = len(listDirectory(self.savePathJoin(\\\"Of\\\"), extension=\\\"png\\\"))\\n if of_images != ori_images - 1 and ori_images != 0:\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Optical flow image number {0} doesn't match video image number {1} - 1 -> Recalculating optical flow\\\".format(\\n of_images, ori_images\\n )\\n )\\n )\\n error_types.append(\\\"NoOf\\\")\\n\\n # Check backward optical flow\\n if self.back_of_exist and not os.path.exists(self.savePathJoin(\\\"Back_Of\\\")):\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Backward optical flow folder {0} doesn't exist -> Recalculating backward optical flow\\\".format(\\n self.savePathJoin(\\\"Back_Of\\\")\\n )\\n )\\n )\\n error_types.append(\\\"NoOf\\\")\\n elif self.back_of_exist:\\n back_of_images = len(\\n listDirectory(self.savePathJoin(\\\"Back_Of\\\"), extension=\\\"png\\\")\\n )\\n if back_of_images != of_images:\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Backward optical flow image number {0} doesn't match optical flow image number {1} -> Recalculating backward optical flow\\\".format(\\n back_of_images, of_images\\n )\\n )\\n )\\n error_types.append(\\\"NoOf\\\")\\n\\n # Check depth estimation\\n if self.depth_exist and not os.path.exists(self.savePathJoin(\\\"Depth\\\")):\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Depth folder {0} doesn't exist -> Recalculating depth\\\".format(\\n self.savePathJoin(\\\"Depth\\\")\\n )\\n )\\n )\\n error_types.append(\\\"NoDepth\\\")\\n elif self.depth_exist:\\n depth_images = len(\\n listDirectory(self.savePathJoin(\\\"Depth\\\"), extension=\\\"png\\\")\\n )\\n if depth_images != ori_images and ori_images != 0:\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Depth image number {0} doesn't match video image number {1} -> Recalculating depth\\\".format(\\n depth_images, ori_images\\n )\\n )\\n )\\n error_types.append(\\\"NoDepth\\\")\\n\\n # Check ground truth\\n if self.gt_exist and not os.path.isfile(self.user[\\\"GT\\\"]):\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Ground Truth file {0} doesn't exist -> File won't be used\\\".format(\\n self.user[\\\"GT\\\"]\\n )\\n )\\n )\\n error_types.append(\\\"NoGT\\\")\\n\\n # Check super pixel labels\\n if (\\n self.super_pixel_method != \\\"\\\"\\n and os.path.exists(\\n os.path.join(self.savePathJoin(\\\"Super_Pixel\\\"), self.super_pixel_method)\\n )\\n and ori_images != 0\\n and len(\\n listDirectory(\\n os.path.join(\\n self.savePathJoin(\\\"Super_Pixel\\\"), self.super_pixel_method\\n ),\\n extension=\\\".npy\\\",\\n )\\n )\\n != ori_images\\n ):\\n errors[\\\"Info\\\"].append(\\n (\\n \\\"Super pixel label number {0} doesn't match image number {1} -> Recalculating super pixel labels\\\".format(\\n len(\\n listDirectory(\\n os.path.join(\\n self.savePathJoin(\\\"Super_Pixel\\\"),\\n self.super_pixel_method,\\n ),\\n extension=\\\".npy\\\",\\n )\\n ),\\n ori_images,\\n )\\n )\\n )\\n error_types.append(\\\"LabelError\\\")\\n\\n # Check object detection\\n if self.ui.c_object_detection.isChecked() and os.path.exists(\\n self.savePathJoin(\\\"ObjectDetection\\\")\\n ):\\n if (\\n len(\\n listDirectory(\\n self.savePathJoin(\\\"ObjectDetection\\\"), extension=\\\".png\\\"\\n )\\n )\\n != ori_images\\n ):\\n errors[\\\"Info\\\"].append(\\n \\\"Object Detection image number {0} doesn't match image number of video {1} -> Recalculating object detection\\\".format(\\n len(\\n listDirectory(\\n self.savePathJoin(\\\"ObjectDetection\\\"), extension=\\\".png\\\"\\n )\\n ),\\n ori_images,\\n )\\n )\\n error_types.append(\\\"ObDetError\\\")\\n elif (\\n len(\\n listDirectory(\\n self.savePathJoin(\\\"ObjectDetection\\\"), extension=\\\".npy\\\"\\n )\\n )\\n != ori_images\\n ):\\n errors[\\\"Info\\\"].append(\\n \\\"Object Detection numpy array number {0} doesn't match image number of video {1} -> Recalculating object detection\\\".format(\\n len(\\n listDirectory(\\n self.savePathJoin(\\\"ObjectDetection\\\"), extension=\\\".npy\\\"\\n )\\n ),\\n ori_images,\\n )\\n )\\n error_types.append(\\\"ObDetError\\\")\\n\\n answer = \\\"\\\"\\n if len(errors[\\\"Info\\\"]) > 0 and len(errors[\\\"Critical\\\"]) == 0:\\n msg = QMessageBox()\\n msg.setIcon(QMessageBox.Information)\\n msg.setText(\\n \\\"Some calculations might not run the way you expect them.\\\\nIn show details check the right side of the arrows to see what will happen.\\\"\\n )\\n msg.setWindowTitle(\\\"Information\\\")\\n all_info = \\\"\\\"\\n for info in errors[\\\"Info\\\"]:\\n all_info += info + \\\"\\\\n\\\\n\\\"\\n msg.setDetailedText(all_info)\\n msg.setStandardButtons(QMessageBox.Ok | QMessageBox.Abort)\\n answer = msg.exec_()\\n elif len(errors[\\\"Critical\\\"]) > 0:\\n msg = QMessageBox()\\n msg.setIcon(QMessageBox.Critical)\\n msg.setText(\\n \\\"Found critical error\\\\nCouldn't start run, see show details for more information\\\"\\n )\\n msg.setWindowTitle(\\\"Critical Error\\\")\\n all_info = \\\"\\\"\\n for info in errors[\\\"Critical\\\"]:\\n all_info += info + \\\"\\\\n\\\"\\n msg.setDetailedText(all_info)\\n msg.setStandardButtons(QMessageBox.Abort)\\n answer = msg.exec_()\\n\\n if answer != int(\\\"0x00040000\\\", 16):\\n for ty in error_types:\\n logging.info(\\\"Solve error: {0}\\\".format(ty))\\n if ty == \\\"NoImage\\\":\\n self.img_exist = False\\n self.of_exist = False\\n self.back_of_exist = False\\n self.depth_exist = False\\n elif ty == \\\"NoOf\\\":\\n self.of_exist = False\\n self.back_of_exist = False\\n elif ty == \\\"NoDepth\\\":\\n self.depth_exist = False\\n elif ty == \\\"NoGT\\\":\\n self.gt_exist = False\\n self.user[\\\"GT\\\"] = \\\"\\\"\\n elif ty == \\\"LabelError\\\":\\n self.create_super_pixel_label = True\\n shutil.rmtree(\\n os.path.join(\\n self.savePathJoin(\\\"Super_Pixel\\\"), self.super_pixel_method\\n )\\n )\\n elif ty == \\\"ObDetError\\\":\\n self.object_detection_dir_exist = False\\n shutil.rmtree(self.savePathJoin(\\\"ObjectDetection\\\"))\\n\\n return answer == int(\\\"0x00040000\\\", 16) or stop_calculation\",\n \"def _checkOutputs(self, outputs, random=False, errorthreshold=0.001):\\n for out in outputs:\\n outFile = os.path.join(self._testDir, self.outputDir, out)\\n fileGoldStd = os.path.join(self.goldDir, out)\\n \\n # Check the expect output file was produced\\n msg = \\\"Missing expected output file:\\\\n output: %s\\\" % outFile\\n self.assertTrue(os.path.exists(outFile), red(msg))\\n \\n if random:\\n print(yellow(\\\"WARNING: %s was created using a random seed, check skipped...\\\" % outFile))\\n else:\\n fnGoldStd = xmippLib.FileName(fileGoldStd)\\n if fnGoldStd.isImage():\\n im1 = xmippLib.Image(fileGoldStd)\\n im2 = xmippLib.Image(outFile)\\n msg = \\\"Images are not equal (+-%f):\\\\n output: %s\\\\n gold: %s\\\" % \\\\\\n (errorthreshold, outFile, fileGoldStd)\\n self.assertTrue(im1.equal(im2, errorthreshold), red(msg))\\n elif fnGoldStd.isMetaData():\\n msg = \\\"MetaDatas are not equal:\\\\n output: %s\\\\n gold: %s\\\" % (outFile, fileGoldStd)\\n self.assertTrue(xmippLib.compareTwoMetadataFiles(outFile, fileGoldStd), red(msg))\\n else:\\n msg = \\\"Files are not equal:\\\\n output: %s\\\\n gold: %s\\\" % (outFile, fileGoldStd)\\n self.assertTrue(xmippLib.compareTwoFiles(outFile, fileGoldStd, 0), red(msg))\",\n \"def collect_errors_and_warnings(self) -> str:\\n # Complete error message\\n message = \\\"----------------ERRORS----------------\\\\n\\\"\\n if self.errors == \\\"\\\":\\n message = \\\"YOUR FILE IS VALIDATED!\\\\n\\\"\\n logger.info(message)\\n else:\\n for error in self.errors.split(\\\"\\\\n\\\"):\\n if error != \\\"\\\":\\n logger.error(error)\\n message += self.errors\\n if self.warnings != \\\"\\\":\\n for warning in self.warnings.split(\\\"\\\\n\\\"):\\n if warning != \\\"\\\":\\n logger.warning(warning)\\n message += \\\"-------------WARNINGS-------------\\\\n\\\" + self.warnings\\n return message\",\n \"def error_check(output_list):\\n #NOTE: Add error messages as you come across them\\n #keys = error messages we are looking for\\n #values = what we log if the key is found\\n known_errors = {\\n \\\"File Not Found\\\":\\\"File was not found\\\",\\n \\\"No such host is known\\\":\\\"Failed to connect to Client\\\"\\n }\\n #Verify the command ran without errors\\n for _line in output_list:\\n for key, value in known_errors.items():\\n if key in _line:\\n log.error(value)\\n return False\\n return True\",\n \"def _go_through_summary_reports(self):\\n\\n for result_file in self.result_files:\\n self.cur_8digit_dir = os.path.split(result_file)[0]\\n try:\\n with open(result_file) as f_in:\\n sum_rep = json.load(f_in)\\n if sum_rep.has_key('Artifacts'):\\n for linked_artifact in sum_rep['Artifacts']:\\n artifact_path = linked_artifact['Path']\\n # For now assume only files are linked (no folders)\\n rel_path_from_results = os.path.join(self.cur_8digit_dir, artifact_path)\\n if os.path.exists(rel_path_from_results):\\n self.files_for_export.append(os.path.join('results',\\n rel_path_from_results))\\n if artifact_path.endswith('.json'):\\n function_tag = artifact_path.replace('.','_').replace('/','_')\\n\\n if hasattr(self, function_tag):\\n getattr(self, function_tag)()\\n except IOError:\\n print '{0} does not exist on this filesystem. I cannot be check for references '\\\\\\n 'to other files.'.format(result_file)\",\n \"def output_main(args):\\n\\t#clean input file (fold and remove escape chars)\\n\\treference = clean_fasta(args.infile)\\n\\tfilterthreshold = args.threshold\\n\\t#look up proper readset using readset module\\n\\treadset = args.readset\\n\\t#if readset is in fasta format, inject fake quality scores\\n\\t\\n\\t#run bwa\\n\\tsamfile = run_bwa(reference, readset)\\n\\t#convert sam to bam file, and sort\\n\\tsortedbam = sam_to_sorted_bam(reference, samfile)\\n\\t#run variant caller freebayes\\n\\tvcffile = run_var_caller(reference, sortedbam)\\n\\t#run hapcut suite\\n\\thapoutfile = run_haplotyper(reference, vcffile, sortedbam, filterthreshold)\\n\\t#convert hapcut output to sequence and gff\\n\\tcalls_to_gff(reference, hapoutfile)\",\n \"def test_main_error_output(runner: CliRunner) -> None:\\n output_random = os.path.join(\\n tempfile.gettempdir(),\\n \\\"\\\".join(secrets.choice(string.hexdigits) for i in range(7)),\\n )\\n\\n with open(output_random, \\\"w\\\") as file:\\n file.write(\\\"This is a test\\\")\\n\\n result = runner.invoke(\\n __main__.main, f\\\"-c tests/clippings-es.txt -o {output_random}\\\"\\n )\\n assert result.exit_code != 0\",\n \"def check_parsing_errors(self, lens: str) -> None:\\n error_files = self.aug.match(\\\"/augeas//error\\\")\\n\\n for path in error_files:\\n # Check to see if it was an error resulting from the use of\\n # the httpd lens\\n lens_path = self.aug.get(path + \\\"/lens\\\")\\n # As aug.get may return null\\n if lens_path and lens in lens_path:\\n msg = (\\n \\\"There has been an error in parsing the file {0} on line {1}: \\\"\\n \\\"{2}\\\".format(\\n # Strip off /augeas/files and /error\\n path[13:len(path) - 6],\\n self.aug.get(path + \\\"/line\\\"),\\n self.aug.get(path + \\\"/message\\\")))\\n raise errors.PluginError(msg)\",\n \"def parse(self, **kwargs):\\n output_filename = self.node.get_option('output_filename')\\n jobname = self.node.get_option('jobname')\\n if jobname is not None:\\n output_filename = \\\"log-\\\" + jobname + \\\".yaml\\\"\\n # Check that folder content is as expected\\n files_retrieved = self.retrieved.list_object_names()\\n files_expected = [output_filename]\\n # Note: set(A) <= set(B) checks whether A is a subset of B\\n if not set(files_expected) <= set(files_retrieved):\\n self.logger.error(\\\"Found files '{}', expected to find '{}'\\\".format(\\n files_retrieved, files_expected))\\n return self.exit_codes.ERROR_MISSING_OUTPUT_FILES\\n\\n # add output file\\n self.logger.info(\\\"Parsing '{}'\\\".format(output_filename))\\n# print(self.retrieved._repository._get_base_folder().get_abs_path(output_filename))\\n output = BigDFTLogfile(self.retrieved._repository._get_base_folder().\\n get_abs_path(output_filename))\\n try:\\n output.store()\\n except ValidationError:\\n self.logger.info(\\\"Impossible to store LogFile - ignoring '{}'\\\".\\n format(output_filename))\\n\\n# with self.retrieved.open(output_filename, 'rb') as handle:\\n# output_node = SinglefileData(file=handle)\\n# output_dict_aiida=orm.Dict(dict=output_dict)\\n# output_dict_aiida.store()\\n# output_log_aiida=BigDFTLogfile(output)\\n self.out('bigdft_logfile', output)\\n\\n return ExitCode(0)\",\n \"def main():\\r\\n# Checking if argument was provided\\r\\n if len(sys.argv) <=1:\\r\\n print_usage()\\r\\n sys.exit(1)\\r\\n \\r\\n for arg in sys.argv:\\r\\n # Checking if help was called\\r\\n if arg == \\\"-h\\\" or arg == \\\"--help\\\":\\r\\n print_usage()\\r\\n sys.exit(1)\\r\\n \\r\\n # Checking for verbose mode \\r\\n if arg == \\\"-v\\\" or arg == \\\"--verbose\\\":\\r\\n global verbose_flag\\r\\n verbose_flag=1\\r\\n\\r\\n # Checking for input file\\r\\n if arg == \\\"-f\\\" or arg == \\\"--file\\\":\\r\\n global default_input_path\\r\\n global default_output_path\\r\\n default_input_path = sys.argv[2]\\r\\n default_output_path=default_input_path[:-4] + \\\"_results.txt\\\"\\r\\n\\r\\n #if arg == \\\"-u\\\" or arg == \\\"--url\\\":\\r\\n # input_url = sys.argv[2]\\r\\n\\t \\r\\n if os.name == \\\"nt\\\":\\r\\n os.system('cls')\\r\\n else:\\r\\n os.system('clear')\\r\\n \\r\\n process_from_file()\",\n \"def run_test(self):\\n\\n # populate *_ps sets\\n self.enter_project_file()\\n\\n # populate *_dir sets\\n self.enter_directories()\\n\\n # The files in the directories makes up the largest possible set of files\\n self.result_files = self.result_files_dir\\n self.design_files = self.design_files_dir\\n self.design_space_files = self.design_space_files_dir\\n self.test_bench_files = self.test_bench_files_dir\\n\\n # populate *_ms sets\\n self.enter_meta_results_file()\\n\\n # populate *_OK sets\\n self.check_analysis_status()\\n\\n df = {'design_files_dir' : list(self.design_files_dir),'design_files_pr' : list(self.design_files_pr),\\n 'design_files_ms' : list(self.design_files_ms), 'design_files_OK' : list(self.design_files_OK)}\\n\\n ds = {'design_space_files_dir' : list(self.design_space_files_dir),\\n 'design_space_files_pr' : list(self.design_space_files_pr)}\\n\\n rs = {'result_files_dir' : list(self.result_files_dir), 'result_files_ms' : list(self.result_files_ms),\\n 'result_files_OK' : list(self.result_files_OK)}\\n\\n tb = {'test_bench_files_dir' : list(self.test_bench_files_dir),\\n 'test_bench_files_ms' : list(self.test_bench_files_ms)}\\n\\n srl = SummaryReportsLinks(self.result_files_dir)\\n\\n lf = {'files_linked_from_sum_reps' : srl.get_files(),\\n 'folders_linked_from_sum_reps' : srl.get_folders()}\\n\\n # 'test_bench_files_pr' : list(self.test_bench_files_pr),\\n \\n json_test = {'design_files' : df, 'design_space_files' : ds, 'result_files' : rs,\\n 'test_bench_files' : tb, 'stat_files' : self.stat_files,\\n 'files_linked_from_sum_reps' : lf}\\n\\n with open('test_run.json','wb') as f_out:\\n json.dump(json_test, f_out, indent=4)\",\n \"def lint_output(tool_source: \\\"ToolSource\\\", lint_ctx: \\\"LintContext\\\"):\\n tool_xml = getattr(tool_source, \\\"xml_tree\\\", None)\\n if tool_xml is None:\\n return\\n profile = tool_source.parse_profile()\\n\\n outputs = tool_xml.findall(\\\"./outputs\\\")\\n # determine node to report for general problems with outputs\\n tool_node = tool_xml.find(\\\"./outputs\\\")\\n if tool_node is None:\\n tool_node = tool_xml.getroot()\\n if len(outputs) == 0:\\n lint_ctx.warn(\\\"Tool contains no outputs section, most tools should produce outputs.\\\", node=tool_node)\\n return\\n if len(outputs) > 1:\\n lint_ctx.warn(\\\"Tool contains multiple output sections, behavior undefined.\\\", node=outputs[1])\\n num_outputs = 0\\n labels = set()\\n names = set()\\n for output in list(outputs[0]):\\n if output.tag is etree.Comment:\\n continue\\n if output.tag not in [\\\"data\\\", \\\"collection\\\"]:\\n lint_ctx.warn(f\\\"Unknown element found in outputs [{output.tag}]\\\", node=output)\\n continue\\n num_outputs += 1\\n if \\\"name\\\" not in output.attrib:\\n lint_ctx.warn(\\\"Tool output doesn't define a name - this is likely a problem.\\\", node=output)\\n # TODO make this an error if there is no discover_datasets / from_work_dir (is this then still a problem)\\n elif not is_valid_cheetah_placeholder(output.attrib[\\\"name\\\"]):\\n lint_ctx.warn(\\n f'Tool output name [{output.attrib[\\\"name\\\"]}] is not a valid Cheetah placeholder.', node=output\\n )\\n\\n name = output.attrib.get(\\\"name\\\")\\n if name is not None:\\n if name in names:\\n lint_ctx.error(f\\\"Tool output [{name}] has duplicated name\\\", node=output)\\n names.add(name)\\n\\n label = output.attrib.get(\\\"label\\\", \\\"${tool.name} on ${on_string}\\\")\\n if label in labels:\\n filter_node = output.find(\\\".//filter\\\")\\n if filter_node is not None:\\n lint_ctx.warn(\\n f\\\"Tool output [{name}] uses duplicated label '{label}', double check if filters imply disjoint cases\\\",\\n node=output,\\n )\\n else:\\n lint_ctx.warn(f\\\"Tool output [{name}] uses duplicated label '{label}'\\\", node=output)\\n labels.add(label)\\n\\n format_set = False\\n if __check_format(output, lint_ctx, profile):\\n format_set = True\\n if output.tag == \\\"data\\\":\\n if \\\"auto_format\\\" in output.attrib and output.attrib[\\\"auto_format\\\"]:\\n format_set = True\\n\\n elif output.tag == \\\"collection\\\":\\n if \\\"type\\\" not in output.attrib:\\n lint_ctx.warn(\\\"Collection output with undefined 'type' found.\\\", node=output)\\n if \\\"structured_like\\\" in output.attrib and \\\"inherit_format\\\" in output.attrib:\\n format_set = True\\n for sub in output:\\n if __check_pattern(sub):\\n format_set = True\\n elif __check_format(sub, lint_ctx, profile, allow_ext=True):\\n format_set = True\\n\\n if not format_set:\\n lint_ctx.warn(\\n f\\\"Tool {output.tag} output {output.attrib.get('name', 'with missing name')} doesn't define an output format.\\\",\\n node=output,\\n )\\n\\n # TODO: check for different labels in case of multiple outputs\\n lint_ctx.info(f\\\"{num_outputs} outputs found.\\\", node=outputs[0])\",\n \"def main(args):\\n p = OptionParser()\\n p.add_option('-d', '--debug',\\n action='store_true', default=False, dest='debug',\\n help='debug')\\n p.add_option('-w', '--w3c',\\n action='store_true', default=False, dest='w3c',\\n help='send file to validator.w3.org')\\n p.add_option('-r', '--rm',\\n action='store_true', default=False, dest='passrm',\\n help='rm validation output on pass')\\n p.add_option('-v', '--verbose',\\n action='store_true', default=False, dest='verbose',\\n help='more output')\\n (o, a) = p.parse_args(args)\\n \\n if o.debug: pdb.set_trace()\\n\\n verbose(o.verbose)\\n \\n if 1 < len(a):\\n flist = a[1:]\\n else:\\n flist = glob.glob(\\\"*.html\\\")\\n\\n for filename in flist:\\n if verbose(): print filename\\n if o.w3c:\\n w3c_validate(filename)\\n else:\\n check_file(filename)\\n\\n sys.exit(exit_value())\",\n \"def StandViz_ReportError( errorobj, args, Header = None ): # error reporting and traceback function\\n (MyPath, MyFile) = os.path.split( args[0] ) # retrieve filename and path of running python script\\n (MyBaseName, MyExt) = os.path.splitext( MyFile ) # separate basefilename from extension\\n errorfilename = \\\"{}.txt\\\".format(MyBaseName) # create new error filename based on base of script filename\\n ERRFILE = open( errorfilename, 'w' ) # open text file for writting\\n if( Header != None ): ERRFILE.write( '%s\\\\n' % Header ) # if Header defined, write Header to file\\n ERRFILE.write( \\\"Error running '{}'\\\\n\\\".format(MyFile) ) # write error message with filename\\n MyTrace = errorobj[2] # retrieve error object\\n while( MyTrace != None ): # loop through stack trace\\n (line, file, name) = ( MyTrace.tb_lineno, MyTrace.tb_frame.f_code.co_filename, MyTrace.tb_frame.f_code.co_name ) # extract line, file, and error name\\n F = open( file, 'r' ) # open source file of Python script\\n L = F.readlines() # read scripot source into memory\\n F.close() # close script file\\n code = L[line-1].strip() # extract line of source code that caused error\\n ERRFILE.write( \\\" File '{}', line {}, in {}\\\\n {}\\\\n\\\".format(file, line, name, code) ) # write filename, source code line, error name, and error code\\n MyTrace = MyTrace.tb_next # step to next level of call stack trace\\n ERRFILE.write( \\\"errorobj: {}\\\\n\\\".format(errorobj) ) # write error object and arguments for call\\n ERRFILE.write( \\\"Calling Argument Vector: {}\\\\n\\\".format(args) ) # write calling arguments\\n ERRFILE.close() # close text file with error stack trace\\n os.system( \\\"notepad.exe {}\\\".format(errorfilename) ) # display error log file with notepad.exe\",\n \"def run_check(output_file,\\n documents,\\n queries,\\n results,\\n ext=\\\".xhtml\\\",\\n formula_bags=False,\\n keep_words=True,\\n keep_math=True\\n ):\\n with open(output_file, \\\"w+\\\") as out:\\n analyzer = Analyzer(formula_bags=formula_bags,\\n keep_words=keep_words,\\n keep_math=keep_math)\\n queries = Queries(queries).get_queries()\\n results = Results(results)\\n print(\\\"{},{},{},{},{},{},{},{},{},{},{}\\\".format(\\\"Query\\\",\\n \\\"Document\\\",\\n \\\"Doc-Length\\\",\\n \\\"Ranking\\\",\\n \\\"Span\\\",\\n \\\"Min-Span\\\",\\n \\\"Normalized-Span\\\",\\n \\\"Normalized-Min-Span\\\",\\n \\\"Min-Distance\\\",\\n \\\"Ave-Distance\\\",\\n \\\"Max-Distance\\\"),\\n file=out)\\n undefined_docs = []\\n for q in tqdm(range(0, len(queries))):\\n query = queries[q]\\n for doc in results.documents_for_query(query):\\n try:\\n document = Document(os.path.join(documents, doc + ext))\\n (tf_dic, __) = document.lookup_dictionaries(analyzer)\\n relevant = lookup_relevant(results.find_score(query, doc))\\n try:\\n dist = calculate_distances(query, tf_dic)\\n doc_length = sum([len(tf_dic[key])\\n for key in tf_dic.keys()])\\n print(\\\"{},{},{},{},{}\\\".format(query,\\n document,\\n doc_length,\\n relevant,\\n \\\",\\\".join([str(d)\\n for d in dist])),\\n file=out)\\n except DistancesUndefinedException:\\n undefined_docs.append((document, relevant, query))\\n except FileNotFoundError:\\n print(\\\"Error in opening document: {}\\\".format(doc))\\n print(\\\"Documents with undefined Distances\\\")\\n for doc in undefined_docs:\\n print(\\\"{}:{}:{}\\\".format(doc[2], doc[0], doc[1]))\",\n \"def call_files():\\n try:\\n predicted_proteins = sys.argv[1]\\n except IndexError:\\n predicted_proteins = input('Please input AUGUSTUS file for analysis: ')\\n try:\\n protein_db = sys.argv[2]\\n except IndexError:\\n protein_db = input('Please input a protein database file: ')\\n\\n try:\\n output_file_aug_to_fasta = sys.argv[3]\\n output_to_file = True\\n except IndexError:\\n output_to_file = input('Write output to file?'\\n + ' [Yes/No]: ')\\n if output_to_file.upper() in 'YES':\\n output_to_file = True\\n output_file_aug_to_fasta = input('Please supply output file name '\\n + 'for AUGUSTUS conversion to '\\n + 'FASTA: ')\\n else:\\n output_to_file = False\\n output_file_aug_to_fasta = None\\n\\n try:\\n output_file_proteins_to_db = sys.argv[4]\\n except IndexError:\\n if output_to_file:\\n output_file_proteins_to_db = input('Please supply output file name'\\n + 'for blast database: ')\\n else:\\n output_file_proteins_to_db = None\\n\\n try:\\n blastp_output = sys.argv[5]\\n except IndexError:\\n if output_to_file:\\n blastp_output = input('Please supply output file name for blastp: ')\\n else:\\n blastp_output = None\\n\\n finally:\\n if len(sys.argv) >= 7:\\n overwrite = sys.argv[6]\\n elif output_file and os.path.exists(output_file):\\n overwrite = input('Output file already exists. Overwrite? '\\n + '[Yes/No]: ')\\n if overwrite.upper() in 'YES':\\n overwrite = True\\n else:\\n overwrite = False\\n else: overwrite = False\\n\\n return (predicted_proteins, protein_db, output_file_aug_to_fasta, \\n output_file_proteins_to_db, blastp_output, \\n output_to_file, overwrite)\",\n \"def test_main_with_titanium_error(self):\\r\\n\\r\\n command = \\\" \\\".join([\\\"denoiser.py\\\",\\r\\n \\\"--force\\\", \\\"-o\\\", self.test_dir,\\r\\n \\\"-i\\\", \\\"%s/qiime/support_files/denoiser/TestData/denoiser_test_set.sff.txt\\\" % PROJECT_HOME,\\r\\n \\\"-f\\\", \\\"%s/qiime/support_files/denoiser/TestData/test_set_seqs.fna\\\" % PROJECT_HOME,\\r\\n \\\"-e\\\", \\\"%s/qiime/support_files/denoiser/Data/Titanium_error_profile.dat\\\" % PROJECT_HOME])\\r\\n\\r\\n result = Popen(command, shell=True, universal_newlines=True,\\r\\n stdout=PIPE, stderr=STDOUT).stdout.read()\\r\\n self.result_dir = self.test_dir\\r\\n\\r\\n observed = \\\"\\\".join(list(open(self.result_dir + \\\"centroids.fasta\\\")))\\r\\n self.assertEqual(observed, self.expected)\\r\\n\\r\\n observed = \\\"\\\".join(\\r\\n list(open(self.result_dir + \\\"denoiser_mapping.txt\\\")))\\r\\n self.assertEqual(observed, self.expected_titanium_map_string)\",\n \"def handle_errors(self, err_list):\\n for (etype, err_cde, err_str, err_value, src_line) in err_list:\\n if etype == 'isa':\\n self.isa_error(err_cde, err_str)\\n elif etype == 'gs':\\n self.gs_error(err_cde, err_str)\\n elif etype == 'st':\\n self.st_error(err_cde, err_str)\\n elif etype == 'seg':\\n self.seg_error(err_cde, err_str, err_value, src_line)\",\n \"def abort(outfile):\\n\\n fout = open(outfile, \\\"w\\\")\\n fout.write(\\\"There was an error parsing the parameter files\\\")\\n fout.close()\\n sys.exit(1)\",\n \"def create_output_files(self):\\n namenode = self.runner.namenode\\n for i in range(self.cnt_reducers):\\n fname = '%s.%s' % (self.output_dir, reduce_output(self.id, i))\\n namenode.create_file(fname)\\n self.result_files.append(fname)\\n self.open_files.append(fname)\\n\\n for j in range(self.cnt_mappers):\\n fname = map_output(self.id, j, i)\\n namenode.create_file(fname)\\n self.open_files.append(fname)\",\n \"def ValidateOutput(self, stdout, stderr, result):\\n # Store .ref and .log files in a platform-specific subdirectory\\n # (avoid possible clashes if several platforms are tested)\\n if \\\"CMTCONFIG\\\" in os.environ:\\n try: os.mkdir( os.environ['CMTCONFIG'] )\\n except OSError: pass\\n stdout_log_path=os.environ['CMTCONFIG']+os.sep\\n else:\\n stdout_log_path=''\\n # Maybe some verbosity is needed here\\n if not(self.stdout_tag==''):\\n strlog='the tag is ' + self.stdout_tag\\n logger.debug('ExecTestBase2:ValidateOutput: '+strlog)\\n if not(self.stdout_tol==0):\\n strlog='the tolerance is ' + repr(self.stdout_tol) \\n logger.debug('ExecTestBase2:ValidateOutput: '+strlog)\\n if not(self.stdout_ref==''):\\n if not(self.stdout_ref_path==''):\\n self.reference_file=self.stdout_ref_path+os.sep+self.stdout_ref \\n else:\\n self.reference_file=self.stdout_ref \\n if os.path.abspath(self.reference_file) != os.path.abspath(stdout_log_path+str(self.stdout_ref)):\\n shutil.copyfile(os.path.abspath(self.reference_file),\\n stdout_log_path+str(self.stdout_ref))\\n ref_file_stdout=''\\n for l in fileinput.input(stdout_log_path+str(self.stdout_ref)): \\n ref_file_stdout=ref_file_stdout+l.strip()+'\\\\n'\\n if not(self.excluded_lines==''):\\n strlog='the excluded lines are ' + self.excluded_lines \\n logger.debug('ExecTestBase2:ValidateOutput: '+strlog) \\n # Copy the log for later use as ref \\n f_ouput=open(stdout_log_path+self.stdout_ref.rstrip('ref')+'log', 'w')\\n f_ouput.write(stdout)\\n f_ouput.close()\\n # Check to see if the standard output matches.\\n self.causes = []\\n if not(self.stdout=='*'):\\n if not(self.stdout_ref==''):\\n # the reference output is described in a\\n # external reference file \\n if not self.__CompareText1(stdout, ref_file_stdout, result):\\n self.causes.append(\\\"standard output\\\") \\n result[\\\"ExecTest.expected_stdout\\\"] = result.Quote(self.stdout)\\n else:\\n # the reference output is described in the test-case\\n if not self.__CompareText1(stdout, self.stdout,result):\\n self.causes.append(\\\"standard output\\\") \\n result[\\\"ExecTest.expected_stdout\\\"] = result.Quote(self.stdout)\\n else:\\n result[\\\"ExecTest.expected_stdout\\\"] = result.Quote(self.stdout)\\n \\n # Check to see if the standard error matches.\\n if not(self.stderr=='*'):\\n if not self.__CompareText(stderr, self.stderr):\\n self.causes.append(\\\"standard error\\\")\\n result[\\\"ExecTest.expected_stderr\\\"] = result.Quote(self.stderr)\\n else: \\n result[\\\"ExecTest.expected_stderr\\\"] = result.Quote(self.stderr)\\n #\\n return self.causes\",\n \"def err(filename, tree, elm, msgtype, msg, error = True):\\n global errors, errexists, warnings, warnexists, fatals, fatalexists\\n\\n # Let user tune whether a warning or error\\n fatal = is_enabled(elm, msgtype, dofatals, error)\\n\\n # By default warnings and errors are enabled, but let user tune it\\n if not is_enabled(elm, msgtype, enables, True):\\n return\\n\\n (prefix, suppr) = elm_suppr(filename, tree, elm, msgtype, True)\\n if suppr in false_positives:\\n # That was actually expected\\n return\\n if suppr in suppressions:\\n # Suppressed\\n suppressions[suppr] = False\\n if fatal:\\n fatalexists += 1\\n if error:\\n errexists += 1\\n else:\\n warnexists += 1\\n return\\n\\n if error:\\n errors += 1\\n else:\\n warnings += 1\\n if fatal:\\n fatals += 1\\n\\n msg = \\\"%s %s%s: %s%s\\\" % (prefix,\\n \\\"FATAL \\\" if fatal else \\\"\\\",\\n \\\"ERROR\\\" if error else \\\"WARNING\\\",\\n elm_name(elm), msg)\\n print(msg)\\n if outfile is not None:\\n print(msg, file=outfile)\",\n \"def get_errors(self, output_str):\\n date_time = get_date_time()\\n trimmed_output = []\\n all_errors = []\\n line_counter = 0\\n temp_lines = ''\\n # trimming unnecessary lines from raw input\\n for line in output_str.split('\\\\n'):\\n if 'protocol' in line or 'input errors' in line:\\n line_counter = line_counter + 1\\n temp_lines = temp_lines + line.strip() + ' '\\n if line_counter == 2:\\n trimmed_output.append(temp_lines)\\n line_counter = 0\\n temp_lines = ''\\n\\n # extracting necessary information from each trimmed line\\n for line in trimmed_output:\\n # extracting port name\\n port = re.search('(FastEthernet|Serial)\\\\d*\\\\W\\\\d*', line).group(0)\\n error_str = re.search('\\\\d* input errors', line).group(0)\\n input_error = re.search('\\\\d*', error_str).group(0)\\n # extracting crc error\\n error_str = re.search('\\\\d* CRC', line).group(0)\\n crc_error = re.search('\\\\d*', error_str).group(0)\\n # extracting frame error\\n error_str = re.search('\\\\d* frame', line).group(0)\\n frame_error = re.search('\\\\d*', error_str).group(0)\\n # extracting overrun error\\n error_str = re.search('\\\\d* overrun', line).group(0)\\n overrun_error = re.search('\\\\d*', error_str).group(0)\\n # extracting ignored error\\n error_str = re.search('\\\\d* ignored', line).group(0)\\n ignored_error = re.search('\\\\d*', error_str).group(0)\\n # appending to a temporary list which will be later converted to a DataFrame\\n all_errors.append([self.device, port, input_error, crc_error, frame_error, overrun_error,\\n ignored_error, date_time])\\n\\n error_df = pd.DataFrame(all_errors, columns=['device_name', 'port', 'input', 'crc', 'frame', 'overrun',\\n 'ignored', 'date_time'])\\n return error_df\",\n \"def report():\\n \\n parser = argparse.ArgumentParser(\\n \\n description='pyrpipe diagnostic utility\\\\nGenerate analysis report.',\\n \\n usage='''pyrpipe_diagnostic report [<args>] <logfile>\\n \\n ''') \\n parser.add_argument('-o', help='out file \\\\ndefault: same as input logfile',action=\\\"store\\\")\\n parser.add_argument('-s','--summary', help='Print quick summary and exit',default=False,dest='summary', action='store_true')\\n parser.add_argument('-e', help='report output type: [md,pdf,html] \\\\ndefault: pdf',default='pdf',action=\\\"store\\\")\\n parser.add_argument('-c',help='Report options [(f)ull,fa(i)l,(p)ass]\\\\ndefault: f',default='f',action=\\\"store\\\")\\n parser.add_argument('-v',help='verbose',action=\\\"store_true\\\")\\n parser.add_argument('logfile', help='The log file generated by pyrpipe',action=\\\"store\\\")\\n args = parser.parse_args(sys.argv[2:])\\n \\n logFile=args.logfile\\n envLog=reports.checkEnvLog(logFile) \\n #parse args\\n if args.summary:\\n #print summary\\n reports.generate_summary(logFile,envLog,coverage='a')\\n return\\n \\n vFlag=args.v\\n if vFlag:\\n print(\\\"Generating report\\\")\\n \\n \\n outFile=\\\"\\\"\\n if args.o is None:\\n outFile=pu.get_file_basename(args.logfile)\\n else:\\n outFile=args.o\\n outFile+='.'+args.e\\n \\n if args.e in ['pdf','html','md']:\\n htmlReport=reports.generateHTMLReport('simpleDiv.html',logFile,envLog,coverage=args.c)\\n if args.e=='pdf':\\n reports.writeHtmlToPdf(htmlReport,outFile)\\n elif args.e=='html':\\n reports.writeHtml(htmlReport,outFile)\\n elif args.e == 'md':\\n reports.writeHtmlToMarkdown(htmlReport,outFile)\\n else:\\n pu.print_boldred(\\\"unknown extension:\\\"+args.e+\\\". Exiting\\\")\",\n \"def poison_all_outputs(self) -> None:\\n assert self.step is not None\\n\\n for pattern in sorted(self.step.output):\\n formatted_pattern = fmt_capture(self.kwargs, optional(pattern))\\n if is_phony(formatted_pattern):\\n Invocation.poisoned.add(formatted_pattern)\\n continue\\n for path in glob_paths(optional(formatted_pattern)):\\n Invocation.poisoned.add(path)\\n global remove_failed_outputs # pylint: disable=invalid-name\\n if remove_failed_outputs.value and not is_precious(path):\\n Logger.file(f\\\"Remove the failed output: {path}\\\")\\n Invocation.remove_output(path)\",\n \"def reportError(self):\\n self.Q['err'].put(sys.exc_info()[:2])\",\n \"def main():\\n parser = CustomArgumentParser()\\n parser.add_argument(\\\"-s\\\", \\\"--simon-sez\\\",\\n help=\\\"Really, Simon sez copy the data!\\\", action=\\\"store_true\\\")\\n parser.add_argument(\\\"-r\\\", \\\"--src-directory\\\",\\n help=\\\"Copy metadata from files in this directory.\\\")\\n parser.add_argument(\\\"-d\\\", \\\"--dst-directory\\\",\\n help=\\\"Copy metadata to matching files in this directory.\\\")\\n parser.add_argument(\\\"-v\\\", \\\"--verbose\\\", help=\\\"Log level to DEBUG.\\\",\\n action=\\\"store_true\\\")\\n args = parser.parse_args()\\n\\n if args.verbose:\\n logging.basicConfig(level=logging.DEBUG)\\n else:\\n logging.basicConfig(level=logging.INFO)\\n\\n error = False\\n\\n # Require these two arguments.\\n for arg in [args.src_directory, args.dst_directory]:\\n if not arg:\\n logger.error(\\n \\\"Required src or dst directory parameter missing.\\\")\\n error = True\\n # XXX: Duplicates exit below. Can't check directory if null.\\n logger.error(\\\"Exiting due to errors.\\\")\\n parser.usage_message()\\n sys.exit(1)\\n\\n if (os.path.exists(args.src_directory) and\\n os.path.isdir(args.src_directory)):\\n src_directory = args.src_directory\\n else:\\n logger.error(\\n \\\"--src-directory={} does not exist or is not a directory.\\\".format(\\n args.dst_directory))\\n error = True\\n\\n if (os.path.exists(args.dst_directory) and\\n os.path.isdir(args.dst_directory)):\\n dst_directory = args.dst_directory\\n else:\\n logger.error(\\n \\\"--dst-directory={} does not exist or is not a directory.\\\".format(\\n args.dst_directory))\\n error = True\\n\\n if error:\\n logger.error(\\\"Exiting due to errors.\\\")\\n parser.usage_message()\\n sys.exit(1)\\n else:\\n process_all_files(src_directory, dst_directory, simon_sez=args.simon_sez)\",\n \"def test_output_otions(rawinputfile, reformfile1, assumpfile1):\\n taxyear = 2021\\n tcio = TaxCalcIO(input_data=rawinputfile.name,\\n tax_year=taxyear,\\n reform=reformfile1.name,\\n assump=assumpfile1.name,\\n growdiff_response=None,\\n aging_input_data=False,\\n exact_calculations=False)\\n outfilepath = tcio.output_filepath()\\n # --ceeu output and standard output\\n try:\\n tcio.static_analysis(writing_output_file=True, output_ceeu=True)\\n except: # pylint: disable=bare-except\\n if os.path.isfile(outfilepath):\\n try:\\n os.remove(outfilepath)\\n except OSError:\\n pass # sometimes we can't remove a generated temporary file\\n assert 'TaxCalcIO.calculate(ceeu)_ok' == 'no'\\n # --dump output\\n try:\\n tcio.static_analysis(writing_output_file=True, output_dump=True)\\n except: # pylint: disable=bare-except\\n if os.path.isfile(outfilepath):\\n try:\\n os.remove(outfilepath)\\n except OSError:\\n pass # sometimes we can't remove a generated temporary file\\n assert 'TaxCalcIO.calculate(dump)_ok' == 'no'\\n # if tries were successful, try to remove the output file\\n if os.path.isfile(outfilepath):\\n try:\\n os.remove(outfilepath)\\n except OSError:\\n pass # sometimes we can't remove a generated temporary file\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.6987194","0.6444478","0.6306633","0.6203654","0.6200872","0.6159186","0.6075979","0.60607296","0.60173655","0.5971868","0.5959482","0.5884925","0.5875602","0.587055","0.5859751","0.5793299","0.5790206","0.5765882","0.5711678","0.5709301","0.57062423","0.5692204","0.5683712","0.5676145","0.5675729","0.564995","0.56208616","0.5617897","0.55910325","0.5587435","0.55588436","0.5548153","0.5536062","0.5531702","0.5523029","0.55130357","0.5511439","0.5503078","0.55011487","0.5498548","0.5492557","0.5490602","0.5487713","0.5478141","0.5475838","0.5458872","0.54494274","0.5447053","0.54440814","0.5440885","0.5429759","0.5422912","0.54158485","0.54030746","0.5392879","0.5377893","0.5376286","0.53602266","0.5346054","0.5339426","0.5313224","0.5311168","0.5306951","0.52993137","0.5290794","0.5290595","0.52840906","0.5283625","0.5274593","0.52739996","0.52737623","0.5269206","0.526332","0.525505","0.5252291","0.52481586","0.5243941","0.5239503","0.5236705","0.5236305","0.5235022","0.5231171","0.52289784","0.52261496","0.5225831","0.5221629","0.5220745","0.5210389","0.5208743","0.52052885","0.52042323","0.52020115","0.51970863","0.51876557","0.51814455","0.51785576","0.5178504","0.5161598","0.5158424","0.515842"],"string":"[\n \"0.6987194\",\n \"0.6444478\",\n \"0.6306633\",\n \"0.6203654\",\n \"0.6200872\",\n \"0.6159186\",\n \"0.6075979\",\n \"0.60607296\",\n \"0.60173655\",\n \"0.5971868\",\n \"0.5959482\",\n \"0.5884925\",\n \"0.5875602\",\n \"0.587055\",\n \"0.5859751\",\n \"0.5793299\",\n \"0.5790206\",\n \"0.5765882\",\n \"0.5711678\",\n \"0.5709301\",\n \"0.57062423\",\n \"0.5692204\",\n \"0.5683712\",\n \"0.5676145\",\n \"0.5675729\",\n \"0.564995\",\n \"0.56208616\",\n \"0.5617897\",\n \"0.55910325\",\n \"0.5587435\",\n \"0.55588436\",\n \"0.5548153\",\n \"0.5536062\",\n \"0.5531702\",\n \"0.5523029\",\n \"0.55130357\",\n \"0.5511439\",\n \"0.5503078\",\n \"0.55011487\",\n \"0.5498548\",\n \"0.5492557\",\n \"0.5490602\",\n \"0.5487713\",\n \"0.5478141\",\n \"0.5475838\",\n \"0.5458872\",\n \"0.54494274\",\n \"0.5447053\",\n \"0.54440814\",\n \"0.5440885\",\n \"0.5429759\",\n \"0.5422912\",\n \"0.54158485\",\n \"0.54030746\",\n \"0.5392879\",\n \"0.5377893\",\n \"0.5376286\",\n \"0.53602266\",\n \"0.5346054\",\n \"0.5339426\",\n \"0.5313224\",\n \"0.5311168\",\n \"0.5306951\",\n \"0.52993137\",\n \"0.5290794\",\n \"0.5290595\",\n \"0.52840906\",\n \"0.5283625\",\n \"0.5274593\",\n \"0.52739996\",\n \"0.52737623\",\n \"0.5269206\",\n \"0.526332\",\n \"0.525505\",\n \"0.5252291\",\n \"0.52481586\",\n \"0.5243941\",\n \"0.5239503\",\n \"0.5236705\",\n \"0.5236305\",\n \"0.5235022\",\n \"0.5231171\",\n \"0.52289784\",\n \"0.52261496\",\n \"0.5225831\",\n \"0.5221629\",\n \"0.5220745\",\n \"0.5210389\",\n \"0.5208743\",\n \"0.52052885\",\n \"0.52042323\",\n \"0.52020115\",\n \"0.51970863\",\n \"0.51876557\",\n \"0.51814455\",\n \"0.51785576\",\n \"0.5178504\",\n \"0.5161598\",\n \"0.5158424\",\n \"0.515842\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.54195714"},"document_rank":{"kind":"string","value":"52"}}},{"rowIdx":17699,"cells":{"query":{"kind":"string","value":"Reports which commands have not been successfully run. Commands found in staplefile are compared with files found in directory stack to identify which commands have failed."},"document":{"kind":"string","value":"def validate_run_results(input_file_parameters, dir_stack):\r\n prev_command_had_output_dir = True\r\n dir_stack_index = -1\r\n command_index = 0\r\n for current_command in input_file_parameters.commands:\r\n # Skip over SPLIT commands\r\n if current_command == 'SPLIT':\r\n continue\r\n\r\n command_index += 1\r\n\r\n if prev_command_had_output_dir:\r\n dir_stack_index += 1\r\n\r\n # Keep track of number of commands created in the current workflow step\r\n number_of_successful_commands = 0\r\n\r\n # Infer command type, parameters, input and output directories\r\n command_type, command_parameters = \\\r\n utils.parse_staplefile_command_line(current_command)\r\n in_dir = dir_stack[dir_stack_index]\r\n if command_type.require_output_dir:\r\n out_dir = dir_stack[dir_stack_index+1]\r\n prev_command_had_output_dir = True\r\n else:\r\n out_dir = in_dir\r\n prev_command_had_output_dir = False\r\n\r\n # Read files until command class finds no more valid input files\r\n number_of_potential_commands = 0\r\n while True:\r\n try:\r\n # The command instance is generated without exceptions if the\r\n # command execution has failed (i.e. expected output\r\n # file does not exist). Otherwise NewFileError is raised.\r\n current_command = command_type(command_parameters, in_dir, out_dir)\r\n except STAPLERerror.NewFileExists:\r\n number_of_successful_commands += 1\r\n number_of_potential_commands += 1\r\n continue\r\n except STAPLERerror.VirtualIOError:\r\n break\r\n number_of_potential_commands += 1\r\n\r\n # Print validation results\r\n if not number_of_successful_commands:\r\n print '{0} command (step number {1}) has not been run.' \\\r\n .format(command_type.name, command_index)\r\n continue\r\n if number_of_successful_commands == number_of_potential_commands:\r\n print '{0} command (step number {1}) has been run succesfully.' \\\r\n .format(command_type.name, command_index)\r\n else:\r\n print '{0} command (step number {1}) workflows have failed {2}/{3} times' \\\r\n .format(command_type.name, command_index,\r\n number_of_potential_commands - number_of_successful_commands,\r\n number_of_potential_commands)"},"metadata":{"kind":"string","value":"{\n \"objective\": {\n \"self\": [],\n \"paired\": [],\n \"triplet\": [\n [\n \"query\",\n \"document\",\n \"negatives\"\n ]\n ]\n }\n}"},"negatives":{"kind":"list like","value":["def check_run_logs(input_file_parameters, dir_stack):\r\n # Check resource manager produced .out and .err files for assumed error\r\n # messages.\r\n print 'Checking runtime log files for error messages...'\r\n file_names = os.listdir(input_file_parameters.output_dir)\r\n\r\n newest_fix_index = 0\r\n files_to_check = []\r\n for file_name in sorted(file_names):\r\n if file_name.endswith('.out') or file_name.endswith('.err'):\r\n if file_name.startswith('FIX_'):\r\n current_fix_index = file_name.split('_')[1]\r\n if int(current_fix_index) > newest_fix_index:\r\n newest_fix_index = current_fix_index\r\n files_to_check = [file_name]\r\n else:\r\n files_to_check.append(file_name)\r\n if newest_fix_index == 0:\r\n files_to_check.append(file_name)\r\n\r\n if newest_fix_index > 0:\r\n print 'Workflow has been fixed {0} times. Checking only the {1} .out ' \\\r\n 'and .err files of the newest run.'.format(newest_fix_index,\r\n len(files_to_check))\r\n\r\n i = 0\r\n number_of_warnings = 0\r\n warning_strings = ['invalid', 'exception', 'warning']\r\n error_strings = ['error', 'segmentation fault', 'canceled', '(err):']\r\n skip_strings = ['adapters with at most',\r\n 'no. of allowed errors',\r\n 'error counts']\r\n for file_name in files_to_check:\r\n handle = open(os.path.join(input_file_parameters.output_dir,\r\n file_name))\r\n\r\n i += 1\r\n finish_string_exists = False\r\n warning_messages = []\r\n error_messages = []\r\n j = 0\r\n for line in handle:\r\n j += 1\r\n line = line.lower()\r\n if any(s in line for s in skip_strings):\r\n continue\r\n if any(w in line for w in warning_strings):\r\n warning_messages.append(j)\r\n number_of_warnings += 1\r\n if any(e in line for e in error_strings):\r\n error_messages.append(j)\r\n number_of_warnings += 1\r\n if 'finished at:' in line:\r\n finish_string_exists = True\r\n if os.path.splitext(file_name)[1] == '.out':\r\n if not finish_string_exists:\r\n error_messages.append('This thread has not been finished:\\n{0}'\r\n .format(os.path.join(input_file_parameters.output_dir,\r\n file_name)))\r\n\r\n if warning_messages or error_messages:\r\n print '\\n\\nThe following file contains possible warning/error messages:'\r\n print os.path.join(input_file_parameters.output_dir, file_name)\r\n if len(warning_messages) != 0:\r\n print '\\nWarning messages on lines:'\r\n print ', '.join(map(str, warning_messages))\r\n if len(error_messages) != 0:\r\n print '\\nError messages on lines:'\r\n print ', '.join(map(str, error_messages))\r\n\r\n print '\\n\\n{0} .out and .err files checked ({1} processes)'.format(i, i/2)\r\n print 'Potential problems detected: {0}'.format(number_of_warnings)","def log_dir_stacks_contents(dir_stacks):\r\n for directory in dir_stacks:\r\n logging.info('-'*80)\r\n logging.info('Predicted directory contents of:\\n{0}'\r\n .format(directory.path))\r\n files = directory.file_names\r\n files = sorted(files)\r\n logging.info('Number of files: {0}'.format(len(files)))\r\n logging.info('Files:')\r\n logging.info('\\t'.join(files))","def sense(self):\n\n partition_folder = self.getPartitionFolder()\n log_folder = os.path.join(partition_folder, 'var/log')\n log_name = 'slapgrid-%s-error.log' % self.getConfig('partition-id')\n slapgrid_error_log_file = os.path.join(partition_folder, '.%s' % log_name)\n link_file = os.path.join(log_folder, log_name)\n monitor_url = self.getConfig('monitor-url')\n message = ''\n if os.path.exists(slapgrid_error_log_file) and \\\n os.stat(slapgrid_error_log_file).st_size:\n message = 'Buildout failed to process %s.' % self.getConfig('partition-id')\n if monitor_url:\n message += '\\nSee %s/log/%s for more information.' % (monitor_url, log_name)\n if not os.path.exists(link_file):\n os.symlink(slapgrid_error_log_file, link_file)\n else:\n if os.path.exists(link_file):\n os.unlink(link_file)\n\n if message:\n self.logger.error(message)\n else:\n self.logger.info(\"buildout is OK\")","def run_commands(commands):\n msg = \"\"\n for cmd, send_stdout in commands: \n msg += \"<hr/>\\n\"\n log.info(\"Attempting to run command {}\".format(cmd))\n try:\n p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE,\n stderr=subprocess.PIPE)\n p.wait()\n except Exception:\n m = (\"<h2 style=\\\"color:red\\\">Failed to run <code>{}</code></h2>\\n\"\n .format(escape(cmd)))\n msg += m\n log.exception(html_to_text(m).strip())\n else:\n if p.returncode == 0:\n m = (\"<h2>Successfully ran <code>{}</code></h2>\\n\"\n .format(escape(cmd)))\n msg += m\n log.info(html_to_text(m).strip())\n else:\n m = (\"<h2 style=\\\"color:red\\\">Failed to run <code>{}</code>\"\n \"</h2>\\n\".format(escape(cmd)))\n msg += m\n log.warn(html_to_text(m).strip())\n\n stderr = p.stderr.read()\n stdout = p.stdout.read() \n \n if (send_stdout or stderr) and stdout:\n msg += (\"<h3>stdout</h3>\\n <pre>{}</pre>\\n\"\n .format(escape(stdout)))\n \n if stderr:\n msg += \"<h3 style=\\\"color:red\\\">stderr</h3>\\n\"\n msg += (\"<pre style=\\\"color:red\\\">{}</pre>\\n\"\n .format(escape(stderr)))\n\n return msg","def validate_services(self, commands):\n for k, v in commands.iteritems():\n for cmd in v:\n output, code = k.run(cmd)\n if code != 0:\n return \"command `{}` returned {}\".format(cmd, str(code))\n return None","def handle_command(self, commands):\n print config.CMD_PROMPT + \" calling commands...\"\n \n success = False\n\n print config.CMD_PROMPT + \" Beginning Command Chain\"\n for command in commands:\n success = self.recursive_execute(command)\n # Is there going to be complex results checking and handling code?\n\n print config.CMD_PROMPT + \" Command Chain Completed\"\n return success","def check_systtests_pickle_files(self):\n # Make sure that there have been no more new scan points run since this\n # last processing. To do this, get the number of output directories\n # Compare this to the number in the pickle files.\n self.num_systematics = {}\n for basename in nsort(os.listdir(self.logdir)):\n if 'pckl' in basename:\n continue\n basename_content = nsort(\n os.listdir(os.path.join(self.logdir, basename))\n )\n # This means it is a directory containing something useful\n if 'config_summary.json' in basename_content:\n bits = basename.split('toy_')[-1].split('_')\n toyname = None\n add_bit = True\n for bit in bits:\n if bit == '' or bit == 'inj':\n add_bit = False\n if add_bit:\n if toyname is None:\n toyname = bit\n else:\n toyname += '_%s'%bit\n if '_full_syst_baseline' in toyname:\n toyname = toyname.split('_full_syst_baseline')[0]\n toyname = 'toy_%s_asimov'%toyname\n if toyname not in self.num_systematics.keys():\n self.num_systematics[toyname] = 0\n if 'wrong' in basename:\n # Only want to include each systematic once, but\n # they will have two directions.\n if 'pve' in basename:\n self.num_systematics[toyname] += 1\n else:\n self.num_systematics[toyname] += 1\n data_sets = from_file(os.path.join(self.logdir,\n 'data_sets.pckl'))\n if sorted(data_sets.keys()) != sorted(self.num_systematics.keys()):\n logging.info(\n 'Found files I assume to be from a previous run of'\n ' this processing script containing these truths: %s. '\n 'However, based on the directories in the overall '\n 'output directory there should be these truths: %s, so '\n 'they will be regenerated.'%(\n sorted(data_sets.keys()),\n sorted(self.num_systematics.keys())\n )\n )\n pickle_there = True\n for toyname in sorted(self.num_systematics.keys()):\n if len(data_sets[toyname].keys()) != self.num_systematics[toyname]:\n pickle_there = False\n if pickle_there:\n logging.info(\n 'Found files I assume to be from a previous run of'\n ' this processing script containing %i sytematics. If '\n 'this seems incorrect please delete the files: '\n 'data_sets.pckl, all_params.pckl and labels.pckl '\n 'from the logdir you have provided.'%(\n self.num_systematics[self.num_systematics.keys()[0]])\n )\n else:\n logging.info(\n 'Found files I assume to be from a previous run of'\n ' this processing script containing %i systematics. '\n 'However, based on the number of directories in the overall '\n 'output directory there should be %i systematics in '\n 'these pickle files, so they will be regenerated.'%(\n len(data_sets[data_sets.keys()[0]].keys()),\n self.num_systematics[self.num_systematics.keys()[0]]\n )\n )\n pickle_there = False\n\n return pickle_there","def _check_for_errors(self, status):\r\n\r\n # Case when test suite name is misspelled or file doesn't exist\r\n if status == 252:\r\n sys.stderr.write('Test suite \"{}\" was not found in path {}\\n'.format(self.name, self.path))\r\n print 'Return code is {}'.format(status)","def error_check(command):\r\n\r\n # TODO\r","def errors(job_name, jenkins_username, jenkins_token):\n global server\n# job_name = 'enterprise_pe-acceptance-tests_integration-system_pe_full-upgrade_weekend_2016.4.x' # 'enterprise_pe-orchestrator_intn-van-sys-pez-multi_2016.4.x-2016.4.x' # 'enterprise_pe-modules-vanagon-suite_intn-van-sys-pez-multi_daily-pe-modules-2016.4.x'\n server = Jenkins('https://cinext-jenkinsmaster-enterprise-prod-1.delivery.puppetlabs.net', username=jenkins_username, password=jenkins_token)\n info = server.get_job_info(job_name)\n builds = [server.get_build_info(job_name, build['number']) for build in info['builds']]\n failed_build_numbers = [b for b in builds if b['result'] == 'FAILURE']\n last_job_errors = None\n\n counts = defaultdict(int)\n similar = set()\n for build in failed_build_numbers:\n output = server.get_build_console_output(job_name, build['number'])\n finder = get_strategy(output)\n errors = finder(output)\n print \"Errors: {}\".format(errors)\n if last_job_errors:\n seq = difflib.SequenceMatcher(a=last_job_errors, b=errors)\n if seq.ratio() == 1.0:\n counts['exact'] += 1\n if seq.ratio() >= 0.7 and seq.ratio() < 1.0:\n counts['similar'] += 1\n similar.append(errors)\n else:\n last_job_errors = errors\n\n if last_job_errors:\n click.echo('Last job errors were:')\n click.echo('\\t{}'.format('\\n\\t'.join(last_job_errors)))\n\n if last_job_errors and 'exact' in counts:\n click.echo('There were {} jobs that failed with errors exactly the same as the last failed job:'.format(counts['exact']))\n click.echo('\\t{}'.format('\\n\\t'.join(last_job_errors)))\n\n if last_job_errors and 'similar' in counts:\n click.echo('There were {} jobs that failed with experienced similar errors as the last failed job:'.format(counts['exact']))\n click.echo('\\t{}'.format('\\n\\t'.join(last_job_errors)))\n for s in similar:\n click.echo('Additional Failed Job:')\n click.echo('\\t{}'.format('\\n\\t'.join(s)))","def all(\n command,\n):\n # If we get to this point all tests listed in 'pre' have passed\n # unless we have run the task with the --warn flag\n if not command.config.run.warn:\n print(\n \"\"\"\nAll Checks Passed Successfully\n==========================================\n\"\"\"\n )","def test_launch_failures(self):\n host = NodeSet(choice(self.server_managers[0].hosts)) # nosec\n self.log.info(\"Creating launch.py failure trigger files on %s\", host)\n failure_trigger = \"00_trigger-launch-failure_00\"\n failure_trigger_dir = os.path.join(self.base_test_dir, failure_trigger)\n failure_trigger_files = [\n os.path.join(self.base_test_dir, \"{}_local.yaml\".format(failure_trigger)),\n os.path.join(os.sep, \"etc\", \"daos\", \"daos_{}.yml\".format(failure_trigger)),\n os.path.join(self.base_test_dir, \"{}.log\".format(failure_trigger)),\n os.path.join(failure_trigger_dir, \"{}.log\".format(failure_trigger)),\n os.path.join(os.sep, \"tmp\", \"daos_dump_{}.txt\".format(failure_trigger)),\n os.path.join(self.tmp, \"valgrind_{}\".format(failure_trigger)),\n ]\n\n self.log.debug(\"Creating %s\", failure_trigger_dir)\n commands = [\n \"sudo -n mkdir -p {}\".format(failure_trigger_dir),\n \"sudo -n {}\".format(get_chown_command(options='-R', file=failure_trigger_dir)),\n ]\n\n local_trigger_file = failure_trigger_files.pop(0)\n self.log.debug(\"Creating %s\", local_trigger_file)\n try:\n with open(local_trigger_file, \"w\", encoding=\"utf-8\") as local_trigger:\n local_trigger.write(\"THIS IS JUST A TEST\\n\")\n except IOError as error:\n self.fail(\"Error writing {}: {}\".format(local_trigger_file, str(error)))\n\n for command in commands:\n if not run_remote(self.log, host, command, timeout=20).passed:\n self.fail(\"Error creating directory {}\".format(failure_trigger_dir))\n\n for failure_trigger_file in failure_trigger_files:\n self.log.debug(\"Creating %s\", failure_trigger_file)\n sudo = \"\" if failure_trigger_file.startswith(self.tmp) else \"sudo -n \"\n commands = [\n \"{}touch {}\".format(sudo, failure_trigger_file),\n \"{}{}\".format(sudo, get_chown_command(options='-R', file=failure_trigger_file)),\n \"echo 'THIS IS JUST A TEST' > {}\".format(failure_trigger_file),\n ]\n for command in commands:\n if not run_remote(self.log, host, command, timeout=20).passed:\n self.fail(\"Error creating file {}\".format(failure_trigger_file))","def error_check(output_list):\n #NOTE: Add error messages as you come across them\n #keys = error messages we are looking for\n #values = what we log if the key is found\n known_errors = {\n \"File Not Found\":\"File was not found\",\n \"No such host is known\":\"Failed to connect to Client\"\n }\n #Verify the command ran without errors\n for _line in output_list:\n for key, value in known_errors.items():\n if key in _line:\n log.error(value)\n return False\n return True","def test_failed():\n build()\n sh(\"%s %s --last-failed\" % (PYTHON, RUNNER_PY))","def try_mitigate_issues_if_any(self, command, code, out):\n if \"Error\" in out or \"Errno\" in out:\n issue_mitigated = self.check_known_issues_and_attempt_fix(out)\n if issue_mitigated:\n self.composite_logger.log_debug('\\nPost mitigation, invoking package manager again using: ' + command)\n code_after_fix_attempt, out_after_fix_attempt = self.env_layer.run_command_output(command, False, False)\n return self.try_mitigate_issues_if_any(command, code_after_fix_attempt, out_after_fix_attempt)\n return code, out","def test_nonexistent_report(self):\n command_line = [\"report\", \"notreport\"]\n for prefix in [[], [\"--propagate\"]]:\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)","def feedback_no_result(self, classname, method):\n logging.debug(\"feedback_no_result(%s, %s)\", classname, method)\n\n logging.info(\"Was not able to find the commit to blame for testcase %s %s\", classname, method)\n\n with open(self.html_file, \"a\") as result_file:\n result_file.write(\"<br/><b>%s - %s is broken</b> but no braking commit found\\n\" % (classname, method))\n with open(self.txt_file, \"a\") as result_file:\n result_file.write(\"%s - %s is broken but no braking commit found\\n\" % (classname, method))\n with open(self.summary_file, \"a\") as result_file:\n result_file.write(\"<br/>Pass on %s#%s\\n\" % (classname.split(\".\")[-1], method))","def _checkCommandStatus(self, lastCommand=False):\n p = self.spawnProc\n p.sendline('echo $?')\n regex = re.compile('^[0-9]+',re.M)\n p.expect(regex, 2)\n msg = '_checkCommandStatus : Execution of command FAILED'\n \tif lastCommand:\n \t msg = '_checkCommandStatus :Execution of command : \"%s\" FAILED' %lastCommand\n if p.after != '0' and p.after != '99':\n raise AssertionError(msg)","def execute():\r\n arcpy.AddMessage(\"START BCA Processing\")\r\n arcpy.env.workspace = config.temp_data_gdb\r\n arcpy.env.overwriteOutput = True\r\n sys.path.append(config.notif_system_script_folder)\r\n\r\n # Other Variables\r\n arcpy.AddMessage(\"Import toolbox\")\r\n arcpy.ImportToolbox(config.notif_toolbox)\r\n REGEX_FOR_INVALID_CHARS = re.compile(r'[^0-9a-zA-Z]+')\r\n todayDate = datetime.datetime.now().strftime(\"%Y%m%d\")\r\n logFile = file(\r\n config.report_processing_log + \"\\\\\" + todayDate + \"_NotificationSystemLog\" + \".txt\", \"a\")\r\n\r\n\r\n # get all unzipped files uploaded to shared folder\r\n configfiles = [os.path.join(dirpath, f)\r\n for dirpath, dirnames, files in os.walk(config.SharedFolder)\r\n for f in files if f.endswith('.csv') or f.endswith('.xls') or f.endswith('.xlsx') or f.endswith('.XLS')]\r\n\r\n correct_config_files = [f for f in configfiles if \"\\BCAWeeklyPermitReport\\\\\" in f]\r\n\r\n # PREPARE workspace\r\n arcpy.AddMessage(\"Preparing workspace...\")\r\n for BCAreport in correct_config_files:\r\n\r\n input_file_name = BCAreport.split(\"\\\\\")[-1]\r\n\r\n MukimConstruct = arcpy.SearchCursor(config.MukimConstructSource)\r\n PermitDateExists = False\r\n\r\n for row in MukimConstruct:\r\n aux = input_file_name[:8]\r\n if \"CORRECTED\" not in BCAreport.upper():\r\n filedate = datetime.datetime.strptime(aux, \"%Y%m%d\")\r\n else:\r\n clean_filename = input_file_name.split(\".\")[0]\r\n filedate = datetime.datetime.strptime(clean_filename[-8:], \"%Y%m%d\")\r\n if filedate == row.PERMIT_DATE and \"CORRECTED\" not in BCAreport.upper():\r\n PermitDateExists = True\r\n break\r\n if PermitDateExists and \"CORRECTED\" not in BCAreport.upper():\r\n PermitDateExistsLog = file(\r\n config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] +\r\n \" file's Permit Date already exists\" + \".log\",\r\n \"a\")\r\n PermitDateExistsLog.write(\r\n \"Permit Date for the file \" + input_file_name + \" already exists in Mukim Construct at \" + str(\r\n datetime.datetime.now()))\r\n logFile.writelines(\r\n \"Permit Date for the file \" + input_file_name + \" already exists in Mukim Construct at \" + str(\r\n datetime.datetime.now()) + \"\\n\")\r\n\r\n else:\r\n\r\n # 00. Creation of geodatabases that will serve as workspaces\r\n logFile.writelines(\"00 Creation of temp gdb starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n if arcpy.Exists(config.TempDataGDB):\r\n arcpy.Delete_management(config.TempDataGDB)\r\n arcpy.CreateFileGDB_management(config.Notification, \"Temp_data.gdb\")\r\n else:\r\n arcpy.CreateFileGDB_management(config.Notification, \"Temp_data.gdb\")\r\n\r\n if arcpy.Exists(config.SDEDataGDB):\r\n arcpy.Delete_management(config.SDEDataGDB)\r\n arcpy.CreateFileGDB_management(config.Notification, \"Source.gdb\")\r\n else:\r\n arcpy.CreateFileGDB_management(config.Notification, \"Source.gdb\")\r\n\r\n if arcpy.Exists(config.CurrentMukimConstructDataGDB):\r\n arcpy.Delete_management(config.CurrentMukimConstructDataGDB)\r\n arcpy.CreateFileGDB_management(config.Notification, \"Final_data.gdb\")\r\n else:\r\n arcpy.CreateFileGDB_management(config.Notification, \"Final_data.gdb\")\r\n\r\n logFile.writelines(\"00 Creation of temp gdb ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 01. Import the base data\r\n logFile.writelines(\"01 Import of base data starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructSource, config.CurrentMukimConstructDataGDB,\r\n \"MUKIM_CONSTRUCT\", \"\", \"\", \"\")\r\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructByProjSource, config.CurrentMukimConstructDataGDB,\r\n \"MUKIM_CONSTRUCT_BYPROJ\", \"\", \"\", \"\")\r\n arcpy.FeatureClassToFeatureClass_conversion(config.DepotSource, config.SDEDataGDB, \"DepotBoundary\", \"\", \"\", \"\")\r\n arcpy.FeatureClassToFeatureClass_conversion(config.CatchmentSource, config.SDEDataGDB, \"CatchmentBoundary\", \"\", \"\", \"\")\r\n arcpy.FeatureClassToFeatureClass_conversion(config.LandlotSource, config.TempDataGDB, \"Land_lot\", \"\", \"\", \"\")\r\n # Calculate the lot key without letter\r\n arcpy.AddField_management(config.LandLot, \"Lotkey_wo_letter\", \"TEXT\", \"\", \"\", \"10\", \"\", \"NULLABLE\", \"NON_REQUIRED\",\r\n \"\")\r\n arcpy.CalculateField_management(config.LandLot, \"Lotkey_wo_letter\", \"!lot_key![:10]\", \"PYTHON\", \"\")\r\n\r\n logFile.writelines(\"01 Import of base data ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n\r\n # START THE LOOP TO PROCESS ALL THE FILES\r\n clcounter = 0\r\n\r\n if len(correct_config_files) == 0:\r\n logFile.writelines(\"No BCA report to process at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n arcpy.AddMessage(\"Processing files...\")\r\n for BCAreport in configfiles:\r\n\r\n clcounter += 1\r\n arcpy.AddMessage(BCAreport)\r\n input_file_name = BCAreport.split(\"\\\\\")[-1]\r\n MukimConstruct = arcpy.SearchCursor(config.MukimConstructSource)\r\n PermitDateExists = False\r\n\r\n # CHEKC FILE DATE EXISTS\r\n for row in MukimConstruct:\r\n aux = input_file_name[:8]\r\n if \"CORRECTED\" not in BCAreport.upper():\r\n filedate = datetime.datetime.strptime(aux, \"%Y%m%d\")\r\n else:\r\n clean_filename = input_file_name.split(\".\")[0]\r\n filedate = datetime.datetime.strptime(clean_filename[-8:], \"%Y%m%d\")\r\n if filedate == row.PERMIT_DATE and \"CORRECTED\" not in input_file_name.upper():\r\n PermitDateExists = True\r\n break\r\n\r\n HEADERVALID = True\r\n with xlrd.open_workbook(BCAreport) as wb:\r\n sh = wb.sheet_by_index(0)\r\n for r in range(sh.nrows):\r\n colcount = 0\r\n if sh.row_values(r)[colcount] == 'Error_Message':\r\n HEADERVALID = True\r\n elif sh.row_values(r)[colcount] == 'Project Ref No' or sh.row_values(r)[colcount] == 'Project_Ref_No':\r\n HEADERVALID = True\r\n else:\r\n PermitDateExistsLog = file(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[\r\n 0] + \" file's header format is not acceptable for processing\" + \".log\", \"a\")\r\n PermitDateExistsLog.write(\r\n \"The header format for the file \" + input_file_name + \" is not acceptable for processing at \" + str(\r\n datetime.datetime.now()))\r\n logFile.writelines(\r\n \"The header format for the file \" + input_file_name + \" is not acceptable for processing at \" + str(\r\n datetime.datetime.now()) + \"\\n\")\r\n HEADERVALID = False\r\n break\r\n\r\n if not PermitDateExists and HEADERVALID:\r\n logFile.writelines(\"Starts processing \" + BCAreport + \" at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # Status update to run/not run the SiteInspection Update\r\n Log_SiteInspectionUpdate = file(config.SiteInspectionUpdate, \"w\")\r\n Log_SiteInspectionUpdate.writelines(\"NO\")\r\n Log_SiteInspectionUpdate.close()\r\n\r\n # 02. Import the BCA report to a geodatabase table\r\n logFile.writelines(\"02 Import of table to gdb starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n if arcpy.Exists(config.TempDataGDB + \"\\\\ConvertedBCAreport_02\"):\r\n arcpy.Delete_management(config.TempDataGDB + \"\\\\ConvertedBCAreport_02\")\r\n arcpy.CreateTable_management(config.TempDataGDB, \"ConvertedBCAreport_02\", config.TemplateConvertedBCAreport)\r\n else:\r\n arcpy.CreateTable_management(config.TempDataGDB, \"ConvertedBCAreport_02\", config.TemplateConvertedBCAreport)\r\n if arcpy.Exists(BCAreport[:-5] + '_err' + '.csv'):\r\n # rename old error report\r\n os.remove(BCAreport[:-5] + '_err' + '.csv')\r\n else:\r\n result = \"Error file does not exist\"\r\n if BCAreport.endswith('.xls') or BCAreport.endswith('.xlsx') or BCAreport.endswith('.XLS'):\r\n rows_out = arcpy.InsertCursor(config.BCAReportGDBTable)\r\n fldlist = arcpy.ListFields(config.BCAReportGDBTable)\r\n fldlist.pop(0)\r\n with xlrd.open_workbook(BCAreport) as wb:\r\n sh = wb.sheet_by_index(0)\r\n for r in range(sh.nrows):\r\n colcount = 0\r\n if sh.row_values(r)[colcount] != 'Error_Message':\r\n colcount = 0\r\n else:\r\n colcount = 1\r\n break\r\n for r in range(sh.nrows):\r\n colcounter = colcount\r\n if r > 0:\r\n new_row_out = rows_out.newRow()\r\n for efld in fldlist:\r\n if efld.name <> 'OBJECTID' and efld.name <> 'ConcatFields':\r\n new_row_out.setValue(efld.name, sh.row_values(r)[colcounter])\r\n colcounter += 1\r\n\r\n logFile.writelines(\"Inserting: \" + str(new_row_out) + \"\\n\")\r\n rows_out.insertRow(new_row_out)\r\n del rows_out, new_row_out\r\n\r\n elif BCAreport.endswith('.csv'):\r\n\r\n BCAreportread = csv.DictReader(open(BCAreport, 'rb'), delimiter=',', quotechar='\"')\r\n rows_out = arcpy.InsertCursor(config.BCAReportGDBTable)\r\n for attribute in BCAreportread:\r\n new_row_out = rows_out.newRow()\r\n new_row_out.Project_Ref_No = attribute['Project_Ref_No']\r\n new_row_out.Project_Title = attribute['Project_Title']\r\n new_row_out.House_Blk_No = attribute['House_Blk_No']\r\n new_row_out.Road_Name = attribute['Road_Name']\r\n new_row_out.Level_No = attribute['Level_No']\r\n new_row_out.Unit_No = attribute['Unit_No']\r\n new_row_out.Building_Name = attribute['Building_Name']\r\n new_row_out.Postal_Code = attribute['Postal_Code']\r\n new_row_out.Project_Mukim_nos = attribute['Project_Mukim_nos']\r\n new_row_out.Project_Lot_nos = attribute['Project_Lot_nos']\r\n new_row_out.Permit_Type_of_Work = attribute['Permit_Type_of_Work']\r\n new_row_out.Type_of_Work = attribute['Type_of_Work']\r\n new_row_out.Owner_s_name = attribute['Owners_name']\r\n new_row_out.Owner_s_firm_name = attribute['Owners_firm_name']\r\n new_row_out.Owner_s_address = attribute['Owners_address']\r\n new_row_out.Owner_s_Tel_No = attribute['Owners_Tel_No']\r\n new_row_out.Owner_s_Email_address = attribute['Owners_Email_address']\r\n new_row_out.Builder_s_name = attribute['Builders_name']\r\n new_row_out.Builder_s_firm_name = attribute['Builders_firm_name']\r\n new_row_out.Builder_s_address = attribute['Builders_address']\r\n new_row_out.Builder_s_Tel_No = attribute['Builders_Tel_No']\r\n new_row_out.Builder_s_email_address = attribute['Builders_email_address']\r\n new_row_out.PE_s_name = attribute['PEs_name']\r\n new_row_out.PE_s_firm_name = attribute['PEs_firm_name']\r\n new_row_out.PE_s_address = attribute['PEs_address']\r\n new_row_out.PE_s_Tel_No = attribute['PEs_Tel_No']\r\n new_row_out.PE_s_Email_address = attribute['PEs_Email_address']\r\n new_row_out.Architect_s_name = attribute['Architects_name']\r\n new_row_out.Architect_s_firm_name = attribute['Architects_firm_name']\r\n new_row_out.Architect_s_address = attribute['Architects_address']\r\n new_row_out.Architect_s_Tel_No = attribute['Architects_Tel_No']\r\n new_row_out.Architect_s_Email_address = attribute['Architects_Email_address']\r\n new_row_out.Project_Cost = attribute['Project_Cost']\r\n new_row_out.Project_Duration = attribute['Project_Duration']\r\n new_row_out.Approval_Date_DD_MM_YYYY_ = attribute['Approval_Date']\r\n rows_out.insertRow(new_row_out)\r\n if new_row_out:\r\n del new_row_out\r\n if rows_out:\r\n del rows_out\r\n\r\n except:\r\n log_error(\"Error in 02 Import of table to gdb: \", logFile)\r\n logFile.writelines(\"02 Import of table to gdb ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 03. Remove spaces in key fields for the concatenation\r\n logFile.writelines(\"03 Removing of spaces starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n rowsSpace = arcpy.UpdateCursor(config.BCAReportGDBTable)\r\n\r\n for row in rowsSpace:\r\n ProjRef = row.Project_Ref_No.strip()\r\n ProjMukim = row.Project_Mukim_nos.strip()\r\n ProjLot = row.Project_Lot_nos.strip()\r\n BuilderN = row.Builder_s_name.strip()\r\n row.Project_Ref_No = ProjRef\r\n row.Project_Mukim_nos = ProjMukim\r\n row.Project_Lot_nos = ProjLot\r\n row.Builder_s_name = BuilderN\r\n rowsSpace.updateRow(row)\r\n if row:\r\n del row\r\n if rowsSpace:\r\n del rowsSpace\r\n except:\r\n log_error(\"Error in 03 Removing of spaces: \", logFile)\r\n logFile.writelines(\"03 Removing of spaces ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 04. Concatenate Project_Ref_No, Project_Mukim_nos, Project_Lot_nos, Builder_s_name\r\n logFile.writelines(\"04 Concatenate the three fields starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n rows = arcpy.UpdateCursor(config.BCAReportGDBTable)\r\n for row in rows:\r\n expression = str(row.Project_Ref_No) + \"-\" + str(row.Project_Mukim_nos) + \"-\" + str(\r\n row.Project_Lot_nos) + \"-\" + str(row.Builder_s_name)\r\n row.ConcatFields = expression\r\n rows.updateRow(row)\r\n if row:\r\n del row\r\n if rows:\r\n del rows\r\n\r\n except:\r\n log_error(\"Error in 04 Concatenate the three fields: \", logFile)\r\n logFile.writelines(\"04 Concatenate the three fields ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 05. Create temporary tables for Unique and Duplicate records\r\n logFile.writelines(\"05 Create temporary tables starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n if arcpy.Exists(config.TempDataGDB + \"\\\\Uniquerows\"):\r\n arcpy.Delete_management(config.TempDataGDB + \"\\\\Uniquerows\")\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Uniquerows\", config.TemplateConcat, \"\")\r\n else:\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Uniquerows\", config.TemplateConcat, \"\")\r\n\r\n if arcpy.Exists(config.TempDataGDB + \"\\\\Duplicaterows\"):\r\n arcpy.Delete_management(config.TempDataGDB + \"\\\\Duplicaterows\")\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Duplicaterows\", config.TemplateConcat, \"\")\r\n else:\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Duplicaterows\", config.TemplateConcat, \"\")\r\n except:\r\n log_error(\"Error in 05 Create temporary tables: \", logFile)\r\n logFile.writelines(\"05 Create temporary tables ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 06. Separate unique and duplicate records\r\n logFile.writelines(\"06 Separate unique and duplicate rows starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n print \"Start step 06\"\r\n rows_inCB02 = arcpy.UpdateCursor(config.BCAReportGDBTable)\r\n rows_outUnique = arcpy.InsertCursor(config.UniqueRecords)\r\n # print rows_outUnique\r\n rows_outDuplicate = arcpy.InsertCursor(config.DuplicateRecords)\r\n\r\n rows_unique = []\r\n rows_duplicates = []\r\n for row in rows_inCB02:\r\n if row.ConcatFields not in rows_unique:\r\n rows_unique = rows_unique + [row.ConcatFields]\r\n else:\r\n rows_duplicates = rows_duplicates + [row.ConcatFields]\r\n\r\n print \"Start step 06 1\"\r\n for item in rows_unique:\r\n print \"clcounter: \" + str(clcounter)\r\n print \"item: \" + str(item)\r\n newrow = rows_outUnique.newRow()\r\n newrow.Concat = item\r\n # print newrow\r\n rows_outUnique.insertRow(newrow)\r\n\r\n print \"Start step 06 2\"\r\n for item in rows_duplicates:\r\n print \"clcounter: \" + str(clcounter)\r\n print \"item: \" + str(item)\r\n newrow = rows_outDuplicate.newRow()\r\n newrow.Concat = item\r\n rows_outDuplicate.insertRow(newrow)\r\n\r\n print \"Start step 06 3\"\r\n\r\n if rows_inCB02:\r\n del rows_inCB02\r\n if rows_outUnique:\r\n del rows_outUnique\r\n if rows_outDuplicate:\r\n del rows_outDuplicate\r\n if row:\r\n del row\r\n except:\r\n log_error(\"Error in 06 Separate unique and duplicate rows: \", logFile)\r\n logFile.writelines(\"06 Separate unique and duplicate rows ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 07. Get the rest of the fields for Uniquerows table\r\n logFile.writelines(\r\n \"07 Get the rest of the fields for unique rows starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.env.workspace = config.TempDataGDB\r\n arcpy.AddMessage(\"Starting toolbox JoinUniqueRestofFields\")\r\n\r\n try:\r\n arcpy.JoinUniqueRestofFields()\r\n except:\r\n log_error(\"Error in 07 Get the rest of the fields for unique rows: \", logFile)\r\n logFile.writelines(\r\n \"07 Get the rest of the fields for unique rows ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 08. Get the rest of the fields for Duplicaterows table\r\n logFile.writelines(\r\n \"08 Get the rest of the fields for duplicate rows starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.AddMessage(\"START toolbox JoinDuplicateRestofFields\")\r\n try:\r\n arcpy.JoinDuplicateRestofFields()\r\n\r\n except:\r\n log_error(\"Error in 08 Get the rest of the fields for duplicate rows: \", logFile)\r\n\r\n logFile.writelines(\r\n \"08 Get the rest of the fields for duplicate rows ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 09. Log duplicate records\r\n logFile.writelines(\"09 Log duplicate records starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.AddMessage(\"Logging duplicate records\")\r\n try:\r\n # Initialize the error log\r\n wbk = xlwt.Workbook()\r\n sheet = wbk.add_sheet('Book 1')\r\n row_count = 0\r\n col_count = 0\r\n header = ['Error_Message', 'Project_Ref_No', 'Project_Title', 'House_Blk_No', 'Road_Name', 'Level_No',\r\n 'Unit_No', 'Building_Name', 'Postal_Code', 'Project_Mukim_nos', 'Project_Lot_nos',\r\n 'Permit_Type_of_Work', 'Type_of_Work', 'Owners_name', 'Owners_firm_name', 'Owners_address',\r\n 'Owners_Tel_No', 'Owners_Email_address', 'Builders_name', 'Builders_firm_name',\r\n 'Builders_address', 'Builders_Tel_No', 'Builders_email_address', 'PEs_name', 'PEs_firm_name',\r\n 'PEs_address', 'PEs_Tel_No', 'PEs_Email_address', 'Architects_name', 'Architects_firm_name',\r\n 'Architects_address', 'Architects_Tel_No', 'Architects_Email_address', 'Project_Cost',\r\n 'Project_Duration', 'Approval_Date']\r\n for fieldname in header:\r\n sheet.write(row_count, col_count, fieldname)\r\n col_count += 1\r\n wbk.save(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\")\r\n\r\n # Log duplicate records\r\n rows = arcpy.SearchCursor(config.DuplicateRows)\r\n\r\n row_count = 1\r\n col_count = 0\r\n row = None\r\n for row in rows:\r\n message = ['Duplicate record in the BCA report', row.Project_Ref_No, row.Project_Title,\r\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\r\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\r\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\r\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\r\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\r\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\r\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\r\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\r\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n wbk.save(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\")\r\n if row:\r\n del row\r\n if rows:\r\n del rows\r\n except:\r\n log_error(\"Error in 09 Log duplicate records: \", logFile)\r\n\r\n logFile.writelines(\"09 Log duplicate records ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 10. Split rows based on Mukim numbers\r\n logFile.writelines(\"10 Splitting of rows based on mukim starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n if arcpy.Exists(config.SplittedMukimRows):\r\n arcpy.Delete_management(config.SplittedMukimRows)\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Splitted_rows_mukim_03\", config.TemplateBCAReport, \"\")\r\n else:\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Splitted_rows_mukim_03\", config.TemplateBCAReport, \"\")\r\n\r\n if arcpy.Exists(config.SplittedProjLotRows):\r\n arcpy.Delete_management(config.SplittedProjLotRows)\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Splitted_rows_projlot_04\", config.TemplateBCAReport, \"\")\r\n else:\r\n arcpy.CreateTable_management(config.TempDataGDB, \"Splitted_rows_projlot_04\", config.TemplateBCAReport, \"\")\r\n\r\n rows_in = arcpy.SearchCursor(config.UniqueRows)\r\n rows_out = arcpy.InsertCursor(config.SplittedMukimRows)\r\n\r\n for row in rows_in:\r\n list_mukim_nos = row.Project_Mukim_nos.split(\",\")\r\n for proj_mukim_nos_id in list_mukim_nos:\r\n new_row_out = rows_out.newRow()\r\n new_row_out.Project_Mukim_nos = proj_mukim_nos_id\r\n new_row_out.PROJECTMUKIM_RAW = row.Project_Mukim_nos\r\n new_row_out.Project_Ref_No = row.Project_Ref_No\r\n new_row_out.Project_Title = row.Project_Title\r\n new_row_out.House_Blk_No = row.House_Blk_No\r\n new_row_out.Road_Name = row.Road_Name\r\n new_row_out.Level_No = row.Level_No\r\n new_row_out.Unit_No = row.Unit_No\r\n new_row_out.Building_Name = row.Building_Name\r\n new_row_out.Postal_Code = row.Postal_Code\r\n new_row_out.Project_Lot_nos = row.Project_Lot_nos\r\n new_row_out.Permit_Type_of_Work = row.Permit_Type_of_Work\r\n new_row_out.Type_of_Work = row.Type_of_Work\r\n new_row_out.Owner_s_name = row.Owner_s_name\r\n new_row_out.Owner_s_firm_name = row.Owner_s_firm_name\r\n new_row_out.Owner_s_address = row.Owner_s_address\r\n new_row_out.Owner_s_Tel_No = row.Owner_s_Tel_No\r\n new_row_out.Owner_s_Email_address = row.Owner_s_Email_address\r\n new_row_out.Builder_s_name = row.Builder_s_name\r\n new_row_out.Builder_s_firm_name = row.Builder_s_firm_name\r\n new_row_out.Builder_s_address = row.Builder_s_address\r\n new_row_out.Builder_s_Tel_No = row.Builder_s_Tel_No\r\n new_row_out.Builder_s_email_address = row.Builder_s_email_address\r\n new_row_out.PE_s_name = row.PE_s_name\r\n new_row_out.PE_s_firm_name = row.PE_s_firm_name\r\n new_row_out.PE_s_address = row.PE_s_address\r\n new_row_out.PE_s_Tel_No = row.PE_s_Tel_No\r\n new_row_out.PE_s_Email_address = row.PE_s_Email_address\r\n new_row_out.Architect_s_name = row.Architect_s_name\r\n new_row_out.Architect_s_firm_name = row.Architect_s_firm_name\r\n new_row_out.Architect_s_address = row.Architect_s_address\r\n new_row_out.Architect_s_Tel_No = row.Architect_s_Tel_No\r\n new_row_out.Architect_s_Email_address = row.Architect_s_Email_address\r\n new_row_out.Project_Cost = row.Project_Cost\r\n new_row_out.Project_Duration = row.Project_Duration\r\n new_row_out.Approval_Date_DD_MM_YYYY_ = row.Approval_Date_DD_MM_YYYY_\r\n rows_out.insertRow(new_row_out)\r\n if row:\r\n del row\r\n if new_row_out:\r\n del new_row_out\r\n if rows_in:\r\n del rows_in\r\n if rows_out:\r\n del rows_out\r\n except:\r\n log_error(\"Error in 10 Splitting of rows based on mukim: \", logFile)\r\n\r\n logFile.writelines(\"10 Splitting of rows based on mukim ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 11.Split rows based on Project lot numbers\r\n arcpy.AddMessage(\"Splitting rows based on project lots\")\r\n\r\n logFile.writelines(\r\n \"11 Splitting of rows based on project lot starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n rows_in03 = arcpy.SearchCursor(config.SplittedMukimRows)\r\n rows_out04 = arcpy.InsertCursor(config.SplittedProjLotRows)\r\n\r\n for row in rows_in03:\r\n list_proj_lot_nos = row.Project_Lot_nos.split(\",\")\r\n print list_proj_lot_nos\r\n for proj_lot_nos_id in list_proj_lot_nos:\r\n print proj_lot_nos_id\r\n new_row_out = rows_out04.newRow()\r\n new_row_out.Project_Lot_nos = proj_lot_nos_id\r\n new_row_out.PROJECTMUKIM_RAW = row.PROJECTMUKIM_RAW\r\n new_row_out.PROJECTLOT_RAW = row.Project_Lot_nos\r\n new_row_out.Project_Ref_No = row.Project_Ref_No\r\n new_row_out.Project_Title = row.Project_Title\r\n new_row_out.House_Blk_No = row.House_Blk_No\r\n new_row_out.Road_Name = row.Road_Name\r\n new_row_out.Level_No = row.Level_No\r\n new_row_out.Unit_No = row.Unit_No\r\n new_row_out.Building_Name = row.Building_Name\r\n new_row_out.Postal_Code = row.Postal_Code\r\n new_row_out.Project_Mukim_nos = row.Project_Mukim_nos\r\n new_row_out.Permit_Type_of_Work = row.Permit_Type_of_Work\r\n new_row_out.Type_of_Work = row.Type_of_Work\r\n new_row_out.Owner_s_name = row.Owner_s_name\r\n new_row_out.Owner_s_firm_name = row.Owner_s_firm_name\r\n new_row_out.Owner_s_address = row.Owner_s_address\r\n new_row_out.Owner_s_Tel_No = row.Owner_s_Tel_No\r\n new_row_out.Owner_s_Email_address = row.Owner_s_Email_address\r\n new_row_out.Builder_s_name = row.Builder_s_name\r\n new_row_out.Builder_s_firm_name = row.Builder_s_firm_name\r\n new_row_out.Builder_s_address = row.Builder_s_address\r\n new_row_out.Builder_s_Tel_No = row.Builder_s_Tel_No\r\n new_row_out.Builder_s_email_address = row.Builder_s_email_address\r\n new_row_out.PE_s_name = row.PE_s_name\r\n new_row_out.PE_s_firm_name = row.PE_s_firm_name\r\n new_row_out.PE_s_address = row.PE_s_address\r\n new_row_out.PE_s_Tel_No = row.PE_s_Tel_No\r\n new_row_out.PE_s_Email_address = row.PE_s_Email_address\r\n new_row_out.Architect_s_name = row.Architect_s_name\r\n new_row_out.Architect_s_firm_name = row.Architect_s_firm_name\r\n new_row_out.Architect_s_address = row.Architect_s_address\r\n new_row_out.Architect_s_Tel_No = row.Architect_s_Tel_No\r\n new_row_out.Architect_s_Email_address = row.Architect_s_Email_address\r\n new_row_out.Project_Cost = row.Project_Cost\r\n new_row_out.Project_Duration = row.Project_Duration\r\n new_row_out.Approval_Date_DD_MM_YYYY_ = row.Approval_Date_DD_MM_YYYY_\r\n rows_out04.insertRow(new_row_out)\r\n\r\n if row:\r\n del row\r\n if new_row_out:\r\n del new_row_out\r\n if rows_in03:\r\n del rows_in03\r\n if rows_out04:\r\n del rows_out04\r\n # print int(arcpy.GetCount_management(SplittedProjLotRows).getOutput(0))\r\n except:\r\n log_error(\"Error in 11 Splitting of rows based on project lot: \", logFile)\r\n logFile.writelines(\r\n \"11 Splitting of rows based on project lot ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 12. Remove spaces in Mukim and Project lot values\r\n logFile.writelines(\r\n \"12 Removing of spaces in mukim and project lot starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.AddMessage(\"Cleaning project lots\")\r\n try:\r\n\r\n rowsSpaces = arcpy.UpdateCursor(config.SplittedProjLotRows)\r\n\r\n for row in rowsSpaces:\r\n lot_no_spaces = row.Project_Lot_nos.strip()\r\n mukim_no_spaces = row.Project_Mukim_nos.strip()\r\n row.Project_Lot_nos = lot_no_spaces\r\n row.Project_Mukim_nos = mukim_no_spaces\r\n rowsSpaces.updateRow(row)\r\n if row:\r\n del row\r\n if rowsSpaces:\r\n del rowsSpaces\r\n except:\r\n log_error(\"Error in 12 Removing of spaces in mukim and project lot: \", logFile)\r\n logFile.writelines(\r\n \"12 Removing of spaces in mukim and project lot ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 13. Log empty Mukimlot or date fields\r\n logFile.writelines(\r\n \"13 Log empty mukim and project lot nos starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n rowsEmpty = arcpy.UpdateCursor(config.SplittedProjLotRows)\r\n\r\n for row in rowsEmpty:\r\n message = ['Missing Project lot or Mukim numbers', row.Project_Ref_No, row.Project_Title,\r\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\r\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\r\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\r\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\r\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\r\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\r\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\r\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\r\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\r\n message2 = ['Missing Project duration or Approval date', row.Project_Ref_No, row.Project_Title,\r\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\r\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\r\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\r\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\r\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\r\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\r\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name,\r\n row.Architect_s_firm_name, row.Architect_s_address, row.Architect_s_Tel_No,\r\n row.Architect_s_Email_address, row.Project_Cost, row.Project_Duration,\r\n row.Approval_Date_DD_MM_YYYY_]\r\n if row.Project_Mukim_nos is None or (len(row.Project_Mukim_nos) < 4):\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsEmpty.deleteRow(row)\r\n elif row.Project_Lot_nos is None or (len(row.Project_Lot_nos) == 0):\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsEmpty.deleteRow(row)\r\n if row.Project_Duration is None or (len(row.Project_Duration) < 1):\r\n col_count = 0\r\n for element in message2:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsEmpty.deleteRow(row)\r\n\r\n elif row.Approval_Date_DD_MM_YYYY_ is None or (len(row.Approval_Date_DD_MM_YYYY_) < 1):\r\n col_count = 0\r\n for element in message2:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsEmpty.deleteRow(row)\r\n wbk.save(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\")\r\n if row:\r\n del row\r\n if rowsEmpty:\r\n del rowsEmpty\r\n except:\r\n log_error(\"Error in 13 Log for empty mukim and project lot nos: \", logFile)\r\n logFile.writelines(\"13 Log empty mukim and project lot nos ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 14. Error log for those with bad values\r\n arcpy.AddMessage(\"14 Logging bad values\")\r\n logFile.writelines(\"14 Log if bad values exist starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsBadValues = arcpy.UpdateCursor(config.SplittedProjLotRows)\r\n\r\n for row in rowsBadValues:\r\n message = ['Mukim or Project lot numbers have bad values', row.Project_Ref_No, row.Project_Title,\r\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\r\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\r\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\r\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\r\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\r\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\r\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\r\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\r\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\r\n if len(REGEX_FOR_INVALID_CHARS.findall(row.Project_Lot_nos)) > 0:\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsBadValues.deleteRow(row)\r\n elif len(REGEX_FOR_INVALID_CHARS.findall(row.Project_Mukim_nos)) > 0:\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsBadValues.deleteRow(row)\r\n elif len(uptodigit(row.Project_Lot_nos)) > 0:\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n rowsBadValues.deleteRow(row)\r\n wbk.save(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\")\r\n\r\n if row:\r\n del row\r\n if rowsBadValues:\r\n del rowsBadValues\r\n except:\r\n log_error(\"Error in 14 Log if bad values exist: \", logFile)\r\n logFile.writelines(\"14 Log if bad values exist ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 15. Add zeros for Project Lot numbers\r\n logFile.writelines(\"15 Add zeros starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsZeros = arcpy.UpdateCursor(config.SplittedProjLotRows)\r\n letters = string.ascii_letters\r\n for row in rowsZeros:\r\n letter_count = len(filter(functools.partial(operator.contains, letters), row.Project_Lot_nos))\r\n filled_string = row.Project_Lot_nos.zfill(5 + letter_count)\r\n row.Project_Lot_nos = filled_string\r\n rowsZeros.updateRow(row)\r\n if row:\r\n del row\r\n if rowsZeros:\r\n del rowsZeros\r\n except:\r\n log_error(\"Error in 15 Add zeros: \", logFile)\r\n logFile.writelines(\"15 Add zeros ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 16. Add and populate fields Mukim_Lot_No, Mukimlot_wo_letter, and Permit_date\r\n logFile.writelines(\"16 Add and populate fields starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsPop = arcpy.UpdateCursor(config.SplittedProjLotRows)\r\n for row in rowsPop:\r\n expression = str(row.Project_Mukim_nos) + \"-\" + str(row.Project_Lot_nos)\r\n row.Mukim_Lot_No = expression\r\n date = filedate.strftime(\"%Y%m%d\")\r\n year = int(date[:4])\r\n month = int(date[4:6])\r\n day = int(date[6:8])\r\n permit_date = datetime.datetime(year, month, day)\r\n row.Permit_date = permit_date\r\n rowsPop.updateRow(row)\r\n if row:\r\n del row\r\n if rowsPop:\r\n del rowsPop\r\n # Calculate Mukimlot_wo_letter\r\n arcpy.CalculateField_management(config.SplittedProjLotRows, \"Mukimlot_wo_letter\", \"!Mukim_Lot_No![:10]\",\r\n \"PYTHON_9.3\", \"\")\r\n\r\n except:\r\n log_error(\"Error in 16 Add and populate fields: \", logFile)\r\n logFile.writelines(\"16 Add and populate fields ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 17.Match mukim lot and land lot\r\n logFile.writelines(\"17 Match mukim lot with landlot starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n arcpy.MatchMukimLandLot()\r\n except:\r\n log_error(\"Error in 17 Match mukim lot with landlot: \", logFile)\r\n logFile.writelines(\"17 Match mukim lot with landlot ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 18.Get unmatched mukim lot with land lot\r\n logFile.writelines(\"18 Get unmatched mukim lot starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.AddMessage(\"18 Get unmatched mukim lot\")\r\n try:\r\n arcpy.GetUnmatchedMukimLot()\r\n\r\n except:\r\n log_error(\"Error in 18 Get unmatched mukim lot: \", logFile)\r\n\r\n logFile.writelines(\"18 Get unmatched mukim lot ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 19. Log errors for unmatched mukim lots\r\n logFile.writelines(\"19 Log unmatched mukim lot starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsUnmatched = arcpy.SearchCursor(config.UnmatchedMukimLot)\r\n row = None\r\n\r\n for row in rowsUnmatched:\r\n message = ['Unmatched mukim lot with the land lot', row.Project_Ref_No, row.Project_Title,\r\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\r\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\r\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\r\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\r\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\r\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\r\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\r\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\r\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\r\n col_count = 0\r\n for element in message:\r\n sheet.write(row_count, col_count, element)\r\n col_count += 1\r\n row_count += 1\r\n wbk.save(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\")\r\n if row:\r\n del row\r\n if rowsUnmatched:\r\n del rowsUnmatched\r\n\r\n with xlrd.open_workbook(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\") as wb:\r\n sh = wb.sheet_by_index(0)\r\n if sh.nrows == 1:\r\n os.remove(config.ErrorLogFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \"_err\" + \".xls\")\r\n\r\n except arcpy.ExecuteError:\r\n log_error(\"Error in 19 Log unmatched mukim lot: \", logFile)\r\n logFile.writelines(\"19 Log unmatched mukim lot ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 20. Prepare the table for MukimConstruct matching (add required fields)\r\n logFile.writelines(\"20 Add fields to be used for matching starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n if arcpy.Exists(config.MUKIMCONSTRUCTImport):\r\n arcpy.Delete_management(config.MUKIMCONSTRUCTImport)\r\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructSource, config.TempDataGDB,\r\n \"MUKIM_CONSTRUCT_Import\")\r\n else:\r\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructSource, config.TempDataGDB,\r\n \"MUKIM_CONSTRUCT_Import\")\r\n\r\n arcpy.AddField_management(config.MatchedMukimLot, \"Concat_4fields\", \"Text\", \"\", \"\", \"\")\r\n arcpy.AddField_management(config.MUKIMCONSTRUCTImport, \"Concat_4fields\", \"Text\", \"\", \"\", \"\")\r\n arcpy.AddField_management(config.MatchedMukimLot, \"PROJ_DURATION_MTHS2\", \"Double\", \"\", \"\", \"\")\r\n except:\r\n log_error(\"Error in 20 Add fields to be used for matching: \", logFile)\r\n logFile.writelines(\"20 Add fields to be used for matching ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 21. Calculate Project Duration as months\r\n logFile.writelines(\"21 Calculate PROJ_DURATION as months starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsProjDur = arcpy.UpdateCursor(config.MatchedMukimLot)\r\n\r\n for row in rowsProjDur:\r\n durationstr = row.PROJ_DURATION_MTHS\r\n if \"Month\" in row.PROJ_DURATION_MTHS:\r\n durationintmth = int(durationstr.split(' ')[0])\r\n row.PROJ_DURATION_MTHS2 = durationintmth\r\n elif \"Year\" in row.PROJ_DURATION_MTHS:\r\n durationintyr = int(durationstr.split(' ')[0]) * 12\r\n row.PROJ_DURATION_MTHS2 = durationintyr\r\n rowsProjDur.updateRow(row)\r\n if rowsProjDur:\r\n del rowsProjDur\r\n if row:\r\n del row\r\n\r\n arcpy.DeleteField_management(config.MatchedMukimLot, \"PROJ_DURATION_MTHS\")\r\n arcpy.AddField_management(config.MatchedMukimLot, \"PROJ_DURATION_MTHS\", \"Double\")\r\n arcpy.CalculateField_management(config.MatchedMukimLot, \"PROJ_DURATION_MTHS\", \"[PROJ_DURATION_MTHS2]\")\r\n except:\r\n log_error(\"Error in 21 Calculate PROJ_DURATION as months: \", logFile)\r\n logFile.writelines(\"21 Calculate PROJ_DURATION as months ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 22. Concatenate 4 fields to be used in checking if mukimlot already exists in MUKIMCONSTRUCT\r\n logFile.writelines(\"22 Concatenate 4 fields starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsConcat1 = arcpy.UpdateCursor(config.MUKIMCONSTRUCTImport)\r\n\r\n for row in rowsConcat1:\r\n expression = str(row.PROJ_REF_NO) + \"-\" + str(row.BUILDER_NAME) + \"-\" + str(\r\n row.LOT_KEY) + \"-\" + str(row.PERMIT_DATE)\r\n row.Concat_4fields = expression\r\n rowsConcat1.updateRow(row)\r\n if row:\r\n del row\r\n if rowsConcat1:\r\n del rowsConcat1\r\n\r\n rowsConcat2 = arcpy.UpdateCursor(config.MatchedMukimLot)\r\n\r\n for row in rowsConcat2:\r\n expression = str(row.PROJ_REF_NO) + \"-\" + str(row.BUILDER_NAME) + \"-\" + str(\r\n row.LOT_KEY) + \"-\" + str(row.PERMIT_DATE)\r\n row.Concat_4fields = expression\r\n rowsConcat2.updateRow(row)\r\n if row:\r\n del row\r\n if rowsConcat2:\r\n del rowsConcat2\r\n except:\r\n log_error(\"Error in 22 Concatenate 4 fields: \", logFile)\r\n logFile.writelines(\"22 Concatenate 4 fields ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 23.Match mukim lot with mukim construct\r\n logFile.writelines(\"23 Match mukimlot with mukim construct at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.env.workspace = config.TempDataGDB # \"G:\\\\Project\\\\GERIUPGRADE\\\\GPTools\\\\NotificationSysTools\\\\BCAReportProcessing\\\\Temp_data.gdb\"\r\n try:\r\n arcpy.MatchedMukimlotMukimConstruct()\r\n except:\r\n log_error(\"Error in 23 Match mukimlot with mukim construct: \", logFile)\r\n logFile.writelines(\"23 Match mukimlot with mukim construct ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 24.Copy raw values to project lot and project mukim columns and delete the 2 fields\r\n logFile.writelines(\"24 Recalculate projlot and projmukim based on original values starts at \" + str(\r\n datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rowsRaw = arcpy.UpdateCursor(config.MatchedMukimLot)\r\n\r\n for row in rowsRaw:\r\n row.PROJ_MUKIM_NOS = row.PROJECTMUKIM_RAW\r\n row.PROJ_LOT_NOS = row.PROJECTLOT_RAW\r\n rowsRaw.updateRow(row)\r\n if row:\r\n del row\r\n if rowsRaw:\r\n del rowsRaw\r\n except:\r\n log_error(\"Error in 24 Recalculate projlot and projmukim based on original values:\", logFile)\r\n logFile.writelines(\"24 Recalculate projlot and projmukim based on original values ends at \" + str(\r\n datetime.datetime.now()) + \"\\n\")\r\n\r\n # 25. Export Cleaned BCA Permit report for CWD\r\n logFile.writelines(\r\n \"25 Export of Cleaned BCA Permit report starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n # Initialize the file\r\n CleanedBCAPermitReport = xlwt.Workbook()\r\n book = CleanedBCAPermitReport.add_sheet('Book 1')\r\n countrow = 0\r\n countcol = 0\r\n fields = ['Project Ref No', 'Project Title', 'House Blk No', 'Road Name', 'Level No', 'Unit No',\r\n 'Building Name', 'Postal Code', 'Project Mukim nos', 'Project Lot nos', 'Permit Type of Work',\r\n 'Type of Work', \"Owner's name\", \"Owner's firm name\", \"Owner's address\", \"Owner's Tel No\",\r\n \"Owner's Email address\", \"Builder's name\", \"Builder's firm name\", \"Builder's address\",\r\n \"Builder's Tel No\", \"Builder's email address\", \"PE's name\", \"PE's firm name\", \"PE's address\",\r\n \"PE's Tel No\", \"PE's Email address\", \"Architect's name\", \"Architect's firm name\",\r\n \"Architect's address\", \"Architect's Tel No\", \"Architect's Email address\", 'Project Cost',\r\n 'Project Duration', 'Approval Date(DD/MM/YYYY)']\r\n for fieldname in fields:\r\n book.write(countrow, countcol, fieldname)\r\n countcol += 1\r\n CleanedBCAPermitReport.save(config.CleanedBCAPermitFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \".xls\")\r\n\r\n # Copy the data to Excel File\r\n data = arcpy.SearchCursor(config.MatchedMukimLot)\r\n\r\n countrow = 1\r\n countcol = 0\r\n for row in data:\r\n message = [row.PROJ_REF_NO, row.PROJ_TITLE, row.HOUSE_BLK_NO, row.ROAD_NAME, row.LEVEL_NO,\r\n row.UNIT_NO, row.BUILDING_NAME, row.POSTAL_CODE, row.PROJ_MUKIM_NOS, row.PROJ_LOT_NOS,\r\n row.PERMIT_WORK_TYPE, row.WORK_TYPE, row.OWNER_NAME, row.OWNER_FIRM_NAME, row.OWNER_ADDR,\r\n row.OWNER_TEL, row.OWNER_EMAIL, row.BUILDER_NAME, row.BUILDER_FIRM_NAME,\r\n row.BUILDER_ADDR, row.BUILDER_TEL, row.BUILDER_EMAIL, row.PE_NAME, row.PE_FIRM_NAME,\r\n row.PE_ADDR, row.PE_TEL, row.PE_EMAIL, row.ARCHITECT_NAME, row.ARCHITECT_FIRM_NAME,\r\n row.ARCHITECT_ADDR, row.ARCHITECT_TEL, row.ARCHITECT_EMAIL, row.PROJ_COST,\r\n row.PROJ_DURATION_MTHS, row.PROJ_APPROVAL_DATE]\r\n countcol = 0\r\n for element in message:\r\n book.write(countrow, countcol, element)\r\n countcol += 1\r\n countrow += 1\r\n CleanedBCAPermitReport.save(config.CleanedBCAPermitFolder + \"\\\\\" + input_file_name.split(\".\")[0] + \".xls\")\r\n if row:\r\n del row\r\n if data:\r\n del data\r\n except:\r\n log_error(\"Error in 25 Export of Cleaned BCA Permit Report: Error in 26 Catchment calculation: \", logFile)\r\n logFile.writelines(\"25 Export of Cleaned BCA Permit Report ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 26. Catchment calculation\r\n arcpy.env.workspace = config.TempDataGDB\r\n logFile.writelines(\"26 Catchment calculation starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n arcpy.CatchmentCalculation()\r\n except:\r\n log_error(\"Error in 26 Catchment calculation: \", logFile)\r\n logFile.writelines(\"26 Catchment calculation ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 27. Depot calculation\r\n logFile.writelines(\"27 Depot calculation starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n arcpy.DepotCalculation()\r\n except:\r\n log_error(\"Error in 27 Depot calculation: \", logFile)\r\n logFile.writelines(\"27 Depot calculation ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 28. Re-add date fields and populate\r\n logFile.writelines(\"28 Re-add date fields and populate starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n arcpy.AddField_management(config.MUKIMCONSTRUCT_Temp, \"PERMIT_DATE\", \"Date\")\r\n arcpy.AddField_management(config.MUKIMCONSTRUCT_Temp, \"PROJ_APPROVAL_DATE2\", \"Date\")\r\n arcpy.AddField_management(config.MUKIMCONSTRUCT_Temp, \"PROJ_END_DATE\", \"Date\")\r\n\r\n rows = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\r\n\r\n for row in rows:\r\n date = filedate.strftime(\"%Y%m%d\")\r\n year = int(date[:4])\r\n month = int(date[4:6])\r\n day = int(date[6:8])\r\n permit_date = datetime.datetime(year, month, day)\r\n row.PERMIT_DATE = permit_date\r\n row.PROJ_APPROVAL_DATE2 = datetime.datetime.strptime(row.PROJ_APPROVAL_DATE, '%d/%m/%Y')\r\n rows.updateRow(row)\r\n if row:\r\n del row\r\n if rows:\r\n del rows\r\n except:\r\n log_error(\"Error in 28 Re-add fields and populate: \", logFile)\r\n logFile.writelines(\"28 Re-add fields and populate ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 29. Calculate the end date field\r\n logFile.writelines(\"29 Calculate the end date field starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n\r\n rowsEndDate = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\r\n\r\n for row in rowsEndDate:\r\n sourcedate = row.PROJ_APPROVAL_DATE2\r\n # sourcedate = datetime.datetime.strptime(row.PROJ_APPROVAL_DATE2 , '%d/%m/%Y')\r\n months = int(row.PROJ_DURATION_MTHS)\r\n d = add_months(sourcedate, months)\r\n row.PROJ_END_DATE = d\r\n rowsEndDate.updateRow(row)\r\n if row:\r\n del row\r\n if rowsEndDate:\r\n del rowsEndDate\r\n except:\r\n log_error(\"Error in 29 Calculate the end date field: \", logFile)\r\n logFile.writelines(\"29 Calculate the end date field ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 30. Calculate Project Total Area\r\n logFile.writelines(\"30 Project total area calculation starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n arcpy.ProjectTotalArea()\r\n except:\r\n log_error(\"Error in 30 Project total area calculation: \", logFile)\r\n logFile.writelines(\"30 Project total area calculation ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 31. Calculate the BCA_CORRECTED_BY\r\n logFile.writelines(\"31 Calculate the BCA_CORRECTED_BY starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n rows_BCA_CB = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\r\n\r\n for row in rows_BCA_CB:\r\n if \"\\WSN\\\\\" in BCAreport:\r\n row.BCA_CORRECTED_BY = \"WSN\"\r\n elif \"\\WRN\\\\\" in BCAreport:\r\n row.BCA_CORRECTED_BY = \"WRN\"\r\n elif \"\\CWD\\\\\" in BCAreport:\r\n row.BCA_CORRECTED_BY = \"CWD\"\r\n rows_BCA_CB.updateRow(row)\r\n if row:\r\n del row\r\n if rows_BCA_CB:\r\n del rows_BCA_CB\r\n except:\r\n log_error(\"Error in 31 Calculate the BCA_CORRECTED_BY: \", logFile)\r\n\r\n # 32. Remove spaces in PROJ_REF_NO\r\n logFile.writelines(\r\n \"32 Removing of spaces in mukim and project lot starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n try:\r\n rowsSpaces = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\r\n\r\n for row in rowsSpaces:\r\n lot_no_spaces = row.PROJ_REF_NO.strip()\r\n row.PROJ_REF_NO = lot_no_spaces\r\n rowsSpaces.updateRow(row)\r\n if row:\r\n del row\r\n if rowsSpaces:\r\n del rowsSpaces\r\n except:\r\n log_error(\"Error in 32 Removing of spaces in mukim and project lot: \", logFile)\r\n logFile.writelines(\r\n \"32 Removing of spaces in mukim and project lot ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 33. Process the Mukim Construct by Project\r\n logFile.writelines(\r\n \"33 Process the Mukim Construct by Project starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.env.overwriteOutput = True\r\n try:\r\n MUKIM_CONSTRUCT_BYPROJ_IMPORT = config.TempDataGDB + \"\\\\MUKIM_CONSTRUCT_BYPROJ_IMPORT\"\r\n MUKIMCONBYPROJ_SORT = config.TempDataGDB + \"\\\\MUKIMCONBYPROJ_SORT\"\r\n MUKIM_CONSTRUCT_BYPROJ_DISS = config.TempDataGDB + \"\\\\MUKIM_CONSTRUCT_BYPROJ_DISS\"\r\n MUKIM_CONSTRUCT_BYPROJ_DISS__2_ = config.TempDataGDB + \"\\\\MUKIM_CONSTRUCT_BYPROJ_DISS\"\r\n\r\n if arcpy.Exists(MUKIM_CONSTRUCT_BYPROJ_IMPORT):\r\n arcpy.Delete_management(MUKIM_CONSTRUCT_BYPROJ_IMPORT)\r\n if arcpy.Exists(MUKIMCONBYPROJ_SORT):\r\n arcpy.Delete_management(MUKIMCONBYPROJ_SORT)\r\n if arcpy.Exists(MUKIM_CONSTRUCT_BYPROJ_DISS):\r\n arcpy.Delete_management(MUKIM_CONSTRUCT_BYPROJ_DISS)\r\n\r\n arcpy.MUKIMCONBYPROJ()\r\n # arcpy.MUKIMCONSTRUCTBYPROJProcess2()\r\n\r\n arcpy.Sort_management(MUKIM_CONSTRUCT_BYPROJ_IMPORT, MUKIMCONBYPROJ_SORT, \"PROJ_END_DATE DESCENDING\",\r\n \"UR\")\r\n arcpy.Dissolve_management(MUKIMCONBYPROJ_SORT, MUKIM_CONSTRUCT_BYPROJ_DISS, \"PROJ_REF_NO\",\r\n \"LOT_KEY FIRST;PROJ_REF_NO FIRST;PROJ_TITLE FIRST;HOUSE_BLK_NO FIRST;ROAD_NAME FIRST;POSTAL_CODE FIRST;LEVEL_NO FIRST;UNIT_NO FIRST;BUILDING_NAME FIRST;PROJ_MUKIM_NOS FIRST;PROJ_LOT_NOS FIRST;PERMIT_WORK_TYPE FIRST;WORK_TYPE FIRST;OWNER_NAME FIRST;OWNER_FIRM_NAME FIRST;OWNER_ADDR FIRST;OWNER_TEL FIRST;OWNER_EMAIL FIRST;BUILDER_NAME FIRST;BUILDER_FIRM_NAME FIRST;BUILDER_ADDR FIRST;BUILDER_TEL FIRST;BUILDER_EMAIL FIRST;PE_NAME FIRST;PE_FIRM_NAME FIRST;PE_ADDR FIRST;PE_TEL FIRST;PE_EMAIL FIRST;ARCHITECT_NAME FIRST;ARCHITECT_FIRM_NAME FIRST;ARCHITECT_ADDR FIRST;ARCHITECT_TEL FIRST;ARCHITECT_EMAIL FIRST;PROJ_TOT_AREA FIRST;PROJ_PARENT_CWDCATCHMENT FIRST;PROJ_PARENT_WSNDEPOT FIRST;PROJ_PARENT_WRPCATCHMENT FIRST;BCA_CORRECTED_BY FIRST;PROJ_DURATION_MTHS FIRST;PROJ_COST FIRST\",\r\n \"MULTI_PART\", \"DISSOLVE_LINES\")\r\n arcpy.JoinField_management(MUKIM_CONSTRUCT_BYPROJ_DISS, \"FIRST_PROJ_REF_NO\", MUKIMCONBYPROJ_SORT,\r\n \"PROJ_REF_NO\", \"PROJ_APPROVAL_DATE;PROJ_END_DATE;PERMIT_DATE\")\r\n arcpy.CalculateField_management(MUKIM_CONSTRUCT_BYPROJ_DISS__2_, \"FIRST_PROJ_TOT_AREA\",\r\n \"[Shape_Area]/10000\", \"VB\", \"\")\r\n\r\n except:\r\n log_error(\"Error in 33 Process the Mukim Construct by Project: \", logFile)\r\n logFile.writelines(\r\n \"33 Process the Mukim Construct by Project ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n arcpy.AddMessage(\"33 END process MUKIM CONSTRUCT\")\r\n\r\n # 34. Filter on-going projects\r\n\r\n logFile.writelines(\"34 Filter on-going projects starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n # TempDataGDB = \"G:\\\\Project\\\\GERIUPGRADE\\\\GPTools\\\\NotificationSysTools\\\\BCAReportProcessing\\\\Temp_data.gdb\"\r\n MUKIM_CONSTRUCT_BYPROJ_DISS = config.TempDataGDB + \"\\\\MUKIM_CONSTRUCT_BYPROJ_DISS\"\r\n rowsIn = arcpy.UpdateCursor(MUKIM_CONSTRUCT_BYPROJ_DISS)\r\n\r\n row = None\r\n for row in rowsIn:\r\n strdays = str(row.PROJ_END_DATE.date() - datetime.date.today())\r\n splitDays = strdays.split()\r\n if splitDays[0] == '0:00:00':\r\n result = \"On-going project (but will end today)\"\r\n else:\r\n if int(splitDays[0]) < 0:\r\n rowsIn.deleteRow(row)\r\n else:\r\n result = \"On-going project\"\r\n if rowsIn:\r\n del rowsIn\r\n if row:\r\n del row\r\n\r\n except:\r\n log_error(\"Error in 34 Filter on-going projects: \", logFile)\r\n logFile.writelines(\"34 Filter on-going projects ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # 35. Append the new data to MUKIM_CONSTRUCT\r\n logFile.writelines(\r\n \"35 Append the new data to MUKIM_CONSTRUCT starts at \" + str(datetime.datetime.now()) + \"\\n\")\r\n try:\r\n arcpy.AppendNewData()\r\n except:\r\n log_error(\"Error in 35 Append the new data to MUKIM_CONSTRUCT: \", logFile)\r\n logFile.writelines(\r\n \"35 Append the new data to MUKIM_CONSTRUCT ends at \" + str(datetime.datetime.now()) + \"\\n\")\r\n\r\n # Clean the memory and the schema lock\r\n arcpy.RefreshCatalog(config.Notification)\r\n arcpy.Compact_management(config.TempDataGDB)\r\n gc.collect()\r\n\r\n # Status update to run/not run the SiteInspection Update\r\n Log_SiteInspectionUpdate = file(config.SiteInspectionUpdate, \"w\")\r\n Log_SiteInspectionUpdate.writelines(\"YES\")\r\n Log_SiteInspectionUpdate.close()\r\n\r\n arcpy.AddMessage(\"END BCA Processing\")\r\n arcpy.AddMessage(\"Passing file date to other functions: \" + repr(filedate))\r\n\r\n # Generate Report\r\n import ReportGeneration_Adhoc_WithProjects as gen_report\r\n gen_report.run(filedate)\r\n #\r\n # # Send email to departments\r\n # import EmailGenerationCompletion_adhoc as send_dept_notification\r\n # if \"CORRECTED\" in BCAreport.upper():\r\n # send_dept_notification.run(filedate, corrected=True)\r\n # else:\r\n # send_dept_notification.run(filedate)\r\n\r\n # Generate advisory letters\r\n import LetterGeneration as letter_gen\r\n letter_gen.run(filedate)\r\n #\r\n # # Send letters to project team\r\n # import EmailGeneration as send_advisory_email\r\n # send_advisory_email.run(filedate)\r\n\r\n\r\n # 36. Move the BCAReport in the backup folder\r\n for BCAreport in correct_config_files:\r\n\r\n input_file_name = BCAreport.split(\"\\\\\")[-1]\r\n bk_file_path = os.path.join(config.BCAreportBackupFolder, input_file_name)\r\n\r\n # if the same file name exists in the backup folder, rename the new file with timestamp and move\r\n if os.path.exists(bk_file_path):\r\n\r\n new_filename = datetime.datetime.now().strftime(\"%Y%m%d-%H%M\") + input_file_name\r\n new_filepath = os.path.join(config.BCAreportBackupFolder, new_filename)\r\n shutil.copy(BCAreport, new_filepath)\r\n os.remove(BCAreport)\r\n\r\n # if the filename does not exist in the backup folder, move the file to backup\r\n else:\r\n shutil.move(BCAreport, config.BCAreportBackupFolder)\r\n\r\n logFile.writelines(\"Moved the BCA report to the backup folder at \" + str(datetime.datetime.now()) + \"\\n\")\r\n logFile.close()","def cmd_error_check(self, cmd_out):\n for err in self.err_strings:\n if re.search('\\\\b%s\\\\b' % (err), cmd_out, re.I):\n _log.info(cmd_out)\n _log.info(\n \"Cmd execution failed! with this Return Error: \\n%s\" % (\n cmd_out))\n return 0","def test_failedCommandProvidesOutput(self):\n bookTeX = FilePath(self.mktemp() + \".tex\")\n builder = BookBuilder()\n inputState = bookTeX.parent().children()\n exc = self.assertRaises(\n CommandFailed,\n builder.buildPDF,\n bookTeX, self.howtoDir, FilePath(self.mktemp()))\n self.assertTrue(exc.output)\n newOutputState = set(bookTeX.parent().children()) - set(inputState)\n self.assertEqual(len(newOutputState), 1)\n workPath = newOutputState.pop()\n self.assertTrue(\n workPath.isdir(),\n \"Expected work path %r was not a directory.\" % (workPath.path,))","def test_check_exit_status(self):\n run_dir_success = 'data/nanopore_data/run4/done_demuxing/20200104_1412_MN19414_AAU644_68125dc2'\n success_run = MinIONqc(run_dir_success, None, None)\n self.assertTrue(success_run.check_exit_status('data/nanopore_data/run4/done_demuxing/20200104_1412_MN19414_AAU644_68125dc2/.exitcode_for_nanoseq'))\n run_dir_fail = 'data/nanopore_data/run8/demux_failed/20200108_1412_MN19414_AAU648_68125dc2'\n fail_run = MinIONqc(run_dir_fail, None, None)\n self.assertFalse(fail_run.check_exit_status('data/nanopore_data/run8/demux_failed/20200108_1412_MN19414_AAU648_68125dc2/.exitcode_for_nanoseq'))","def run_command_check(self):\n pass","def check_commands(self):\n pass","def run_test_second():\n os.system(\n \"sed -n '/(Failed)$/p' test_op_log.txt | awk '{print $3}' >& rerun_op.txt\"\n )\n rerun_list = get_op_list('rerun_op.txt')\n if len(rerun_list):\n print(\n \"-------there are \"\n + str(len(rerun_list))\n + \" op(s) need to rerun!!!-------\"\n )\n for failed_op in rerun_list:\n os.system(\"ctest -R \\\"(\" + failed_op + \")\\\" \")\n else:\n print(\"-------all op passed successfully!!!-------\")","def extract_failed_tests_info():\n global g_failed_testnames\n global g_failed_test_paths\n\n if os.path.isfile(g_temp_filename):\n console_file = open(g_temp_filename,'r') # open temp file that stored jenkins job console output\n try:\n for each_line in console_file: # go through each line of console output to extract build ID, data/time ...\n each_line.strip()\n print(each_line)\n if (\"Test Result\" in each_line) and (\"failure\" in each_line): # the next few lines will contain failed tests\n temp = each_line.split(\"testReport\")\n if (\"Test Result\" in temp[1]) and (\"failure\" in temp[1]): # grab number of failed tests\n try:\n tempCount = int(temp[1].split(\"</a>\")[1].split(\" \")[0].split(\"(\")[1])\n\n if isinstance(tempCount, int) and tempCount > 0: # temp[1], temp[2],... should contain failed tests\n for findex in range(2,len(temp)):\n tempMess = temp[findex].split(\">\")\n g_failed_test_paths.append(tempMess[0].strip('\"'))\n ftestname = tempMess[1].strip(\"</a\")\n nameLen = len(ftestname)\n true_testname = ftestname[8:nameLen] if 'r_suite.' in ftestname else ftestname\n g_failed_testnames.append(true_testname)\n break # done. Only one spot contains failed test info.\n except:\n break # file probably does not have failures captured.\n finally:\n console_file.close()","def test_stratis_bad_subcommand(self):\n for command_line in [\n [\"notasub\"],\n [\"daemon\", \"notasub\"],\n [\"pool\", \"notasub\"],\n [\"blockdev\", \"notasub\"],\n [\"filesystem\", \"notasub\"],\n ]:\n for prefix in [[], [\"--propagate\"]]:\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)","def testError(self):\n cmds = \"\"\"chown 0 missingFile\npwd\nexit\n\"\"\"\n\n def _cbCheckResult(res):\n self.assertNotIn(self.testDir.asBytesMode().path, res)\n\n d = self._getBatchOutput(cmds)\n d.addCallback(_cbCheckResult)\n return d","def slurm_check(path='.'):\n for file in shrunner.get_files(path, '.out'):\n with open(file, 'r') as f:\n for line in f.read().splitlines():\n if 'issue' in line.lower():\n print(file)\n print(line)\n print('-' * 40)","def checkForCommand(quickLogger, commandList):\n\n for command in commandList:\n\n cmd = \"which -s \" + command + \" > \" + os.devnull + \" 2>&1\"\n retcode = os.system(cmd)\n \n if(retcode):\n quickLogger.critical(\"unix command \"+command+\" not found.\")\n raise CommandNotFound","def has_failed_outputs(self):\n return False","def test_duplicatefslabels_run_exception(self, get_label_dict_mock):\n with contextlib.redirect_stdout(self.output):\n self.assertFalse(moduletests.src.duplicatefslabels.run())\n self.assertTrue(self.output.getvalue().endswith(\"Review the logs to determine the cause of the issue.\\n\"))\n self.assertTrue(get_label_dict_mock.called)","def test_process_host_commands(self):\n\n command = [\"df\", \"-h\"]\n output = run(verification.process_host_commands(command))\n self.assertTrue(\"```\\nThat command is not available.```\" not in output)\n\n command = [\"ls\", \"-la\"]\n output = run(verification.process_host_commands(command))\n self.assertEqual(\"```\\nThat command is not available.```\", output)","def report():\n\n global COUNTER\n \n if COUNTER > 0:\n print('\\n\\n')\n\n print('Searched {0} files'.format(SEARCHED))\n print('Found {0} TODOs in {1} files'.format(COUNTER, F_COUNTER))","def test_fixture_missing_results(tmp_sample_project):\n config_dir = tmp_sample_project\n output = subprocess.run([\"smif\", \"missing_results\", \"energy_central\", \"-d\", config_dir],\n stdout=subprocess.PIPE)\n\n out_str = str(output.stdout)\n assert(out_str.count('model run: energy_central') == 1)\n assert(out_str.count('sos model: energy') == 1)\n assert(out_str.count('sector model:') == 1)\n assert(out_str.count('output:') == 2)\n assert(out_str.count('output: cost') == 1)\n assert(out_str.count('output: water_demand') == 1)\n assert(out_str.count('no missing results') == 0)\n assert(out_str.count('results missing for:') == 2)\n\n # Run energy_central and re-check output with optional flag for completed results\n subprocess.run([\"smif\", \"run\", \"energy_central\", \"-d\", config_dir], stdout=subprocess.PIPE)\n output = subprocess.run([\"smif\", \"missing_results\", \"energy_central\", \"-d\", config_dir],\n stdout=subprocess.PIPE)\n\n out_str = str(output.stdout)\n assert(out_str.count('model run: energy_central') == 1)\n assert(out_str.count('sos model: energy') == 1)\n assert(out_str.count('sector model:') == 1)\n assert(out_str.count('output:') == 2)\n assert(out_str.count('output: cost') == 1)\n assert(out_str.count('output: water_demand') == 1)\n assert(out_str.count('no missing results') == 2)\n assert(out_str.count('results missing for:') == 0)","def test_error_before_all_processes_complete(self):\n first = \"\"\"file://B <- file://A\n sleep 1\n echo A produces B > B\n error\n \nfile://C <- file://A\n sleep 2\n echo A produces C > C\n \"\"\"\n\n rcode, output = run_tuttle_file(first, nb_workers=2)\n assert rcode == 2\n assert isfile('B')\n assert not isfile('C')\n w = Workflow.load()\n p = w.find_process_that_creates(\"file://C\")\n assert not p.success, \"Process that creates C should be in error in the dump\"","def files_exist(self):\n\n passed = []\n warned = []\n failed = []\n ignored = []\n\n # NB: Should all be files, not directories\n # List of lists. Passes if any of the files in the sublist are found.\n #: test autodoc\n try:\n _, short_name = self.nf_config[\"manifest.name\"].strip(\"\\\"'\").split(\"/\")\n except ValueError:\n log.warning(\"Expected manifest.name to be in the format '<repo>/<pipeline>'. Will assume it is '<pipeline>'.\")\n short_name = self.nf_config[\"manifest.name\"].strip(\"\\\"'\").split(\"/\")\n\n files_fail = [\n [\".gitattributes\"],\n [\".gitignore\"],\n [\".nf-core.yml\"],\n [\".editorconfig\"],\n [\".prettierignore\"],\n [\".prettierrc.yml\"],\n [\"CHANGELOG.md\"],\n [\"CITATIONS.md\"],\n [\"CODE_OF_CONDUCT.md\"],\n [\"CODE_OF_CONDUCT.md\"],\n [\"LICENSE\", \"LICENSE.md\", \"LICENCE\", \"LICENCE.md\"], # NB: British / American spelling\n [\"nextflow_schema.json\"],\n [\"nextflow.config\"],\n [\"README.md\"],\n [os.path.join(\".github\", \".dockstore.yml\")],\n [os.path.join(\".github\", \"CONTRIBUTING.md\")],\n [os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"bug_report.yml\")],\n [os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"config.yml\")],\n [os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"feature_request.yml\")],\n [os.path.join(\".github\", \"PULL_REQUEST_TEMPLATE.md\")],\n [os.path.join(\".github\", \"workflows\", \"branch.yml\")],\n [os.path.join(\".github\", \"workflows\", \"ci.yml\")],\n [os.path.join(\".github\", \"workflows\", \"linting_comment.yml\")],\n [os.path.join(\".github\", \"workflows\", \"linting.yml\")],\n [os.path.join(\"assets\", \"email_template.html\")],\n [os.path.join(\"assets\", \"email_template.txt\")],\n [os.path.join(\"assets\", \"sendmail_template.txt\")],\n [os.path.join(\"assets\", f\"nf-core-{short_name}_logo_light.png\")],\n [os.path.join(\"conf\", \"modules.config\")],\n [os.path.join(\"conf\", \"test.config\")],\n [os.path.join(\"conf\", \"test_full.config\")],\n [os.path.join(\"docs\", \"images\", f\"nf-core-{short_name}_logo_light.png\")],\n [os.path.join(\"docs\", \"images\", f\"nf-core-{short_name}_logo_dark.png\")],\n [os.path.join(\"docs\", \"output.md\")],\n [os.path.join(\"docs\", \"README.md\")],\n [os.path.join(\"docs\", \"README.md\")],\n [os.path.join(\"docs\", \"usage.md\")],\n [os.path.join(\"lib\", \"nfcore_external_java_deps.jar\")],\n [os.path.join(\"lib\", \"NfcoreTemplate.groovy\")],\n [os.path.join(\"lib\", \"Utils.groovy\")],\n [os.path.join(\"lib\", \"WorkflowMain.groovy\")],\n ]\n\n files_warn = [\n [\"main.nf\"],\n [os.path.join(\"assets\", \"multiqc_config.yml\")],\n [os.path.join(\"conf\", \"base.config\")],\n [os.path.join(\"conf\", \"igenomes.config\")],\n [os.path.join(\".github\", \"workflows\", \"awstest.yml\")],\n [os.path.join(\".github\", \"workflows\", \"awsfulltest.yml\")],\n [os.path.join(\"lib\", f\"Workflow{short_name[0].upper()}{short_name[1:]}.groovy\")],\n [\"modules.json\"],\n [\"pyproject.toml\"],\n ]\n\n # List of strings. Fails / warns if any of the strings exist.\n files_fail_ifexists = [\n \"Singularity\",\n \"parameters.settings.json\",\n \".nf-core.yaml\", # yml not yaml\n os.path.join(\"bin\", \"markdown_to_html.r\"),\n os.path.join(\"conf\", \"aws.config\"),\n os.path.join(\".github\", \"workflows\", \"push_dockerhub.yml\"),\n os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"bug_report.md\"),\n os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"feature_request.md\"),\n os.path.join(\"docs\", \"images\", f\"nf-core-{short_name}_logo.png\"),\n \".markdownlint.yml\",\n \".yamllint.yml\",\n os.path.join(\"lib\", \"Checks.groovy\"),\n os.path.join(\"lib\", \"Completion.groovy\"),\n os.path.join(\"lib\", \"Workflow.groovy\"),\n ]\n files_warn_ifexists = [\".travis.yml\"]\n\n # Remove files that should be ignored according to the linting config\n ignore_files = self.lint_config.get(\"files_exist\", [])\n\n def pf(file_path):\n return os.path.join(self.wf_path, file_path)\n\n # First - critical files. Check that this is actually a Nextflow pipeline\n if not os.path.isfile(pf(\"nextflow.config\")) and not os.path.isfile(pf(\"main.nf\")):\n failed.append(\"File not found: nextflow.config or main.nf\")\n raise AssertionError(\"Neither nextflow.config or main.nf found! Is this a Nextflow pipeline?\")\n\n # Files that cause an error if they don't exist\n for files in files_fail:\n if any([f in ignore_files for f in files]):\n continue\n if any([os.path.isfile(pf(f)) for f in files]):\n passed.append(f\"File found: {self._wrap_quotes(files)}\")\n else:\n failed.append(f\"File not found: {self._wrap_quotes(files)}\")\n\n # Files that cause a warning if they don't exist\n for files in files_warn:\n if any([f in ignore_files for f in files]):\n continue\n if any([os.path.isfile(pf(f)) for f in files]):\n passed.append(f\"File found: {self._wrap_quotes(files)}\")\n else:\n warned.append(f\"File not found: {self._wrap_quotes(files)}\")\n\n # Files that cause an error if they exist\n for file in files_fail_ifexists:\n if file in ignore_files:\n continue\n if os.path.isfile(pf(file)):\n failed.append(f\"File must be removed: {self._wrap_quotes(file)}\")\n else:\n passed.append(f\"File not found check: {self._wrap_quotes(file)}\")\n\n # Files that cause a warning if they exist\n for file in files_warn_ifexists:\n if file in ignore_files:\n continue\n if os.path.isfile(pf(file)):\n warned.append(f\"File should be removed: {self._wrap_quotes(file)}\")\n else:\n passed.append(f\"File not found check: {self._wrap_quotes(file)}\")\n\n # Files that are ignoed\n for file in ignore_files:\n ignored.append(f\"File is ignored: {self._wrap_quotes(file)}\")\n\n return {\"passed\": passed, \"warned\": warned, \"failed\": failed, \"ignored\": ignored}","def _verifyCommand(self):\n for i in range(3):\n rc = self.subdevice.command_test() # Verify command is correct\n if rc is None:\n break","def test_otter_check_script(self):\n # run for each individual test\n for file in glob(TEST_FILES_PATH + \"tests/*.py\"):\n # capture stdout\n output = StringIO()\n with contextlib.redirect_stdout(output):\n\n # mock block_print otherwise it interferes with capture of stdout\n with mock.patch(\"otter.check.block_print\"):\n check(\n TEST_FILES_PATH + \"file0.py\", \n question = os.path.split(file)[1][:-3],\n tests_path = os.path.split(file)[0],\n )\n\n if os.path.split(file)[1] != \"q2.py\":\n self.assertEqual(\n output.getvalue().strip().split(\"\\n\")[-1].strip(), \n \"All tests passed!\", \n \"Did not pass test at {}\".format(file)\n )\n\n # run the file for all questions\n output = StringIO()\n with contextlib.redirect_stdout(output):\n with mock.patch(\"otter.check.block_print\"):\n check(\n TEST_FILES_PATH + \"file0.py\", \n tests_path = os.path.split(file)[0],\n )\n self.assertEqual(\n output.getvalue().strip(), \n dedent(\"\"\"\\\n [0. 0.02002002 0.04004004 0.06006006 0.08008008]\n q1 results: All test cases passed!\n q2 results:\n q2 - 1 result:\n Trying:\n 1 == 1\n Expecting:\n False\n **********************************************************************\n Line 2, in q2 0\n Failed example:\n 1 == 1\n Expected:\n False\n Got:\n True\n\n q2 - 2 result:\n Test case passed!\n q3 results: All test cases passed!\n q4 results: All test cases passed!\n q5 results: All test cases passed!\"\"\"), \n \"Did not pass correct tests\"\n )","def syntax_check(self, working_dir, disco_ver):\n\n bar = ''\n spinner = ''\n if progressbar:\n progressbar.streams.flush()\n progressbar.streams.wrap_stdout()\n widgets = [progressbar.AnimatedMarker(),\n ' Checking syntax. ',\n progressbar.Timer()]\n bar = progressbar.ProgressBar(widgets=widgets,\n max_value=progressbar.UnknownLength,\n redirect_stdout=True)\n else:\n spinner = itertools.cycle(['-', '/', '|', '\\\\'])\n log.debug(\"Module progressbar2 is not installed, will show progress in usual manner.\")\n pass\n\n tpl_mod_dir = os.path.abspath(os.path.join(__file__ , \"../..\"))\n tplint_exe_path = tpl_mod_dir + '\\\\tplint\\\\tplint.exe'\n tplint_tax_path = tpl_mod_dir+'\\\\taxonomy\\\\00taxonomy.xml'\n syntax_passed = False\n\n # errors_re = re.compile(\"\\s+Errors:\\s+(.+)\")\n # mod_re = re.compile(\"Module:\\s+(.+)\")\n match_result = re.compile(\"(?P<error>\\w+\\s\\w+) at or near '(?P<near>\\S+)', \"\n \"line (?P<line>\\d+), in (?P<module>\\S+)\")\n\n log.debug(\"Syntax: Will check_ide all files in path: \" + str(working_dir))\n\n if disco_ver not in self.SYNTAX_SUPPORTED:\n log.info(\"NOTE: tplint was updated in 2016 last time, \"\n \"so we can use only version which is not greater then 11.0\")\n disco_ver = 11.0\n\n # Lines will be collected in list:\n result_out = []\n if os.path.exists(tplint_exe_path) and os.path.exists(tplint_tax_path):\n cmd = \" --discovery-versions=\"+str(disco_ver)+\" --loglevel=WARN -t \"+tplint_tax_path\n\n # noinspection PyBroadException\n try:\n open_path = subprocess.Popen(tplint_exe_path+cmd, cwd=working_dir, stdout=subprocess.PIPE)\n\n # Show progress with fancy progressbar:\n while open_path.stdout is not None:\n if progressbar:\n bar.update()\n else:\n sys.stdout.write(next(spinner))\n sys.stdout.flush()\n sys.stdout.write('\\b') # Working fine in win CMD but not in PyCharm.\n\n out = open_path.stdout.readline()\n result_out.append(out.decode('UTF-8').rstrip('\\r'))\n\n if not out:\n break\n time.sleep(0.01)\n # Final result:\n result = ''.join(result_out)\n if \"No issues found!\" in result:\n # Close bar, do not forget to.\n if progressbar:\n bar.finish()\n log.info(\"Build OK: Syntax: PASSED!\")\n syntax_passed = True\n sys.stdout.flush()\n\n elif match_result.findall(result):\n # Close bar, do not forget to.\n if progressbar:\n bar.finish()\n # error_modules = mod_re.findall(result)\n # errors = errors_re.findall(result)\n log.error(\"Syntax: ERROR: Some issues found!\"\"\\n\" + str(result))\n sys.stdout.flush()\n else:\n log.error(\"Syntax: Something is not OK \\n\" + str(result))\n except:\n log.error(\"Syntax: Tplint cannot run, check_ide if working dir is present!\")\n log.error(\"Syntax: Tplint use path: \" + tpl_mod_dir)\n else:\n log.warning(\"Path to tplint module is not exist. Please check_ide this: \"\n \"https://github.com/trianglesis/BMC_TPL_IDE#syntax-check_ide\")\n # noinspection PyPep8\n log.debug(\"Those paths expected: \"\n \"\\ntplint_exe_path - \"+str(tplint_exe_path) +\n \"\\ntplint_tax_path - \"+str(tplint_tax_path))\n\n return syntax_passed","def run_checks(hooks_all, hooks_modified, modified, path):\n retcode = 0\n for command in hooks_all:\n if not isinstance(command, list):\n command = shlex.split(command)\n retcode |= subprocess.call(command, env={'PATH': path})\n\n for pattern, command in hooks_modified:\n if not isinstance(command, list):\n command = shlex.split(command)\n for filename in modified:\n if not fnmatch.fnmatch(filename, pattern):\n continue\n printed_filename = False\n proc = subprocess.Popen(command + [filename],\n env={'PATH': path},\n stdout=subprocess.PIPE,\n stderr=subprocess.STDOUT)\n output = proc.communicate()[0]\n if proc.returncode != 0:\n if not printed_filename:\n print(filename)\n print('=' * len(filename))\n printed_filename = True\n print(command[0])\n print('-' * len(command[0]))\n print(output)\n retcode |= proc.returncode\n\n return retcode","def execute(self, collectedDir):\n success = 0\n failure = 0\n\n targets = os.listdir(collectedDir)\n for target in targets:\n fileName = \"%s/%s\" % (collectedDir, target)\n\n wxXmlParser = WxXmlParser()\n wxXmlParser.execute(fileName)\n\n station_id = wxXmlParser.key_value['station_id']\n if len(station_id) < 1:\n failure = failure+1\n else:\n wxLoader = WxLoader()\n if wxLoader.execute(wxXmlParser.key_value):\n success = success+1\n else:\n failure = failure+1\n\n print \"end success:%d failure:%d\" % (success, failure)","def run_command(cmd, log_file, time_file):\r\n sts = 0\r\n try_times = -1\r\n while True:\r\n try_times += 1\r\n if try_times > 2: # try to run the command 4 times --> change to 3 times\r\n break\r\n etime = ElapsedTime()\r\n etime.play()\r\n log = \"Running Command: %s [%s]\" % (cmd, etime.get_play_time())\r\n if try_times:\r\n log += \"-- TryTime: %d\" % try_times\r\n say_it(log)\r\n say_it(\" <%s>\" % os.getcwd())\r\n sts, text = get_status_output(cmd)\r\n etime.stop()\r\n append_file(log_file, [\"=\" * 30,cmd, etime] + text)\r\n append_file(time_file, [cmd, \"rem %s\" % etime])\r\n if sts:\r\n t = \"Status: Failed.\"\r\n else:\r\n t = \"Status: Pass.\"\r\n say_it(\"%s %s\" % (t, etime))\r\n time.sleep(3.14)\r\n if not sts:\r\n break\r\n # flow failed!\r\n have_license_error = simple_parser(log_file, p_license_error, 100)\r\n if have_license_error:\r\n # backup log file and re-launch the command after 1 minute\r\n backup_log_file = log_file+str(try_times)\r\n if os.path.isfile(backup_log_file):\r\n os.remove(backup_log_file)\r\n os.rename(log_file, backup_log_file)\r\n time.sleep(30) # change 60 --> 30\r\n else:\r\n if abnormal_exit(log_file):\r\n time.sleep(30)\r\n else:\r\n break\r\n if sts:\r\n error_msg_line = simple_parser(log_file, p_error_msg, 100)\r\n if error_msg_line:\r\n say_it(error_msg_line[0])\r\n say_it(\"\")\r\n return sts","def test_dump_and_report_workflow(self):\n project = \"\"\"file://result <- file://A\n echo result > result\n error\n \"\"\"\n rcode, output = run_tuttle_file(project)\n assert rcode == 2\n assert path.isfile(path.join(\".tuttle\", \"last_workflow.pickle\"))","def test_governed_folders_high(tmp_trestle_dir: pathlib.Path, command_string: str, return_code: int) -> None:\n with mock.patch.object(sys, 'argv', command_string.split()):\n with pytest.raises(SystemExit) as wrapped_error:\n trestle.cli.run()\n # FIXME: Needs to be changed once implemented.\n assert wrapped_error.type == SystemExit\n assert wrapped_error.value.code == return_code","def run(self, uname):\n\n out = []\n\n sol_dir = get_ex_solution(self.exname, uname)\n exec_path = join(sol_dir, \"solution\")\n test_out = join(sol_dir, \"test_out\")\n\n if not isfile(exec_path):\n return\n\n for test in self.testcases:\n in_path = get_test_in_path(test)\n out_path = get_test_out_path(test)\n\n test_proc = subprocess.Popen([exec_path],\n stdin=open(in_path),\n stdout=open(test_out, \"w+\"))\n try:\n test_proc.wait(timeout=self.timeout)\n except:\n out.append({\n 'comment': \"Execution timed out after {0}s.\".format(self.timeout),\n 'percentage': 0,\n 'suggestion': True,\n 'description': []\n })\n\n # Compare output to expected output\n with open(test_out) as actual_out:\n with open(out_path) as expected_out:\n res = list(unified_diff(\n list(actual_out), list(expected_out),\n fromfile=\"actual\", tofile=\"expected\"))\n\n if res:\n out.append({\n 'comment': \"Incorrect output in testcase {0}.\".format(test),\n 'percentage': 30,\n 'suggestion': False,\n 'description': res\n })\n\n\n\n return out","def test_bad_file() -> None:\n\n bad = random_string()\n rv, out = getstatusoutput(f'{RUN} {bad}')\n assert rv != 0\n assert out.lower().startswith('usage:')\n assert re.search(f\"No such file or directory: '{bad}'\", out)","def test_stats(tool):\n\n with pytest.raises(Exceptions.Error):\n tool.command(\"stats\", f\"-f 'bad_function' {tool.good_paths[0]}\")","def _check_results(self):\n if not 'EXECUTION OF GAMESS TERMINATED NORMALLY' in self.file_dic['output']:\n print self.job_name + \" didn't finish\"\n raise TypeError('Calculation didn\\'t finish')","def check_errors():\n\n for error in errors:\n ERROR('%s' % str(error))\n\n if len(errors) != 0:\n sys.exit(1)","def files_unchanged(self):\n\n passed = []\n failed = []\n ignored = []\n fixed = []\n could_fix = False\n\n # Check that we have the minimum required config\n required_pipeline_config = {\"manifest.name\", \"manifest.description\", \"manifest.author\"}\n missing_pipeline_config = required_pipeline_config.difference(self.nf_config)\n if missing_pipeline_config:\n return {\"ignored\": [f\"Required pipeline config not found - {missing_pipeline_config}\"]}\n try:\n prefix, short_name = self.nf_config[\"manifest.name\"].strip(\"\\\"'\").split(\"/\")\n except ValueError:\n log.warning(\n \"Expected manifest.name to be in the format '<repo>/<pipeline>'. Will assume it is <pipeline> and default to repo 'nf-core'\"\n )\n short_name = self.nf_config[\"manifest.name\"].strip(\"\\\"'\")\n prefix = \"nf-core\"\n\n # NB: Should all be files, not directories\n # List of lists. Passes if any of the files in the sublist are found.\n files_exact = [\n [\".gitattributes\"],\n [\".prettierrc.yml\"],\n [\"CODE_OF_CONDUCT.md\"],\n [\"LICENSE\", \"LICENSE.md\", \"LICENCE\", \"LICENCE.md\"], # NB: British / American spelling\n [os.path.join(\".github\", \".dockstore.yml\")],\n [os.path.join(\".github\", \"CONTRIBUTING.md\")],\n [os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"bug_report.yml\")],\n [os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"config.yml\")],\n [os.path.join(\".github\", \"ISSUE_TEMPLATE\", \"feature_request.yml\")],\n [os.path.join(\".github\", \"PULL_REQUEST_TEMPLATE.md\")],\n [os.path.join(\".github\", \"workflows\", \"branch.yml\")],\n [os.path.join(\".github\", \"workflows\", \"linting_comment.yml\")],\n [os.path.join(\".github\", \"workflows\", \"linting.yml\")],\n [os.path.join(\"assets\", \"email_template.html\")],\n [os.path.join(\"assets\", \"email_template.txt\")],\n [os.path.join(\"assets\", \"sendmail_template.txt\")],\n [os.path.join(\"assets\", f\"nf-core-{short_name}_logo_light.png\")],\n [os.path.join(\"docs\", \"images\", f\"nf-core-{short_name}_logo_light.png\")],\n [os.path.join(\"docs\", \"images\", f\"nf-core-{short_name}_logo_dark.png\")],\n [os.path.join(\"docs\", \"README.md\")],\n [os.path.join(\"lib\", \"nfcore_external_java_deps.jar\")],\n [os.path.join(\"lib\", \"NfcoreTemplate.groovy\")],\n ]\n files_partial = [\n [\".gitignore\", \".prettierignore\", \"pyproject.toml\"],\n ]\n\n # Only show error messages from pipeline creation\n logging.getLogger(\"nf_core.create\").setLevel(logging.ERROR)\n\n # Generate a new pipeline with nf-core create that we can compare to\n tmp_dir = tempfile.mkdtemp()\n\n # Create a template.yaml file for the pipeline creation\n template_yaml = {\n \"name\": short_name,\n \"description\": self.nf_config[\"manifest.description\"].strip(\"\\\"'\"),\n \"author\": self.nf_config[\"manifest.author\"].strip(\"\\\"'\"),\n \"prefix\": prefix,\n }\n\n template_yaml_path = os.path.join(tmp_dir, \"template.yaml\")\n with open(template_yaml_path, \"w\") as fh:\n yaml.dump(template_yaml, fh, default_flow_style=False)\n\n test_pipeline_dir = os.path.join(tmp_dir, f\"{prefix}-{short_name}\")\n create_obj = nf_core.create.PipelineCreate(\n None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path\n )\n create_obj.init_pipeline()\n\n # Helper functions for file paths\n def _pf(file_path):\n \"\"\"Helper function - get file path for pipeline file\"\"\"\n return os.path.join(self.wf_path, file_path)\n\n def _tf(file_path):\n \"\"\"Helper function - get file path for template file\"\"\"\n return os.path.join(test_pipeline_dir, file_path)\n\n # Files that must be completely unchanged from template\n for files in files_exact:\n # Ignore if file specified in linting config\n ignore_files = self.lint_config.get(\"files_unchanged\", [])\n if any([f in ignore_files for f in files]):\n ignored.append(f\"File ignored due to lint config: {self._wrap_quotes(files)}\")\n\n # Ignore if we can't find the file\n elif not any([os.path.isfile(_pf(f)) for f in files]):\n ignored.append(f\"File does not exist: {self._wrap_quotes(files)}\")\n\n # Check that the file has an identical match\n else:\n for f in files:\n try:\n if filecmp.cmp(_pf(f), _tf(f), shallow=True):\n passed.append(f\"`{f}` matches the template\")\n else:\n if \"files_unchanged\" in self.fix:\n # Try to fix the problem by overwriting the pipeline file\n shutil.copy(_tf(f), _pf(f))\n passed.append(f\"`{f}` matches the template\")\n fixed.append(f\"`{f}` overwritten with template file\")\n else:\n failed.append(f\"`{f}` does not match the template\")\n could_fix = True\n except FileNotFoundError:\n pass\n\n # Files that can be added to, but that must contain the template contents\n for files in files_partial:\n # Ignore if file specified in linting config\n ignore_files = self.lint_config.get(\"files_unchanged\", [])\n if any([f in ignore_files for f in files]):\n ignored.append(f\"File ignored due to lint config: {self._wrap_quotes(files)}\")\n\n # Ignore if we can't find the file\n elif not any([os.path.isfile(_pf(f)) for f in files]):\n ignored.append(f\"File does not exist: {self._wrap_quotes(files)}\")\n\n # Check that the file contains the template file contents\n else:\n for f in files:\n try:\n with open(_pf(f), \"r\") as fh:\n pipeline_file = fh.read()\n with open(_tf(f), \"r\") as fh:\n template_file = fh.read()\n if template_file in pipeline_file:\n passed.append(f\"`{f}` matches the template\")\n else:\n if \"files_unchanged\" in self.fix:\n # Try to fix the problem by overwriting the pipeline file\n with open(_tf(f), \"r\") as fh:\n template_file = fh.read()\n with open(_pf(f), \"w\") as fh:\n fh.write(template_file)\n passed.append(f\"`{f}` matches the template\")\n fixed.append(f\"`{f}` overwritten with template file\")\n else:\n failed.append(f\"`{f}` does not match the template\")\n could_fix = True\n except FileNotFoundError:\n pass\n\n # cleaning up temporary dir\n shutil.rmtree(tmp_dir)\n\n return {\"passed\": passed, \"failed\": failed, \"ignored\": ignored, \"fixed\": fixed, \"could_fix\": could_fix}","def show_errors(self):\n\n if self.errors:\n print('Clean error in:')\n for file in self.errors:\n print(' %s' % file)","def CheckFilesMatch(config):\n\n diff_errors = []\n\n file_pairs = _GetFilePairs(config)\n missing_files, stale_files = _GetMissingAndStaleFiles(file_pairs)\n\n for pair in missing_files:\n diff_errors.append(\"File %s does not exist\" % pair.target)\n continue\n\n for pair in stale_files:\n diff_errors.append(\"File %s is out of date\" % pair.target)\n\n if diff_errors:\n error_msg = \"Files out of date!\\n\\n\"\n error_msg += \"To fix run THIS command:\\n\"\n error_msg += \" bazel-bin/%s/%s --fix\\n\\n\" % (config.package_name,\n config.target_name)\n error_msg += \"Errors:\\n\"\n error_msg += \" \" + \"\\n \".join(diff_errors)\n return error_msg\n else:\n return None","def _check_for_commands(keep_path):\n if not os.path.exists(keep_path):\n click.echo(\"You have not registered any command yet.\")\n quit()","def RunCheckMate(parserDict):\n t0 = time.time()\n parser = ConfigParserExt()\n parser.read_dict(parserDict)\n\n pars = parser.toDict(raw=False)[\"options\"]\n\n outputFolder = os.path.abspath(parser.get(\"CheckMateParameters\",\"OutputDirectory\"))\n resultFolder = os.path.join(outputFolder,parser.get(\"CheckMateParameters\",\"Name\"))\n if os.path.isdir(resultFolder):\n logger.info(\"Results folder %s found.\" %resultFolder)\n if parser.get(\"CheckMateParameters\",\"OutputExists\") == 'overwrite':\n logger.info(\"Overwriting\")\n shutil.rmtree(resultFolder)\n else:\n logger.info(\"Skipping\" %resultFolder)\n return \"---- %s skipped\" %resultFolder\n cardFile = getCheckMateCard(parser)\n logger.debug('Steering card %s created' %cardFile)\n\n #Create output dirs, if do not exist:\n try:\n os.makedirs(outputFolder)\n except:\n pass\n\n #Run CheckMate\n checkmatePath = os.path.abspath(pars['checkmateFolder'])\n checkmateBin = os.path.join(checkmatePath,'bin')\n logger.info('Running checkmate with steering card: %s ' %cardFile)\n logger.debug('Running: python2 ./CheckMATE %s at %s' %(cardFile,checkmateBin))\n run = subprocess.Popen('python2 ./CheckMATE %s' %(cardFile)\n ,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE,cwd=checkmateBin)\n output,errorMsg= run.communicate()\n logger.debug('CheckMATE error:\\n %s \\n' %errorMsg)\n logger.debug('CheckMATE output:\\n %s \\n' %output)\n\n os.remove(cardFile)\n\n logger.info(\"Done in %3.2f min\" %((time.time()-t0)/60.))\n\n #Remove parton level events:\n if pars['cleanUp'] is True:\n mg5folder = os.path.join(resultFolder,'mg5amcatnlo')\n if os.path.isdir(mg5folder):\n logger.debug('Removing data from: %s \\n' %mg5folder)\n for f in os.listdir(mg5folder):\n file_path = os.path.join(mg5folder, f)\n if os.path.isdir(file_path):\n shutil.rmtree(file_path)\n analysisfolder = os.path.join(resultFolder,'analysis')\n if os.path.isfile(os.path.join(analysisfolder,'analysisstdout_atlas_1712_02118_ew.log')):\n os.remove(os.path.join(analysisfolder,'analysisstdout_atlas_1712_02118_ew.log'))\n\n now = datetime.datetime.now()\n\n return \"Finished running CheckMATE at %s\" %(now.strftime(\"%Y-%m-%d %H:%M\"))","def test_duplicatefslabels_run_failure(self, get_label_dict_mock):\n get_label_dict_mock.return_value = {\"/\": [\"/dev/xvda1\", \"/dev/xvdf1\"],\n \"TEST\": [\"/dev/xvdg1\"]}\n with contextlib.redirect_stdout(self.output):\n self.assertTrue(moduletests.src.duplicatefslabels.run())\n self.assertTrue(\"[FAILURE] Duplicate label, /, found on the following filesystems: /dev/xvda1, /dev/xvdf1\\n\"\n in self.output.getvalue())\n self.assertTrue(get_label_dict_mock.called)","def testIgnoredError(self):\n cmds = \"\"\"-chown 0 missingFile\npwd\nexit\n\"\"\"\n def _cbCheckResult(res):\n self.assertIn(self.testDir.asBytesMode().path, res)\n\n d = self._getBatchOutput(cmds)\n d.addCallback(_cbCheckResult)\n return d","def errors(conf, daemon):\n # persisted dict interface for long term memory\n errors = Shove('file://{0}'.format(conf.app.errors), protocol=2, flag='r')\n if any(errors):\n print(\"errors found\")\n for path, error in six.iteritems(errors):\n pp(error)\n errors.close()\n exit(1)\n # ⏏ exit the program with an error\n else:\n print(\"no errors found - OK\")\n print()\n errors.close()","def test_bad_protein_file():\n\n bad = random_filename()\n rv, out = getstatusoutput(f'{prg} --cdhit {cdhit} -p {bad}')\n assert rv > 0\n assert out.lower().startswith('usage:')\n assert re.search(f\"No such file or directory: '{bad}'\", out)","def command_failed_error(cmd):\n\n output_1 = colored(' - Error: Failed to run command ', 'red')\n output_2 = command(cmd)\n return output_1 + output_2 + '\\n'","def test_bad_cdhit_file():\n\n bad = random_filename()\n rv, out = getstatusoutput(f'{prg} --cdhit {bad} -p {proteins}')\n assert rv > 0\n assert out.lower().startswith('usage:')\n assert re.search(f\"No such file or directory: '{bad}'\", out)","def assert_cmd_success(self, cmds):\n print('@ %s' % cmds)\n try:\n self.cc.batch_command(cmds)\n except MakeFailed as e:\n print('Detected MakeFailed')\n print('Failed jobs: %s' % e.failed)\n for job_id in e.failed:\n self.cc.interpret_commands_wrap('details %s' % job_id)\n\n except CommandFailed:\n # msg = 'Command %r failed. (res=%s)' % (cmds, res)\n raise\n\n self.cc.interpret_commands_wrap('check_consistency raise_if_error=1')","def test_errors_on_output(self):\n mb = self.maria_backup\n\n # normal run\n errors = b\"\"\"\n 220309 11:19:09 Finished backing up non-InnoDB tables and files\n 220309 11:19:09 Executing FLUSH NO_WRITE_TO_BINLOG ENGINE LOGS...\n xtrabackup: The latest check point (for incremental): '92134324'\n xtrabackup: Stopping log copying thread..\n 220309 11:19:10 >> log scanned up to (900123121)\n 220309 11:19:10 Executing UNLOCK TABLES\n 220309 11:19:10 All tables unlocked\n 220309 11:19:10 Backup created in directory '/a/dir'\n 220309 11:19:10 [00] Writing backup-my.cnf\n 220309 11:19:10 [00] ...done\n 220309 11:19:10 [00] Writing xtrabackup_info\n 220309 11:19:10 [00] ...done\n xtrabackup: Transaction log of lsn (89423125) to (900123121) was copied.\n 220309 11:19:10 completed OK!\n \"\"\"\n self.assertFalse(mb.errors_on_output(b'', errors))\n\n # failed run\n errors = b\"\"\"\n xtrabackup: error: log block numbers mismatch:\n xtrabackup: error: expected log block no. 293842034, but got no. 13324598 from the log file.\n xtrabackup: error: it looks like InnoDB log has wrapped around before xtrabackup\n could process all records due to either log copying being too slow, or log files being too small.\n xtrabackup: Error: xtrabackup_copy_logfile() failed\n \"\"\"\n self.assertTrue(mb.errors_on_output(b'', errors))","def exechost_status():\n\n exechost = socket.gethostname()\n\n # free\n try:\n subp = subprocess.Popen([\"free\", \"-m\"], stdout=subprocess.PIPE)\n output = subp.communicate()[0]\n print \"EXECSTAT %s FREE\\n%s\" % (exechost, output)\n except:\n print \"Problem running free command\"\n (extype, exvalue, trback) = sys.exc_info()\n traceback.print_exception(extype, exvalue, trback, limit=1, file=sys.stdout)\n print \"Ignoring error and continuing...\\n\"\n\n # df\n try:\n cwd = os.getcwd()\n subp = subprocess.Popen([\"df\", \"-h\", cwd], stdout=subprocess.PIPE)\n output = subp.communicate()[0]\n print \"EXECSTAT %s DF\\n%s\" % (exechost, output)\n except:\n print \"Problem running df command\"\n (extype, exvalue, trback) = sys.exc_info()\n traceback.print_exception(extype, exvalue, trback, limit=1, file=sys.stdout)\n print \"Ignoring error and continuing...\\n\"","def check_tools_exist(WARNINGS):\n tools_list = []\n Warning_out = WARNINGS + \"Tool executable warning: \"\n try:\n flash.Flash(args.flash)\n tools_list.append(\"flash\")\n except ValueError:\n Warning_out = Warning_out + \"Flash not in path\"\n try:\n error_correction.Error_Correction(args.spades)\n tools_list.append(\"error_correction\")\n except ValueError:\n Warning_out = Warning_out + \"spades.py not in path\\n\"\n try:\n vsearch.Vsearch(args.vsearch)\n tools_list.append(\"vsearch\")\n except ValueError:\n Warning_out = Warning_out + \"vsearch not in path\\n\"\n try:\n trimmomatic.Trimmomatic(args.trimmomatic)\n tools_list.append(\"trimmomatic\")\n except ValueError:\n Warning_out = Warning_out + \"trimmomatic not in path\\n\"\n try:\n swarm.Swarm(args.swarm)\n tools_list.append(\"swarm\")\n except ValueError:\n Warning_out = Warning_out + \"swarm not in path\\n\"\n try:\n samtools_index.Samtools_Index(args.samtools)\n tools_list.append(\"samtools\")\n except ValueError:\n Warning_out = Warning_out + \"samtools not in path\\n\"\n try:\n pear.Pear(args.pear)\n tools_list.append(\"pear\")\n except ValueError:\n Warning_out = Warning_out + \"pear not in path\\n\"\n try:\n muscle.Muscle(args.muscle)\n tools_list.append(\"muscle\")\n except ValueError:\n Warning_out = Warning_out + \"muscle not in path\\n\"\n try:\n fastqc.FastQC(args.fastqc)\n tools_list.append(\"fastqc\")\n except ValueError:\n Warning_out = Warning_out + \"fastqc not in path\\n\"\n try:\n cd_hit.Cd_hit(args.cd_hit)\n tools_list.append(\"cd-hit-est\")\n except ValueError:\n Warning_out = Warning_out + \"cd-hit-est not in path\\n\"\n try:\n bowtie_map.Bowtie2_Map(args.bowtie2)\n tools_list.append(\"bowtie2\")\n except ValueError:\n Warning_out = Warning_out + \"bowtie2 not in path\\n\"\n try:\n blast.Blastclust(args.blastclust)\n tools_list.append(\"blastclust\")\n except ValueError:\n Warning_out = Warning_out + \"blastclust not in path\\n\"\n return tools_list, Warning_out","def step_impl(context):\n log.info(\"====> verify the NSA files are not placed under container_nsa directory\")\n\n nsa_container = get_nsa_container_string(context)\n container_nsa_path = \"/tmp/cme/local/GFD/{nsa_container}/container_nsa\".format(nsa_container=nsa_container)\n log.info(\" ****> DEBUG: nsa container path is: {container_nsa_path}\".format(container_nsa_path=container_nsa_path))\n\n command = \"cd {container_nsa_path}; ls -a | wc -l\".format(container_nsa_path=container_nsa_path)\n if \"2\" in context.cme_session.send_ssh_command(command=command): # Means that directory is empty\n log.info(\" ****> Passed The NSA files are placed under the container_nsa directory - As expected.\")\n else:\n assert False, \" ****> Failed: The NSA files are placed under the container_nsa directory - While they should not be there.\"","def not_found(client, server, command):\n server.logger.info(\"BLACKLIST {} : {}\".format(client.ip, command))\n client.send(\"sh: {}: command not found\\n\".format(command))\n client.exit_status = 127","def test_deploy_log_messages(deploy_result: Result) -> None:\n expected_lines = [\n \"deployment_1:processing deployment (in progress)\",\n \"deployment_1:processing regions sequentially...\",\n \"\",\n \"deployment_1.test_raw_cfn:processing module in us-east-1 (in progress)\",\n \"cfngin.yml:init (in progress)\",\n \"skipped; cfngin_bucket not defined\",\n \"cfngin.yml:init (complete)\",\n \"cfngin.yml:deploy (in progress)\",\n \"raw-template-vpc:submitted (creating new stack)\",\n \"raw-template-vpc:complete (creating new stack)\",\n \"cfngin.yml:deploy (complete)\",\n \"deployment_1.test_raw_cfn:processing module in us-east-1 (complete)\",\n \"deployment_1:processing deployment (complete)\",\n ]\n expected = \"\\n\".join(f\"[runway] {msg}\" for msg in expected_lines)\n assert expected in deploy_result.stdout, (\n \"stdout does not match expected\\n\\nEXPECTED:\\n\"\n f\"{expected}\\n\\nSTDOUT:\\n{deploy_result.stdout}\"\n )","def run(self):\n list_test_scenarios = self.__get_list_scenarios_in_folder()\n\n if not list_test_scenarios:\n utils.print_error(\n \"\\n{}\\n\".format(constant.ERR_CANNOT_FIND_ANY_TEST_SCENARIOS))\n exit(1)\n\n (tests_pass, tests_fail) = self.__execute_tests(list_test_scenarios)\n\n complete_message = constant.INFO_TEST_PASS_FAIL.format(\n tests_pass, tests_fail)\n\n print(complete_message)\n\n self.__execute_reporter()","def get_fatal_alerts(self, path):","def test_do_not_need_alternate(self):\n os.unlink(os.path.join(self.reports_dir,\n 'TEST-testutil.manual_test.LintTest-fail.xml'\n ))\n os.unlink(os.path.join(self.reports_dir,\n 'TEST-testutil.manual_test.LintTest-success.xml'\n ))\n actual = self._analyze_make_output()\n self.assertEqual(1, actual)\n self.assertIn('E999 lint error from txt-file.', self.errors[0])","def test_generate_logs(self):\n debug = True\n # Extra \"dummy\" files will be generated to the system to get the system to\n # the total_file_count\n total_file_count = 1020\n # Time in days to erase files\n erase_threshold = 7 \n filename_header = 'event-log-'\n log_directory = '/hd/logs'\n #log_directory = '/hdp/logs'\n\n \n \n password = get_hidden_password()\n self.ssx.open_hidden_shell(password)\n \n ###########\n ## Warning!\n ###########\n self.myLog.info(\"Warning:\")\n self.myLog.info(\"This automatoin makes use of tail and head\")\n self.myLog.info(\"Those binaries are not already on the SSX\")\n self.myLog.info(\"You need to copy both of them from the script directory to:\")\n self.myLog.info(\"/hd/logs otherwise the script will FAIL!\")\n \n #################################\n ## 1. Check the state of /hd/logs\n #################################\n self.myLog.info(\"Testing the %s location\" % log_directory)\n self.myLog.info(\"--------------------------------------\")\n ####################\n ## Get the file list\n \n command = 'cd ' + log_directory\n # This may cause a bug here!\n #raw_output = self.ssx.hidden_cmd(\"cd \\/hd\\/logs\", timeout=30)\n raw_output = self.ssx.hidden_cmd(command, timeout 30)\n if debug:\n print 'the return value was'\n print raw_output\n\n raw_output = self.ssx.hidden_cmd(\"pwd\", timeout=30)\n if debug:\n print 'the return value was'\n print raw_output\n\n raw_output = self.ssx.hidden_cmd(\"ls | grep event-log | wc\", timeout=30)\n if debug:\n print 'the return value was'\n print raw_output\n\n try:\n raw_file_count = raw_output.split()\n file_count = int(raw_file_count[0])\n except:\n self.myLog.error(\"Unable to parse the file count: %s\" % raw_file_count)\n \n # We have placed a copy of the following two tools onto the ssx in /hd/logs\n # tail, head\n # There is a retarded bug in tail that causes it to not be able to read files\n # via stdin. A work around for this bug is as follows:\n self.myLog.info(\"Executing workaround to make tail work\")\n raw_output = self.ssx.hidden_cmd(\"touch stdin\", timeout=10)\n \n \n self.myLog.info(\"Finding the oldest log file\")\n raw_output = self.ssx.hidden_cmd(\"ls event-log* | /hd/logs/head -1\")\n oldest_file = raw_output\n self.myLog.info(\"The oldest logs fils is %s\" % oldest_file)\n \n # Newest is the file with the highest date. (means it was created recently)\n self.myLog.info(\"Finding the newest file\") \n raw_output = self.ssx.hidden_cmd(\"ls event-log* | /hd/logs/tail -1\")\n newest_file = raw_output\n self.myLog.info(\"The newest log file is %s\" % newest_file)\n \n \n self.myLog.info(\"Checking the difference in date/time between the two logs\")\n newest_log_parts = newest_file.split(\"-\")\n newest_log_date = newest_log_parts[2]\n newest_log_time = newest_log_parts[3]\n newest_log_year = newest_log_date[0:4]\n newest_log_month = newest_log_date[4:6]\n newest_log_day = newest_log_date[6:8]\n \n oldest_log_parts = oldest_file.split(\"-\")\n oldest_log_date = oldest_log_parts[2]\n oldest_log_time = oldest_log_parts[3]\n oldest_log_year = oldest_log_date[0:4]\n oldest_log_month = oldest_log_date[4:6]\n oldest_log_day = oldest_log_date[6:8] \n \n \n self.myLog.info(\"Checking to see if the oldest file on the system 'should' be errased\")\n # Now we have all the parts of the date/time we need to compare them to see \n # if the time delta is greater then 7 days or some user defined value\n should_be_errased = False\n # If the years are different then errase\n if newest_log_year > oldest_log_year:\n self.myLog.info(\"files will be errased\")\n should_be_errased = True\n # If the day value is larger\n elif newest_log_day > oldest_log_day:\n if int(newest_log_day) - int(oldest_log_day) >= erase_threshold:\n self.myLog.info(\"files will be errased\")\n should_be_errased = True\n else:\n self.myLog.info(\"The oldest file is not old enough to be errased\")\n self.myLog.info(\"The oldest file is not old enough to be errased\")\n \n self.myLog.info(\"------------------------------------------------------------------------\")\n self.myLog.info(\"We will now generate files that are newer then the file errasal threshold\")\n self.myLog.info(\"This will cause ALL files that are newer then the date to be errased\")\n \n\n self.myLog.info(\"We found %s files in /hd/logs\" % file_count)\n files_to_generate = total_file_count - file_count\n self.myLog.info(\"For this test we will generate %s files\" % files_to_generate)\n \n \n #file_date = int(raw_file_date[2]) - 1\n if debug:\n self.myLog.debug(\"These are the variables we will use:\")\n self.myLog.debug(\"newest_log_year: %s\" % newest_log_year)\n self.myLog.debug(\"newest_log_day: %s\" % newest_log_day)\n self.myLog.debug(\"newest_log_month: %s\" % newest_log_month)\n self.myLog.debug(\"erase_threshold: %s\" % erase_threshold)\n file_date = str(newest_log_year) + str(newest_log_month)\n self.myLog.debug(\"file_date: %s\" % file_date)\n erase_day = int(newest_log_day) + int(erase_threshold) + 1\n self.myLog.debug(\"erase_day: %s\" % erase_day)\n file_date = file_date + str(erase_day)\n self.myLog.debug(\"file_date: %s\" % file_date)\n self.myLog.info(\"The fake log files will be generated with date: %s\" % file_date)\n \n \n ##########################\n ## Generate Fake log files\n ##########################\n \n for i in range(0,files_to_generate):\n if debug:\n print '===================================='\n print 'Workin on file number:', i, 'of:', files_to_generate\n complete_file_name = filename_header + str(file_date) + '-' + str.rjust(str(i), 6, '0')\n if debug:\n print 'The fake file will be called:', complete_file_name\n \n #command = 'cp ' + oldest_file + ' ' + complete_file_name\n command = 'touch ' + complete_file_name\n if debug:\n print 'The command will be:'\n print command\n \n raw_output = self.ssx.hidden_cmd(command)\n\n\n self.myLog.info(\"Done generating fake log files\")\n self.myLog.info(\"--------------------------------------\")\n #self.ssx.hidden_cmd(\"\\n\")\n self.ssx.close_hidden_shell()\n \n self.myLog.info(\"Checking to see the status of the log buffers\")\n log_counters = show_logging(self.ssx)\n self.myLog.info(\"The log files will be errased when:\")\n self.myLog.info(\"%s = %s\" % (log_counters['Glob-D']['Next-Ix 1'], log_counters['Glob-D']['Next Save-Ix 1']))\n log_events_to_generate = int(log_counters['Glob-D']['Next Save-Ix 1']) - int(log_counters['Glob-D']['Next-Ix 1'])\n self.myLog.info(\"We need to generate %s log events to cause the log to flush to disk\" % log_events_to_generate)","def verify_git_clean(path):\n\n sys.stdout.write(\" - Checking for uncommitted changes:\")\n result = run_in_component(path, ['git', 'status', '--porcelain=v1'])\n\n lines = [x for x in result.splitlines() if len(x) > 0]\n\n if len(lines) == 0:\n print(\" OKAY\")\n return\n\n print(\" FAILED\")\n\n raise GenericError(\"There are uncommitted changes in the component, please commit or stash them\")","def status(self, exe_paths=False):\n if self.status_msg is None:\n self.check_all(exe_paths=exe_paths)\n return self.status_msg","def main():\n\n# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n# ~~~~ Reads config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n print('\\n\\nInterpreting command line options\\n'+'~'*72+'\\n')\n\n parser = ArgumentParser()\n subparser = parser.add_subparsers(\\\n help='run_selafin commands to do', dest='command')\n\n subparser = chop_parser(subparser)\n subparser = scan_parser(subparser)\n subparser = spec_parser(subparser)\n subparser = alter_parser(subparser)\n subparser = merge_parser(subparser)\n subparser = diff_parser(subparser)\n subparser = calcs_parser(subparser, 'calcs', '???')\n subparser = calcs_parser(subparser, 'crunch', '???')\n subparser = calcs_parser(subparser, 'transf', '???')\n subparser = sample_parser(subparser)\n subparser = subdivide_parser(subparser)\n subparser = tesselate_parser(subparser)\n\n options = parser.parse_args()\n\n# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n# ~~~~ Reads code name ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n if options.command == 'scan':\n scan(options)\n elif options.command == 'spec':\n spec(options)\n elif options.command == 'chop':\n chop(options)\n elif options.command == 'alter':\n alter(options)\n elif options.command == 'merge':\n merge(options)\n elif options.command == 'diff':\n diff(options)\n elif options.command == 'sample':\n sample(options)\n elif options.command in ['calcs', 'crunch', 'transf']:\n calcs(options, options.command)\n elif options.command == 'subdivide':\n subdivide(options)\n elif options.command == 'tessellate':\n tesselate(options)\n else:\n raise TelemacException(\\\n '\\nDo not know what to do with '\n 'this code name: {}'.format(options.command))\n\n# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n# ~~~~ Jenkins' success message ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n print('\\n\\nMy work is done\\n\\n')\n\n sys.exit(0)","def check_for_errors(self):\n\n with open(\"output.dat\", \"r\") as log:\n for line in log:\n if \"*** Psi4 exiting successfully.\" in line:\n return {\"success\": True}\n\n elif \"*** Psi4 encountered an error.\" in line:\n return {\"success\": False, \"error\": \"Not known\"}\n\n return {\"success\": False, \"error\": \"Segfault\"}","def failure_cmd(self) -> str:\n return \"{} --enable=all -f -q {}\".format(\n self.conf.get_executable(), constants.ROOT_PATH + \"/data/cppcheck-152/trial-fail.cpp\"\n )","def test_bad_file():\n\n bad = ''.join(random.choices(string.ascii_uppercase + string.digits, k=5))\n rv, out = getstatusoutput(f'{prg} -f {bad}')\n assert rv != 0\n assert re.match('usage:', out, re.I)\n assert re.search(f\"No such file or directory: '{bad}'\", out)","def test_run_cmd_simple_negative(caplog):\n caplog.set_level(logging.DEBUG)\n cmd = \"ls /tmp/this/file/isindeednotthereatall\"\n with pytest.raises(CommandFailed) as excinfo:\n utils.run_cmd(cmd)\n assert \"No such file or directory\" in str(excinfo.value)\n # check that run_cmd logged the run as expected\n assert caplog.records[0].levelname == 'INFO'\n assert caplog.records[0].message == f'Executing command: {cmd}'\n assert caplog.records[1].levelname == 'DEBUG'\n assert caplog.records[1].message == 'Command stdout is empty'\n assert caplog.records[2].levelname == 'WARNING'\n assert caplog.records[2].message.startswith(\"Command stderr: ls:\")\n assert \"No such file or directory\" in caplog.records[2].message\n assert caplog.records[3].levelname == 'DEBUG'\n assert caplog.records[3].message == 'Command return code: 2'","def test_stratis_no_subcommand(self):\n for command_line in [[], [\"daemon\"]]:\n for prefix in [[], [\"--propagate\"]]:\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)","def run_commands(self, commands):\n if isinstance(commands, str):\n commands = commands.split('\\n')\n for item in commands:\n if item.strip().startswith(\"#\"):\n continue\n should_exit, result = self.cmd_with_result(item)\n if not result:\n break","def run(self, server):\n diagnostics = \"unknown\"\n save_stdout = sys.stdout\n try:\n self.skip = False\n if os.path.exists(self.skip_cond):\n sys.stdout = FilteredStream(self.tmp_result)\n stdout_fileno = sys.stdout.stream.fileno()\n execfile(self.skip_cond, dict(locals(), **server.__dict__))\n sys.stdout.close()\n sys.stdout = save_stdout\n if not self.skip:\n sys.stdout = FilteredStream(self.tmp_result)\n stdout_fileno = sys.stdout.stream.fileno()\n self.execute(server)\n sys.stdout.flush()\n self.is_executed_ok = True\n except Exception as e:\n traceback.print_exc(e)\n diagnostics = str(e)\n finally:\n if sys.stdout and sys.stdout != save_stdout:\n sys.stdout.close()\n sys.stdout = save_stdout\n self.is_executed = True\n sys.stdout.flush()\n\n if not self.skip:\n if self.is_executed_ok and os.path.isfile(self.result):\n self.is_equal_result = filecmp.cmp(self.result, self.tmp_result)\n else:\n self.is_equal_result = 1\n\n if self.args.valgrind:\n self.is_valgrind_clean = (check_valgrind_log(server.valgrind_log) == False)\n\n if self.skip:\n color_stdout(\"[ skip ]\\n\", schema='test_skip')\n if os.path.exists(self.tmp_result):\n os.remove(self.tmp_result)\n elif self.is_executed_ok and self.is_equal_result and self.is_valgrind_clean:\n color_stdout(\"[ pass ]\\n\", schema='test_pass')\n if os.path.exists(self.tmp_result):\n os.remove(self.tmp_result)\n elif (self.is_executed_ok and not self.is_equal_result and not\n os.path.isfile(self.result)):\n os.rename(self.tmp_result, self.result)\n color_stdout(\"[ new ]\\n\", schema='test_new')\n else:\n os.rename(self.tmp_result, self.reject)\n color_stdout(\"[ fail ]\\n\", schema='test_fail')\n\n where = \"\"\n if not self.is_executed_ok:\n self.print_diagnostics(self.reject, \"Test failed! Last 10 lines of the result file:\\n\")\n server.print_log(15)\n where = \": test execution aborted, reason '{0}'\".format(diagnostics)\n elif not self.is_equal_result:\n self.print_unidiff()\n server.print_log(15)\n where = \": wrong test output\"\n elif not self.is_valgrind_clean:\n os.remove(self.reject)\n self.print_diagnostics(server.valgrind_log, \"Test failed! Last 10 lines of valgrind.log:\\n\")\n where = \": there were warnings in valgrind.log\"\n\n if not self.args.is_force:\n raise RuntimeError(\"Failed to run test \" + self.name + where)","def test_explain_non_existent_code(self):\n command_line = [\"pool\", \"explain\", \"bogus\"]\n for prefix in [[], [\"--propagate\"]]:\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)","def check_analysis_pickle_files(self):\n # Make sure that there have been no more trials run since this\n # last processing. To do this, get the number of output files\n for basename in nsort(os.listdir(self.logdir)):\n m = self.labels.subdir_re.match(basename)\n if m is None or 'pckl' in basename:\n continue\n # Here is the output directory which contains the files\n subdir = os.path.join(self.logdir, basename)\n # Account for failed jobs. Get the set of file numbers that\n # exist for all h0 and h1 combinations\n self.get_set_file_nums(\n filedir=subdir\n )\n # Take one of the pickle files to see how many data\n # entries it has.\n data_sets = from_file(os.path.join(self.logdir,\n 'data_sets.pckl'))\n # Take the first data key and then the h0 fit to h0 fid\n # which should always exist. The length of this is then\n # the number of trials in the pickle files.\n if 'h0_fit_to_h0_fid' in data_sets[data_sets.keys()[0]].keys():\n pckl_trials = len(data_sets[data_sets.keys()[0]][\n 'h0_fit_to_h0_fid'].keys())\n # The number of pickle trials should match the number of\n # trials derived from the output directory.\n if self.num_trials == pckl_trials:\n logging.info(\n 'Found files I assume to be from a previous run of'\n ' this processing script containing %i trials. If '\n 'this seems incorrect please delete the files: '\n 'data_sets.pckl, all_params.pckl and labels.pckl '\n 'from the logdir you have provided.'%pckl_trials\n )\n pickle_there = True\n else:\n logging.info(\n 'Found files I assume to be from a previous run of'\n ' this processing script containing %i trials. '\n 'However, based on the number of json files in the '\n 'output directory there should be %i trials in '\n 'these pickle files, so they will be regenerated.'%(\n pckl_trials, self.num_trials)\n )\n pickle_there = False\n else:\n logging.info(\n 'Found files I assume to be from a previous run of'\n ' this processing script which do not seem to '\n 'contain any trials, so they will be regenerated.'\n )\n pickle_there = False\n \n return pickle_there","def run_commands(commands: List[str], dry_run: bool) -> List[str]:\n result = []\n for cmd in commands:\n if dry_run:\n logging.info(cmd)\n else:\n p = safe_exec(cmd)\n if p.stdout:\n for line in p.stdout.decode().split('\\n'):\n if line:\n if line.startswith('No resources found'):\n # nothing was deleted\n break\n fields = line.rstrip().split()\n if len(fields) > 1:\n result.append(fields[1])\n else:\n result.append(fields[0])\n return result","def __statistics_students_failing(self):\n students_list = self.__grade_controller.get_list_of_failing_students()\n if len(students_list) == 0:\n print(\"There is no student failing!\")\n return\n\n for student in students_list:\n print(str(student) + \"\\n\")","def check():\n \n overall_report = dict()\n\n # source code analysis\n # ====================\n # currently empty\n \n # compile\n # =======\n ret_makefile = subprocess.run([config.compiler] + config.compiler_args, # command\n stdout=subprocess.PIPE, # capture stdout\n stderr=subprocess.PIPE, # capture stderr\n universal_newlines=True) # use text mode for std* file objects\n overall_report['makefile'] = ret_makefile\n \n # runtime analysis\n # ================\n with open('compile.txt', 'r') as f:\n if 'error' not in f.read().lower(): # if compilation succeeded\n overall_report, test_case_report_list = runtime_analysis(config, overall_report)\n \n # pass this info to next tools for subsequent processing\n # ======================================================\n pp(overall_report)\n # results from runtime analysis\n if 'runtime_analysis_done' in overall_report:\n success_count = 0\n for report in test_case_report_list:\n if 'timeout' in report:\n util.addFinding(\"Time limit exceeded!\", 0, \"\", \"TEST_080006\")\n elif report['return_code'] != 0:\n if report['stderr_stream'] != '': # ASan/LeakSan/Stack protector probably reported something\n pass # but these findings will be added by analyze.py\n else:\n util.addFinding(\"It seems your program might have crashed.\", 0,\"\",\"TEST_100006\")\n # output_match == None means the user might have tried to print to outfile\n elif report['stdout_stream'] != '' or report['output_match'] is None:\n util.addFinding(\"A test case failed! Make sure you are not trying to print something.\",\n 0,\"\",\"TEST_100006\")\n elif not all(report['output_match']): # not all test cases passed\n util.addFinding(\"A test case failed!\", 0, \"\", \"TEST_100006\")\n else:\n success_count += 1\n\n with open('stderr.txt', 'a') as f:\n f.write(report['stderr_stream'])\n with open('stdout.txt', 'a') as f:\n f.write(report['outfile'])\n\n if success_count == len(test_case_report_list):\n util.addFinding(\"Program behaves as expected!\", 1, \"CHALLENGE_PASS\", \"TEST_900006\")\n \n util.dumpFindings()\n \n # next tools\n subprocess.run([\"./analyse.py\"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n subprocess.run([\"./ai.py\"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)","def CompareResults(ref_dir, results_dir):\n logging.info(\"Comparing results to \" + ref_dir)\n\n diff_result = os.path.join(results_dir, \"layout_tests_diff.txt\") \n if os.path.exists(diff_result):\n os.remove(diff_result)\n\n files=[\"passed\", \"failed\", \"nontext\", \"crashed\"]\n for f in files:\n result_file_name = \"layout_tests_\" + f + \".txt\"\n DiffResults(f, os.path.join(results_dir, result_file_name),\n os.path.join(ref_dir, result_file_name), diff_result,\n f == \"failed\")\n logging.info(\"Detailed diffs are in \" + diff_result)","def errdump_analysis(errdump_df, switchshow_df, switch_params_aggregated_df, \n portshow_aggregated_df, project_constants_lst):\n \n # imported project constants required for module execution\n project_steps_df, max_title, io_data_names_df, _, report_headers_df, report_columns_usage_sr, *_ = project_constants_lst\n\n # data titles obtained after module execution (output data)\n # data titles which module is dependent on (input data)\n data_names, analyzed_data_names = dfop.list_from_dataframe(io_data_names_df, 'errorlog_analysis_out', 'errorlog_analysis_in')\n # module information\n meop.show_module_info(project_steps_df, data_names)\n # read data from database if they were saved on previos program execution iteration\n data_lst = dbop.read_database(project_constants_lst, *data_names)\n \n # force run when any output data from data_lst is not found in database or \n # procedure execution explicitly requested (force_run flag is on) for any output or input data \n force_run = meop.verify_force_run(data_names, data_lst, project_steps_df, \n max_title, analyzed_data_names)\n if force_run:\n # data imported from init file (regular expression patterns) to extract values from data columns\n pattern_dct, _ = sfop.regex_pattern_import('raslog_split', max_title)\n raslog_message_details_df = sfop.dataframe_import('raslog_details', max_title)\n raslog_message_id_details_df = sfop.dataframe_import('raslog_id_details', max_title, columns=['Message_ID', 'Details', 'Recommended_action'])\n\n # current operation information string\n info = f'Counting RASLog messages'\n print(info, end =\" \")\n\n # get aggregated DataFrames\n errdump_aggregated_df = errdump_aggregated(errdump_df, switchshow_df, switch_params_aggregated_df, \n portshow_aggregated_df, pattern_dct)\n # count how many times event appears during one month for the last six months \n raslog_counter_df, raslog_frequent_df = errdump_statistics(errdump_aggregated_df, raslog_message_details_df, raslog_message_id_details_df)\n # after finish display status\n meop.status_info('ok', max_title, len(info)) \n # partition aggregated DataFrame to required tables\n raslog_report_df = raslog_report(raslog_frequent_df, data_names, report_headers_df, report_columns_usage_sr)\n\n # create list with partitioned DataFrames\n data_lst = [errdump_aggregated_df, raslog_counter_df, raslog_report_df]\n # writing data to sql\n dbop.write_database(project_constants_lst, data_names, *data_lst)\n # verify if loaded data is empty and replace information string with empty DataFrame\n else:\n data_lst = dbop.verify_read_data(max_title, data_names, *data_lst)\n errdump_aggregated_df, raslog_counter_df, *_ = data_lst\n # save data to service file if it's required\n for data_name, data_frame in zip(data_names, data_lst):\n report.dataframe_to_excel(data_frame, data_name, project_constants_lst)\n return errdump_aggregated_df, raslog_counter_df","def find_stack_status(indir):\n\n if not indir.is_dir():\n raise ValueError(f\"'{indir} is not a directory\")\n\n stacks = {}\n for inst in [\"acis\", \"hrc\"]:\n\n infile = indir / f\"{inst}_stacks_unchanged.txt\"\n for stack in read_unchanged(infile):\n assert stack not in stacks\n stacks[stack] = \"unchanged\"\n\n for status in [\"updated\", \"new\"]:\n infile = indir / f\"{inst}_stacks_{status}.txt\"\n\n for stack in read_changed(infile):\n assert stack not in stacks\n stacks[stack] = status\n\n return stacks","def usage(status=0):\n print(\"finds copy pasted blocks in a set of files\")\n print()\n print(\n \"Usage: symilar [-d|--duplicates min_duplicated_lines] \\\n[-i|--ignore-comments] [--ignore-docstrings] [--ignore-imports] file1...\"\n )\n sys.exit(status)","def run_silent(self, opts):\n\n if not opts.add_to_svn and not opts.export_locally:\n print \"This execution will probably not have any effect. Make sure at least one of \"\\\n \"the options -l and -a are activated.\"\n\n svn_OK = False\n if opts.add_to_svn:\n svn_OK = check_svn()\n\n # look for and enter project file\n if not self.enter_project_file():\n raw_input(\"Execution aborted!\\nPress any key to close.\")\n return\n\n # which files are in directories\n self.enter_directories()\n\n self.result_files = self.result_files_dir\n self.design_files = self.design_files_dir\n self.design_space_files = self.design_space_files_dir\n self.test_bench_files = self.test_bench_files_dir\n\n if opts.project_file_link:\n self._pr_intersect()\n\n if opts.meta_results_file_link:\n if not self.enter_meta_results_file():\n raw_input(\"Execution aborted!\\nPress any key to close.\")\n return\n self._ms_intersect()\n\n if opts.summary_reports_must_be_ok:\n self.check_analysis_status()\n self._OK_intersect()\n\n if opts.clean_up_missing_references:\n project_file_references_valid, meta_results_file_references_valid =\\\n self._check_pr_and_ms_references()\n\n if not project_file_references_valid:\n self._clean_up_project_file()\n if not meta_results_file_references_valid:\n self._clean_up_meta_results_file()\n\n # go through all summary.report.json files and extract linked files\n srl = SummaryReportsLinks(self.result_files)\n self.files_linked_from_sum_reps = srl.get_files()\n self.folders_linked_from_sum_reps = srl.get_folders()\n\n include_dashboard = not opts.do_not_export_dashboard\n if svn_OK:\n self.add_to_svn(include_dashboard)\n\n if opts.export_locally:\n self.export_locally(include_dashboard)","def test_conformance_tests_test_output(self):\n style = pycodestyle.StyleGuide(quiet=True)\n result = style.check_files(['tests/test_output.py'])\n self.assertEqual(result.total_errors, 0,\n \"Found code style errors (and warnings).\")","def assertExecutedOnce(self, component: Text) -> None:\n component_path = os.path.join(self._pipeline_root, component)\n self.assertTrue(fileio.exists(component_path))\n outputs = fileio.listdir(component_path)\n\n self.assertIn(\".system\", outputs)\n outputs.remove(\".system\")\n system_paths = [\n os.path.join(\".system\", path)\n for path in fileio.listdir(os.path.join(component_path, \".system\"))\n ]\n self.assertNotEmpty(system_paths)\n self.assertIn(\".system/executor_execution\", system_paths)\n outputs.extend(system_paths)\n self.assertNotEmpty(outputs)\n for output in outputs:\n execution = fileio.listdir(os.path.join(component_path, output))\n self.assertLen(execution, 1)","def test_deploy_no_change_log_messages(deploy_no_change_result: Result) -> None:\n expected_lines = [\n \"deployment_1:processing deployment (in progress)\",\n \"deployment_1:processing regions sequentially...\",\n \"\",\n \"deployment_1.test_raw_cfn:processing module in us-east-1 (in progress)\",\n \"cfngin.yml:init (in progress)\",\n \"skipped; cfngin_bucket not defined\",\n \"cfngin.yml:init (complete)\",\n \"cfngin.yml:deploy (in progress)\",\n \"raw-template-vpc:skipped (nochange)\",\n \"cfngin.yml:deploy (complete)\",\n \"deployment_1.test_raw_cfn:processing module in us-east-1 (complete)\",\n \"deployment_1:processing deployment (complete)\",\n ]\n expected = \"\\n\".join(f\"[runway] {msg}\" for msg in expected_lines)\n assert expected in deploy_no_change_result.stdout, (\n \"stdout does not match expected\\n\\nEXPECTED:\\n\"\n f\"{expected}\\n\\nSTDOUT:\\n{deploy_no_change_result.stdout}\"\n )","def _execute_commands_file(self, commands_file_path):\n print(\"Executing commands from file \" + commands_file_path)\n stop = False\n with io.open(commands_file_path, 'r', encoding=\"utf-8\") as f:\n for l in f:\n if not l.isspace() and not l.lstrip().startswith(\"//\"):\n stop = self.interpret_command(l.rstrip(), quiet=True)\n if stop:\n break\n print(\"Execution of file over.\")\n return stop","def printErrors(self):\n if self.dots:\n self.stream.writeln()\n\n # Skipped Test Report\n if not self.args.no_skip_report:\n for test, reason in self.skipped:\n self.stream.writeln(\n \"\\n{} {} - {}\".format(\n self.colors.blue(\"Skipped\"),\n self.colors.bold(test.dotted_name),\n reason,\n )\n )\n\n # Captured output for non-failing tests\n if not self.args.quiet_stdout:\n failing_tests = {x[0] for x in self.all_errors}\n for test in list(self.stdout_output) + list(self.stderr_errput):\n if test not in failing_tests:\n self.displayStdout(test)\n self.displayStderr(test)\n\n # Actual tracebacks and captured output for failing tests\n for test, color_func, outcome, err in self.all_errors:\n # Header Line\n self.stream.writeln(\n f\"\\n{color_func(outcome)} in {self.colors.bold(test.dotted_name)}\"\n )\n\n # Traceback\n if not self.args.no_tracebacks:\n relevant_frames = []\n for i, frame in enumerate(err.traceback_lines):\n # Python2 tracebacks containing unicode need some special handling\n # This doesn't always make it readable, but at least it doesn't\n # crash\n if sys.version_info[0] == 2: # pragma: no cover\n try:\n \"\".join([frame]) # intentionally trigger exceptions\n except UnicodeDecodeError:\n frame = frame.decode(\"utf-8\")\n debug(\n \"\\n\"\n f\"{'*' * 30}Frame {i}:{'*' * 30}\\n\" + self.colors.yellow(frame),\n level=3,\n )\n # Ignore useless frames\n if self.verbose < 4:\n if frame.strip() == \"Traceback (most recent call last):\":\n continue\n # Done with this frame, capture it.\n relevant_frames.append(frame)\n self.stream.write(\"\".join(relevant_frames))\n\n # Captured output for failing tests\n self.displayStdout(test)\n self.displayStderr(test)","def log_result(self, result_list, directory=None):\n if not result_list:\n result = \"No cleaning was required\"\n else:\n if self.dry_run:\n file_verb = (\"file\" if len(result_list) == 1 else \"files\") + \" would be\"\n else:\n file_verb = \"file was\" if len(result_list) == 1 else \"files were\"\n directory_verb = f\" to directory {directory}\" if directory else \"\"\n result = f\"{len(result_list)} {file_verb} moved{directory_verb}:\\n{', '.join(result_list)}\"\n print(result)","def error_message(self):\n summary = format(\"%i out of %s failed unexpectedly:\",\n self.pool.num_failed,\n pluralize(self.pool.num_commands, \"command\"))\n details = \"\\n\".join(\" - %s\" % cmd.error_message for cmd in self.commands)\n return summary + \"\\n\\n\" + details","def validate_command(ctx, path):\n context = SceptreContext(\n command_path=path,\n project_path=ctx.obj.get(\"project_path\"),\n user_variables=ctx.obj.get(\"user_variables\"),\n options=ctx.obj.get(\"options\"),\n output_format=ctx.obj.get(\"output_format\"),\n ignore_dependencies=ctx.obj.get(\"ignore_dependencies\")\n )\n\n plan = SceptrePlan(context)\n responses = plan.validate()\n\n for stack, response in responses.items():\n if response['ResponseMetadata']['HTTPStatusCode'] == 200:\n del response['ResponseMetadata']\n click.echo(\"Template {} is valid. Template details:\\n\".format(stack.name))\n write(response, context.output_format)"],"string":"[\n \"def check_run_logs(input_file_parameters, dir_stack):\\r\\n # Check resource manager produced .out and .err files for assumed error\\r\\n # messages.\\r\\n print 'Checking runtime log files for error messages...'\\r\\n file_names = os.listdir(input_file_parameters.output_dir)\\r\\n\\r\\n newest_fix_index = 0\\r\\n files_to_check = []\\r\\n for file_name in sorted(file_names):\\r\\n if file_name.endswith('.out') or file_name.endswith('.err'):\\r\\n if file_name.startswith('FIX_'):\\r\\n current_fix_index = file_name.split('_')[1]\\r\\n if int(current_fix_index) > newest_fix_index:\\r\\n newest_fix_index = current_fix_index\\r\\n files_to_check = [file_name]\\r\\n else:\\r\\n files_to_check.append(file_name)\\r\\n if newest_fix_index == 0:\\r\\n files_to_check.append(file_name)\\r\\n\\r\\n if newest_fix_index > 0:\\r\\n print 'Workflow has been fixed {0} times. Checking only the {1} .out ' \\\\\\r\\n 'and .err files of the newest run.'.format(newest_fix_index,\\r\\n len(files_to_check))\\r\\n\\r\\n i = 0\\r\\n number_of_warnings = 0\\r\\n warning_strings = ['invalid', 'exception', 'warning']\\r\\n error_strings = ['error', 'segmentation fault', 'canceled', '(err):']\\r\\n skip_strings = ['adapters with at most',\\r\\n 'no. of allowed errors',\\r\\n 'error counts']\\r\\n for file_name in files_to_check:\\r\\n handle = open(os.path.join(input_file_parameters.output_dir,\\r\\n file_name))\\r\\n\\r\\n i += 1\\r\\n finish_string_exists = False\\r\\n warning_messages = []\\r\\n error_messages = []\\r\\n j = 0\\r\\n for line in handle:\\r\\n j += 1\\r\\n line = line.lower()\\r\\n if any(s in line for s in skip_strings):\\r\\n continue\\r\\n if any(w in line for w in warning_strings):\\r\\n warning_messages.append(j)\\r\\n number_of_warnings += 1\\r\\n if any(e in line for e in error_strings):\\r\\n error_messages.append(j)\\r\\n number_of_warnings += 1\\r\\n if 'finished at:' in line:\\r\\n finish_string_exists = True\\r\\n if os.path.splitext(file_name)[1] == '.out':\\r\\n if not finish_string_exists:\\r\\n error_messages.append('This thread has not been finished:\\\\n{0}'\\r\\n .format(os.path.join(input_file_parameters.output_dir,\\r\\n file_name)))\\r\\n\\r\\n if warning_messages or error_messages:\\r\\n print '\\\\n\\\\nThe following file contains possible warning/error messages:'\\r\\n print os.path.join(input_file_parameters.output_dir, file_name)\\r\\n if len(warning_messages) != 0:\\r\\n print '\\\\nWarning messages on lines:'\\r\\n print ', '.join(map(str, warning_messages))\\r\\n if len(error_messages) != 0:\\r\\n print '\\\\nError messages on lines:'\\r\\n print ', '.join(map(str, error_messages))\\r\\n\\r\\n print '\\\\n\\\\n{0} .out and .err files checked ({1} processes)'.format(i, i/2)\\r\\n print 'Potential problems detected: {0}'.format(number_of_warnings)\",\n \"def log_dir_stacks_contents(dir_stacks):\\r\\n for directory in dir_stacks:\\r\\n logging.info('-'*80)\\r\\n logging.info('Predicted directory contents of:\\\\n{0}'\\r\\n .format(directory.path))\\r\\n files = directory.file_names\\r\\n files = sorted(files)\\r\\n logging.info('Number of files: {0}'.format(len(files)))\\r\\n logging.info('Files:')\\r\\n logging.info('\\\\t'.join(files))\",\n \"def sense(self):\\n\\n partition_folder = self.getPartitionFolder()\\n log_folder = os.path.join(partition_folder, 'var/log')\\n log_name = 'slapgrid-%s-error.log' % self.getConfig('partition-id')\\n slapgrid_error_log_file = os.path.join(partition_folder, '.%s' % log_name)\\n link_file = os.path.join(log_folder, log_name)\\n monitor_url = self.getConfig('monitor-url')\\n message = ''\\n if os.path.exists(slapgrid_error_log_file) and \\\\\\n os.stat(slapgrid_error_log_file).st_size:\\n message = 'Buildout failed to process %s.' % self.getConfig('partition-id')\\n if monitor_url:\\n message += '\\\\nSee %s/log/%s for more information.' % (monitor_url, log_name)\\n if not os.path.exists(link_file):\\n os.symlink(slapgrid_error_log_file, link_file)\\n else:\\n if os.path.exists(link_file):\\n os.unlink(link_file)\\n\\n if message:\\n self.logger.error(message)\\n else:\\n self.logger.info(\\\"buildout is OK\\\")\",\n \"def run_commands(commands):\\n msg = \\\"\\\"\\n for cmd, send_stdout in commands: \\n msg += \\\"<hr/>\\\\n\\\"\\n log.info(\\\"Attempting to run command {}\\\".format(cmd))\\n try:\\n p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE,\\n stderr=subprocess.PIPE)\\n p.wait()\\n except Exception:\\n m = (\\\"<h2 style=\\\\\\\"color:red\\\\\\\">Failed to run <code>{}</code></h2>\\\\n\\\"\\n .format(escape(cmd)))\\n msg += m\\n log.exception(html_to_text(m).strip())\\n else:\\n if p.returncode == 0:\\n m = (\\\"<h2>Successfully ran <code>{}</code></h2>\\\\n\\\"\\n .format(escape(cmd)))\\n msg += m\\n log.info(html_to_text(m).strip())\\n else:\\n m = (\\\"<h2 style=\\\\\\\"color:red\\\\\\\">Failed to run <code>{}</code>\\\"\\n \\\"</h2>\\\\n\\\".format(escape(cmd)))\\n msg += m\\n log.warn(html_to_text(m).strip())\\n\\n stderr = p.stderr.read()\\n stdout = p.stdout.read() \\n \\n if (send_stdout or stderr) and stdout:\\n msg += (\\\"<h3>stdout</h3>\\\\n <pre>{}</pre>\\\\n\\\"\\n .format(escape(stdout)))\\n \\n if stderr:\\n msg += \\\"<h3 style=\\\\\\\"color:red\\\\\\\">stderr</h3>\\\\n\\\"\\n msg += (\\\"<pre style=\\\\\\\"color:red\\\\\\\">{}</pre>\\\\n\\\"\\n .format(escape(stderr)))\\n\\n return msg\",\n \"def validate_services(self, commands):\\n for k, v in commands.iteritems():\\n for cmd in v:\\n output, code = k.run(cmd)\\n if code != 0:\\n return \\\"command `{}` returned {}\\\".format(cmd, str(code))\\n return None\",\n \"def handle_command(self, commands):\\n print config.CMD_PROMPT + \\\" calling commands...\\\"\\n \\n success = False\\n\\n print config.CMD_PROMPT + \\\" Beginning Command Chain\\\"\\n for command in commands:\\n success = self.recursive_execute(command)\\n # Is there going to be complex results checking and handling code?\\n\\n print config.CMD_PROMPT + \\\" Command Chain Completed\\\"\\n return success\",\n \"def check_systtests_pickle_files(self):\\n # Make sure that there have been no more new scan points run since this\\n # last processing. To do this, get the number of output directories\\n # Compare this to the number in the pickle files.\\n self.num_systematics = {}\\n for basename in nsort(os.listdir(self.logdir)):\\n if 'pckl' in basename:\\n continue\\n basename_content = nsort(\\n os.listdir(os.path.join(self.logdir, basename))\\n )\\n # This means it is a directory containing something useful\\n if 'config_summary.json' in basename_content:\\n bits = basename.split('toy_')[-1].split('_')\\n toyname = None\\n add_bit = True\\n for bit in bits:\\n if bit == '' or bit == 'inj':\\n add_bit = False\\n if add_bit:\\n if toyname is None:\\n toyname = bit\\n else:\\n toyname += '_%s'%bit\\n if '_full_syst_baseline' in toyname:\\n toyname = toyname.split('_full_syst_baseline')[0]\\n toyname = 'toy_%s_asimov'%toyname\\n if toyname not in self.num_systematics.keys():\\n self.num_systematics[toyname] = 0\\n if 'wrong' in basename:\\n # Only want to include each systematic once, but\\n # they will have two directions.\\n if 'pve' in basename:\\n self.num_systematics[toyname] += 1\\n else:\\n self.num_systematics[toyname] += 1\\n data_sets = from_file(os.path.join(self.logdir,\\n 'data_sets.pckl'))\\n if sorted(data_sets.keys()) != sorted(self.num_systematics.keys()):\\n logging.info(\\n 'Found files I assume to be from a previous run of'\\n ' this processing script containing these truths: %s. '\\n 'However, based on the directories in the overall '\\n 'output directory there should be these truths: %s, so '\\n 'they will be regenerated.'%(\\n sorted(data_sets.keys()),\\n sorted(self.num_systematics.keys())\\n )\\n )\\n pickle_there = True\\n for toyname in sorted(self.num_systematics.keys()):\\n if len(data_sets[toyname].keys()) != self.num_systematics[toyname]:\\n pickle_there = False\\n if pickle_there:\\n logging.info(\\n 'Found files I assume to be from a previous run of'\\n ' this processing script containing %i sytematics. If '\\n 'this seems incorrect please delete the files: '\\n 'data_sets.pckl, all_params.pckl and labels.pckl '\\n 'from the logdir you have provided.'%(\\n self.num_systematics[self.num_systematics.keys()[0]])\\n )\\n else:\\n logging.info(\\n 'Found files I assume to be from a previous run of'\\n ' this processing script containing %i systematics. '\\n 'However, based on the number of directories in the overall '\\n 'output directory there should be %i systematics in '\\n 'these pickle files, so they will be regenerated.'%(\\n len(data_sets[data_sets.keys()[0]].keys()),\\n self.num_systematics[self.num_systematics.keys()[0]]\\n )\\n )\\n pickle_there = False\\n\\n return pickle_there\",\n \"def _check_for_errors(self, status):\\r\\n\\r\\n # Case when test suite name is misspelled or file doesn't exist\\r\\n if status == 252:\\r\\n sys.stderr.write('Test suite \\\"{}\\\" was not found in path {}\\\\n'.format(self.name, self.path))\\r\\n print 'Return code is {}'.format(status)\",\n \"def error_check(command):\\r\\n\\r\\n # TODO\\r\",\n \"def errors(job_name, jenkins_username, jenkins_token):\\n global server\\n# job_name = 'enterprise_pe-acceptance-tests_integration-system_pe_full-upgrade_weekend_2016.4.x' # 'enterprise_pe-orchestrator_intn-van-sys-pez-multi_2016.4.x-2016.4.x' # 'enterprise_pe-modules-vanagon-suite_intn-van-sys-pez-multi_daily-pe-modules-2016.4.x'\\n server = Jenkins('https://cinext-jenkinsmaster-enterprise-prod-1.delivery.puppetlabs.net', username=jenkins_username, password=jenkins_token)\\n info = server.get_job_info(job_name)\\n builds = [server.get_build_info(job_name, build['number']) for build in info['builds']]\\n failed_build_numbers = [b for b in builds if b['result'] == 'FAILURE']\\n last_job_errors = None\\n\\n counts = defaultdict(int)\\n similar = set()\\n for build in failed_build_numbers:\\n output = server.get_build_console_output(job_name, build['number'])\\n finder = get_strategy(output)\\n errors = finder(output)\\n print \\\"Errors: {}\\\".format(errors)\\n if last_job_errors:\\n seq = difflib.SequenceMatcher(a=last_job_errors, b=errors)\\n if seq.ratio() == 1.0:\\n counts['exact'] += 1\\n if seq.ratio() >= 0.7 and seq.ratio() < 1.0:\\n counts['similar'] += 1\\n similar.append(errors)\\n else:\\n last_job_errors = errors\\n\\n if last_job_errors:\\n click.echo('Last job errors were:')\\n click.echo('\\\\t{}'.format('\\\\n\\\\t'.join(last_job_errors)))\\n\\n if last_job_errors and 'exact' in counts:\\n click.echo('There were {} jobs that failed with errors exactly the same as the last failed job:'.format(counts['exact']))\\n click.echo('\\\\t{}'.format('\\\\n\\\\t'.join(last_job_errors)))\\n\\n if last_job_errors and 'similar' in counts:\\n click.echo('There were {} jobs that failed with experienced similar errors as the last failed job:'.format(counts['exact']))\\n click.echo('\\\\t{}'.format('\\\\n\\\\t'.join(last_job_errors)))\\n for s in similar:\\n click.echo('Additional Failed Job:')\\n click.echo('\\\\t{}'.format('\\\\n\\\\t'.join(s)))\",\n \"def all(\\n command,\\n):\\n # If we get to this point all tests listed in 'pre' have passed\\n # unless we have run the task with the --warn flag\\n if not command.config.run.warn:\\n print(\\n \\\"\\\"\\\"\\nAll Checks Passed Successfully\\n==========================================\\n\\\"\\\"\\\"\\n )\",\n \"def test_launch_failures(self):\\n host = NodeSet(choice(self.server_managers[0].hosts)) # nosec\\n self.log.info(\\\"Creating launch.py failure trigger files on %s\\\", host)\\n failure_trigger = \\\"00_trigger-launch-failure_00\\\"\\n failure_trigger_dir = os.path.join(self.base_test_dir, failure_trigger)\\n failure_trigger_files = [\\n os.path.join(self.base_test_dir, \\\"{}_local.yaml\\\".format(failure_trigger)),\\n os.path.join(os.sep, \\\"etc\\\", \\\"daos\\\", \\\"daos_{}.yml\\\".format(failure_trigger)),\\n os.path.join(self.base_test_dir, \\\"{}.log\\\".format(failure_trigger)),\\n os.path.join(failure_trigger_dir, \\\"{}.log\\\".format(failure_trigger)),\\n os.path.join(os.sep, \\\"tmp\\\", \\\"daos_dump_{}.txt\\\".format(failure_trigger)),\\n os.path.join(self.tmp, \\\"valgrind_{}\\\".format(failure_trigger)),\\n ]\\n\\n self.log.debug(\\\"Creating %s\\\", failure_trigger_dir)\\n commands = [\\n \\\"sudo -n mkdir -p {}\\\".format(failure_trigger_dir),\\n \\\"sudo -n {}\\\".format(get_chown_command(options='-R', file=failure_trigger_dir)),\\n ]\\n\\n local_trigger_file = failure_trigger_files.pop(0)\\n self.log.debug(\\\"Creating %s\\\", local_trigger_file)\\n try:\\n with open(local_trigger_file, \\\"w\\\", encoding=\\\"utf-8\\\") as local_trigger:\\n local_trigger.write(\\\"THIS IS JUST A TEST\\\\n\\\")\\n except IOError as error:\\n self.fail(\\\"Error writing {}: {}\\\".format(local_trigger_file, str(error)))\\n\\n for command in commands:\\n if not run_remote(self.log, host, command, timeout=20).passed:\\n self.fail(\\\"Error creating directory {}\\\".format(failure_trigger_dir))\\n\\n for failure_trigger_file in failure_trigger_files:\\n self.log.debug(\\\"Creating %s\\\", failure_trigger_file)\\n sudo = \\\"\\\" if failure_trigger_file.startswith(self.tmp) else \\\"sudo -n \\\"\\n commands = [\\n \\\"{}touch {}\\\".format(sudo, failure_trigger_file),\\n \\\"{}{}\\\".format(sudo, get_chown_command(options='-R', file=failure_trigger_file)),\\n \\\"echo 'THIS IS JUST A TEST' > {}\\\".format(failure_trigger_file),\\n ]\\n for command in commands:\\n if not run_remote(self.log, host, command, timeout=20).passed:\\n self.fail(\\\"Error creating file {}\\\".format(failure_trigger_file))\",\n \"def error_check(output_list):\\n #NOTE: Add error messages as you come across them\\n #keys = error messages we are looking for\\n #values = what we log if the key is found\\n known_errors = {\\n \\\"File Not Found\\\":\\\"File was not found\\\",\\n \\\"No such host is known\\\":\\\"Failed to connect to Client\\\"\\n }\\n #Verify the command ran without errors\\n for _line in output_list:\\n for key, value in known_errors.items():\\n if key in _line:\\n log.error(value)\\n return False\\n return True\",\n \"def test_failed():\\n build()\\n sh(\\\"%s %s --last-failed\\\" % (PYTHON, RUNNER_PY))\",\n \"def try_mitigate_issues_if_any(self, command, code, out):\\n if \\\"Error\\\" in out or \\\"Errno\\\" in out:\\n issue_mitigated = self.check_known_issues_and_attempt_fix(out)\\n if issue_mitigated:\\n self.composite_logger.log_debug('\\\\nPost mitigation, invoking package manager again using: ' + command)\\n code_after_fix_attempt, out_after_fix_attempt = self.env_layer.run_command_output(command, False, False)\\n return self.try_mitigate_issues_if_any(command, code_after_fix_attempt, out_after_fix_attempt)\\n return code, out\",\n \"def test_nonexistent_report(self):\\n command_line = [\\\"report\\\", \\\"notreport\\\"]\\n for prefix in [[], [\\\"--propagate\\\"]]:\\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)\",\n \"def feedback_no_result(self, classname, method):\\n logging.debug(\\\"feedback_no_result(%s, %s)\\\", classname, method)\\n\\n logging.info(\\\"Was not able to find the commit to blame for testcase %s %s\\\", classname, method)\\n\\n with open(self.html_file, \\\"a\\\") as result_file:\\n result_file.write(\\\"<br/><b>%s - %s is broken</b> but no braking commit found\\\\n\\\" % (classname, method))\\n with open(self.txt_file, \\\"a\\\") as result_file:\\n result_file.write(\\\"%s - %s is broken but no braking commit found\\\\n\\\" % (classname, method))\\n with open(self.summary_file, \\\"a\\\") as result_file:\\n result_file.write(\\\"<br/>Pass on %s#%s\\\\n\\\" % (classname.split(\\\".\\\")[-1], method))\",\n \"def _checkCommandStatus(self, lastCommand=False):\\n p = self.spawnProc\\n p.sendline('echo $?')\\n regex = re.compile('^[0-9]+',re.M)\\n p.expect(regex, 2)\\n msg = '_checkCommandStatus : Execution of command FAILED'\\n \\tif lastCommand:\\n \\t msg = '_checkCommandStatus :Execution of command : \\\"%s\\\" FAILED' %lastCommand\\n if p.after != '0' and p.after != '99':\\n raise AssertionError(msg)\",\n \"def execute():\\r\\n arcpy.AddMessage(\\\"START BCA Processing\\\")\\r\\n arcpy.env.workspace = config.temp_data_gdb\\r\\n arcpy.env.overwriteOutput = True\\r\\n sys.path.append(config.notif_system_script_folder)\\r\\n\\r\\n # Other Variables\\r\\n arcpy.AddMessage(\\\"Import toolbox\\\")\\r\\n arcpy.ImportToolbox(config.notif_toolbox)\\r\\n REGEX_FOR_INVALID_CHARS = re.compile(r'[^0-9a-zA-Z]+')\\r\\n todayDate = datetime.datetime.now().strftime(\\\"%Y%m%d\\\")\\r\\n logFile = file(\\r\\n config.report_processing_log + \\\"\\\\\\\\\\\" + todayDate + \\\"_NotificationSystemLog\\\" + \\\".txt\\\", \\\"a\\\")\\r\\n\\r\\n\\r\\n # get all unzipped files uploaded to shared folder\\r\\n configfiles = [os.path.join(dirpath, f)\\r\\n for dirpath, dirnames, files in os.walk(config.SharedFolder)\\r\\n for f in files if f.endswith('.csv') or f.endswith('.xls') or f.endswith('.xlsx') or f.endswith('.XLS')]\\r\\n\\r\\n correct_config_files = [f for f in configfiles if \\\"\\\\BCAWeeklyPermitReport\\\\\\\\\\\" in f]\\r\\n\\r\\n # PREPARE workspace\\r\\n arcpy.AddMessage(\\\"Preparing workspace...\\\")\\r\\n for BCAreport in correct_config_files:\\r\\n\\r\\n input_file_name = BCAreport.split(\\\"\\\\\\\\\\\")[-1]\\r\\n\\r\\n MukimConstruct = arcpy.SearchCursor(config.MukimConstructSource)\\r\\n PermitDateExists = False\\r\\n\\r\\n for row in MukimConstruct:\\r\\n aux = input_file_name[:8]\\r\\n if \\\"CORRECTED\\\" not in BCAreport.upper():\\r\\n filedate = datetime.datetime.strptime(aux, \\\"%Y%m%d\\\")\\r\\n else:\\r\\n clean_filename = input_file_name.split(\\\".\\\")[0]\\r\\n filedate = datetime.datetime.strptime(clean_filename[-8:], \\\"%Y%m%d\\\")\\r\\n if filedate == row.PERMIT_DATE and \\\"CORRECTED\\\" not in BCAreport.upper():\\r\\n PermitDateExists = True\\r\\n break\\r\\n if PermitDateExists and \\\"CORRECTED\\\" not in BCAreport.upper():\\r\\n PermitDateExistsLog = file(\\r\\n config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] +\\r\\n \\\" file's Permit Date already exists\\\" + \\\".log\\\",\\r\\n \\\"a\\\")\\r\\n PermitDateExistsLog.write(\\r\\n \\\"Permit Date for the file \\\" + input_file_name + \\\" already exists in Mukim Construct at \\\" + str(\\r\\n datetime.datetime.now()))\\r\\n logFile.writelines(\\r\\n \\\"Permit Date for the file \\\" + input_file_name + \\\" already exists in Mukim Construct at \\\" + str(\\r\\n datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n else:\\r\\n\\r\\n # 00. Creation of geodatabases that will serve as workspaces\\r\\n logFile.writelines(\\\"00 Creation of temp gdb starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n if arcpy.Exists(config.TempDataGDB):\\r\\n arcpy.Delete_management(config.TempDataGDB)\\r\\n arcpy.CreateFileGDB_management(config.Notification, \\\"Temp_data.gdb\\\")\\r\\n else:\\r\\n arcpy.CreateFileGDB_management(config.Notification, \\\"Temp_data.gdb\\\")\\r\\n\\r\\n if arcpy.Exists(config.SDEDataGDB):\\r\\n arcpy.Delete_management(config.SDEDataGDB)\\r\\n arcpy.CreateFileGDB_management(config.Notification, \\\"Source.gdb\\\")\\r\\n else:\\r\\n arcpy.CreateFileGDB_management(config.Notification, \\\"Source.gdb\\\")\\r\\n\\r\\n if arcpy.Exists(config.CurrentMukimConstructDataGDB):\\r\\n arcpy.Delete_management(config.CurrentMukimConstructDataGDB)\\r\\n arcpy.CreateFileGDB_management(config.Notification, \\\"Final_data.gdb\\\")\\r\\n else:\\r\\n arcpy.CreateFileGDB_management(config.Notification, \\\"Final_data.gdb\\\")\\r\\n\\r\\n logFile.writelines(\\\"00 Creation of temp gdb ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 01. Import the base data\\r\\n logFile.writelines(\\\"01 Import of base data starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructSource, config.CurrentMukimConstructDataGDB,\\r\\n \\\"MUKIM_CONSTRUCT\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructByProjSource, config.CurrentMukimConstructDataGDB,\\r\\n \\\"MUKIM_CONSTRUCT_BYPROJ\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.DepotSource, config.SDEDataGDB, \\\"DepotBoundary\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.CatchmentSource, config.SDEDataGDB, \\\"CatchmentBoundary\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.LandlotSource, config.TempDataGDB, \\\"Land_lot\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n # Calculate the lot key without letter\\r\\n arcpy.AddField_management(config.LandLot, \\\"Lotkey_wo_letter\\\", \\\"TEXT\\\", \\\"\\\", \\\"\\\", \\\"10\\\", \\\"\\\", \\\"NULLABLE\\\", \\\"NON_REQUIRED\\\",\\r\\n \\\"\\\")\\r\\n arcpy.CalculateField_management(config.LandLot, \\\"Lotkey_wo_letter\\\", \\\"!lot_key![:10]\\\", \\\"PYTHON\\\", \\\"\\\")\\r\\n\\r\\n logFile.writelines(\\\"01 Import of base data ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n\\r\\n # START THE LOOP TO PROCESS ALL THE FILES\\r\\n clcounter = 0\\r\\n\\r\\n if len(correct_config_files) == 0:\\r\\n logFile.writelines(\\\"No BCA report to process at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n arcpy.AddMessage(\\\"Processing files...\\\")\\r\\n for BCAreport in configfiles:\\r\\n\\r\\n clcounter += 1\\r\\n arcpy.AddMessage(BCAreport)\\r\\n input_file_name = BCAreport.split(\\\"\\\\\\\\\\\")[-1]\\r\\n MukimConstruct = arcpy.SearchCursor(config.MukimConstructSource)\\r\\n PermitDateExists = False\\r\\n\\r\\n # CHEKC FILE DATE EXISTS\\r\\n for row in MukimConstruct:\\r\\n aux = input_file_name[:8]\\r\\n if \\\"CORRECTED\\\" not in BCAreport.upper():\\r\\n filedate = datetime.datetime.strptime(aux, \\\"%Y%m%d\\\")\\r\\n else:\\r\\n clean_filename = input_file_name.split(\\\".\\\")[0]\\r\\n filedate = datetime.datetime.strptime(clean_filename[-8:], \\\"%Y%m%d\\\")\\r\\n if filedate == row.PERMIT_DATE and \\\"CORRECTED\\\" not in input_file_name.upper():\\r\\n PermitDateExists = True\\r\\n break\\r\\n\\r\\n HEADERVALID = True\\r\\n with xlrd.open_workbook(BCAreport) as wb:\\r\\n sh = wb.sheet_by_index(0)\\r\\n for r in range(sh.nrows):\\r\\n colcount = 0\\r\\n if sh.row_values(r)[colcount] == 'Error_Message':\\r\\n HEADERVALID = True\\r\\n elif sh.row_values(r)[colcount] == 'Project Ref No' or sh.row_values(r)[colcount] == 'Project_Ref_No':\\r\\n HEADERVALID = True\\r\\n else:\\r\\n PermitDateExistsLog = file(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[\\r\\n 0] + \\\" file's header format is not acceptable for processing\\\" + \\\".log\\\", \\\"a\\\")\\r\\n PermitDateExistsLog.write(\\r\\n \\\"The header format for the file \\\" + input_file_name + \\\" is not acceptable for processing at \\\" + str(\\r\\n datetime.datetime.now()))\\r\\n logFile.writelines(\\r\\n \\\"The header format for the file \\\" + input_file_name + \\\" is not acceptable for processing at \\\" + str(\\r\\n datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n HEADERVALID = False\\r\\n break\\r\\n\\r\\n if not PermitDateExists and HEADERVALID:\\r\\n logFile.writelines(\\\"Starts processing \\\" + BCAreport + \\\" at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # Status update to run/not run the SiteInspection Update\\r\\n Log_SiteInspectionUpdate = file(config.SiteInspectionUpdate, \\\"w\\\")\\r\\n Log_SiteInspectionUpdate.writelines(\\\"NO\\\")\\r\\n Log_SiteInspectionUpdate.close()\\r\\n\\r\\n # 02. Import the BCA report to a geodatabase table\\r\\n logFile.writelines(\\\"02 Import of table to gdb starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n if arcpy.Exists(config.TempDataGDB + \\\"\\\\\\\\ConvertedBCAreport_02\\\"):\\r\\n arcpy.Delete_management(config.TempDataGDB + \\\"\\\\\\\\ConvertedBCAreport_02\\\")\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"ConvertedBCAreport_02\\\", config.TemplateConvertedBCAreport)\\r\\n else:\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"ConvertedBCAreport_02\\\", config.TemplateConvertedBCAreport)\\r\\n if arcpy.Exists(BCAreport[:-5] + '_err' + '.csv'):\\r\\n # rename old error report\\r\\n os.remove(BCAreport[:-5] + '_err' + '.csv')\\r\\n else:\\r\\n result = \\\"Error file does not exist\\\"\\r\\n if BCAreport.endswith('.xls') or BCAreport.endswith('.xlsx') or BCAreport.endswith('.XLS'):\\r\\n rows_out = arcpy.InsertCursor(config.BCAReportGDBTable)\\r\\n fldlist = arcpy.ListFields(config.BCAReportGDBTable)\\r\\n fldlist.pop(0)\\r\\n with xlrd.open_workbook(BCAreport) as wb:\\r\\n sh = wb.sheet_by_index(0)\\r\\n for r in range(sh.nrows):\\r\\n colcount = 0\\r\\n if sh.row_values(r)[colcount] != 'Error_Message':\\r\\n colcount = 0\\r\\n else:\\r\\n colcount = 1\\r\\n break\\r\\n for r in range(sh.nrows):\\r\\n colcounter = colcount\\r\\n if r > 0:\\r\\n new_row_out = rows_out.newRow()\\r\\n for efld in fldlist:\\r\\n if efld.name <> 'OBJECTID' and efld.name <> 'ConcatFields':\\r\\n new_row_out.setValue(efld.name, sh.row_values(r)[colcounter])\\r\\n colcounter += 1\\r\\n\\r\\n logFile.writelines(\\\"Inserting: \\\" + str(new_row_out) + \\\"\\\\n\\\")\\r\\n rows_out.insertRow(new_row_out)\\r\\n del rows_out, new_row_out\\r\\n\\r\\n elif BCAreport.endswith('.csv'):\\r\\n\\r\\n BCAreportread = csv.DictReader(open(BCAreport, 'rb'), delimiter=',', quotechar='\\\"')\\r\\n rows_out = arcpy.InsertCursor(config.BCAReportGDBTable)\\r\\n for attribute in BCAreportread:\\r\\n new_row_out = rows_out.newRow()\\r\\n new_row_out.Project_Ref_No = attribute['Project_Ref_No']\\r\\n new_row_out.Project_Title = attribute['Project_Title']\\r\\n new_row_out.House_Blk_No = attribute['House_Blk_No']\\r\\n new_row_out.Road_Name = attribute['Road_Name']\\r\\n new_row_out.Level_No = attribute['Level_No']\\r\\n new_row_out.Unit_No = attribute['Unit_No']\\r\\n new_row_out.Building_Name = attribute['Building_Name']\\r\\n new_row_out.Postal_Code = attribute['Postal_Code']\\r\\n new_row_out.Project_Mukim_nos = attribute['Project_Mukim_nos']\\r\\n new_row_out.Project_Lot_nos = attribute['Project_Lot_nos']\\r\\n new_row_out.Permit_Type_of_Work = attribute['Permit_Type_of_Work']\\r\\n new_row_out.Type_of_Work = attribute['Type_of_Work']\\r\\n new_row_out.Owner_s_name = attribute['Owners_name']\\r\\n new_row_out.Owner_s_firm_name = attribute['Owners_firm_name']\\r\\n new_row_out.Owner_s_address = attribute['Owners_address']\\r\\n new_row_out.Owner_s_Tel_No = attribute['Owners_Tel_No']\\r\\n new_row_out.Owner_s_Email_address = attribute['Owners_Email_address']\\r\\n new_row_out.Builder_s_name = attribute['Builders_name']\\r\\n new_row_out.Builder_s_firm_name = attribute['Builders_firm_name']\\r\\n new_row_out.Builder_s_address = attribute['Builders_address']\\r\\n new_row_out.Builder_s_Tel_No = attribute['Builders_Tel_No']\\r\\n new_row_out.Builder_s_email_address = attribute['Builders_email_address']\\r\\n new_row_out.PE_s_name = attribute['PEs_name']\\r\\n new_row_out.PE_s_firm_name = attribute['PEs_firm_name']\\r\\n new_row_out.PE_s_address = attribute['PEs_address']\\r\\n new_row_out.PE_s_Tel_No = attribute['PEs_Tel_No']\\r\\n new_row_out.PE_s_Email_address = attribute['PEs_Email_address']\\r\\n new_row_out.Architect_s_name = attribute['Architects_name']\\r\\n new_row_out.Architect_s_firm_name = attribute['Architects_firm_name']\\r\\n new_row_out.Architect_s_address = attribute['Architects_address']\\r\\n new_row_out.Architect_s_Tel_No = attribute['Architects_Tel_No']\\r\\n new_row_out.Architect_s_Email_address = attribute['Architects_Email_address']\\r\\n new_row_out.Project_Cost = attribute['Project_Cost']\\r\\n new_row_out.Project_Duration = attribute['Project_Duration']\\r\\n new_row_out.Approval_Date_DD_MM_YYYY_ = attribute['Approval_Date']\\r\\n rows_out.insertRow(new_row_out)\\r\\n if new_row_out:\\r\\n del new_row_out\\r\\n if rows_out:\\r\\n del rows_out\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 02 Import of table to gdb: \\\", logFile)\\r\\n logFile.writelines(\\\"02 Import of table to gdb ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 03. Remove spaces in key fields for the concatenation\\r\\n logFile.writelines(\\\"03 Removing of spaces starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n rowsSpace = arcpy.UpdateCursor(config.BCAReportGDBTable)\\r\\n\\r\\n for row in rowsSpace:\\r\\n ProjRef = row.Project_Ref_No.strip()\\r\\n ProjMukim = row.Project_Mukim_nos.strip()\\r\\n ProjLot = row.Project_Lot_nos.strip()\\r\\n BuilderN = row.Builder_s_name.strip()\\r\\n row.Project_Ref_No = ProjRef\\r\\n row.Project_Mukim_nos = ProjMukim\\r\\n row.Project_Lot_nos = ProjLot\\r\\n row.Builder_s_name = BuilderN\\r\\n rowsSpace.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsSpace:\\r\\n del rowsSpace\\r\\n except:\\r\\n log_error(\\\"Error in 03 Removing of spaces: \\\", logFile)\\r\\n logFile.writelines(\\\"03 Removing of spaces ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 04. Concatenate Project_Ref_No, Project_Mukim_nos, Project_Lot_nos, Builder_s_name\\r\\n logFile.writelines(\\\"04 Concatenate the three fields starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n rows = arcpy.UpdateCursor(config.BCAReportGDBTable)\\r\\n for row in rows:\\r\\n expression = str(row.Project_Ref_No) + \\\"-\\\" + str(row.Project_Mukim_nos) + \\\"-\\\" + str(\\r\\n row.Project_Lot_nos) + \\\"-\\\" + str(row.Builder_s_name)\\r\\n row.ConcatFields = expression\\r\\n rows.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rows:\\r\\n del rows\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 04 Concatenate the three fields: \\\", logFile)\\r\\n logFile.writelines(\\\"04 Concatenate the three fields ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 05. Create temporary tables for Unique and Duplicate records\\r\\n logFile.writelines(\\\"05 Create temporary tables starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n if arcpy.Exists(config.TempDataGDB + \\\"\\\\\\\\Uniquerows\\\"):\\r\\n arcpy.Delete_management(config.TempDataGDB + \\\"\\\\\\\\Uniquerows\\\")\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Uniquerows\\\", config.TemplateConcat, \\\"\\\")\\r\\n else:\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Uniquerows\\\", config.TemplateConcat, \\\"\\\")\\r\\n\\r\\n if arcpy.Exists(config.TempDataGDB + \\\"\\\\\\\\Duplicaterows\\\"):\\r\\n arcpy.Delete_management(config.TempDataGDB + \\\"\\\\\\\\Duplicaterows\\\")\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Duplicaterows\\\", config.TemplateConcat, \\\"\\\")\\r\\n else:\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Duplicaterows\\\", config.TemplateConcat, \\\"\\\")\\r\\n except:\\r\\n log_error(\\\"Error in 05 Create temporary tables: \\\", logFile)\\r\\n logFile.writelines(\\\"05 Create temporary tables ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 06. Separate unique and duplicate records\\r\\n logFile.writelines(\\\"06 Separate unique and duplicate rows starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n print \\\"Start step 06\\\"\\r\\n rows_inCB02 = arcpy.UpdateCursor(config.BCAReportGDBTable)\\r\\n rows_outUnique = arcpy.InsertCursor(config.UniqueRecords)\\r\\n # print rows_outUnique\\r\\n rows_outDuplicate = arcpy.InsertCursor(config.DuplicateRecords)\\r\\n\\r\\n rows_unique = []\\r\\n rows_duplicates = []\\r\\n for row in rows_inCB02:\\r\\n if row.ConcatFields not in rows_unique:\\r\\n rows_unique = rows_unique + [row.ConcatFields]\\r\\n else:\\r\\n rows_duplicates = rows_duplicates + [row.ConcatFields]\\r\\n\\r\\n print \\\"Start step 06 1\\\"\\r\\n for item in rows_unique:\\r\\n print \\\"clcounter: \\\" + str(clcounter)\\r\\n print \\\"item: \\\" + str(item)\\r\\n newrow = rows_outUnique.newRow()\\r\\n newrow.Concat = item\\r\\n # print newrow\\r\\n rows_outUnique.insertRow(newrow)\\r\\n\\r\\n print \\\"Start step 06 2\\\"\\r\\n for item in rows_duplicates:\\r\\n print \\\"clcounter: \\\" + str(clcounter)\\r\\n print \\\"item: \\\" + str(item)\\r\\n newrow = rows_outDuplicate.newRow()\\r\\n newrow.Concat = item\\r\\n rows_outDuplicate.insertRow(newrow)\\r\\n\\r\\n print \\\"Start step 06 3\\\"\\r\\n\\r\\n if rows_inCB02:\\r\\n del rows_inCB02\\r\\n if rows_outUnique:\\r\\n del rows_outUnique\\r\\n if rows_outDuplicate:\\r\\n del rows_outDuplicate\\r\\n if row:\\r\\n del row\\r\\n except:\\r\\n log_error(\\\"Error in 06 Separate unique and duplicate rows: \\\", logFile)\\r\\n logFile.writelines(\\\"06 Separate unique and duplicate rows ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 07. Get the rest of the fields for Uniquerows table\\r\\n logFile.writelines(\\r\\n \\\"07 Get the rest of the fields for unique rows starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.env.workspace = config.TempDataGDB\\r\\n arcpy.AddMessage(\\\"Starting toolbox JoinUniqueRestofFields\\\")\\r\\n\\r\\n try:\\r\\n arcpy.JoinUniqueRestofFields()\\r\\n except:\\r\\n log_error(\\\"Error in 07 Get the rest of the fields for unique rows: \\\", logFile)\\r\\n logFile.writelines(\\r\\n \\\"07 Get the rest of the fields for unique rows ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 08. Get the rest of the fields for Duplicaterows table\\r\\n logFile.writelines(\\r\\n \\\"08 Get the rest of the fields for duplicate rows starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.AddMessage(\\\"START toolbox JoinDuplicateRestofFields\\\")\\r\\n try:\\r\\n arcpy.JoinDuplicateRestofFields()\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 08 Get the rest of the fields for duplicate rows: \\\", logFile)\\r\\n\\r\\n logFile.writelines(\\r\\n \\\"08 Get the rest of the fields for duplicate rows ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 09. Log duplicate records\\r\\n logFile.writelines(\\\"09 Log duplicate records starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.AddMessage(\\\"Logging duplicate records\\\")\\r\\n try:\\r\\n # Initialize the error log\\r\\n wbk = xlwt.Workbook()\\r\\n sheet = wbk.add_sheet('Book 1')\\r\\n row_count = 0\\r\\n col_count = 0\\r\\n header = ['Error_Message', 'Project_Ref_No', 'Project_Title', 'House_Blk_No', 'Road_Name', 'Level_No',\\r\\n 'Unit_No', 'Building_Name', 'Postal_Code', 'Project_Mukim_nos', 'Project_Lot_nos',\\r\\n 'Permit_Type_of_Work', 'Type_of_Work', 'Owners_name', 'Owners_firm_name', 'Owners_address',\\r\\n 'Owners_Tel_No', 'Owners_Email_address', 'Builders_name', 'Builders_firm_name',\\r\\n 'Builders_address', 'Builders_Tel_No', 'Builders_email_address', 'PEs_name', 'PEs_firm_name',\\r\\n 'PEs_address', 'PEs_Tel_No', 'PEs_Email_address', 'Architects_name', 'Architects_firm_name',\\r\\n 'Architects_address', 'Architects_Tel_No', 'Architects_Email_address', 'Project_Cost',\\r\\n 'Project_Duration', 'Approval_Date']\\r\\n for fieldname in header:\\r\\n sheet.write(row_count, col_count, fieldname)\\r\\n col_count += 1\\r\\n wbk.save(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\")\\r\\n\\r\\n # Log duplicate records\\r\\n rows = arcpy.SearchCursor(config.DuplicateRows)\\r\\n\\r\\n row_count = 1\\r\\n col_count = 0\\r\\n row = None\\r\\n for row in rows:\\r\\n message = ['Duplicate record in the BCA report', row.Project_Ref_No, row.Project_Title,\\r\\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\\r\\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\\r\\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\\r\\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\\r\\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\\r\\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\\r\\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\\r\\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\\r\\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n wbk.save(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\")\\r\\n if row:\\r\\n del row\\r\\n if rows:\\r\\n del rows\\r\\n except:\\r\\n log_error(\\\"Error in 09 Log duplicate records: \\\", logFile)\\r\\n\\r\\n logFile.writelines(\\\"09 Log duplicate records ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 10. Split rows based on Mukim numbers\\r\\n logFile.writelines(\\\"10 Splitting of rows based on mukim starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n if arcpy.Exists(config.SplittedMukimRows):\\r\\n arcpy.Delete_management(config.SplittedMukimRows)\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Splitted_rows_mukim_03\\\", config.TemplateBCAReport, \\\"\\\")\\r\\n else:\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Splitted_rows_mukim_03\\\", config.TemplateBCAReport, \\\"\\\")\\r\\n\\r\\n if arcpy.Exists(config.SplittedProjLotRows):\\r\\n arcpy.Delete_management(config.SplittedProjLotRows)\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Splitted_rows_projlot_04\\\", config.TemplateBCAReport, \\\"\\\")\\r\\n else:\\r\\n arcpy.CreateTable_management(config.TempDataGDB, \\\"Splitted_rows_projlot_04\\\", config.TemplateBCAReport, \\\"\\\")\\r\\n\\r\\n rows_in = arcpy.SearchCursor(config.UniqueRows)\\r\\n rows_out = arcpy.InsertCursor(config.SplittedMukimRows)\\r\\n\\r\\n for row in rows_in:\\r\\n list_mukim_nos = row.Project_Mukim_nos.split(\\\",\\\")\\r\\n for proj_mukim_nos_id in list_mukim_nos:\\r\\n new_row_out = rows_out.newRow()\\r\\n new_row_out.Project_Mukim_nos = proj_mukim_nos_id\\r\\n new_row_out.PROJECTMUKIM_RAW = row.Project_Mukim_nos\\r\\n new_row_out.Project_Ref_No = row.Project_Ref_No\\r\\n new_row_out.Project_Title = row.Project_Title\\r\\n new_row_out.House_Blk_No = row.House_Blk_No\\r\\n new_row_out.Road_Name = row.Road_Name\\r\\n new_row_out.Level_No = row.Level_No\\r\\n new_row_out.Unit_No = row.Unit_No\\r\\n new_row_out.Building_Name = row.Building_Name\\r\\n new_row_out.Postal_Code = row.Postal_Code\\r\\n new_row_out.Project_Lot_nos = row.Project_Lot_nos\\r\\n new_row_out.Permit_Type_of_Work = row.Permit_Type_of_Work\\r\\n new_row_out.Type_of_Work = row.Type_of_Work\\r\\n new_row_out.Owner_s_name = row.Owner_s_name\\r\\n new_row_out.Owner_s_firm_name = row.Owner_s_firm_name\\r\\n new_row_out.Owner_s_address = row.Owner_s_address\\r\\n new_row_out.Owner_s_Tel_No = row.Owner_s_Tel_No\\r\\n new_row_out.Owner_s_Email_address = row.Owner_s_Email_address\\r\\n new_row_out.Builder_s_name = row.Builder_s_name\\r\\n new_row_out.Builder_s_firm_name = row.Builder_s_firm_name\\r\\n new_row_out.Builder_s_address = row.Builder_s_address\\r\\n new_row_out.Builder_s_Tel_No = row.Builder_s_Tel_No\\r\\n new_row_out.Builder_s_email_address = row.Builder_s_email_address\\r\\n new_row_out.PE_s_name = row.PE_s_name\\r\\n new_row_out.PE_s_firm_name = row.PE_s_firm_name\\r\\n new_row_out.PE_s_address = row.PE_s_address\\r\\n new_row_out.PE_s_Tel_No = row.PE_s_Tel_No\\r\\n new_row_out.PE_s_Email_address = row.PE_s_Email_address\\r\\n new_row_out.Architect_s_name = row.Architect_s_name\\r\\n new_row_out.Architect_s_firm_name = row.Architect_s_firm_name\\r\\n new_row_out.Architect_s_address = row.Architect_s_address\\r\\n new_row_out.Architect_s_Tel_No = row.Architect_s_Tel_No\\r\\n new_row_out.Architect_s_Email_address = row.Architect_s_Email_address\\r\\n new_row_out.Project_Cost = row.Project_Cost\\r\\n new_row_out.Project_Duration = row.Project_Duration\\r\\n new_row_out.Approval_Date_DD_MM_YYYY_ = row.Approval_Date_DD_MM_YYYY_\\r\\n rows_out.insertRow(new_row_out)\\r\\n if row:\\r\\n del row\\r\\n if new_row_out:\\r\\n del new_row_out\\r\\n if rows_in:\\r\\n del rows_in\\r\\n if rows_out:\\r\\n del rows_out\\r\\n except:\\r\\n log_error(\\\"Error in 10 Splitting of rows based on mukim: \\\", logFile)\\r\\n\\r\\n logFile.writelines(\\\"10 Splitting of rows based on mukim ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 11.Split rows based on Project lot numbers\\r\\n arcpy.AddMessage(\\\"Splitting rows based on project lots\\\")\\r\\n\\r\\n logFile.writelines(\\r\\n \\\"11 Splitting of rows based on project lot starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n rows_in03 = arcpy.SearchCursor(config.SplittedMukimRows)\\r\\n rows_out04 = arcpy.InsertCursor(config.SplittedProjLotRows)\\r\\n\\r\\n for row in rows_in03:\\r\\n list_proj_lot_nos = row.Project_Lot_nos.split(\\\",\\\")\\r\\n print list_proj_lot_nos\\r\\n for proj_lot_nos_id in list_proj_lot_nos:\\r\\n print proj_lot_nos_id\\r\\n new_row_out = rows_out04.newRow()\\r\\n new_row_out.Project_Lot_nos = proj_lot_nos_id\\r\\n new_row_out.PROJECTMUKIM_RAW = row.PROJECTMUKIM_RAW\\r\\n new_row_out.PROJECTLOT_RAW = row.Project_Lot_nos\\r\\n new_row_out.Project_Ref_No = row.Project_Ref_No\\r\\n new_row_out.Project_Title = row.Project_Title\\r\\n new_row_out.House_Blk_No = row.House_Blk_No\\r\\n new_row_out.Road_Name = row.Road_Name\\r\\n new_row_out.Level_No = row.Level_No\\r\\n new_row_out.Unit_No = row.Unit_No\\r\\n new_row_out.Building_Name = row.Building_Name\\r\\n new_row_out.Postal_Code = row.Postal_Code\\r\\n new_row_out.Project_Mukim_nos = row.Project_Mukim_nos\\r\\n new_row_out.Permit_Type_of_Work = row.Permit_Type_of_Work\\r\\n new_row_out.Type_of_Work = row.Type_of_Work\\r\\n new_row_out.Owner_s_name = row.Owner_s_name\\r\\n new_row_out.Owner_s_firm_name = row.Owner_s_firm_name\\r\\n new_row_out.Owner_s_address = row.Owner_s_address\\r\\n new_row_out.Owner_s_Tel_No = row.Owner_s_Tel_No\\r\\n new_row_out.Owner_s_Email_address = row.Owner_s_Email_address\\r\\n new_row_out.Builder_s_name = row.Builder_s_name\\r\\n new_row_out.Builder_s_firm_name = row.Builder_s_firm_name\\r\\n new_row_out.Builder_s_address = row.Builder_s_address\\r\\n new_row_out.Builder_s_Tel_No = row.Builder_s_Tel_No\\r\\n new_row_out.Builder_s_email_address = row.Builder_s_email_address\\r\\n new_row_out.PE_s_name = row.PE_s_name\\r\\n new_row_out.PE_s_firm_name = row.PE_s_firm_name\\r\\n new_row_out.PE_s_address = row.PE_s_address\\r\\n new_row_out.PE_s_Tel_No = row.PE_s_Tel_No\\r\\n new_row_out.PE_s_Email_address = row.PE_s_Email_address\\r\\n new_row_out.Architect_s_name = row.Architect_s_name\\r\\n new_row_out.Architect_s_firm_name = row.Architect_s_firm_name\\r\\n new_row_out.Architect_s_address = row.Architect_s_address\\r\\n new_row_out.Architect_s_Tel_No = row.Architect_s_Tel_No\\r\\n new_row_out.Architect_s_Email_address = row.Architect_s_Email_address\\r\\n new_row_out.Project_Cost = row.Project_Cost\\r\\n new_row_out.Project_Duration = row.Project_Duration\\r\\n new_row_out.Approval_Date_DD_MM_YYYY_ = row.Approval_Date_DD_MM_YYYY_\\r\\n rows_out04.insertRow(new_row_out)\\r\\n\\r\\n if row:\\r\\n del row\\r\\n if new_row_out:\\r\\n del new_row_out\\r\\n if rows_in03:\\r\\n del rows_in03\\r\\n if rows_out04:\\r\\n del rows_out04\\r\\n # print int(arcpy.GetCount_management(SplittedProjLotRows).getOutput(0))\\r\\n except:\\r\\n log_error(\\\"Error in 11 Splitting of rows based on project lot: \\\", logFile)\\r\\n logFile.writelines(\\r\\n \\\"11 Splitting of rows based on project lot ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 12. Remove spaces in Mukim and Project lot values\\r\\n logFile.writelines(\\r\\n \\\"12 Removing of spaces in mukim and project lot starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.AddMessage(\\\"Cleaning project lots\\\")\\r\\n try:\\r\\n\\r\\n rowsSpaces = arcpy.UpdateCursor(config.SplittedProjLotRows)\\r\\n\\r\\n for row in rowsSpaces:\\r\\n lot_no_spaces = row.Project_Lot_nos.strip()\\r\\n mukim_no_spaces = row.Project_Mukim_nos.strip()\\r\\n row.Project_Lot_nos = lot_no_spaces\\r\\n row.Project_Mukim_nos = mukim_no_spaces\\r\\n rowsSpaces.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsSpaces:\\r\\n del rowsSpaces\\r\\n except:\\r\\n log_error(\\\"Error in 12 Removing of spaces in mukim and project lot: \\\", logFile)\\r\\n logFile.writelines(\\r\\n \\\"12 Removing of spaces in mukim and project lot ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 13. Log empty Mukimlot or date fields\\r\\n logFile.writelines(\\r\\n \\\"13 Log empty mukim and project lot nos starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n rowsEmpty = arcpy.UpdateCursor(config.SplittedProjLotRows)\\r\\n\\r\\n for row in rowsEmpty:\\r\\n message = ['Missing Project lot or Mukim numbers', row.Project_Ref_No, row.Project_Title,\\r\\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\\r\\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\\r\\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\\r\\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\\r\\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\\r\\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\\r\\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\\r\\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\\r\\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\\r\\n message2 = ['Missing Project duration or Approval date', row.Project_Ref_No, row.Project_Title,\\r\\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\\r\\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\\r\\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\\r\\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\\r\\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\\r\\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\\r\\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name,\\r\\n row.Architect_s_firm_name, row.Architect_s_address, row.Architect_s_Tel_No,\\r\\n row.Architect_s_Email_address, row.Project_Cost, row.Project_Duration,\\r\\n row.Approval_Date_DD_MM_YYYY_]\\r\\n if row.Project_Mukim_nos is None or (len(row.Project_Mukim_nos) < 4):\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsEmpty.deleteRow(row)\\r\\n elif row.Project_Lot_nos is None or (len(row.Project_Lot_nos) == 0):\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsEmpty.deleteRow(row)\\r\\n if row.Project_Duration is None or (len(row.Project_Duration) < 1):\\r\\n col_count = 0\\r\\n for element in message2:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsEmpty.deleteRow(row)\\r\\n\\r\\n elif row.Approval_Date_DD_MM_YYYY_ is None or (len(row.Approval_Date_DD_MM_YYYY_) < 1):\\r\\n col_count = 0\\r\\n for element in message2:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsEmpty.deleteRow(row)\\r\\n wbk.save(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\")\\r\\n if row:\\r\\n del row\\r\\n if rowsEmpty:\\r\\n del rowsEmpty\\r\\n except:\\r\\n log_error(\\\"Error in 13 Log for empty mukim and project lot nos: \\\", logFile)\\r\\n logFile.writelines(\\\"13 Log empty mukim and project lot nos ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 14. Error log for those with bad values\\r\\n arcpy.AddMessage(\\\"14 Logging bad values\\\")\\r\\n logFile.writelines(\\\"14 Log if bad values exist starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsBadValues = arcpy.UpdateCursor(config.SplittedProjLotRows)\\r\\n\\r\\n for row in rowsBadValues:\\r\\n message = ['Mukim or Project lot numbers have bad values', row.Project_Ref_No, row.Project_Title,\\r\\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\\r\\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\\r\\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\\r\\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\\r\\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\\r\\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\\r\\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\\r\\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\\r\\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\\r\\n if len(REGEX_FOR_INVALID_CHARS.findall(row.Project_Lot_nos)) > 0:\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsBadValues.deleteRow(row)\\r\\n elif len(REGEX_FOR_INVALID_CHARS.findall(row.Project_Mukim_nos)) > 0:\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsBadValues.deleteRow(row)\\r\\n elif len(uptodigit(row.Project_Lot_nos)) > 0:\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n rowsBadValues.deleteRow(row)\\r\\n wbk.save(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\")\\r\\n\\r\\n if row:\\r\\n del row\\r\\n if rowsBadValues:\\r\\n del rowsBadValues\\r\\n except:\\r\\n log_error(\\\"Error in 14 Log if bad values exist: \\\", logFile)\\r\\n logFile.writelines(\\\"14 Log if bad values exist ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 15. Add zeros for Project Lot numbers\\r\\n logFile.writelines(\\\"15 Add zeros starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsZeros = arcpy.UpdateCursor(config.SplittedProjLotRows)\\r\\n letters = string.ascii_letters\\r\\n for row in rowsZeros:\\r\\n letter_count = len(filter(functools.partial(operator.contains, letters), row.Project_Lot_nos))\\r\\n filled_string = row.Project_Lot_nos.zfill(5 + letter_count)\\r\\n row.Project_Lot_nos = filled_string\\r\\n rowsZeros.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsZeros:\\r\\n del rowsZeros\\r\\n except:\\r\\n log_error(\\\"Error in 15 Add zeros: \\\", logFile)\\r\\n logFile.writelines(\\\"15 Add zeros ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 16. Add and populate fields Mukim_Lot_No, Mukimlot_wo_letter, and Permit_date\\r\\n logFile.writelines(\\\"16 Add and populate fields starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsPop = arcpy.UpdateCursor(config.SplittedProjLotRows)\\r\\n for row in rowsPop:\\r\\n expression = str(row.Project_Mukim_nos) + \\\"-\\\" + str(row.Project_Lot_nos)\\r\\n row.Mukim_Lot_No = expression\\r\\n date = filedate.strftime(\\\"%Y%m%d\\\")\\r\\n year = int(date[:4])\\r\\n month = int(date[4:6])\\r\\n day = int(date[6:8])\\r\\n permit_date = datetime.datetime(year, month, day)\\r\\n row.Permit_date = permit_date\\r\\n rowsPop.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsPop:\\r\\n del rowsPop\\r\\n # Calculate Mukimlot_wo_letter\\r\\n arcpy.CalculateField_management(config.SplittedProjLotRows, \\\"Mukimlot_wo_letter\\\", \\\"!Mukim_Lot_No![:10]\\\",\\r\\n \\\"PYTHON_9.3\\\", \\\"\\\")\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 16 Add and populate fields: \\\", logFile)\\r\\n logFile.writelines(\\\"16 Add and populate fields ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 17.Match mukim lot and land lot\\r\\n logFile.writelines(\\\"17 Match mukim lot with landlot starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n arcpy.MatchMukimLandLot()\\r\\n except:\\r\\n log_error(\\\"Error in 17 Match mukim lot with landlot: \\\", logFile)\\r\\n logFile.writelines(\\\"17 Match mukim lot with landlot ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 18.Get unmatched mukim lot with land lot\\r\\n logFile.writelines(\\\"18 Get unmatched mukim lot starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.AddMessage(\\\"18 Get unmatched mukim lot\\\")\\r\\n try:\\r\\n arcpy.GetUnmatchedMukimLot()\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 18 Get unmatched mukim lot: \\\", logFile)\\r\\n\\r\\n logFile.writelines(\\\"18 Get unmatched mukim lot ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 19. Log errors for unmatched mukim lots\\r\\n logFile.writelines(\\\"19 Log unmatched mukim lot starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsUnmatched = arcpy.SearchCursor(config.UnmatchedMukimLot)\\r\\n row = None\\r\\n\\r\\n for row in rowsUnmatched:\\r\\n message = ['Unmatched mukim lot with the land lot', row.Project_Ref_No, row.Project_Title,\\r\\n row.House_Blk_No, row.Road_Name, row.Level_No, row.Unit_No, row.Building_Name,\\r\\n row.Postal_Code, row.Project_Mukim_nos, row.Project_Lot_nos, row.Permit_Type_of_Work,\\r\\n row.Type_of_Work, row.Owner_s_name, row.Owner_s_firm_name, row.Owner_s_address,\\r\\n row.Owner_s_Tel_No, row.Owner_s_Email_address, row.Builder_s_name,\\r\\n row.Builder_s_firm_name, row.Builder_s_address, row.Builder_s_Tel_No,\\r\\n row.Builder_s_email_address, row.PE_s_name, row.PE_s_firm_name, row.PE_s_address,\\r\\n row.PE_s_Tel_No, row.PE_s_Email_address, row.Architect_s_name, row.Architect_s_firm_name,\\r\\n row.Architect_s_address, row.Architect_s_Tel_No, row.Architect_s_Email_address,\\r\\n row.Project_Cost, row.Project_Duration, row.Approval_Date_DD_MM_YYYY_]\\r\\n col_count = 0\\r\\n for element in message:\\r\\n sheet.write(row_count, col_count, element)\\r\\n col_count += 1\\r\\n row_count += 1\\r\\n wbk.save(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\")\\r\\n if row:\\r\\n del row\\r\\n if rowsUnmatched:\\r\\n del rowsUnmatched\\r\\n\\r\\n with xlrd.open_workbook(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\") as wb:\\r\\n sh = wb.sheet_by_index(0)\\r\\n if sh.nrows == 1:\\r\\n os.remove(config.ErrorLogFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\"_err\\\" + \\\".xls\\\")\\r\\n\\r\\n except arcpy.ExecuteError:\\r\\n log_error(\\\"Error in 19 Log unmatched mukim lot: \\\", logFile)\\r\\n logFile.writelines(\\\"19 Log unmatched mukim lot ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 20. Prepare the table for MukimConstruct matching (add required fields)\\r\\n logFile.writelines(\\\"20 Add fields to be used for matching starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n if arcpy.Exists(config.MUKIMCONSTRUCTImport):\\r\\n arcpy.Delete_management(config.MUKIMCONSTRUCTImport)\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructSource, config.TempDataGDB,\\r\\n \\\"MUKIM_CONSTRUCT_Import\\\")\\r\\n else:\\r\\n arcpy.FeatureClassToFeatureClass_conversion(config.MukimConstructSource, config.TempDataGDB,\\r\\n \\\"MUKIM_CONSTRUCT_Import\\\")\\r\\n\\r\\n arcpy.AddField_management(config.MatchedMukimLot, \\\"Concat_4fields\\\", \\\"Text\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n arcpy.AddField_management(config.MUKIMCONSTRUCTImport, \\\"Concat_4fields\\\", \\\"Text\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n arcpy.AddField_management(config.MatchedMukimLot, \\\"PROJ_DURATION_MTHS2\\\", \\\"Double\\\", \\\"\\\", \\\"\\\", \\\"\\\")\\r\\n except:\\r\\n log_error(\\\"Error in 20 Add fields to be used for matching: \\\", logFile)\\r\\n logFile.writelines(\\\"20 Add fields to be used for matching ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 21. Calculate Project Duration as months\\r\\n logFile.writelines(\\\"21 Calculate PROJ_DURATION as months starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsProjDur = arcpy.UpdateCursor(config.MatchedMukimLot)\\r\\n\\r\\n for row in rowsProjDur:\\r\\n durationstr = row.PROJ_DURATION_MTHS\\r\\n if \\\"Month\\\" in row.PROJ_DURATION_MTHS:\\r\\n durationintmth = int(durationstr.split(' ')[0])\\r\\n row.PROJ_DURATION_MTHS2 = durationintmth\\r\\n elif \\\"Year\\\" in row.PROJ_DURATION_MTHS:\\r\\n durationintyr = int(durationstr.split(' ')[0]) * 12\\r\\n row.PROJ_DURATION_MTHS2 = durationintyr\\r\\n rowsProjDur.updateRow(row)\\r\\n if rowsProjDur:\\r\\n del rowsProjDur\\r\\n if row:\\r\\n del row\\r\\n\\r\\n arcpy.DeleteField_management(config.MatchedMukimLot, \\\"PROJ_DURATION_MTHS\\\")\\r\\n arcpy.AddField_management(config.MatchedMukimLot, \\\"PROJ_DURATION_MTHS\\\", \\\"Double\\\")\\r\\n arcpy.CalculateField_management(config.MatchedMukimLot, \\\"PROJ_DURATION_MTHS\\\", \\\"[PROJ_DURATION_MTHS2]\\\")\\r\\n except:\\r\\n log_error(\\\"Error in 21 Calculate PROJ_DURATION as months: \\\", logFile)\\r\\n logFile.writelines(\\\"21 Calculate PROJ_DURATION as months ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 22. Concatenate 4 fields to be used in checking if mukimlot already exists in MUKIMCONSTRUCT\\r\\n logFile.writelines(\\\"22 Concatenate 4 fields starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsConcat1 = arcpy.UpdateCursor(config.MUKIMCONSTRUCTImport)\\r\\n\\r\\n for row in rowsConcat1:\\r\\n expression = str(row.PROJ_REF_NO) + \\\"-\\\" + str(row.BUILDER_NAME) + \\\"-\\\" + str(\\r\\n row.LOT_KEY) + \\\"-\\\" + str(row.PERMIT_DATE)\\r\\n row.Concat_4fields = expression\\r\\n rowsConcat1.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsConcat1:\\r\\n del rowsConcat1\\r\\n\\r\\n rowsConcat2 = arcpy.UpdateCursor(config.MatchedMukimLot)\\r\\n\\r\\n for row in rowsConcat2:\\r\\n expression = str(row.PROJ_REF_NO) + \\\"-\\\" + str(row.BUILDER_NAME) + \\\"-\\\" + str(\\r\\n row.LOT_KEY) + \\\"-\\\" + str(row.PERMIT_DATE)\\r\\n row.Concat_4fields = expression\\r\\n rowsConcat2.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsConcat2:\\r\\n del rowsConcat2\\r\\n except:\\r\\n log_error(\\\"Error in 22 Concatenate 4 fields: \\\", logFile)\\r\\n logFile.writelines(\\\"22 Concatenate 4 fields ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 23.Match mukim lot with mukim construct\\r\\n logFile.writelines(\\\"23 Match mukimlot with mukim construct at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.env.workspace = config.TempDataGDB # \\\"G:\\\\\\\\Project\\\\\\\\GERIUPGRADE\\\\\\\\GPTools\\\\\\\\NotificationSysTools\\\\\\\\BCAReportProcessing\\\\\\\\Temp_data.gdb\\\"\\r\\n try:\\r\\n arcpy.MatchedMukimlotMukimConstruct()\\r\\n except:\\r\\n log_error(\\\"Error in 23 Match mukimlot with mukim construct: \\\", logFile)\\r\\n logFile.writelines(\\\"23 Match mukimlot with mukim construct ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 24.Copy raw values to project lot and project mukim columns and delete the 2 fields\\r\\n logFile.writelines(\\\"24 Recalculate projlot and projmukim based on original values starts at \\\" + str(\\r\\n datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rowsRaw = arcpy.UpdateCursor(config.MatchedMukimLot)\\r\\n\\r\\n for row in rowsRaw:\\r\\n row.PROJ_MUKIM_NOS = row.PROJECTMUKIM_RAW\\r\\n row.PROJ_LOT_NOS = row.PROJECTLOT_RAW\\r\\n rowsRaw.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsRaw:\\r\\n del rowsRaw\\r\\n except:\\r\\n log_error(\\\"Error in 24 Recalculate projlot and projmukim based on original values:\\\", logFile)\\r\\n logFile.writelines(\\\"24 Recalculate projlot and projmukim based on original values ends at \\\" + str(\\r\\n datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 25. Export Cleaned BCA Permit report for CWD\\r\\n logFile.writelines(\\r\\n \\\"25 Export of Cleaned BCA Permit report starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n # Initialize the file\\r\\n CleanedBCAPermitReport = xlwt.Workbook()\\r\\n book = CleanedBCAPermitReport.add_sheet('Book 1')\\r\\n countrow = 0\\r\\n countcol = 0\\r\\n fields = ['Project Ref No', 'Project Title', 'House Blk No', 'Road Name', 'Level No', 'Unit No',\\r\\n 'Building Name', 'Postal Code', 'Project Mukim nos', 'Project Lot nos', 'Permit Type of Work',\\r\\n 'Type of Work', \\\"Owner's name\\\", \\\"Owner's firm name\\\", \\\"Owner's address\\\", \\\"Owner's Tel No\\\",\\r\\n \\\"Owner's Email address\\\", \\\"Builder's name\\\", \\\"Builder's firm name\\\", \\\"Builder's address\\\",\\r\\n \\\"Builder's Tel No\\\", \\\"Builder's email address\\\", \\\"PE's name\\\", \\\"PE's firm name\\\", \\\"PE's address\\\",\\r\\n \\\"PE's Tel No\\\", \\\"PE's Email address\\\", \\\"Architect's name\\\", \\\"Architect's firm name\\\",\\r\\n \\\"Architect's address\\\", \\\"Architect's Tel No\\\", \\\"Architect's Email address\\\", 'Project Cost',\\r\\n 'Project Duration', 'Approval Date(DD/MM/YYYY)']\\r\\n for fieldname in fields:\\r\\n book.write(countrow, countcol, fieldname)\\r\\n countcol += 1\\r\\n CleanedBCAPermitReport.save(config.CleanedBCAPermitFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\".xls\\\")\\r\\n\\r\\n # Copy the data to Excel File\\r\\n data = arcpy.SearchCursor(config.MatchedMukimLot)\\r\\n\\r\\n countrow = 1\\r\\n countcol = 0\\r\\n for row in data:\\r\\n message = [row.PROJ_REF_NO, row.PROJ_TITLE, row.HOUSE_BLK_NO, row.ROAD_NAME, row.LEVEL_NO,\\r\\n row.UNIT_NO, row.BUILDING_NAME, row.POSTAL_CODE, row.PROJ_MUKIM_NOS, row.PROJ_LOT_NOS,\\r\\n row.PERMIT_WORK_TYPE, row.WORK_TYPE, row.OWNER_NAME, row.OWNER_FIRM_NAME, row.OWNER_ADDR,\\r\\n row.OWNER_TEL, row.OWNER_EMAIL, row.BUILDER_NAME, row.BUILDER_FIRM_NAME,\\r\\n row.BUILDER_ADDR, row.BUILDER_TEL, row.BUILDER_EMAIL, row.PE_NAME, row.PE_FIRM_NAME,\\r\\n row.PE_ADDR, row.PE_TEL, row.PE_EMAIL, row.ARCHITECT_NAME, row.ARCHITECT_FIRM_NAME,\\r\\n row.ARCHITECT_ADDR, row.ARCHITECT_TEL, row.ARCHITECT_EMAIL, row.PROJ_COST,\\r\\n row.PROJ_DURATION_MTHS, row.PROJ_APPROVAL_DATE]\\r\\n countcol = 0\\r\\n for element in message:\\r\\n book.write(countrow, countcol, element)\\r\\n countcol += 1\\r\\n countrow += 1\\r\\n CleanedBCAPermitReport.save(config.CleanedBCAPermitFolder + \\\"\\\\\\\\\\\" + input_file_name.split(\\\".\\\")[0] + \\\".xls\\\")\\r\\n if row:\\r\\n del row\\r\\n if data:\\r\\n del data\\r\\n except:\\r\\n log_error(\\\"Error in 25 Export of Cleaned BCA Permit Report: Error in 26 Catchment calculation: \\\", logFile)\\r\\n logFile.writelines(\\\"25 Export of Cleaned BCA Permit Report ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 26. Catchment calculation\\r\\n arcpy.env.workspace = config.TempDataGDB\\r\\n logFile.writelines(\\\"26 Catchment calculation starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n arcpy.CatchmentCalculation()\\r\\n except:\\r\\n log_error(\\\"Error in 26 Catchment calculation: \\\", logFile)\\r\\n logFile.writelines(\\\"26 Catchment calculation ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 27. Depot calculation\\r\\n logFile.writelines(\\\"27 Depot calculation starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n arcpy.DepotCalculation()\\r\\n except:\\r\\n log_error(\\\"Error in 27 Depot calculation: \\\", logFile)\\r\\n logFile.writelines(\\\"27 Depot calculation ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 28. Re-add date fields and populate\\r\\n logFile.writelines(\\\"28 Re-add date fields and populate starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n arcpy.AddField_management(config.MUKIMCONSTRUCT_Temp, \\\"PERMIT_DATE\\\", \\\"Date\\\")\\r\\n arcpy.AddField_management(config.MUKIMCONSTRUCT_Temp, \\\"PROJ_APPROVAL_DATE2\\\", \\\"Date\\\")\\r\\n arcpy.AddField_management(config.MUKIMCONSTRUCT_Temp, \\\"PROJ_END_DATE\\\", \\\"Date\\\")\\r\\n\\r\\n rows = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\\r\\n\\r\\n for row in rows:\\r\\n date = filedate.strftime(\\\"%Y%m%d\\\")\\r\\n year = int(date[:4])\\r\\n month = int(date[4:6])\\r\\n day = int(date[6:8])\\r\\n permit_date = datetime.datetime(year, month, day)\\r\\n row.PERMIT_DATE = permit_date\\r\\n row.PROJ_APPROVAL_DATE2 = datetime.datetime.strptime(row.PROJ_APPROVAL_DATE, '%d/%m/%Y')\\r\\n rows.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rows:\\r\\n del rows\\r\\n except:\\r\\n log_error(\\\"Error in 28 Re-add fields and populate: \\\", logFile)\\r\\n logFile.writelines(\\\"28 Re-add fields and populate ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 29. Calculate the end date field\\r\\n logFile.writelines(\\\"29 Calculate the end date field starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n\\r\\n rowsEndDate = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\\r\\n\\r\\n for row in rowsEndDate:\\r\\n sourcedate = row.PROJ_APPROVAL_DATE2\\r\\n # sourcedate = datetime.datetime.strptime(row.PROJ_APPROVAL_DATE2 , '%d/%m/%Y')\\r\\n months = int(row.PROJ_DURATION_MTHS)\\r\\n d = add_months(sourcedate, months)\\r\\n row.PROJ_END_DATE = d\\r\\n rowsEndDate.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsEndDate:\\r\\n del rowsEndDate\\r\\n except:\\r\\n log_error(\\\"Error in 29 Calculate the end date field: \\\", logFile)\\r\\n logFile.writelines(\\\"29 Calculate the end date field ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 30. Calculate Project Total Area\\r\\n logFile.writelines(\\\"30 Project total area calculation starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n arcpy.ProjectTotalArea()\\r\\n except:\\r\\n log_error(\\\"Error in 30 Project total area calculation: \\\", logFile)\\r\\n logFile.writelines(\\\"30 Project total area calculation ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 31. Calculate the BCA_CORRECTED_BY\\r\\n logFile.writelines(\\\"31 Calculate the BCA_CORRECTED_BY starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n rows_BCA_CB = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\\r\\n\\r\\n for row in rows_BCA_CB:\\r\\n if \\\"\\\\WSN\\\\\\\\\\\" in BCAreport:\\r\\n row.BCA_CORRECTED_BY = \\\"WSN\\\"\\r\\n elif \\\"\\\\WRN\\\\\\\\\\\" in BCAreport:\\r\\n row.BCA_CORRECTED_BY = \\\"WRN\\\"\\r\\n elif \\\"\\\\CWD\\\\\\\\\\\" in BCAreport:\\r\\n row.BCA_CORRECTED_BY = \\\"CWD\\\"\\r\\n rows_BCA_CB.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rows_BCA_CB:\\r\\n del rows_BCA_CB\\r\\n except:\\r\\n log_error(\\\"Error in 31 Calculate the BCA_CORRECTED_BY: \\\", logFile)\\r\\n\\r\\n # 32. Remove spaces in PROJ_REF_NO\\r\\n logFile.writelines(\\r\\n \\\"32 Removing of spaces in mukim and project lot starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n try:\\r\\n rowsSpaces = arcpy.UpdateCursor(config.MUKIMCONSTRUCT_Temp)\\r\\n\\r\\n for row in rowsSpaces:\\r\\n lot_no_spaces = row.PROJ_REF_NO.strip()\\r\\n row.PROJ_REF_NO = lot_no_spaces\\r\\n rowsSpaces.updateRow(row)\\r\\n if row:\\r\\n del row\\r\\n if rowsSpaces:\\r\\n del rowsSpaces\\r\\n except:\\r\\n log_error(\\\"Error in 32 Removing of spaces in mukim and project lot: \\\", logFile)\\r\\n logFile.writelines(\\r\\n \\\"32 Removing of spaces in mukim and project lot ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 33. Process the Mukim Construct by Project\\r\\n logFile.writelines(\\r\\n \\\"33 Process the Mukim Construct by Project starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.env.overwriteOutput = True\\r\\n try:\\r\\n MUKIM_CONSTRUCT_BYPROJ_IMPORT = config.TempDataGDB + \\\"\\\\\\\\MUKIM_CONSTRUCT_BYPROJ_IMPORT\\\"\\r\\n MUKIMCONBYPROJ_SORT = config.TempDataGDB + \\\"\\\\\\\\MUKIMCONBYPROJ_SORT\\\"\\r\\n MUKIM_CONSTRUCT_BYPROJ_DISS = config.TempDataGDB + \\\"\\\\\\\\MUKIM_CONSTRUCT_BYPROJ_DISS\\\"\\r\\n MUKIM_CONSTRUCT_BYPROJ_DISS__2_ = config.TempDataGDB + \\\"\\\\\\\\MUKIM_CONSTRUCT_BYPROJ_DISS\\\"\\r\\n\\r\\n if arcpy.Exists(MUKIM_CONSTRUCT_BYPROJ_IMPORT):\\r\\n arcpy.Delete_management(MUKIM_CONSTRUCT_BYPROJ_IMPORT)\\r\\n if arcpy.Exists(MUKIMCONBYPROJ_SORT):\\r\\n arcpy.Delete_management(MUKIMCONBYPROJ_SORT)\\r\\n if arcpy.Exists(MUKIM_CONSTRUCT_BYPROJ_DISS):\\r\\n arcpy.Delete_management(MUKIM_CONSTRUCT_BYPROJ_DISS)\\r\\n\\r\\n arcpy.MUKIMCONBYPROJ()\\r\\n # arcpy.MUKIMCONSTRUCTBYPROJProcess2()\\r\\n\\r\\n arcpy.Sort_management(MUKIM_CONSTRUCT_BYPROJ_IMPORT, MUKIMCONBYPROJ_SORT, \\\"PROJ_END_DATE DESCENDING\\\",\\r\\n \\\"UR\\\")\\r\\n arcpy.Dissolve_management(MUKIMCONBYPROJ_SORT, MUKIM_CONSTRUCT_BYPROJ_DISS, \\\"PROJ_REF_NO\\\",\\r\\n \\\"LOT_KEY FIRST;PROJ_REF_NO FIRST;PROJ_TITLE FIRST;HOUSE_BLK_NO FIRST;ROAD_NAME FIRST;POSTAL_CODE FIRST;LEVEL_NO FIRST;UNIT_NO FIRST;BUILDING_NAME FIRST;PROJ_MUKIM_NOS FIRST;PROJ_LOT_NOS FIRST;PERMIT_WORK_TYPE FIRST;WORK_TYPE FIRST;OWNER_NAME FIRST;OWNER_FIRM_NAME FIRST;OWNER_ADDR FIRST;OWNER_TEL FIRST;OWNER_EMAIL FIRST;BUILDER_NAME FIRST;BUILDER_FIRM_NAME FIRST;BUILDER_ADDR FIRST;BUILDER_TEL FIRST;BUILDER_EMAIL FIRST;PE_NAME FIRST;PE_FIRM_NAME FIRST;PE_ADDR FIRST;PE_TEL FIRST;PE_EMAIL FIRST;ARCHITECT_NAME FIRST;ARCHITECT_FIRM_NAME FIRST;ARCHITECT_ADDR FIRST;ARCHITECT_TEL FIRST;ARCHITECT_EMAIL FIRST;PROJ_TOT_AREA FIRST;PROJ_PARENT_CWDCATCHMENT FIRST;PROJ_PARENT_WSNDEPOT FIRST;PROJ_PARENT_WRPCATCHMENT FIRST;BCA_CORRECTED_BY FIRST;PROJ_DURATION_MTHS FIRST;PROJ_COST FIRST\\\",\\r\\n \\\"MULTI_PART\\\", \\\"DISSOLVE_LINES\\\")\\r\\n arcpy.JoinField_management(MUKIM_CONSTRUCT_BYPROJ_DISS, \\\"FIRST_PROJ_REF_NO\\\", MUKIMCONBYPROJ_SORT,\\r\\n \\\"PROJ_REF_NO\\\", \\\"PROJ_APPROVAL_DATE;PROJ_END_DATE;PERMIT_DATE\\\")\\r\\n arcpy.CalculateField_management(MUKIM_CONSTRUCT_BYPROJ_DISS__2_, \\\"FIRST_PROJ_TOT_AREA\\\",\\r\\n \\\"[Shape_Area]/10000\\\", \\\"VB\\\", \\\"\\\")\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 33 Process the Mukim Construct by Project: \\\", logFile)\\r\\n logFile.writelines(\\r\\n \\\"33 Process the Mukim Construct by Project ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n arcpy.AddMessage(\\\"33 END process MUKIM CONSTRUCT\\\")\\r\\n\\r\\n # 34. Filter on-going projects\\r\\n\\r\\n logFile.writelines(\\\"34 Filter on-going projects starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n # TempDataGDB = \\\"G:\\\\\\\\Project\\\\\\\\GERIUPGRADE\\\\\\\\GPTools\\\\\\\\NotificationSysTools\\\\\\\\BCAReportProcessing\\\\\\\\Temp_data.gdb\\\"\\r\\n MUKIM_CONSTRUCT_BYPROJ_DISS = config.TempDataGDB + \\\"\\\\\\\\MUKIM_CONSTRUCT_BYPROJ_DISS\\\"\\r\\n rowsIn = arcpy.UpdateCursor(MUKIM_CONSTRUCT_BYPROJ_DISS)\\r\\n\\r\\n row = None\\r\\n for row in rowsIn:\\r\\n strdays = str(row.PROJ_END_DATE.date() - datetime.date.today())\\r\\n splitDays = strdays.split()\\r\\n if splitDays[0] == '0:00:00':\\r\\n result = \\\"On-going project (but will end today)\\\"\\r\\n else:\\r\\n if int(splitDays[0]) < 0:\\r\\n rowsIn.deleteRow(row)\\r\\n else:\\r\\n result = \\\"On-going project\\\"\\r\\n if rowsIn:\\r\\n del rowsIn\\r\\n if row:\\r\\n del row\\r\\n\\r\\n except:\\r\\n log_error(\\\"Error in 34 Filter on-going projects: \\\", logFile)\\r\\n logFile.writelines(\\\"34 Filter on-going projects ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # 35. Append the new data to MUKIM_CONSTRUCT\\r\\n logFile.writelines(\\r\\n \\\"35 Append the new data to MUKIM_CONSTRUCT starts at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n try:\\r\\n arcpy.AppendNewData()\\r\\n except:\\r\\n log_error(\\\"Error in 35 Append the new data to MUKIM_CONSTRUCT: \\\", logFile)\\r\\n logFile.writelines(\\r\\n \\\"35 Append the new data to MUKIM_CONSTRUCT ends at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n\\r\\n # Clean the memory and the schema lock\\r\\n arcpy.RefreshCatalog(config.Notification)\\r\\n arcpy.Compact_management(config.TempDataGDB)\\r\\n gc.collect()\\r\\n\\r\\n # Status update to run/not run the SiteInspection Update\\r\\n Log_SiteInspectionUpdate = file(config.SiteInspectionUpdate, \\\"w\\\")\\r\\n Log_SiteInspectionUpdate.writelines(\\\"YES\\\")\\r\\n Log_SiteInspectionUpdate.close()\\r\\n\\r\\n arcpy.AddMessage(\\\"END BCA Processing\\\")\\r\\n arcpy.AddMessage(\\\"Passing file date to other functions: \\\" + repr(filedate))\\r\\n\\r\\n # Generate Report\\r\\n import ReportGeneration_Adhoc_WithProjects as gen_report\\r\\n gen_report.run(filedate)\\r\\n #\\r\\n # # Send email to departments\\r\\n # import EmailGenerationCompletion_adhoc as send_dept_notification\\r\\n # if \\\"CORRECTED\\\" in BCAreport.upper():\\r\\n # send_dept_notification.run(filedate, corrected=True)\\r\\n # else:\\r\\n # send_dept_notification.run(filedate)\\r\\n\\r\\n # Generate advisory letters\\r\\n import LetterGeneration as letter_gen\\r\\n letter_gen.run(filedate)\\r\\n #\\r\\n # # Send letters to project team\\r\\n # import EmailGeneration as send_advisory_email\\r\\n # send_advisory_email.run(filedate)\\r\\n\\r\\n\\r\\n # 36. Move the BCAReport in the backup folder\\r\\n for BCAreport in correct_config_files:\\r\\n\\r\\n input_file_name = BCAreport.split(\\\"\\\\\\\\\\\")[-1]\\r\\n bk_file_path = os.path.join(config.BCAreportBackupFolder, input_file_name)\\r\\n\\r\\n # if the same file name exists in the backup folder, rename the new file with timestamp and move\\r\\n if os.path.exists(bk_file_path):\\r\\n\\r\\n new_filename = datetime.datetime.now().strftime(\\\"%Y%m%d-%H%M\\\") + input_file_name\\r\\n new_filepath = os.path.join(config.BCAreportBackupFolder, new_filename)\\r\\n shutil.copy(BCAreport, new_filepath)\\r\\n os.remove(BCAreport)\\r\\n\\r\\n # if the filename does not exist in the backup folder, move the file to backup\\r\\n else:\\r\\n shutil.move(BCAreport, config.BCAreportBackupFolder)\\r\\n\\r\\n logFile.writelines(\\\"Moved the BCA report to the backup folder at \\\" + str(datetime.datetime.now()) + \\\"\\\\n\\\")\\r\\n logFile.close()\",\n \"def cmd_error_check(self, cmd_out):\\n for err in self.err_strings:\\n if re.search('\\\\\\\\b%s\\\\\\\\b' % (err), cmd_out, re.I):\\n _log.info(cmd_out)\\n _log.info(\\n \\\"Cmd execution failed! with this Return Error: \\\\n%s\\\" % (\\n cmd_out))\\n return 0\",\n \"def test_failedCommandProvidesOutput(self):\\n bookTeX = FilePath(self.mktemp() + \\\".tex\\\")\\n builder = BookBuilder()\\n inputState = bookTeX.parent().children()\\n exc = self.assertRaises(\\n CommandFailed,\\n builder.buildPDF,\\n bookTeX, self.howtoDir, FilePath(self.mktemp()))\\n self.assertTrue(exc.output)\\n newOutputState = set(bookTeX.parent().children()) - set(inputState)\\n self.assertEqual(len(newOutputState), 1)\\n workPath = newOutputState.pop()\\n self.assertTrue(\\n workPath.isdir(),\\n \\\"Expected work path %r was not a directory.\\\" % (workPath.path,))\",\n \"def test_check_exit_status(self):\\n run_dir_success = 'data/nanopore_data/run4/done_demuxing/20200104_1412_MN19414_AAU644_68125dc2'\\n success_run = MinIONqc(run_dir_success, None, None)\\n self.assertTrue(success_run.check_exit_status('data/nanopore_data/run4/done_demuxing/20200104_1412_MN19414_AAU644_68125dc2/.exitcode_for_nanoseq'))\\n run_dir_fail = 'data/nanopore_data/run8/demux_failed/20200108_1412_MN19414_AAU648_68125dc2'\\n fail_run = MinIONqc(run_dir_fail, None, None)\\n self.assertFalse(fail_run.check_exit_status('data/nanopore_data/run8/demux_failed/20200108_1412_MN19414_AAU648_68125dc2/.exitcode_for_nanoseq'))\",\n \"def run_command_check(self):\\n pass\",\n \"def check_commands(self):\\n pass\",\n \"def run_test_second():\\n os.system(\\n \\\"sed -n '/(Failed)$/p' test_op_log.txt | awk '{print $3}' >& rerun_op.txt\\\"\\n )\\n rerun_list = get_op_list('rerun_op.txt')\\n if len(rerun_list):\\n print(\\n \\\"-------there are \\\"\\n + str(len(rerun_list))\\n + \\\" op(s) need to rerun!!!-------\\\"\\n )\\n for failed_op in rerun_list:\\n os.system(\\\"ctest -R \\\\\\\"(\\\" + failed_op + \\\")\\\\\\\" \\\")\\n else:\\n print(\\\"-------all op passed successfully!!!-------\\\")\",\n \"def extract_failed_tests_info():\\n global g_failed_testnames\\n global g_failed_test_paths\\n\\n if os.path.isfile(g_temp_filename):\\n console_file = open(g_temp_filename,'r') # open temp file that stored jenkins job console output\\n try:\\n for each_line in console_file: # go through each line of console output to extract build ID, data/time ...\\n each_line.strip()\\n print(each_line)\\n if (\\\"Test Result\\\" in each_line) and (\\\"failure\\\" in each_line): # the next few lines will contain failed tests\\n temp = each_line.split(\\\"testReport\\\")\\n if (\\\"Test Result\\\" in temp[1]) and (\\\"failure\\\" in temp[1]): # grab number of failed tests\\n try:\\n tempCount = int(temp[1].split(\\\"</a>\\\")[1].split(\\\" \\\")[0].split(\\\"(\\\")[1])\\n\\n if isinstance(tempCount, int) and tempCount > 0: # temp[1], temp[2],... should contain failed tests\\n for findex in range(2,len(temp)):\\n tempMess = temp[findex].split(\\\">\\\")\\n g_failed_test_paths.append(tempMess[0].strip('\\\"'))\\n ftestname = tempMess[1].strip(\\\"</a\\\")\\n nameLen = len(ftestname)\\n true_testname = ftestname[8:nameLen] if 'r_suite.' in ftestname else ftestname\\n g_failed_testnames.append(true_testname)\\n break # done. Only one spot contains failed test info.\\n except:\\n break # file probably does not have failures captured.\\n finally:\\n console_file.close()\",\n \"def test_stratis_bad_subcommand(self):\\n for command_line in [\\n [\\\"notasub\\\"],\\n [\\\"daemon\\\", \\\"notasub\\\"],\\n [\\\"pool\\\", \\\"notasub\\\"],\\n [\\\"blockdev\\\", \\\"notasub\\\"],\\n [\\\"filesystem\\\", \\\"notasub\\\"],\\n ]:\\n for prefix in [[], [\\\"--propagate\\\"]]:\\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)\",\n \"def testError(self):\\n cmds = \\\"\\\"\\\"chown 0 missingFile\\npwd\\nexit\\n\\\"\\\"\\\"\\n\\n def _cbCheckResult(res):\\n self.assertNotIn(self.testDir.asBytesMode().path, res)\\n\\n d = self._getBatchOutput(cmds)\\n d.addCallback(_cbCheckResult)\\n return d\",\n \"def slurm_check(path='.'):\\n for file in shrunner.get_files(path, '.out'):\\n with open(file, 'r') as f:\\n for line in f.read().splitlines():\\n if 'issue' in line.lower():\\n print(file)\\n print(line)\\n print('-' * 40)\",\n \"def checkForCommand(quickLogger, commandList):\\n\\n for command in commandList:\\n\\n cmd = \\\"which -s \\\" + command + \\\" > \\\" + os.devnull + \\\" 2>&1\\\"\\n retcode = os.system(cmd)\\n \\n if(retcode):\\n quickLogger.critical(\\\"unix command \\\"+command+\\\" not found.\\\")\\n raise CommandNotFound\",\n \"def has_failed_outputs(self):\\n return False\",\n \"def test_duplicatefslabels_run_exception(self, get_label_dict_mock):\\n with contextlib.redirect_stdout(self.output):\\n self.assertFalse(moduletests.src.duplicatefslabels.run())\\n self.assertTrue(self.output.getvalue().endswith(\\\"Review the logs to determine the cause of the issue.\\\\n\\\"))\\n self.assertTrue(get_label_dict_mock.called)\",\n \"def test_process_host_commands(self):\\n\\n command = [\\\"df\\\", \\\"-h\\\"]\\n output = run(verification.process_host_commands(command))\\n self.assertTrue(\\\"```\\\\nThat command is not available.```\\\" not in output)\\n\\n command = [\\\"ls\\\", \\\"-la\\\"]\\n output = run(verification.process_host_commands(command))\\n self.assertEqual(\\\"```\\\\nThat command is not available.```\\\", output)\",\n \"def report():\\n\\n global COUNTER\\n \\n if COUNTER > 0:\\n print('\\\\n\\\\n')\\n\\n print('Searched {0} files'.format(SEARCHED))\\n print('Found {0} TODOs in {1} files'.format(COUNTER, F_COUNTER))\",\n \"def test_fixture_missing_results(tmp_sample_project):\\n config_dir = tmp_sample_project\\n output = subprocess.run([\\\"smif\\\", \\\"missing_results\\\", \\\"energy_central\\\", \\\"-d\\\", config_dir],\\n stdout=subprocess.PIPE)\\n\\n out_str = str(output.stdout)\\n assert(out_str.count('model run: energy_central') == 1)\\n assert(out_str.count('sos model: energy') == 1)\\n assert(out_str.count('sector model:') == 1)\\n assert(out_str.count('output:') == 2)\\n assert(out_str.count('output: cost') == 1)\\n assert(out_str.count('output: water_demand') == 1)\\n assert(out_str.count('no missing results') == 0)\\n assert(out_str.count('results missing for:') == 2)\\n\\n # Run energy_central and re-check output with optional flag for completed results\\n subprocess.run([\\\"smif\\\", \\\"run\\\", \\\"energy_central\\\", \\\"-d\\\", config_dir], stdout=subprocess.PIPE)\\n output = subprocess.run([\\\"smif\\\", \\\"missing_results\\\", \\\"energy_central\\\", \\\"-d\\\", config_dir],\\n stdout=subprocess.PIPE)\\n\\n out_str = str(output.stdout)\\n assert(out_str.count('model run: energy_central') == 1)\\n assert(out_str.count('sos model: energy') == 1)\\n assert(out_str.count('sector model:') == 1)\\n assert(out_str.count('output:') == 2)\\n assert(out_str.count('output: cost') == 1)\\n assert(out_str.count('output: water_demand') == 1)\\n assert(out_str.count('no missing results') == 2)\\n assert(out_str.count('results missing for:') == 0)\",\n \"def test_error_before_all_processes_complete(self):\\n first = \\\"\\\"\\\"file://B <- file://A\\n sleep 1\\n echo A produces B > B\\n error\\n \\nfile://C <- file://A\\n sleep 2\\n echo A produces C > C\\n \\\"\\\"\\\"\\n\\n rcode, output = run_tuttle_file(first, nb_workers=2)\\n assert rcode == 2\\n assert isfile('B')\\n assert not isfile('C')\\n w = Workflow.load()\\n p = w.find_process_that_creates(\\\"file://C\\\")\\n assert not p.success, \\\"Process that creates C should be in error in the dump\\\"\",\n \"def files_exist(self):\\n\\n passed = []\\n warned = []\\n failed = []\\n ignored = []\\n\\n # NB: Should all be files, not directories\\n # List of lists. Passes if any of the files in the sublist are found.\\n #: test autodoc\\n try:\\n _, short_name = self.nf_config[\\\"manifest.name\\\"].strip(\\\"\\\\\\\"'\\\").split(\\\"/\\\")\\n except ValueError:\\n log.warning(\\\"Expected manifest.name to be in the format '<repo>/<pipeline>'. Will assume it is '<pipeline>'.\\\")\\n short_name = self.nf_config[\\\"manifest.name\\\"].strip(\\\"\\\\\\\"'\\\").split(\\\"/\\\")\\n\\n files_fail = [\\n [\\\".gitattributes\\\"],\\n [\\\".gitignore\\\"],\\n [\\\".nf-core.yml\\\"],\\n [\\\".editorconfig\\\"],\\n [\\\".prettierignore\\\"],\\n [\\\".prettierrc.yml\\\"],\\n [\\\"CHANGELOG.md\\\"],\\n [\\\"CITATIONS.md\\\"],\\n [\\\"CODE_OF_CONDUCT.md\\\"],\\n [\\\"CODE_OF_CONDUCT.md\\\"],\\n [\\\"LICENSE\\\", \\\"LICENSE.md\\\", \\\"LICENCE\\\", \\\"LICENCE.md\\\"], # NB: British / American spelling\\n [\\\"nextflow_schema.json\\\"],\\n [\\\"nextflow.config\\\"],\\n [\\\"README.md\\\"],\\n [os.path.join(\\\".github\\\", \\\".dockstore.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"CONTRIBUTING.md\\\")],\\n [os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"bug_report.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"config.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"feature_request.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"PULL_REQUEST_TEMPLATE.md\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"branch.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"ci.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"linting_comment.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"linting.yml\\\")],\\n [os.path.join(\\\"assets\\\", \\\"email_template.html\\\")],\\n [os.path.join(\\\"assets\\\", \\\"email_template.txt\\\")],\\n [os.path.join(\\\"assets\\\", \\\"sendmail_template.txt\\\")],\\n [os.path.join(\\\"assets\\\", f\\\"nf-core-{short_name}_logo_light.png\\\")],\\n [os.path.join(\\\"conf\\\", \\\"modules.config\\\")],\\n [os.path.join(\\\"conf\\\", \\\"test.config\\\")],\\n [os.path.join(\\\"conf\\\", \\\"test_full.config\\\")],\\n [os.path.join(\\\"docs\\\", \\\"images\\\", f\\\"nf-core-{short_name}_logo_light.png\\\")],\\n [os.path.join(\\\"docs\\\", \\\"images\\\", f\\\"nf-core-{short_name}_logo_dark.png\\\")],\\n [os.path.join(\\\"docs\\\", \\\"output.md\\\")],\\n [os.path.join(\\\"docs\\\", \\\"README.md\\\")],\\n [os.path.join(\\\"docs\\\", \\\"README.md\\\")],\\n [os.path.join(\\\"docs\\\", \\\"usage.md\\\")],\\n [os.path.join(\\\"lib\\\", \\\"nfcore_external_java_deps.jar\\\")],\\n [os.path.join(\\\"lib\\\", \\\"NfcoreTemplate.groovy\\\")],\\n [os.path.join(\\\"lib\\\", \\\"Utils.groovy\\\")],\\n [os.path.join(\\\"lib\\\", \\\"WorkflowMain.groovy\\\")],\\n ]\\n\\n files_warn = [\\n [\\\"main.nf\\\"],\\n [os.path.join(\\\"assets\\\", \\\"multiqc_config.yml\\\")],\\n [os.path.join(\\\"conf\\\", \\\"base.config\\\")],\\n [os.path.join(\\\"conf\\\", \\\"igenomes.config\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"awstest.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"awsfulltest.yml\\\")],\\n [os.path.join(\\\"lib\\\", f\\\"Workflow{short_name[0].upper()}{short_name[1:]}.groovy\\\")],\\n [\\\"modules.json\\\"],\\n [\\\"pyproject.toml\\\"],\\n ]\\n\\n # List of strings. Fails / warns if any of the strings exist.\\n files_fail_ifexists = [\\n \\\"Singularity\\\",\\n \\\"parameters.settings.json\\\",\\n \\\".nf-core.yaml\\\", # yml not yaml\\n os.path.join(\\\"bin\\\", \\\"markdown_to_html.r\\\"),\\n os.path.join(\\\"conf\\\", \\\"aws.config\\\"),\\n os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"push_dockerhub.yml\\\"),\\n os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"bug_report.md\\\"),\\n os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"feature_request.md\\\"),\\n os.path.join(\\\"docs\\\", \\\"images\\\", f\\\"nf-core-{short_name}_logo.png\\\"),\\n \\\".markdownlint.yml\\\",\\n \\\".yamllint.yml\\\",\\n os.path.join(\\\"lib\\\", \\\"Checks.groovy\\\"),\\n os.path.join(\\\"lib\\\", \\\"Completion.groovy\\\"),\\n os.path.join(\\\"lib\\\", \\\"Workflow.groovy\\\"),\\n ]\\n files_warn_ifexists = [\\\".travis.yml\\\"]\\n\\n # Remove files that should be ignored according to the linting config\\n ignore_files = self.lint_config.get(\\\"files_exist\\\", [])\\n\\n def pf(file_path):\\n return os.path.join(self.wf_path, file_path)\\n\\n # First - critical files. Check that this is actually a Nextflow pipeline\\n if not os.path.isfile(pf(\\\"nextflow.config\\\")) and not os.path.isfile(pf(\\\"main.nf\\\")):\\n failed.append(\\\"File not found: nextflow.config or main.nf\\\")\\n raise AssertionError(\\\"Neither nextflow.config or main.nf found! Is this a Nextflow pipeline?\\\")\\n\\n # Files that cause an error if they don't exist\\n for files in files_fail:\\n if any([f in ignore_files for f in files]):\\n continue\\n if any([os.path.isfile(pf(f)) for f in files]):\\n passed.append(f\\\"File found: {self._wrap_quotes(files)}\\\")\\n else:\\n failed.append(f\\\"File not found: {self._wrap_quotes(files)}\\\")\\n\\n # Files that cause a warning if they don't exist\\n for files in files_warn:\\n if any([f in ignore_files for f in files]):\\n continue\\n if any([os.path.isfile(pf(f)) for f in files]):\\n passed.append(f\\\"File found: {self._wrap_quotes(files)}\\\")\\n else:\\n warned.append(f\\\"File not found: {self._wrap_quotes(files)}\\\")\\n\\n # Files that cause an error if they exist\\n for file in files_fail_ifexists:\\n if file in ignore_files:\\n continue\\n if os.path.isfile(pf(file)):\\n failed.append(f\\\"File must be removed: {self._wrap_quotes(file)}\\\")\\n else:\\n passed.append(f\\\"File not found check: {self._wrap_quotes(file)}\\\")\\n\\n # Files that cause a warning if they exist\\n for file in files_warn_ifexists:\\n if file in ignore_files:\\n continue\\n if os.path.isfile(pf(file)):\\n warned.append(f\\\"File should be removed: {self._wrap_quotes(file)}\\\")\\n else:\\n passed.append(f\\\"File not found check: {self._wrap_quotes(file)}\\\")\\n\\n # Files that are ignoed\\n for file in ignore_files:\\n ignored.append(f\\\"File is ignored: {self._wrap_quotes(file)}\\\")\\n\\n return {\\\"passed\\\": passed, \\\"warned\\\": warned, \\\"failed\\\": failed, \\\"ignored\\\": ignored}\",\n \"def _verifyCommand(self):\\n for i in range(3):\\n rc = self.subdevice.command_test() # Verify command is correct\\n if rc is None:\\n break\",\n \"def test_otter_check_script(self):\\n # run for each individual test\\n for file in glob(TEST_FILES_PATH + \\\"tests/*.py\\\"):\\n # capture stdout\\n output = StringIO()\\n with contextlib.redirect_stdout(output):\\n\\n # mock block_print otherwise it interferes with capture of stdout\\n with mock.patch(\\\"otter.check.block_print\\\"):\\n check(\\n TEST_FILES_PATH + \\\"file0.py\\\", \\n question = os.path.split(file)[1][:-3],\\n tests_path = os.path.split(file)[0],\\n )\\n\\n if os.path.split(file)[1] != \\\"q2.py\\\":\\n self.assertEqual(\\n output.getvalue().strip().split(\\\"\\\\n\\\")[-1].strip(), \\n \\\"All tests passed!\\\", \\n \\\"Did not pass test at {}\\\".format(file)\\n )\\n\\n # run the file for all questions\\n output = StringIO()\\n with contextlib.redirect_stdout(output):\\n with mock.patch(\\\"otter.check.block_print\\\"):\\n check(\\n TEST_FILES_PATH + \\\"file0.py\\\", \\n tests_path = os.path.split(file)[0],\\n )\\n self.assertEqual(\\n output.getvalue().strip(), \\n dedent(\\\"\\\"\\\"\\\\\\n [0. 0.02002002 0.04004004 0.06006006 0.08008008]\\n q1 results: All test cases passed!\\n q2 results:\\n q2 - 1 result:\\n Trying:\\n 1 == 1\\n Expecting:\\n False\\n **********************************************************************\\n Line 2, in q2 0\\n Failed example:\\n 1 == 1\\n Expected:\\n False\\n Got:\\n True\\n\\n q2 - 2 result:\\n Test case passed!\\n q3 results: All test cases passed!\\n q4 results: All test cases passed!\\n q5 results: All test cases passed!\\\"\\\"\\\"), \\n \\\"Did not pass correct tests\\\"\\n )\",\n \"def syntax_check(self, working_dir, disco_ver):\\n\\n bar = ''\\n spinner = ''\\n if progressbar:\\n progressbar.streams.flush()\\n progressbar.streams.wrap_stdout()\\n widgets = [progressbar.AnimatedMarker(),\\n ' Checking syntax. ',\\n progressbar.Timer()]\\n bar = progressbar.ProgressBar(widgets=widgets,\\n max_value=progressbar.UnknownLength,\\n redirect_stdout=True)\\n else:\\n spinner = itertools.cycle(['-', '/', '|', '\\\\\\\\'])\\n log.debug(\\\"Module progressbar2 is not installed, will show progress in usual manner.\\\")\\n pass\\n\\n tpl_mod_dir = os.path.abspath(os.path.join(__file__ , \\\"../..\\\"))\\n tplint_exe_path = tpl_mod_dir + '\\\\\\\\tplint\\\\\\\\tplint.exe'\\n tplint_tax_path = tpl_mod_dir+'\\\\\\\\taxonomy\\\\\\\\00taxonomy.xml'\\n syntax_passed = False\\n\\n # errors_re = re.compile(\\\"\\\\s+Errors:\\\\s+(.+)\\\")\\n # mod_re = re.compile(\\\"Module:\\\\s+(.+)\\\")\\n match_result = re.compile(\\\"(?P<error>\\\\w+\\\\s\\\\w+) at or near '(?P<near>\\\\S+)', \\\"\\n \\\"line (?P<line>\\\\d+), in (?P<module>\\\\S+)\\\")\\n\\n log.debug(\\\"Syntax: Will check_ide all files in path: \\\" + str(working_dir))\\n\\n if disco_ver not in self.SYNTAX_SUPPORTED:\\n log.info(\\\"NOTE: tplint was updated in 2016 last time, \\\"\\n \\\"so we can use only version which is not greater then 11.0\\\")\\n disco_ver = 11.0\\n\\n # Lines will be collected in list:\\n result_out = []\\n if os.path.exists(tplint_exe_path) and os.path.exists(tplint_tax_path):\\n cmd = \\\" --discovery-versions=\\\"+str(disco_ver)+\\\" --loglevel=WARN -t \\\"+tplint_tax_path\\n\\n # noinspection PyBroadException\\n try:\\n open_path = subprocess.Popen(tplint_exe_path+cmd, cwd=working_dir, stdout=subprocess.PIPE)\\n\\n # Show progress with fancy progressbar:\\n while open_path.stdout is not None:\\n if progressbar:\\n bar.update()\\n else:\\n sys.stdout.write(next(spinner))\\n sys.stdout.flush()\\n sys.stdout.write('\\\\b') # Working fine in win CMD but not in PyCharm.\\n\\n out = open_path.stdout.readline()\\n result_out.append(out.decode('UTF-8').rstrip('\\\\r'))\\n\\n if not out:\\n break\\n time.sleep(0.01)\\n # Final result:\\n result = ''.join(result_out)\\n if \\\"No issues found!\\\" in result:\\n # Close bar, do not forget to.\\n if progressbar:\\n bar.finish()\\n log.info(\\\"Build OK: Syntax: PASSED!\\\")\\n syntax_passed = True\\n sys.stdout.flush()\\n\\n elif match_result.findall(result):\\n # Close bar, do not forget to.\\n if progressbar:\\n bar.finish()\\n # error_modules = mod_re.findall(result)\\n # errors = errors_re.findall(result)\\n log.error(\\\"Syntax: ERROR: Some issues found!\\\"\\\"\\\\n\\\" + str(result))\\n sys.stdout.flush()\\n else:\\n log.error(\\\"Syntax: Something is not OK \\\\n\\\" + str(result))\\n except:\\n log.error(\\\"Syntax: Tplint cannot run, check_ide if working dir is present!\\\")\\n log.error(\\\"Syntax: Tplint use path: \\\" + tpl_mod_dir)\\n else:\\n log.warning(\\\"Path to tplint module is not exist. Please check_ide this: \\\"\\n \\\"https://github.com/trianglesis/BMC_TPL_IDE#syntax-check_ide\\\")\\n # noinspection PyPep8\\n log.debug(\\\"Those paths expected: \\\"\\n \\\"\\\\ntplint_exe_path - \\\"+str(tplint_exe_path) +\\n \\\"\\\\ntplint_tax_path - \\\"+str(tplint_tax_path))\\n\\n return syntax_passed\",\n \"def run_checks(hooks_all, hooks_modified, modified, path):\\n retcode = 0\\n for command in hooks_all:\\n if not isinstance(command, list):\\n command = shlex.split(command)\\n retcode |= subprocess.call(command, env={'PATH': path})\\n\\n for pattern, command in hooks_modified:\\n if not isinstance(command, list):\\n command = shlex.split(command)\\n for filename in modified:\\n if not fnmatch.fnmatch(filename, pattern):\\n continue\\n printed_filename = False\\n proc = subprocess.Popen(command + [filename],\\n env={'PATH': path},\\n stdout=subprocess.PIPE,\\n stderr=subprocess.STDOUT)\\n output = proc.communicate()[0]\\n if proc.returncode != 0:\\n if not printed_filename:\\n print(filename)\\n print('=' * len(filename))\\n printed_filename = True\\n print(command[0])\\n print('-' * len(command[0]))\\n print(output)\\n retcode |= proc.returncode\\n\\n return retcode\",\n \"def execute(self, collectedDir):\\n success = 0\\n failure = 0\\n\\n targets = os.listdir(collectedDir)\\n for target in targets:\\n fileName = \\\"%s/%s\\\" % (collectedDir, target)\\n\\n wxXmlParser = WxXmlParser()\\n wxXmlParser.execute(fileName)\\n\\n station_id = wxXmlParser.key_value['station_id']\\n if len(station_id) < 1:\\n failure = failure+1\\n else:\\n wxLoader = WxLoader()\\n if wxLoader.execute(wxXmlParser.key_value):\\n success = success+1\\n else:\\n failure = failure+1\\n\\n print \\\"end success:%d failure:%d\\\" % (success, failure)\",\n \"def run_command(cmd, log_file, time_file):\\r\\n sts = 0\\r\\n try_times = -1\\r\\n while True:\\r\\n try_times += 1\\r\\n if try_times > 2: # try to run the command 4 times --> change to 3 times\\r\\n break\\r\\n etime = ElapsedTime()\\r\\n etime.play()\\r\\n log = \\\"Running Command: %s [%s]\\\" % (cmd, etime.get_play_time())\\r\\n if try_times:\\r\\n log += \\\"-- TryTime: %d\\\" % try_times\\r\\n say_it(log)\\r\\n say_it(\\\" <%s>\\\" % os.getcwd())\\r\\n sts, text = get_status_output(cmd)\\r\\n etime.stop()\\r\\n append_file(log_file, [\\\"=\\\" * 30,cmd, etime] + text)\\r\\n append_file(time_file, [cmd, \\\"rem %s\\\" % etime])\\r\\n if sts:\\r\\n t = \\\"Status: Failed.\\\"\\r\\n else:\\r\\n t = \\\"Status: Pass.\\\"\\r\\n say_it(\\\"%s %s\\\" % (t, etime))\\r\\n time.sleep(3.14)\\r\\n if not sts:\\r\\n break\\r\\n # flow failed!\\r\\n have_license_error = simple_parser(log_file, p_license_error, 100)\\r\\n if have_license_error:\\r\\n # backup log file and re-launch the command after 1 minute\\r\\n backup_log_file = log_file+str(try_times)\\r\\n if os.path.isfile(backup_log_file):\\r\\n os.remove(backup_log_file)\\r\\n os.rename(log_file, backup_log_file)\\r\\n time.sleep(30) # change 60 --> 30\\r\\n else:\\r\\n if abnormal_exit(log_file):\\r\\n time.sleep(30)\\r\\n else:\\r\\n break\\r\\n if sts:\\r\\n error_msg_line = simple_parser(log_file, p_error_msg, 100)\\r\\n if error_msg_line:\\r\\n say_it(error_msg_line[0])\\r\\n say_it(\\\"\\\")\\r\\n return sts\",\n \"def test_dump_and_report_workflow(self):\\n project = \\\"\\\"\\\"file://result <- file://A\\n echo result > result\\n error\\n \\\"\\\"\\\"\\n rcode, output = run_tuttle_file(project)\\n assert rcode == 2\\n assert path.isfile(path.join(\\\".tuttle\\\", \\\"last_workflow.pickle\\\"))\",\n \"def test_governed_folders_high(tmp_trestle_dir: pathlib.Path, command_string: str, return_code: int) -> None:\\n with mock.patch.object(sys, 'argv', command_string.split()):\\n with pytest.raises(SystemExit) as wrapped_error:\\n trestle.cli.run()\\n # FIXME: Needs to be changed once implemented.\\n assert wrapped_error.type == SystemExit\\n assert wrapped_error.value.code == return_code\",\n \"def run(self, uname):\\n\\n out = []\\n\\n sol_dir = get_ex_solution(self.exname, uname)\\n exec_path = join(sol_dir, \\\"solution\\\")\\n test_out = join(sol_dir, \\\"test_out\\\")\\n\\n if not isfile(exec_path):\\n return\\n\\n for test in self.testcases:\\n in_path = get_test_in_path(test)\\n out_path = get_test_out_path(test)\\n\\n test_proc = subprocess.Popen([exec_path],\\n stdin=open(in_path),\\n stdout=open(test_out, \\\"w+\\\"))\\n try:\\n test_proc.wait(timeout=self.timeout)\\n except:\\n out.append({\\n 'comment': \\\"Execution timed out after {0}s.\\\".format(self.timeout),\\n 'percentage': 0,\\n 'suggestion': True,\\n 'description': []\\n })\\n\\n # Compare output to expected output\\n with open(test_out) as actual_out:\\n with open(out_path) as expected_out:\\n res = list(unified_diff(\\n list(actual_out), list(expected_out),\\n fromfile=\\\"actual\\\", tofile=\\\"expected\\\"))\\n\\n if res:\\n out.append({\\n 'comment': \\\"Incorrect output in testcase {0}.\\\".format(test),\\n 'percentage': 30,\\n 'suggestion': False,\\n 'description': res\\n })\\n\\n\\n\\n return out\",\n \"def test_bad_file() -> None:\\n\\n bad = random_string()\\n rv, out = getstatusoutput(f'{RUN} {bad}')\\n assert rv != 0\\n assert out.lower().startswith('usage:')\\n assert re.search(f\\\"No such file or directory: '{bad}'\\\", out)\",\n \"def test_stats(tool):\\n\\n with pytest.raises(Exceptions.Error):\\n tool.command(\\\"stats\\\", f\\\"-f 'bad_function' {tool.good_paths[0]}\\\")\",\n \"def _check_results(self):\\n if not 'EXECUTION OF GAMESS TERMINATED NORMALLY' in self.file_dic['output']:\\n print self.job_name + \\\" didn't finish\\\"\\n raise TypeError('Calculation didn\\\\'t finish')\",\n \"def check_errors():\\n\\n for error in errors:\\n ERROR('%s' % str(error))\\n\\n if len(errors) != 0:\\n sys.exit(1)\",\n \"def files_unchanged(self):\\n\\n passed = []\\n failed = []\\n ignored = []\\n fixed = []\\n could_fix = False\\n\\n # Check that we have the minimum required config\\n required_pipeline_config = {\\\"manifest.name\\\", \\\"manifest.description\\\", \\\"manifest.author\\\"}\\n missing_pipeline_config = required_pipeline_config.difference(self.nf_config)\\n if missing_pipeline_config:\\n return {\\\"ignored\\\": [f\\\"Required pipeline config not found - {missing_pipeline_config}\\\"]}\\n try:\\n prefix, short_name = self.nf_config[\\\"manifest.name\\\"].strip(\\\"\\\\\\\"'\\\").split(\\\"/\\\")\\n except ValueError:\\n log.warning(\\n \\\"Expected manifest.name to be in the format '<repo>/<pipeline>'. Will assume it is <pipeline> and default to repo 'nf-core'\\\"\\n )\\n short_name = self.nf_config[\\\"manifest.name\\\"].strip(\\\"\\\\\\\"'\\\")\\n prefix = \\\"nf-core\\\"\\n\\n # NB: Should all be files, not directories\\n # List of lists. Passes if any of the files in the sublist are found.\\n files_exact = [\\n [\\\".gitattributes\\\"],\\n [\\\".prettierrc.yml\\\"],\\n [\\\"CODE_OF_CONDUCT.md\\\"],\\n [\\\"LICENSE\\\", \\\"LICENSE.md\\\", \\\"LICENCE\\\", \\\"LICENCE.md\\\"], # NB: British / American spelling\\n [os.path.join(\\\".github\\\", \\\".dockstore.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"CONTRIBUTING.md\\\")],\\n [os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"bug_report.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"config.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"ISSUE_TEMPLATE\\\", \\\"feature_request.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"PULL_REQUEST_TEMPLATE.md\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"branch.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"linting_comment.yml\\\")],\\n [os.path.join(\\\".github\\\", \\\"workflows\\\", \\\"linting.yml\\\")],\\n [os.path.join(\\\"assets\\\", \\\"email_template.html\\\")],\\n [os.path.join(\\\"assets\\\", \\\"email_template.txt\\\")],\\n [os.path.join(\\\"assets\\\", \\\"sendmail_template.txt\\\")],\\n [os.path.join(\\\"assets\\\", f\\\"nf-core-{short_name}_logo_light.png\\\")],\\n [os.path.join(\\\"docs\\\", \\\"images\\\", f\\\"nf-core-{short_name}_logo_light.png\\\")],\\n [os.path.join(\\\"docs\\\", \\\"images\\\", f\\\"nf-core-{short_name}_logo_dark.png\\\")],\\n [os.path.join(\\\"docs\\\", \\\"README.md\\\")],\\n [os.path.join(\\\"lib\\\", \\\"nfcore_external_java_deps.jar\\\")],\\n [os.path.join(\\\"lib\\\", \\\"NfcoreTemplate.groovy\\\")],\\n ]\\n files_partial = [\\n [\\\".gitignore\\\", \\\".prettierignore\\\", \\\"pyproject.toml\\\"],\\n ]\\n\\n # Only show error messages from pipeline creation\\n logging.getLogger(\\\"nf_core.create\\\").setLevel(logging.ERROR)\\n\\n # Generate a new pipeline with nf-core create that we can compare to\\n tmp_dir = tempfile.mkdtemp()\\n\\n # Create a template.yaml file for the pipeline creation\\n template_yaml = {\\n \\\"name\\\": short_name,\\n \\\"description\\\": self.nf_config[\\\"manifest.description\\\"].strip(\\\"\\\\\\\"'\\\"),\\n \\\"author\\\": self.nf_config[\\\"manifest.author\\\"].strip(\\\"\\\\\\\"'\\\"),\\n \\\"prefix\\\": prefix,\\n }\\n\\n template_yaml_path = os.path.join(tmp_dir, \\\"template.yaml\\\")\\n with open(template_yaml_path, \\\"w\\\") as fh:\\n yaml.dump(template_yaml, fh, default_flow_style=False)\\n\\n test_pipeline_dir = os.path.join(tmp_dir, f\\\"{prefix}-{short_name}\\\")\\n create_obj = nf_core.create.PipelineCreate(\\n None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path\\n )\\n create_obj.init_pipeline()\\n\\n # Helper functions for file paths\\n def _pf(file_path):\\n \\\"\\\"\\\"Helper function - get file path for pipeline file\\\"\\\"\\\"\\n return os.path.join(self.wf_path, file_path)\\n\\n def _tf(file_path):\\n \\\"\\\"\\\"Helper function - get file path for template file\\\"\\\"\\\"\\n return os.path.join(test_pipeline_dir, file_path)\\n\\n # Files that must be completely unchanged from template\\n for files in files_exact:\\n # Ignore if file specified in linting config\\n ignore_files = self.lint_config.get(\\\"files_unchanged\\\", [])\\n if any([f in ignore_files for f in files]):\\n ignored.append(f\\\"File ignored due to lint config: {self._wrap_quotes(files)}\\\")\\n\\n # Ignore if we can't find the file\\n elif not any([os.path.isfile(_pf(f)) for f in files]):\\n ignored.append(f\\\"File does not exist: {self._wrap_quotes(files)}\\\")\\n\\n # Check that the file has an identical match\\n else:\\n for f in files:\\n try:\\n if filecmp.cmp(_pf(f), _tf(f), shallow=True):\\n passed.append(f\\\"`{f}` matches the template\\\")\\n else:\\n if \\\"files_unchanged\\\" in self.fix:\\n # Try to fix the problem by overwriting the pipeline file\\n shutil.copy(_tf(f), _pf(f))\\n passed.append(f\\\"`{f}` matches the template\\\")\\n fixed.append(f\\\"`{f}` overwritten with template file\\\")\\n else:\\n failed.append(f\\\"`{f}` does not match the template\\\")\\n could_fix = True\\n except FileNotFoundError:\\n pass\\n\\n # Files that can be added to, but that must contain the template contents\\n for files in files_partial:\\n # Ignore if file specified in linting config\\n ignore_files = self.lint_config.get(\\\"files_unchanged\\\", [])\\n if any([f in ignore_files for f in files]):\\n ignored.append(f\\\"File ignored due to lint config: {self._wrap_quotes(files)}\\\")\\n\\n # Ignore if we can't find the file\\n elif not any([os.path.isfile(_pf(f)) for f in files]):\\n ignored.append(f\\\"File does not exist: {self._wrap_quotes(files)}\\\")\\n\\n # Check that the file contains the template file contents\\n else:\\n for f in files:\\n try:\\n with open(_pf(f), \\\"r\\\") as fh:\\n pipeline_file = fh.read()\\n with open(_tf(f), \\\"r\\\") as fh:\\n template_file = fh.read()\\n if template_file in pipeline_file:\\n passed.append(f\\\"`{f}` matches the template\\\")\\n else:\\n if \\\"files_unchanged\\\" in self.fix:\\n # Try to fix the problem by overwriting the pipeline file\\n with open(_tf(f), \\\"r\\\") as fh:\\n template_file = fh.read()\\n with open(_pf(f), \\\"w\\\") as fh:\\n fh.write(template_file)\\n passed.append(f\\\"`{f}` matches the template\\\")\\n fixed.append(f\\\"`{f}` overwritten with template file\\\")\\n else:\\n failed.append(f\\\"`{f}` does not match the template\\\")\\n could_fix = True\\n except FileNotFoundError:\\n pass\\n\\n # cleaning up temporary dir\\n shutil.rmtree(tmp_dir)\\n\\n return {\\\"passed\\\": passed, \\\"failed\\\": failed, \\\"ignored\\\": ignored, \\\"fixed\\\": fixed, \\\"could_fix\\\": could_fix}\",\n \"def show_errors(self):\\n\\n if self.errors:\\n print('Clean error in:')\\n for file in self.errors:\\n print(' %s' % file)\",\n \"def CheckFilesMatch(config):\\n\\n diff_errors = []\\n\\n file_pairs = _GetFilePairs(config)\\n missing_files, stale_files = _GetMissingAndStaleFiles(file_pairs)\\n\\n for pair in missing_files:\\n diff_errors.append(\\\"File %s does not exist\\\" % pair.target)\\n continue\\n\\n for pair in stale_files:\\n diff_errors.append(\\\"File %s is out of date\\\" % pair.target)\\n\\n if diff_errors:\\n error_msg = \\\"Files out of date!\\\\n\\\\n\\\"\\n error_msg += \\\"To fix run THIS command:\\\\n\\\"\\n error_msg += \\\" bazel-bin/%s/%s --fix\\\\n\\\\n\\\" % (config.package_name,\\n config.target_name)\\n error_msg += \\\"Errors:\\\\n\\\"\\n error_msg += \\\" \\\" + \\\"\\\\n \\\".join(diff_errors)\\n return error_msg\\n else:\\n return None\",\n \"def _check_for_commands(keep_path):\\n if not os.path.exists(keep_path):\\n click.echo(\\\"You have not registered any command yet.\\\")\\n quit()\",\n \"def RunCheckMate(parserDict):\\n t0 = time.time()\\n parser = ConfigParserExt()\\n parser.read_dict(parserDict)\\n\\n pars = parser.toDict(raw=False)[\\\"options\\\"]\\n\\n outputFolder = os.path.abspath(parser.get(\\\"CheckMateParameters\\\",\\\"OutputDirectory\\\"))\\n resultFolder = os.path.join(outputFolder,parser.get(\\\"CheckMateParameters\\\",\\\"Name\\\"))\\n if os.path.isdir(resultFolder):\\n logger.info(\\\"Results folder %s found.\\\" %resultFolder)\\n if parser.get(\\\"CheckMateParameters\\\",\\\"OutputExists\\\") == 'overwrite':\\n logger.info(\\\"Overwriting\\\")\\n shutil.rmtree(resultFolder)\\n else:\\n logger.info(\\\"Skipping\\\" %resultFolder)\\n return \\\"---- %s skipped\\\" %resultFolder\\n cardFile = getCheckMateCard(parser)\\n logger.debug('Steering card %s created' %cardFile)\\n\\n #Create output dirs, if do not exist:\\n try:\\n os.makedirs(outputFolder)\\n except:\\n pass\\n\\n #Run CheckMate\\n checkmatePath = os.path.abspath(pars['checkmateFolder'])\\n checkmateBin = os.path.join(checkmatePath,'bin')\\n logger.info('Running checkmate with steering card: %s ' %cardFile)\\n logger.debug('Running: python2 ./CheckMATE %s at %s' %(cardFile,checkmateBin))\\n run = subprocess.Popen('python2 ./CheckMATE %s' %(cardFile)\\n ,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE,cwd=checkmateBin)\\n output,errorMsg= run.communicate()\\n logger.debug('CheckMATE error:\\\\n %s \\\\n' %errorMsg)\\n logger.debug('CheckMATE output:\\\\n %s \\\\n' %output)\\n\\n os.remove(cardFile)\\n\\n logger.info(\\\"Done in %3.2f min\\\" %((time.time()-t0)/60.))\\n\\n #Remove parton level events:\\n if pars['cleanUp'] is True:\\n mg5folder = os.path.join(resultFolder,'mg5amcatnlo')\\n if os.path.isdir(mg5folder):\\n logger.debug('Removing data from: %s \\\\n' %mg5folder)\\n for f in os.listdir(mg5folder):\\n file_path = os.path.join(mg5folder, f)\\n if os.path.isdir(file_path):\\n shutil.rmtree(file_path)\\n analysisfolder = os.path.join(resultFolder,'analysis')\\n if os.path.isfile(os.path.join(analysisfolder,'analysisstdout_atlas_1712_02118_ew.log')):\\n os.remove(os.path.join(analysisfolder,'analysisstdout_atlas_1712_02118_ew.log'))\\n\\n now = datetime.datetime.now()\\n\\n return \\\"Finished running CheckMATE at %s\\\" %(now.strftime(\\\"%Y-%m-%d %H:%M\\\"))\",\n \"def test_duplicatefslabels_run_failure(self, get_label_dict_mock):\\n get_label_dict_mock.return_value = {\\\"/\\\": [\\\"/dev/xvda1\\\", \\\"/dev/xvdf1\\\"],\\n \\\"TEST\\\": [\\\"/dev/xvdg1\\\"]}\\n with contextlib.redirect_stdout(self.output):\\n self.assertTrue(moduletests.src.duplicatefslabels.run())\\n self.assertTrue(\\\"[FAILURE] Duplicate label, /, found on the following filesystems: /dev/xvda1, /dev/xvdf1\\\\n\\\"\\n in self.output.getvalue())\\n self.assertTrue(get_label_dict_mock.called)\",\n \"def testIgnoredError(self):\\n cmds = \\\"\\\"\\\"-chown 0 missingFile\\npwd\\nexit\\n\\\"\\\"\\\"\\n def _cbCheckResult(res):\\n self.assertIn(self.testDir.asBytesMode().path, res)\\n\\n d = self._getBatchOutput(cmds)\\n d.addCallback(_cbCheckResult)\\n return d\",\n \"def errors(conf, daemon):\\n # persisted dict interface for long term memory\\n errors = Shove('file://{0}'.format(conf.app.errors), protocol=2, flag='r')\\n if any(errors):\\n print(\\\"errors found\\\")\\n for path, error in six.iteritems(errors):\\n pp(error)\\n errors.close()\\n exit(1)\\n # ⏏ exit the program with an error\\n else:\\n print(\\\"no errors found - OK\\\")\\n print()\\n errors.close()\",\n \"def test_bad_protein_file():\\n\\n bad = random_filename()\\n rv, out = getstatusoutput(f'{prg} --cdhit {cdhit} -p {bad}')\\n assert rv > 0\\n assert out.lower().startswith('usage:')\\n assert re.search(f\\\"No such file or directory: '{bad}'\\\", out)\",\n \"def command_failed_error(cmd):\\n\\n output_1 = colored(' - Error: Failed to run command ', 'red')\\n output_2 = command(cmd)\\n return output_1 + output_2 + '\\\\n'\",\n \"def test_bad_cdhit_file():\\n\\n bad = random_filename()\\n rv, out = getstatusoutput(f'{prg} --cdhit {bad} -p {proteins}')\\n assert rv > 0\\n assert out.lower().startswith('usage:')\\n assert re.search(f\\\"No such file or directory: '{bad}'\\\", out)\",\n \"def assert_cmd_success(self, cmds):\\n print('@ %s' % cmds)\\n try:\\n self.cc.batch_command(cmds)\\n except MakeFailed as e:\\n print('Detected MakeFailed')\\n print('Failed jobs: %s' % e.failed)\\n for job_id in e.failed:\\n self.cc.interpret_commands_wrap('details %s' % job_id)\\n\\n except CommandFailed:\\n # msg = 'Command %r failed. (res=%s)' % (cmds, res)\\n raise\\n\\n self.cc.interpret_commands_wrap('check_consistency raise_if_error=1')\",\n \"def test_errors_on_output(self):\\n mb = self.maria_backup\\n\\n # normal run\\n errors = b\\\"\\\"\\\"\\n 220309 11:19:09 Finished backing up non-InnoDB tables and files\\n 220309 11:19:09 Executing FLUSH NO_WRITE_TO_BINLOG ENGINE LOGS...\\n xtrabackup: The latest check point (for incremental): '92134324'\\n xtrabackup: Stopping log copying thread..\\n 220309 11:19:10 >> log scanned up to (900123121)\\n 220309 11:19:10 Executing UNLOCK TABLES\\n 220309 11:19:10 All tables unlocked\\n 220309 11:19:10 Backup created in directory '/a/dir'\\n 220309 11:19:10 [00] Writing backup-my.cnf\\n 220309 11:19:10 [00] ...done\\n 220309 11:19:10 [00] Writing xtrabackup_info\\n 220309 11:19:10 [00] ...done\\n xtrabackup: Transaction log of lsn (89423125) to (900123121) was copied.\\n 220309 11:19:10 completed OK!\\n \\\"\\\"\\\"\\n self.assertFalse(mb.errors_on_output(b'', errors))\\n\\n # failed run\\n errors = b\\\"\\\"\\\"\\n xtrabackup: error: log block numbers mismatch:\\n xtrabackup: error: expected log block no. 293842034, but got no. 13324598 from the log file.\\n xtrabackup: error: it looks like InnoDB log has wrapped around before xtrabackup\\n could process all records due to either log copying being too slow, or log files being too small.\\n xtrabackup: Error: xtrabackup_copy_logfile() failed\\n \\\"\\\"\\\"\\n self.assertTrue(mb.errors_on_output(b'', errors))\",\n \"def exechost_status():\\n\\n exechost = socket.gethostname()\\n\\n # free\\n try:\\n subp = subprocess.Popen([\\\"free\\\", \\\"-m\\\"], stdout=subprocess.PIPE)\\n output = subp.communicate()[0]\\n print \\\"EXECSTAT %s FREE\\\\n%s\\\" % (exechost, output)\\n except:\\n print \\\"Problem running free command\\\"\\n (extype, exvalue, trback) = sys.exc_info()\\n traceback.print_exception(extype, exvalue, trback, limit=1, file=sys.stdout)\\n print \\\"Ignoring error and continuing...\\\\n\\\"\\n\\n # df\\n try:\\n cwd = os.getcwd()\\n subp = subprocess.Popen([\\\"df\\\", \\\"-h\\\", cwd], stdout=subprocess.PIPE)\\n output = subp.communicate()[0]\\n print \\\"EXECSTAT %s DF\\\\n%s\\\" % (exechost, output)\\n except:\\n print \\\"Problem running df command\\\"\\n (extype, exvalue, trback) = sys.exc_info()\\n traceback.print_exception(extype, exvalue, trback, limit=1, file=sys.stdout)\\n print \\\"Ignoring error and continuing...\\\\n\\\"\",\n \"def check_tools_exist(WARNINGS):\\n tools_list = []\\n Warning_out = WARNINGS + \\\"Tool executable warning: \\\"\\n try:\\n flash.Flash(args.flash)\\n tools_list.append(\\\"flash\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"Flash not in path\\\"\\n try:\\n error_correction.Error_Correction(args.spades)\\n tools_list.append(\\\"error_correction\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"spades.py not in path\\\\n\\\"\\n try:\\n vsearch.Vsearch(args.vsearch)\\n tools_list.append(\\\"vsearch\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"vsearch not in path\\\\n\\\"\\n try:\\n trimmomatic.Trimmomatic(args.trimmomatic)\\n tools_list.append(\\\"trimmomatic\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"trimmomatic not in path\\\\n\\\"\\n try:\\n swarm.Swarm(args.swarm)\\n tools_list.append(\\\"swarm\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"swarm not in path\\\\n\\\"\\n try:\\n samtools_index.Samtools_Index(args.samtools)\\n tools_list.append(\\\"samtools\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"samtools not in path\\\\n\\\"\\n try:\\n pear.Pear(args.pear)\\n tools_list.append(\\\"pear\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"pear not in path\\\\n\\\"\\n try:\\n muscle.Muscle(args.muscle)\\n tools_list.append(\\\"muscle\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"muscle not in path\\\\n\\\"\\n try:\\n fastqc.FastQC(args.fastqc)\\n tools_list.append(\\\"fastqc\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"fastqc not in path\\\\n\\\"\\n try:\\n cd_hit.Cd_hit(args.cd_hit)\\n tools_list.append(\\\"cd-hit-est\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"cd-hit-est not in path\\\\n\\\"\\n try:\\n bowtie_map.Bowtie2_Map(args.bowtie2)\\n tools_list.append(\\\"bowtie2\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"bowtie2 not in path\\\\n\\\"\\n try:\\n blast.Blastclust(args.blastclust)\\n tools_list.append(\\\"blastclust\\\")\\n except ValueError:\\n Warning_out = Warning_out + \\\"blastclust not in path\\\\n\\\"\\n return tools_list, Warning_out\",\n \"def step_impl(context):\\n log.info(\\\"====> verify the NSA files are not placed under container_nsa directory\\\")\\n\\n nsa_container = get_nsa_container_string(context)\\n container_nsa_path = \\\"/tmp/cme/local/GFD/{nsa_container}/container_nsa\\\".format(nsa_container=nsa_container)\\n log.info(\\\" ****> DEBUG: nsa container path is: {container_nsa_path}\\\".format(container_nsa_path=container_nsa_path))\\n\\n command = \\\"cd {container_nsa_path}; ls -a | wc -l\\\".format(container_nsa_path=container_nsa_path)\\n if \\\"2\\\" in context.cme_session.send_ssh_command(command=command): # Means that directory is empty\\n log.info(\\\" ****> Passed The NSA files are placed under the container_nsa directory - As expected.\\\")\\n else:\\n assert False, \\\" ****> Failed: The NSA files are placed under the container_nsa directory - While they should not be there.\\\"\",\n \"def not_found(client, server, command):\\n server.logger.info(\\\"BLACKLIST {} : {}\\\".format(client.ip, command))\\n client.send(\\\"sh: {}: command not found\\\\n\\\".format(command))\\n client.exit_status = 127\",\n \"def test_deploy_log_messages(deploy_result: Result) -> None:\\n expected_lines = [\\n \\\"deployment_1:processing deployment (in progress)\\\",\\n \\\"deployment_1:processing regions sequentially...\\\",\\n \\\"\\\",\\n \\\"deployment_1.test_raw_cfn:processing module in us-east-1 (in progress)\\\",\\n \\\"cfngin.yml:init (in progress)\\\",\\n \\\"skipped; cfngin_bucket not defined\\\",\\n \\\"cfngin.yml:init (complete)\\\",\\n \\\"cfngin.yml:deploy (in progress)\\\",\\n \\\"raw-template-vpc:submitted (creating new stack)\\\",\\n \\\"raw-template-vpc:complete (creating new stack)\\\",\\n \\\"cfngin.yml:deploy (complete)\\\",\\n \\\"deployment_1.test_raw_cfn:processing module in us-east-1 (complete)\\\",\\n \\\"deployment_1:processing deployment (complete)\\\",\\n ]\\n expected = \\\"\\\\n\\\".join(f\\\"[runway] {msg}\\\" for msg in expected_lines)\\n assert expected in deploy_result.stdout, (\\n \\\"stdout does not match expected\\\\n\\\\nEXPECTED:\\\\n\\\"\\n f\\\"{expected}\\\\n\\\\nSTDOUT:\\\\n{deploy_result.stdout}\\\"\\n )\",\n \"def run(self):\\n list_test_scenarios = self.__get_list_scenarios_in_folder()\\n\\n if not list_test_scenarios:\\n utils.print_error(\\n \\\"\\\\n{}\\\\n\\\".format(constant.ERR_CANNOT_FIND_ANY_TEST_SCENARIOS))\\n exit(1)\\n\\n (tests_pass, tests_fail) = self.__execute_tests(list_test_scenarios)\\n\\n complete_message = constant.INFO_TEST_PASS_FAIL.format(\\n tests_pass, tests_fail)\\n\\n print(complete_message)\\n\\n self.__execute_reporter()\",\n \"def get_fatal_alerts(self, path):\",\n \"def test_do_not_need_alternate(self):\\n os.unlink(os.path.join(self.reports_dir,\\n 'TEST-testutil.manual_test.LintTest-fail.xml'\\n ))\\n os.unlink(os.path.join(self.reports_dir,\\n 'TEST-testutil.manual_test.LintTest-success.xml'\\n ))\\n actual = self._analyze_make_output()\\n self.assertEqual(1, actual)\\n self.assertIn('E999 lint error from txt-file.', self.errors[0])\",\n \"def test_generate_logs(self):\\n debug = True\\n # Extra \\\"dummy\\\" files will be generated to the system to get the system to\\n # the total_file_count\\n total_file_count = 1020\\n # Time in days to erase files\\n erase_threshold = 7 \\n filename_header = 'event-log-'\\n log_directory = '/hd/logs'\\n #log_directory = '/hdp/logs'\\n\\n \\n \\n password = get_hidden_password()\\n self.ssx.open_hidden_shell(password)\\n \\n ###########\\n ## Warning!\\n ###########\\n self.myLog.info(\\\"Warning:\\\")\\n self.myLog.info(\\\"This automatoin makes use of tail and head\\\")\\n self.myLog.info(\\\"Those binaries are not already on the SSX\\\")\\n self.myLog.info(\\\"You need to copy both of them from the script directory to:\\\")\\n self.myLog.info(\\\"/hd/logs otherwise the script will FAIL!\\\")\\n \\n #################################\\n ## 1. Check the state of /hd/logs\\n #################################\\n self.myLog.info(\\\"Testing the %s location\\\" % log_directory)\\n self.myLog.info(\\\"--------------------------------------\\\")\\n ####################\\n ## Get the file list\\n \\n command = 'cd ' + log_directory\\n # This may cause a bug here!\\n #raw_output = self.ssx.hidden_cmd(\\\"cd \\\\/hd\\\\/logs\\\", timeout=30)\\n raw_output = self.ssx.hidden_cmd(command, timeout 30)\\n if debug:\\n print 'the return value was'\\n print raw_output\\n\\n raw_output = self.ssx.hidden_cmd(\\\"pwd\\\", timeout=30)\\n if debug:\\n print 'the return value was'\\n print raw_output\\n\\n raw_output = self.ssx.hidden_cmd(\\\"ls | grep event-log | wc\\\", timeout=30)\\n if debug:\\n print 'the return value was'\\n print raw_output\\n\\n try:\\n raw_file_count = raw_output.split()\\n file_count = int(raw_file_count[0])\\n except:\\n self.myLog.error(\\\"Unable to parse the file count: %s\\\" % raw_file_count)\\n \\n # We have placed a copy of the following two tools onto the ssx in /hd/logs\\n # tail, head\\n # There is a retarded bug in tail that causes it to not be able to read files\\n # via stdin. A work around for this bug is as follows:\\n self.myLog.info(\\\"Executing workaround to make tail work\\\")\\n raw_output = self.ssx.hidden_cmd(\\\"touch stdin\\\", timeout=10)\\n \\n \\n self.myLog.info(\\\"Finding the oldest log file\\\")\\n raw_output = self.ssx.hidden_cmd(\\\"ls event-log* | /hd/logs/head -1\\\")\\n oldest_file = raw_output\\n self.myLog.info(\\\"The oldest logs fils is %s\\\" % oldest_file)\\n \\n # Newest is the file with the highest date. (means it was created recently)\\n self.myLog.info(\\\"Finding the newest file\\\") \\n raw_output = self.ssx.hidden_cmd(\\\"ls event-log* | /hd/logs/tail -1\\\")\\n newest_file = raw_output\\n self.myLog.info(\\\"The newest log file is %s\\\" % newest_file)\\n \\n \\n self.myLog.info(\\\"Checking the difference in date/time between the two logs\\\")\\n newest_log_parts = newest_file.split(\\\"-\\\")\\n newest_log_date = newest_log_parts[2]\\n newest_log_time = newest_log_parts[3]\\n newest_log_year = newest_log_date[0:4]\\n newest_log_month = newest_log_date[4:6]\\n newest_log_day = newest_log_date[6:8]\\n \\n oldest_log_parts = oldest_file.split(\\\"-\\\")\\n oldest_log_date = oldest_log_parts[2]\\n oldest_log_time = oldest_log_parts[3]\\n oldest_log_year = oldest_log_date[0:4]\\n oldest_log_month = oldest_log_date[4:6]\\n oldest_log_day = oldest_log_date[6:8] \\n \\n \\n self.myLog.info(\\\"Checking to see if the oldest file on the system 'should' be errased\\\")\\n # Now we have all the parts of the date/time we need to compare them to see \\n # if the time delta is greater then 7 days or some user defined value\\n should_be_errased = False\\n # If the years are different then errase\\n if newest_log_year > oldest_log_year:\\n self.myLog.info(\\\"files will be errased\\\")\\n should_be_errased = True\\n # If the day value is larger\\n elif newest_log_day > oldest_log_day:\\n if int(newest_log_day) - int(oldest_log_day) >= erase_threshold:\\n self.myLog.info(\\\"files will be errased\\\")\\n should_be_errased = True\\n else:\\n self.myLog.info(\\\"The oldest file is not old enough to be errased\\\")\\n self.myLog.info(\\\"The oldest file is not old enough to be errased\\\")\\n \\n self.myLog.info(\\\"------------------------------------------------------------------------\\\")\\n self.myLog.info(\\\"We will now generate files that are newer then the file errasal threshold\\\")\\n self.myLog.info(\\\"This will cause ALL files that are newer then the date to be errased\\\")\\n \\n\\n self.myLog.info(\\\"We found %s files in /hd/logs\\\" % file_count)\\n files_to_generate = total_file_count - file_count\\n self.myLog.info(\\\"For this test we will generate %s files\\\" % files_to_generate)\\n \\n \\n #file_date = int(raw_file_date[2]) - 1\\n if debug:\\n self.myLog.debug(\\\"These are the variables we will use:\\\")\\n self.myLog.debug(\\\"newest_log_year: %s\\\" % newest_log_year)\\n self.myLog.debug(\\\"newest_log_day: %s\\\" % newest_log_day)\\n self.myLog.debug(\\\"newest_log_month: %s\\\" % newest_log_month)\\n self.myLog.debug(\\\"erase_threshold: %s\\\" % erase_threshold)\\n file_date = str(newest_log_year) + str(newest_log_month)\\n self.myLog.debug(\\\"file_date: %s\\\" % file_date)\\n erase_day = int(newest_log_day) + int(erase_threshold) + 1\\n self.myLog.debug(\\\"erase_day: %s\\\" % erase_day)\\n file_date = file_date + str(erase_day)\\n self.myLog.debug(\\\"file_date: %s\\\" % file_date)\\n self.myLog.info(\\\"The fake log files will be generated with date: %s\\\" % file_date)\\n \\n \\n ##########################\\n ## Generate Fake log files\\n ##########################\\n \\n for i in range(0,files_to_generate):\\n if debug:\\n print '===================================='\\n print 'Workin on file number:', i, 'of:', files_to_generate\\n complete_file_name = filename_header + str(file_date) + '-' + str.rjust(str(i), 6, '0')\\n if debug:\\n print 'The fake file will be called:', complete_file_name\\n \\n #command = 'cp ' + oldest_file + ' ' + complete_file_name\\n command = 'touch ' + complete_file_name\\n if debug:\\n print 'The command will be:'\\n print command\\n \\n raw_output = self.ssx.hidden_cmd(command)\\n\\n\\n self.myLog.info(\\\"Done generating fake log files\\\")\\n self.myLog.info(\\\"--------------------------------------\\\")\\n #self.ssx.hidden_cmd(\\\"\\\\n\\\")\\n self.ssx.close_hidden_shell()\\n \\n self.myLog.info(\\\"Checking to see the status of the log buffers\\\")\\n log_counters = show_logging(self.ssx)\\n self.myLog.info(\\\"The log files will be errased when:\\\")\\n self.myLog.info(\\\"%s = %s\\\" % (log_counters['Glob-D']['Next-Ix 1'], log_counters['Glob-D']['Next Save-Ix 1']))\\n log_events_to_generate = int(log_counters['Glob-D']['Next Save-Ix 1']) - int(log_counters['Glob-D']['Next-Ix 1'])\\n self.myLog.info(\\\"We need to generate %s log events to cause the log to flush to disk\\\" % log_events_to_generate)\",\n \"def verify_git_clean(path):\\n\\n sys.stdout.write(\\\" - Checking for uncommitted changes:\\\")\\n result = run_in_component(path, ['git', 'status', '--porcelain=v1'])\\n\\n lines = [x for x in result.splitlines() if len(x) > 0]\\n\\n if len(lines) == 0:\\n print(\\\" OKAY\\\")\\n return\\n\\n print(\\\" FAILED\\\")\\n\\n raise GenericError(\\\"There are uncommitted changes in the component, please commit or stash them\\\")\",\n \"def status(self, exe_paths=False):\\n if self.status_msg is None:\\n self.check_all(exe_paths=exe_paths)\\n return self.status_msg\",\n \"def main():\\n\\n# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\\n# ~~~~ Reads config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\\n print('\\\\n\\\\nInterpreting command line options\\\\n'+'~'*72+'\\\\n')\\n\\n parser = ArgumentParser()\\n subparser = parser.add_subparsers(\\\\\\n help='run_selafin commands to do', dest='command')\\n\\n subparser = chop_parser(subparser)\\n subparser = scan_parser(subparser)\\n subparser = spec_parser(subparser)\\n subparser = alter_parser(subparser)\\n subparser = merge_parser(subparser)\\n subparser = diff_parser(subparser)\\n subparser = calcs_parser(subparser, 'calcs', '???')\\n subparser = calcs_parser(subparser, 'crunch', '???')\\n subparser = calcs_parser(subparser, 'transf', '???')\\n subparser = sample_parser(subparser)\\n subparser = subdivide_parser(subparser)\\n subparser = tesselate_parser(subparser)\\n\\n options = parser.parse_args()\\n\\n# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\\n# ~~~~ Reads code name ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\\n\\n if options.command == 'scan':\\n scan(options)\\n elif options.command == 'spec':\\n spec(options)\\n elif options.command == 'chop':\\n chop(options)\\n elif options.command == 'alter':\\n alter(options)\\n elif options.command == 'merge':\\n merge(options)\\n elif options.command == 'diff':\\n diff(options)\\n elif options.command == 'sample':\\n sample(options)\\n elif options.command in ['calcs', 'crunch', 'transf']:\\n calcs(options, options.command)\\n elif options.command == 'subdivide':\\n subdivide(options)\\n elif options.command == 'tessellate':\\n tesselate(options)\\n else:\\n raise TelemacException(\\\\\\n '\\\\nDo not know what to do with '\\n 'this code name: {}'.format(options.command))\\n\\n# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\\n# ~~~~ Jenkins' success message ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\\n print('\\\\n\\\\nMy work is done\\\\n\\\\n')\\n\\n sys.exit(0)\",\n \"def check_for_errors(self):\\n\\n with open(\\\"output.dat\\\", \\\"r\\\") as log:\\n for line in log:\\n if \\\"*** Psi4 exiting successfully.\\\" in line:\\n return {\\\"success\\\": True}\\n\\n elif \\\"*** Psi4 encountered an error.\\\" in line:\\n return {\\\"success\\\": False, \\\"error\\\": \\\"Not known\\\"}\\n\\n return {\\\"success\\\": False, \\\"error\\\": \\\"Segfault\\\"}\",\n \"def failure_cmd(self) -> str:\\n return \\\"{} --enable=all -f -q {}\\\".format(\\n self.conf.get_executable(), constants.ROOT_PATH + \\\"/data/cppcheck-152/trial-fail.cpp\\\"\\n )\",\n \"def test_bad_file():\\n\\n bad = ''.join(random.choices(string.ascii_uppercase + string.digits, k=5))\\n rv, out = getstatusoutput(f'{prg} -f {bad}')\\n assert rv != 0\\n assert re.match('usage:', out, re.I)\\n assert re.search(f\\\"No such file or directory: '{bad}'\\\", out)\",\n \"def test_run_cmd_simple_negative(caplog):\\n caplog.set_level(logging.DEBUG)\\n cmd = \\\"ls /tmp/this/file/isindeednotthereatall\\\"\\n with pytest.raises(CommandFailed) as excinfo:\\n utils.run_cmd(cmd)\\n assert \\\"No such file or directory\\\" in str(excinfo.value)\\n # check that run_cmd logged the run as expected\\n assert caplog.records[0].levelname == 'INFO'\\n assert caplog.records[0].message == f'Executing command: {cmd}'\\n assert caplog.records[1].levelname == 'DEBUG'\\n assert caplog.records[1].message == 'Command stdout is empty'\\n assert caplog.records[2].levelname == 'WARNING'\\n assert caplog.records[2].message.startswith(\\\"Command stderr: ls:\\\")\\n assert \\\"No such file or directory\\\" in caplog.records[2].message\\n assert caplog.records[3].levelname == 'DEBUG'\\n assert caplog.records[3].message == 'Command return code: 2'\",\n \"def test_stratis_no_subcommand(self):\\n for command_line in [[], [\\\"daemon\\\"]]:\\n for prefix in [[], [\\\"--propagate\\\"]]:\\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)\",\n \"def run_commands(self, commands):\\n if isinstance(commands, str):\\n commands = commands.split('\\\\n')\\n for item in commands:\\n if item.strip().startswith(\\\"#\\\"):\\n continue\\n should_exit, result = self.cmd_with_result(item)\\n if not result:\\n break\",\n \"def run(self, server):\\n diagnostics = \\\"unknown\\\"\\n save_stdout = sys.stdout\\n try:\\n self.skip = False\\n if os.path.exists(self.skip_cond):\\n sys.stdout = FilteredStream(self.tmp_result)\\n stdout_fileno = sys.stdout.stream.fileno()\\n execfile(self.skip_cond, dict(locals(), **server.__dict__))\\n sys.stdout.close()\\n sys.stdout = save_stdout\\n if not self.skip:\\n sys.stdout = FilteredStream(self.tmp_result)\\n stdout_fileno = sys.stdout.stream.fileno()\\n self.execute(server)\\n sys.stdout.flush()\\n self.is_executed_ok = True\\n except Exception as e:\\n traceback.print_exc(e)\\n diagnostics = str(e)\\n finally:\\n if sys.stdout and sys.stdout != save_stdout:\\n sys.stdout.close()\\n sys.stdout = save_stdout\\n self.is_executed = True\\n sys.stdout.flush()\\n\\n if not self.skip:\\n if self.is_executed_ok and os.path.isfile(self.result):\\n self.is_equal_result = filecmp.cmp(self.result, self.tmp_result)\\n else:\\n self.is_equal_result = 1\\n\\n if self.args.valgrind:\\n self.is_valgrind_clean = (check_valgrind_log(server.valgrind_log) == False)\\n\\n if self.skip:\\n color_stdout(\\\"[ skip ]\\\\n\\\", schema='test_skip')\\n if os.path.exists(self.tmp_result):\\n os.remove(self.tmp_result)\\n elif self.is_executed_ok and self.is_equal_result and self.is_valgrind_clean:\\n color_stdout(\\\"[ pass ]\\\\n\\\", schema='test_pass')\\n if os.path.exists(self.tmp_result):\\n os.remove(self.tmp_result)\\n elif (self.is_executed_ok and not self.is_equal_result and not\\n os.path.isfile(self.result)):\\n os.rename(self.tmp_result, self.result)\\n color_stdout(\\\"[ new ]\\\\n\\\", schema='test_new')\\n else:\\n os.rename(self.tmp_result, self.reject)\\n color_stdout(\\\"[ fail ]\\\\n\\\", schema='test_fail')\\n\\n where = \\\"\\\"\\n if not self.is_executed_ok:\\n self.print_diagnostics(self.reject, \\\"Test failed! Last 10 lines of the result file:\\\\n\\\")\\n server.print_log(15)\\n where = \\\": test execution aborted, reason '{0}'\\\".format(diagnostics)\\n elif not self.is_equal_result:\\n self.print_unidiff()\\n server.print_log(15)\\n where = \\\": wrong test output\\\"\\n elif not self.is_valgrind_clean:\\n os.remove(self.reject)\\n self.print_diagnostics(server.valgrind_log, \\\"Test failed! Last 10 lines of valgrind.log:\\\\n\\\")\\n where = \\\": there were warnings in valgrind.log\\\"\\n\\n if not self.args.is_force:\\n raise RuntimeError(\\\"Failed to run test \\\" + self.name + where)\",\n \"def test_explain_non_existent_code(self):\\n command_line = [\\\"pool\\\", \\\"explain\\\", \\\"bogus\\\"]\\n for prefix in [[], [\\\"--propagate\\\"]]:\\n self.check_system_exit(prefix + command_line, _PARSE_ERROR)\",\n \"def check_analysis_pickle_files(self):\\n # Make sure that there have been no more trials run since this\\n # last processing. To do this, get the number of output files\\n for basename in nsort(os.listdir(self.logdir)):\\n m = self.labels.subdir_re.match(basename)\\n if m is None or 'pckl' in basename:\\n continue\\n # Here is the output directory which contains the files\\n subdir = os.path.join(self.logdir, basename)\\n # Account for failed jobs. Get the set of file numbers that\\n # exist for all h0 and h1 combinations\\n self.get_set_file_nums(\\n filedir=subdir\\n )\\n # Take one of the pickle files to see how many data\\n # entries it has.\\n data_sets = from_file(os.path.join(self.logdir,\\n 'data_sets.pckl'))\\n # Take the first data key and then the h0 fit to h0 fid\\n # which should always exist. The length of this is then\\n # the number of trials in the pickle files.\\n if 'h0_fit_to_h0_fid' in data_sets[data_sets.keys()[0]].keys():\\n pckl_trials = len(data_sets[data_sets.keys()[0]][\\n 'h0_fit_to_h0_fid'].keys())\\n # The number of pickle trials should match the number of\\n # trials derived from the output directory.\\n if self.num_trials == pckl_trials:\\n logging.info(\\n 'Found files I assume to be from a previous run of'\\n ' this processing script containing %i trials. If '\\n 'this seems incorrect please delete the files: '\\n 'data_sets.pckl, all_params.pckl and labels.pckl '\\n 'from the logdir you have provided.'%pckl_trials\\n )\\n pickle_there = True\\n else:\\n logging.info(\\n 'Found files I assume to be from a previous run of'\\n ' this processing script containing %i trials. '\\n 'However, based on the number of json files in the '\\n 'output directory there should be %i trials in '\\n 'these pickle files, so they will be regenerated.'%(\\n pckl_trials, self.num_trials)\\n )\\n pickle_there = False\\n else:\\n logging.info(\\n 'Found files I assume to be from a previous run of'\\n ' this processing script which do not seem to '\\n 'contain any trials, so they will be regenerated.'\\n )\\n pickle_there = False\\n \\n return pickle_there\",\n \"def run_commands(commands: List[str], dry_run: bool) -> List[str]:\\n result = []\\n for cmd in commands:\\n if dry_run:\\n logging.info(cmd)\\n else:\\n p = safe_exec(cmd)\\n if p.stdout:\\n for line in p.stdout.decode().split('\\\\n'):\\n if line:\\n if line.startswith('No resources found'):\\n # nothing was deleted\\n break\\n fields = line.rstrip().split()\\n if len(fields) > 1:\\n result.append(fields[1])\\n else:\\n result.append(fields[0])\\n return result\",\n \"def __statistics_students_failing(self):\\n students_list = self.__grade_controller.get_list_of_failing_students()\\n if len(students_list) == 0:\\n print(\\\"There is no student failing!\\\")\\n return\\n\\n for student in students_list:\\n print(str(student) + \\\"\\\\n\\\")\",\n \"def check():\\n \\n overall_report = dict()\\n\\n # source code analysis\\n # ====================\\n # currently empty\\n \\n # compile\\n # =======\\n ret_makefile = subprocess.run([config.compiler] + config.compiler_args, # command\\n stdout=subprocess.PIPE, # capture stdout\\n stderr=subprocess.PIPE, # capture stderr\\n universal_newlines=True) # use text mode for std* file objects\\n overall_report['makefile'] = ret_makefile\\n \\n # runtime analysis\\n # ================\\n with open('compile.txt', 'r') as f:\\n if 'error' not in f.read().lower(): # if compilation succeeded\\n overall_report, test_case_report_list = runtime_analysis(config, overall_report)\\n \\n # pass this info to next tools for subsequent processing\\n # ======================================================\\n pp(overall_report)\\n # results from runtime analysis\\n if 'runtime_analysis_done' in overall_report:\\n success_count = 0\\n for report in test_case_report_list:\\n if 'timeout' in report:\\n util.addFinding(\\\"Time limit exceeded!\\\", 0, \\\"\\\", \\\"TEST_080006\\\")\\n elif report['return_code'] != 0:\\n if report['stderr_stream'] != '': # ASan/LeakSan/Stack protector probably reported something\\n pass # but these findings will be added by analyze.py\\n else:\\n util.addFinding(\\\"It seems your program might have crashed.\\\", 0,\\\"\\\",\\\"TEST_100006\\\")\\n # output_match == None means the user might have tried to print to outfile\\n elif report['stdout_stream'] != '' or report['output_match'] is None:\\n util.addFinding(\\\"A test case failed! Make sure you are not trying to print something.\\\",\\n 0,\\\"\\\",\\\"TEST_100006\\\")\\n elif not all(report['output_match']): # not all test cases passed\\n util.addFinding(\\\"A test case failed!\\\", 0, \\\"\\\", \\\"TEST_100006\\\")\\n else:\\n success_count += 1\\n\\n with open('stderr.txt', 'a') as f:\\n f.write(report['stderr_stream'])\\n with open('stdout.txt', 'a') as f:\\n f.write(report['outfile'])\\n\\n if success_count == len(test_case_report_list):\\n util.addFinding(\\\"Program behaves as expected!\\\", 1, \\\"CHALLENGE_PASS\\\", \\\"TEST_900006\\\")\\n \\n util.dumpFindings()\\n \\n # next tools\\n subprocess.run([\\\"./analyse.py\\\"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)\\n subprocess.run([\\\"./ai.py\\\"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)\",\n \"def CompareResults(ref_dir, results_dir):\\n logging.info(\\\"Comparing results to \\\" + ref_dir)\\n\\n diff_result = os.path.join(results_dir, \\\"layout_tests_diff.txt\\\") \\n if os.path.exists(diff_result):\\n os.remove(diff_result)\\n\\n files=[\\\"passed\\\", \\\"failed\\\", \\\"nontext\\\", \\\"crashed\\\"]\\n for f in files:\\n result_file_name = \\\"layout_tests_\\\" + f + \\\".txt\\\"\\n DiffResults(f, os.path.join(results_dir, result_file_name),\\n os.path.join(ref_dir, result_file_name), diff_result,\\n f == \\\"failed\\\")\\n logging.info(\\\"Detailed diffs are in \\\" + diff_result)\",\n \"def errdump_analysis(errdump_df, switchshow_df, switch_params_aggregated_df, \\n portshow_aggregated_df, project_constants_lst):\\n \\n # imported project constants required for module execution\\n project_steps_df, max_title, io_data_names_df, _, report_headers_df, report_columns_usage_sr, *_ = project_constants_lst\\n\\n # data titles obtained after module execution (output data)\\n # data titles which module is dependent on (input data)\\n data_names, analyzed_data_names = dfop.list_from_dataframe(io_data_names_df, 'errorlog_analysis_out', 'errorlog_analysis_in')\\n # module information\\n meop.show_module_info(project_steps_df, data_names)\\n # read data from database if they were saved on previos program execution iteration\\n data_lst = dbop.read_database(project_constants_lst, *data_names)\\n \\n # force run when any output data from data_lst is not found in database or \\n # procedure execution explicitly requested (force_run flag is on) for any output or input data \\n force_run = meop.verify_force_run(data_names, data_lst, project_steps_df, \\n max_title, analyzed_data_names)\\n if force_run:\\n # data imported from init file (regular expression patterns) to extract values from data columns\\n pattern_dct, _ = sfop.regex_pattern_import('raslog_split', max_title)\\n raslog_message_details_df = sfop.dataframe_import('raslog_details', max_title)\\n raslog_message_id_details_df = sfop.dataframe_import('raslog_id_details', max_title, columns=['Message_ID', 'Details', 'Recommended_action'])\\n\\n # current operation information string\\n info = f'Counting RASLog messages'\\n print(info, end =\\\" \\\")\\n\\n # get aggregated DataFrames\\n errdump_aggregated_df = errdump_aggregated(errdump_df, switchshow_df, switch_params_aggregated_df, \\n portshow_aggregated_df, pattern_dct)\\n # count how many times event appears during one month for the last six months \\n raslog_counter_df, raslog_frequent_df = errdump_statistics(errdump_aggregated_df, raslog_message_details_df, raslog_message_id_details_df)\\n # after finish display status\\n meop.status_info('ok', max_title, len(info)) \\n # partition aggregated DataFrame to required tables\\n raslog_report_df = raslog_report(raslog_frequent_df, data_names, report_headers_df, report_columns_usage_sr)\\n\\n # create list with partitioned DataFrames\\n data_lst = [errdump_aggregated_df, raslog_counter_df, raslog_report_df]\\n # writing data to sql\\n dbop.write_database(project_constants_lst, data_names, *data_lst)\\n # verify if loaded data is empty and replace information string with empty DataFrame\\n else:\\n data_lst = dbop.verify_read_data(max_title, data_names, *data_lst)\\n errdump_aggregated_df, raslog_counter_df, *_ = data_lst\\n # save data to service file if it's required\\n for data_name, data_frame in zip(data_names, data_lst):\\n report.dataframe_to_excel(data_frame, data_name, project_constants_lst)\\n return errdump_aggregated_df, raslog_counter_df\",\n \"def find_stack_status(indir):\\n\\n if not indir.is_dir():\\n raise ValueError(f\\\"'{indir} is not a directory\\\")\\n\\n stacks = {}\\n for inst in [\\\"acis\\\", \\\"hrc\\\"]:\\n\\n infile = indir / f\\\"{inst}_stacks_unchanged.txt\\\"\\n for stack in read_unchanged(infile):\\n assert stack not in stacks\\n stacks[stack] = \\\"unchanged\\\"\\n\\n for status in [\\\"updated\\\", \\\"new\\\"]:\\n infile = indir / f\\\"{inst}_stacks_{status}.txt\\\"\\n\\n for stack in read_changed(infile):\\n assert stack not in stacks\\n stacks[stack] = status\\n\\n return stacks\",\n \"def usage(status=0):\\n print(\\\"finds copy pasted blocks in a set of files\\\")\\n print()\\n print(\\n \\\"Usage: symilar [-d|--duplicates min_duplicated_lines] \\\\\\n[-i|--ignore-comments] [--ignore-docstrings] [--ignore-imports] file1...\\\"\\n )\\n sys.exit(status)\",\n \"def run_silent(self, opts):\\n\\n if not opts.add_to_svn and not opts.export_locally:\\n print \\\"This execution will probably not have any effect. Make sure at least one of \\\"\\\\\\n \\\"the options -l and -a are activated.\\\"\\n\\n svn_OK = False\\n if opts.add_to_svn:\\n svn_OK = check_svn()\\n\\n # look for and enter project file\\n if not self.enter_project_file():\\n raw_input(\\\"Execution aborted!\\\\nPress any key to close.\\\")\\n return\\n\\n # which files are in directories\\n self.enter_directories()\\n\\n self.result_files = self.result_files_dir\\n self.design_files = self.design_files_dir\\n self.design_space_files = self.design_space_files_dir\\n self.test_bench_files = self.test_bench_files_dir\\n\\n if opts.project_file_link:\\n self._pr_intersect()\\n\\n if opts.meta_results_file_link:\\n if not self.enter_meta_results_file():\\n raw_input(\\\"Execution aborted!\\\\nPress any key to close.\\\")\\n return\\n self._ms_intersect()\\n\\n if opts.summary_reports_must_be_ok:\\n self.check_analysis_status()\\n self._OK_intersect()\\n\\n if opts.clean_up_missing_references:\\n project_file_references_valid, meta_results_file_references_valid =\\\\\\n self._check_pr_and_ms_references()\\n\\n if not project_file_references_valid:\\n self._clean_up_project_file()\\n if not meta_results_file_references_valid:\\n self._clean_up_meta_results_file()\\n\\n # go through all summary.report.json files and extract linked files\\n srl = SummaryReportsLinks(self.result_files)\\n self.files_linked_from_sum_reps = srl.get_files()\\n self.folders_linked_from_sum_reps = srl.get_folders()\\n\\n include_dashboard = not opts.do_not_export_dashboard\\n if svn_OK:\\n self.add_to_svn(include_dashboard)\\n\\n if opts.export_locally:\\n self.export_locally(include_dashboard)\",\n \"def test_conformance_tests_test_output(self):\\n style = pycodestyle.StyleGuide(quiet=True)\\n result = style.check_files(['tests/test_output.py'])\\n self.assertEqual(result.total_errors, 0,\\n \\\"Found code style errors (and warnings).\\\")\",\n \"def assertExecutedOnce(self, component: Text) -> None:\\n component_path = os.path.join(self._pipeline_root, component)\\n self.assertTrue(fileio.exists(component_path))\\n outputs = fileio.listdir(component_path)\\n\\n self.assertIn(\\\".system\\\", outputs)\\n outputs.remove(\\\".system\\\")\\n system_paths = [\\n os.path.join(\\\".system\\\", path)\\n for path in fileio.listdir(os.path.join(component_path, \\\".system\\\"))\\n ]\\n self.assertNotEmpty(system_paths)\\n self.assertIn(\\\".system/executor_execution\\\", system_paths)\\n outputs.extend(system_paths)\\n self.assertNotEmpty(outputs)\\n for output in outputs:\\n execution = fileio.listdir(os.path.join(component_path, output))\\n self.assertLen(execution, 1)\",\n \"def test_deploy_no_change_log_messages(deploy_no_change_result: Result) -> None:\\n expected_lines = [\\n \\\"deployment_1:processing deployment (in progress)\\\",\\n \\\"deployment_1:processing regions sequentially...\\\",\\n \\\"\\\",\\n \\\"deployment_1.test_raw_cfn:processing module in us-east-1 (in progress)\\\",\\n \\\"cfngin.yml:init (in progress)\\\",\\n \\\"skipped; cfngin_bucket not defined\\\",\\n \\\"cfngin.yml:init (complete)\\\",\\n \\\"cfngin.yml:deploy (in progress)\\\",\\n \\\"raw-template-vpc:skipped (nochange)\\\",\\n \\\"cfngin.yml:deploy (complete)\\\",\\n \\\"deployment_1.test_raw_cfn:processing module in us-east-1 (complete)\\\",\\n \\\"deployment_1:processing deployment (complete)\\\",\\n ]\\n expected = \\\"\\\\n\\\".join(f\\\"[runway] {msg}\\\" for msg in expected_lines)\\n assert expected in deploy_no_change_result.stdout, (\\n \\\"stdout does not match expected\\\\n\\\\nEXPECTED:\\\\n\\\"\\n f\\\"{expected}\\\\n\\\\nSTDOUT:\\\\n{deploy_no_change_result.stdout}\\\"\\n )\",\n \"def _execute_commands_file(self, commands_file_path):\\n print(\\\"Executing commands from file \\\" + commands_file_path)\\n stop = False\\n with io.open(commands_file_path, 'r', encoding=\\\"utf-8\\\") as f:\\n for l in f:\\n if not l.isspace() and not l.lstrip().startswith(\\\"//\\\"):\\n stop = self.interpret_command(l.rstrip(), quiet=True)\\n if stop:\\n break\\n print(\\\"Execution of file over.\\\")\\n return stop\",\n \"def printErrors(self):\\n if self.dots:\\n self.stream.writeln()\\n\\n # Skipped Test Report\\n if not self.args.no_skip_report:\\n for test, reason in self.skipped:\\n self.stream.writeln(\\n \\\"\\\\n{} {} - {}\\\".format(\\n self.colors.blue(\\\"Skipped\\\"),\\n self.colors.bold(test.dotted_name),\\n reason,\\n )\\n )\\n\\n # Captured output for non-failing tests\\n if not self.args.quiet_stdout:\\n failing_tests = {x[0] for x in self.all_errors}\\n for test in list(self.stdout_output) + list(self.stderr_errput):\\n if test not in failing_tests:\\n self.displayStdout(test)\\n self.displayStderr(test)\\n\\n # Actual tracebacks and captured output for failing tests\\n for test, color_func, outcome, err in self.all_errors:\\n # Header Line\\n self.stream.writeln(\\n f\\\"\\\\n{color_func(outcome)} in {self.colors.bold(test.dotted_name)}\\\"\\n )\\n\\n # Traceback\\n if not self.args.no_tracebacks:\\n relevant_frames = []\\n for i, frame in enumerate(err.traceback_lines):\\n # Python2 tracebacks containing unicode need some special handling\\n # This doesn't always make it readable, but at least it doesn't\\n # crash\\n if sys.version_info[0] == 2: # pragma: no cover\\n try:\\n \\\"\\\".join([frame]) # intentionally trigger exceptions\\n except UnicodeDecodeError:\\n frame = frame.decode(\\\"utf-8\\\")\\n debug(\\n \\\"\\\\n\\\"\\n f\\\"{'*' * 30}Frame {i}:{'*' * 30}\\\\n\\\" + self.colors.yellow(frame),\\n level=3,\\n )\\n # Ignore useless frames\\n if self.verbose < 4:\\n if frame.strip() == \\\"Traceback (most recent call last):\\\":\\n continue\\n # Done with this frame, capture it.\\n relevant_frames.append(frame)\\n self.stream.write(\\\"\\\".join(relevant_frames))\\n\\n # Captured output for failing tests\\n self.displayStdout(test)\\n self.displayStderr(test)\",\n \"def log_result(self, result_list, directory=None):\\n if not result_list:\\n result = \\\"No cleaning was required\\\"\\n else:\\n if self.dry_run:\\n file_verb = (\\\"file\\\" if len(result_list) == 1 else \\\"files\\\") + \\\" would be\\\"\\n else:\\n file_verb = \\\"file was\\\" if len(result_list) == 1 else \\\"files were\\\"\\n directory_verb = f\\\" to directory {directory}\\\" if directory else \\\"\\\"\\n result = f\\\"{len(result_list)} {file_verb} moved{directory_verb}:\\\\n{', '.join(result_list)}\\\"\\n print(result)\",\n \"def error_message(self):\\n summary = format(\\\"%i out of %s failed unexpectedly:\\\",\\n self.pool.num_failed,\\n pluralize(self.pool.num_commands, \\\"command\\\"))\\n details = \\\"\\\\n\\\".join(\\\" - %s\\\" % cmd.error_message for cmd in self.commands)\\n return summary + \\\"\\\\n\\\\n\\\" + details\",\n \"def validate_command(ctx, path):\\n context = SceptreContext(\\n command_path=path,\\n project_path=ctx.obj.get(\\\"project_path\\\"),\\n user_variables=ctx.obj.get(\\\"user_variables\\\"),\\n options=ctx.obj.get(\\\"options\\\"),\\n output_format=ctx.obj.get(\\\"output_format\\\"),\\n ignore_dependencies=ctx.obj.get(\\\"ignore_dependencies\\\")\\n )\\n\\n plan = SceptrePlan(context)\\n responses = plan.validate()\\n\\n for stack, response in responses.items():\\n if response['ResponseMetadata']['HTTPStatusCode'] == 200:\\n del response['ResponseMetadata']\\n click.echo(\\\"Template {} is valid. Template details:\\\\n\\\".format(stack.name))\\n write(response, context.output_format)\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.6216581","0.5714732","0.56718695","0.56527007","0.5601208","0.55626947","0.5551729","0.5527082","0.5517359","0.54875124","0.5445772","0.5432267","0.54280514","0.54172146","0.5366206","0.5357607","0.5353905","0.5338872","0.5335011","0.5333496","0.53188115","0.53051627","0.52903223","0.5280883","0.52702796","0.52629435","0.5249522","0.5249344","0.52456796","0.52426404","0.52363306","0.5228205","0.5228077","0.52272016","0.52200264","0.5211221","0.52056134","0.51911765","0.5175241","0.5174306","0.5166538","0.51628065","0.51564175","0.51530236","0.51505333","0.51474726","0.5145515","0.51440245","0.5123874","0.51176256","0.5113551","0.5100023","0.50964993","0.50935346","0.5092651","0.5091986","0.5087511","0.5087403","0.5081809","0.50790197","0.5073292","0.5069744","0.50631505","0.5062479","0.5059656","0.5056621","0.50537163","0.5049862","0.50484765","0.50461274","0.5041241","0.50378716","0.5036819","0.5033528","0.5032412","0.50275505","0.50265193","0.50199306","0.50169104","0.5016083","0.5011925","0.5010238","0.5006531","0.50053465","0.49986193","0.49962094","0.499093","0.49873674","0.49869233","0.49864247","0.49838108","0.49814054","0.49809638","0.49762112","0.49761373","0.49724016","0.49722722","0.49598595","0.49578485","0.49444133"],"string":"[\n \"0.6216581\",\n \"0.5714732\",\n \"0.56718695\",\n \"0.56527007\",\n \"0.5601208\",\n \"0.55626947\",\n \"0.5551729\",\n \"0.5527082\",\n \"0.5517359\",\n \"0.54875124\",\n \"0.5445772\",\n \"0.5432267\",\n \"0.54280514\",\n \"0.54172146\",\n \"0.5366206\",\n \"0.5357607\",\n \"0.5353905\",\n \"0.5338872\",\n \"0.5335011\",\n \"0.5333496\",\n \"0.53188115\",\n \"0.53051627\",\n \"0.52903223\",\n \"0.5280883\",\n \"0.52702796\",\n \"0.52629435\",\n \"0.5249522\",\n \"0.5249344\",\n \"0.52456796\",\n \"0.52426404\",\n \"0.52363306\",\n \"0.5228205\",\n \"0.5228077\",\n \"0.52272016\",\n \"0.52200264\",\n \"0.5211221\",\n \"0.52056134\",\n \"0.51911765\",\n \"0.5175241\",\n \"0.5174306\",\n \"0.5166538\",\n \"0.51628065\",\n \"0.51564175\",\n \"0.51530236\",\n \"0.51505333\",\n \"0.51474726\",\n \"0.5145515\",\n \"0.51440245\",\n \"0.5123874\",\n \"0.51176256\",\n \"0.5113551\",\n \"0.5100023\",\n \"0.50964993\",\n \"0.50935346\",\n \"0.5092651\",\n \"0.5091986\",\n \"0.5087511\",\n \"0.5087403\",\n \"0.5081809\",\n \"0.50790197\",\n \"0.5073292\",\n \"0.5069744\",\n \"0.50631505\",\n \"0.5062479\",\n \"0.5059656\",\n \"0.5056621\",\n \"0.50537163\",\n \"0.5049862\",\n \"0.50484765\",\n \"0.50461274\",\n \"0.5041241\",\n \"0.50378716\",\n \"0.5036819\",\n \"0.5033528\",\n \"0.5032412\",\n \"0.50275505\",\n \"0.50265193\",\n \"0.50199306\",\n \"0.50169104\",\n \"0.5016083\",\n \"0.5011925\",\n \"0.5010238\",\n \"0.5006531\",\n \"0.50053465\",\n \"0.49986193\",\n \"0.49962094\",\n \"0.499093\",\n \"0.49873674\",\n \"0.49869233\",\n \"0.49864247\",\n \"0.49838108\",\n \"0.49814054\",\n \"0.49809638\",\n \"0.49762112\",\n \"0.49761373\",\n \"0.49724016\",\n \"0.49722722\",\n \"0.49598595\",\n \"0.49578485\",\n \"0.49444133\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.67288995"},"document_rank":{"kind":"string","value":"0"}}}],"truncated":false,"partial":true},"paginationData":{"pageIndex":176,"numItemsPerPage":100,"numTotalItems":95772,"offset":17600,"length":100}},"jwt":"eyJhbGciOiJFZERTQSIsImtpZCI6IjVHZDBvd0g5MTM2eDZjc1FvbE1zcktNWUZoRVFoUm5PVVVybEpjOUhaUEEifQ.eyJyZWFkIjp0cnVlLCJwZXJtaXNzaW9ucyI6eyJyZXBvLmNvbnRlbnQucmVhZCI6dHJ1ZX0sImlhdCI6MTc4NjIyOTk0MCwianRpIjoiMDcxZTdlNzgtYTM4ZC00MzZmLWJkYzUtYWU5YTZlMjcyNTRjIiwic3ViIjoiL2RhdGFzZXRzL25vbWljLWFpL2Nvcm5zdGFjay1weXRob24tdjEiLCJleHAiOjE3ODYyMzM1NDAsImlzcyI6Imh0dHBzOi8vaHVnZ2luZ2ZhY2UuY28ifQ.-ImX6lUTzSJ_xh25BzHUHOqFR0vWspb6XoTPn06-mTvgpdtpEkle5IqZGcv5b9GeHwFa3C7uTc6ce-G9LKO9AA","displayUrls":true,"splitSizeSummaries":[{"config":"default","split":"train","numRows":95772,"numBytesParquet":1928375891}]},"discussionsStats":{"closed":1,"open":1,"total":2},"fullWidth":true,"hasGatedAccess":true,"hasFullAccess":true,"isEmbedded":false,"savedQueries":{"community":[],"user":[]}}">
query stringlengths 9 3.4k | document stringlengths 9 87.4k | metadata dict | negatives listlengths 4 101 | negative_scores listlengths 4 101 | document_score stringlengths 3 10 | document_rank stringclasses 102
values |
|---|---|---|---|---|---|---|
Print out all attributes, with an indentation level. | def printout_all(self, indent_level):
indent = " "*indent_level*INDENTATION_MULTIPLIER
print(indent, "Cloud Virtual Resource ID:", self.ID, sep='')
print(indent, "|-name:", self.name, sep='')
print(indent, "|-info:", self.info, sep='')
print(indent, "|-IP address:", self.IP_add... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def print_attrs(self):\n for attribute in self.__dict__.keys():\n print(attribute)",
"def print_attribute(attributes):\n for attribute in attributes:\n print ' ',\n change_color_by_tag(attribute)\n if attribute['ExtAttributes']:\n print_extattributes_of_mem... | [
"0.7907038",
"0.7637966",
"0.7155113",
"0.7127499",
"0.699982",
"0.69641304",
"0.6960341",
"0.6898987",
"0.684572",
"0.6805746",
"0.67901194",
"0.67732644",
"0.67293435",
"0.6668916",
"0.6649524",
"0.6606475",
"0.65686685",
"0.65122306",
"0.64923453",
"0.6455977",
"0.64494777... | 0.5749131 | 70 |
Function to initialize cloud virtual resource data. | def init_cloud_virtual_resources():
test_cldvirt_resources = []
# add info to list in memory, one by one, following signature values
cldvirtres_ID = 1
cldvirtres_name = "nova-compute-1"
cldvirtres_info = "nova VM in Arm pod"
cldvirtres_IPAddress = "50.60.70.80"
cldvirtres_URL = "http://50.6... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(__self__,\n resource_name: str,\n args: VirtualHardDiskArgs,\n opts: Optional[pulumi.ResourceOptions] = None):\n ...",
"def pre_virtual_machine_create(self, resource_dict):\n pass",
"def __init__(__self__,\n resource_nam... | [
"0.65209603",
"0.64640987",
"0.63841754",
"0.63472927",
"0.63000673",
"0.62648845",
"0.625409",
"0.62490654",
"0.62399304",
"0.6233856",
"0.62064767",
"0.61925113",
"0.61889744",
"0.61788136",
"0.6159353",
"0.6158444",
"0.61480516",
"0.6146311",
"0.6145305",
"0.6139789",
"0.6... | 0.7303633 | 0 |
Print out all attributes, with an indentation level. | def printout_all(self, indent_level):
indent = " "*indent_level*INDENTATION_MULTIPLIER
print(indent, "VNF or e2e Service ID:", self.ID, sep='')
print(indent, "|-name:", self.name, sep='')
print(indent, "|-info:", self.info, sep='')
print(indent, "|-IP address:", self.IP_address... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def print_attrs(self):\n for attribute in self.__dict__.keys():\n print(attribute)",
"def print_attribute(attributes):\n for attribute in attributes:\n print ' ',\n change_color_by_tag(attribute)\n if attribute['ExtAttributes']:\n print_extattributes_of_mem... | [
"0.79098475",
"0.76404846",
"0.71579635",
"0.7130595",
"0.7002356",
"0.6967273",
"0.6959917",
"0.68992954",
"0.6844863",
"0.6809012",
"0.6792403",
"0.6774788",
"0.6733136",
"0.6671675",
"0.6648593",
"0.6605866",
"0.6567369",
"0.651564",
"0.649377",
"0.64581263",
"0.64466727",... | 0.55880797 | 98 |
Function to initialize VNFs and e2e Services data. | def init_VNFs_Services():
test_VNFs_Services = []
# add info to list in memory, one by one, following signature values
vnf_serv_ID = 1
vnf_serv_name = "vCPE-1"
vnf_serv_info = "virtual CPE in Arm pod"
vnf_serv_IPAddress = "5.4.3.2"
vnf_serv_URL = "http://5.4.3.2:8080"
vnf_serv_related_p... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def initialize(self):\n self.initialize_edges()\n self.initialize_prob()\n self.initialize_total_input_dict()\n\n self.initialize_fpmusigv_dict()",
"def _initialize_data(self):\n self.reset_count = 0\n self._idn_no_firmware = \"KEPCO,BOP 50-20,E1234,\"\n self._fir... | [
"0.6000072",
"0.5982209",
"0.59133905",
"0.58482045",
"0.5846955",
"0.5802692",
"0.57983714",
"0.57908916",
"0.57861805",
"0.57234365",
"0.5716901",
"0.57001555",
"0.56514275",
"0.5569302",
"0.553498",
"0.5508897",
"0.5441034",
"0.54278976",
"0.5421931",
"0.5419489",
"0.54168... | 0.6732011 | 0 |
Append an object to a list of strings and adds a timestamp. | def append_to_list(self, string_to_append):
if type(string_to_append)==str:
current_time = datetime.now()
self.__string_list.append(string_to_append)
self.__timestamp_list.append(current_time) # timestamp will have the same index as string
else:
print("ap... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def add(self, timestamp):\n self.total_count += 1\n self.times.append(timestamp)",
"def append(self, object):\r\n raise NotImplementedError()",
"def append(self, obj):\r\n raise NotImplementedError",
"def append(self, ts: Union[str, datetime.datetime, None], attribute: Any, raise_... | [
"0.63131636",
"0.60031503",
"0.5990919",
"0.5893538",
"0.58589745",
"0.58204615",
"0.5716781",
"0.56838316",
"0.5644069",
"0.56173307",
"0.56059915",
"0.5589093",
"0.5588692",
"0.55833554",
"0.55797154",
"0.5551652",
"0.55227566",
"0.55158985",
"0.5504161",
"0.5495428",
"0.54... | 0.78029543 | 0 |
return a list of strings with timestamps as prefixes (not showing microseconds). | def get_timestamped_strings(self):
ret_list = []
i = 0
while i < len(self.__string_list):
ret_list.append(self.__timestamp_list[i].strftime("%Y-%m-%d %H:%M:%S")+" "+self.__string_list[i])
i += 1
return ret_list | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_time_strs(self):\n\n log(\"Getting time strings starting at {}\".format(self._t0))\n tz = dt.timezone.utc\n mkdt = lambda n: dt.datetime.fromtimestamp(\n self._t0 - (self._delta * n),\n tz=tz\n )\n ns = range(self._frames, 0, -1)\n return [mkd... | [
"0.7256951",
"0.6693242",
"0.6453684",
"0.6298663",
"0.62940955",
"0.61848104",
"0.6147845",
"0.6098919",
"0.6096851",
"0.6066497",
"0.6043481",
"0.603737",
"0.59519106",
"0.58646226",
"0.5857015",
"0.58160734",
"0.5814002",
"0.5814002",
"0.5812247",
"0.5737909",
"0.57244587"... | 0.78146636 | 0 |
Generic function to dump all Challenge Execution data in a CSV file. | def write_to_csv(self):
dump_list = []
# add rows one by one, each as a list, even if only 1 element
dump_list.append(["challenge execution ID",self.ID])
dump_list.append(["challenge execution name",self.name])
dump_list.append(["challenge definition ID",self.challenge_def_ID... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def write_to_csv(self):\n\n dump_list = []\n\n # add rows one by one, each as a list, even if only 1 element\n\n dump_list.append([\"test execution ID\",self.ID])\n dump_list.append([\"test execution name\",self.name])\n\n dump_list.append([\"test definition ID\",self.test_def_ID... | [
"0.67913586",
"0.6477758",
"0.6425062",
"0.62495226",
"0.6236619",
"0.6227798",
"0.6211598",
"0.61715055",
"0.6133314",
"0.61221945",
"0.6114023",
"0.6110165",
"0.60603863",
"0.6050782",
"0.6025989",
"0.5951282",
"0.5934519",
"0.5933892",
"0.59329176",
"0.59259146",
"0.591796... | 0.75044805 | 0 |
Append a metric value (MetricValue) to the list. MetricValue already has a timestamp attribute. | def append_to_list(self, metric_value_to_append):
if type(metric_value_to_append)==MetricValue:
self.__metric_value_list.append(metric_value_to_append)
else:
print("appended object must be a MetricValue, metric_value_to_append=",metric_value_to_append)
sys.exit() # s... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def append(self, value):\n self.values.append(value)\n return value",
"def log(self, metric_name: str, value: float) -> None:\n if metric_name in self.metrics:\n self.metrics[metric_name].append(value)\n else:\n self.metrics[metric_name] = [value]",
"def append... | [
"0.6807644",
"0.67213684",
"0.6580341",
"0.65766835",
"0.6570106",
"0.6512985",
"0.6349774",
"0.62712246",
"0.62586963",
"0.6248036",
"0.6227115",
"0.62080497",
"0.6151301",
"0.6121657",
"0.6113878",
"0.60947984",
"0.6074452",
"0.60592484",
"0.6024408",
"0.6023302",
"0.600047... | 0.7759538 | 0 |
Return a list of strings with metric values and timestamps as prefixes (not showing microseconds). Also show the metric def ID in parentheses. | def get_timestamped_metric_values_as_strings(self):
ret_list = []
i = 0
while i < len(self.__metric_value_list):
ret_list.append(self.__metric_value_list[i].timestamp.strftime("%Y-%m-%d %H:%M:%S") + " " +
str(self.__metric_value_list[i].value) +
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_metric_list(self) -> List[str]:\n ...",
"def get_metric(ms):\n\treturn '['+','.join(str(m) for m in ms)+']'",
"def __str__(self):\n columns = list(self.metrics.keys())\n columns.sort()\n out = '%s\\n' % ','.join(columns)\n values = [str(self.metrics[c]) for c in columns]\n out += ... | [
"0.7170015",
"0.7163434",
"0.614878",
"0.598899",
"0.5964182",
"0.5915469",
"0.5894196",
"0.5894196",
"0.5894196",
"0.58587414",
"0.58564055",
"0.5797499",
"0.5731772",
"0.5715355",
"0.57042557",
"0.56763",
"0.5675049",
"0.56671524",
"0.565569",
"0.5654457",
"0.5632019",
"0... | 0.73370224 | 0 |
Generic function to dump all Test Execution data in a CSV file. | def write_to_csv(self):
dump_list = []
# add rows one by one, each as a list, even if only 1 element
dump_list.append(["test execution ID",self.ID])
dump_list.append(["test execution name",self.name])
dump_list.append(["test definition ID",self.test_def_ID])
test_def_... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def Dump():\n with open(path.join(MAIN_PATH, INST), \"wb\") as f:\n writer = csv.writer(f, delimiter=\",\")\n\n for inst in instances:\n writer.writerow(inst)\n \n with open(path.join(MAIN_PATH, \"test_instances.csv\"), \"wb\") as f:\n writer = csv.writer(f, delimit... | [
"0.67293197",
"0.6513849",
"0.6487891",
"0.633611",
"0.62388986",
"0.6189851",
"0.61873883",
"0.6097543",
"0.608892",
"0.6053703",
"0.60277325",
"0.5961769",
"0.5952618",
"0.5923491",
"0.59027004",
"0.588059",
"0.58773726",
"0.5876296",
"0.5853088",
"0.583685",
"0.5753217",
... | 0.7351433 | 0 |
Get all content from all Definition data binary files, and dump everything in a snapshot CSV file. | def dump_all_binaries_to_CSV():
## TODO
timenow = datetime.now() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def main(output_filepath):\n logger = logging.getLogger(__name__)\n logger.info('making final data set from raw data')\n\n baseurl = 'http://codeandbeer.org/virtual/BigData/Labs/'\n files = ['Booking-20151012-1322.csv', 'Booking-20181025-1232.csv']\n for filename in files:\n r = requests.get(... | [
"0.6119058",
"0.584404",
"0.5760777",
"0.5618853",
"0.55985814",
"0.5554482",
"0.5531929",
"0.552771",
"0.5514406",
"0.5481521",
"0.5466135",
"0.5440491",
"0.5430171",
"0.54249936",
"0.53819466",
"0.5378581",
"0.53638315",
"0.5349894",
"0.53484917",
"0.5341942",
"0.5338703",
... | 0.5712153 | 3 |
Saves parameters to json file | def save(self, json_path):
with open(json_path, 'w') as f:
json.dump(self.__dict__, f, indent=4) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def save_json(self, path=None):\n if path is None:\n path = self.parampath\n\n params = {str(key): str(value) for key, value in self.__dict__.items()}\n # with open(f'{path}/params_{self.mode}.json', 'w') as f:\n with open(os.path.join(path, f'params_{self.mode}.json'), 'w') ... | [
"0.82312053",
"0.8181947",
"0.8057166",
"0.7808885",
"0.77812463",
"0.775106",
"0.7710382",
"0.7706769",
"0.76148814",
"0.75990826",
"0.7574917",
"0.75643057",
"0.7448175",
"0.7373087",
"0.7341731",
"0.7261098",
"0.719621",
"0.7154501",
"0.714766",
"0.7143015",
"0.71297264",
... | 0.6701761 | 64 |
Loads parameters from json file | def update(self, json_path):
with open(json_path) as f:
params = json.load(f)
self.__dict__.update(params) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_parameters(self):\n json_data = open(\"param.json\")\n data = json.load(json_data)\n self.items = data[\"items\"]\n self.pollInterval = self.items[0]['poll_interval']",
"def load_params_from_file(self, fn):\n f = file(fn, 'r')\n params = json.load(f)\n re... | [
"0.80815786",
"0.8032984",
"0.77628386",
"0.7658748",
"0.7499289",
"0.7396562",
"0.7371273",
"0.7343756",
"0.7205131",
"0.71630406",
"0.7145317",
"0.71170235",
"0.70144874",
"0.6910112",
"0.6828196",
"0.6777038",
"0.6745744",
"0.670805",
"0.6676465",
"0.66282165",
"0.6626882"... | 0.0 | -1 |
Gives dictlike access to Params instance by `params.dict['learning_rate']` | def dict(self):
return self.__dict__ | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def update_params(self, learning_rate):\n\t\t#######################################################################\n\t\t# ** START OF YOUR CODE **\n\t\t#######################################################################\n\n\t\tfor layer in self._layers:\n\t\t\tlayer.update_params(learni... | [
"0.67212766",
"0.65639395",
"0.64237636",
"0.63552547",
"0.63375807",
"0.6335523",
"0.6291742",
"0.62781876",
"0.62616247",
"0.6256042",
"0.6244642",
"0.62040687",
"0.61626947",
"0.61462617",
"0.6137591",
"0.6134931",
"0.6117105",
"0.6034695",
"0.6009135",
"0.59249216",
"0.59... | 0.0 | -1 |
Gives dictlike access to Params instance by `params.dict['learning_rate']` | def dict(self):
return self.__dict__ | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def update_params(self, learning_rate):\n\t\t#######################################################################\n\t\t# ** START OF YOUR CODE **\n\t\t#######################################################################\n\n\t\tfor layer in self._layers:\n\t\t\tlayer.update_params(learni... | [
"0.6720487",
"0.65625185",
"0.64225143",
"0.63549536",
"0.6335197",
"0.63333946",
"0.6289275",
"0.62763816",
"0.6261218",
"0.6254811",
"0.6242165",
"0.62025636",
"0.61608726",
"0.6144572",
"0.6134815",
"0.61332786",
"0.6115073",
"0.6032413",
"0.6008105",
"0.5924919",
"0.59114... | 0.0 | -1 |
Save the codes and configuration file. During the training, we may modify the codes. It will be problematic when we try to extract embeddings using the old model and the new code. So we save the codes when we train the model and use the saved codes to extract embeddings. | def save_codes_and_config(cont, model, config):
if cont:
# If we want to continue the model training, we need to check the existence of the checkpoint.
if not os.path.isdir(os.path.join(model, "nnet")) or not os.path.isdir(os.path.join(model, "codes")):
sys.exit("To continue training the... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def saveOutput(self,code):\r\n\t\tCodeSaver().save(code,self.savePath)",
"def save_model(self):\n filename=self.name + '_words'\n file_write(filename, self.words)\n\n filename2=self.name+'_word_lengths'\n file_write(filename2, self.word_lengths)\n\n filename3=self.name+'_stems'... | [
"0.66678596",
"0.65298474",
"0.65280056",
"0.65230376",
"0.65037274",
"0.64659584",
"0.6451233",
"0.6426465",
"0.6415432",
"0.63984126",
"0.6397235",
"0.6397206",
"0.6392341",
"0.63780564",
"0.63757557",
"0.6353628",
"0.63431454",
"0.62933993",
"0.627987",
"0.6270623",
"0.625... | 0.7381167 | 0 |
Get the pretrained model and copy to the target model as the initial version. | def get_pretrain_model(pretrain_model, target_model, checkpoint='-1'):
if not os.path.isfile(os.path.join(pretrain_model, "checkpoint")):
sys.exit("[ERROR] Cannot find checkpoint in %s." % pretrain_model)
ckpt = tf.train.get_checkpoint_state(pretrain_model)
model_checkpoint_path = ckpt.model_checkp... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_pretrained_model(destination):\n url = \"https://storage.googleapis.com/download.magenta.tensorflow.org/models/ \\\n arbitrary_style_transfer.tar.gz\"\n\n os.system(\"curl -o arbitrary_style_transfer.tar.gz {0}\".format(url))\n with tarfile.open(\"arbitrary_style_transfer.tar.gz\") as ta... | [
"0.6822754",
"0.6722586",
"0.6549904",
"0.6507627",
"0.6432653",
"0.64292246",
"0.6409875",
"0.6334059",
"0.6267043",
"0.6259309",
"0.6258022",
"0.6249631",
"0.6218196",
"0.6192777",
"0.618744",
"0.6157598",
"0.6148145",
"0.6140525",
"0.61373776",
"0.6136138",
"0.6130443",
... | 0.69689536 | 0 |
Load learning rate from a saved file | def load_lr(filename):
learning_rate_array = []
with open(filename, "r") as f:
for line in f.readlines():
_, lr = line.strip().split(" ")
learning_rate_array.append(float(lr))
return learning_rate_array | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load(self, filename):\n param_dict = pickle.load(open('%s' % filename, 'rb'))\n self.learningrate = param_dict['learningrate']\n self.verbose = param_dict['verbose']\n self._loadsize = param_dict['loadsize']\n self._batchsize = param_dict['batchsize']\n self.momentum =... | [
"0.67811286",
"0.6583575",
"0.6550467",
"0.6278531",
"0.62552196",
"0.619063",
"0.61676574",
"0.6159735",
"0.61502033",
"0.614148",
"0.61373883",
"0.61225915",
"0.61004525",
"0.6077979",
"0.605477",
"0.59805137",
"0.59794164",
"0.5961897",
"0.5954225",
"0.5944981",
"0.5944981... | 0.71505105 | 0 |
Load valid loss from a saved file | def load_valid_loss(filename):
min_loss = ValidLoss()
with open(filename, "r") as f:
for line in f.readlines():
epoch, loss = line.strip().split(" ")[:2]
epoch = int(epoch)
loss = float(loss)
if loss < min_loss.min_loss:
min_loss.min_loss =... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_checkpoint(self, file):\n \"\"\"Load \"\"\"\n chkpnt = torch.load(file)\n self.load_state_dict(chkpnt['model_state_dict'])",
"def load_network(self, sess, filename):\n dir_path = os.path.dirname(os.path.realpath(__file__))\n dir_path += '/Models/'\n dir_path += ... | [
"0.6473382",
"0.63657707",
"0.61991316",
"0.6178769",
"0.6170918",
"0.59643334",
"0.5960667",
"0.5960353",
"0.5944361",
"0.59310794",
"0.5908972",
"0.5874426",
"0.58355534",
"0.5824624",
"0.5812557",
"0.5805543",
"0.580154",
"0.57972693",
"0.5791554",
"0.57738537",
"0.5772561... | 0.75367886 | 0 |
Set the checkpoint in the model directory and return the name of the checkpoint | def get_checkpoint(model, checkpoint='-1'):
if not os.path.isfile(os.path.join(model, "checkpoint")):
sys.exit("[ERROR] Cannot find checkpoint in %s." % model)
ckpt = tf.train.get_checkpoint_state(model)
model_checkpoint_path = ckpt.model_checkpoint_path
all_model_checkpoint_paths = ckpt.all_mo... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_checkpoint_name(self):\n dataset_basename = Path(self._train_dataset_path).resolve().stem\n filename = \"model_cpt_{}.pkl\".format(dataset_basename)\n return filename",
"def test_model_checkpoint_path(tmpdir, logger_version, expected):\n tutils.reset_seed()\n model = EvalModel... | [
"0.74503803",
"0.7105686",
"0.69459254",
"0.6914723",
"0.6896195",
"0.68212557",
"0.68031454",
"0.6800865",
"0.6794284",
"0.67591476",
"0.6740254",
"0.66765016",
"0.6662393",
"0.66157246",
"0.6609026",
"0.66063094",
"0.6599918",
"0.6598686",
"0.65768677",
"0.6550074",
"0.6542... | 0.62566173 | 44 |
Compute pairwise EER using cosine similarity. The EER is estimated by interp1d and brentq, so it is not the exact value and may be a little different each time. | def compute_cos_pairwise_eer(embeddings, labels, max_num_embeddings=1000):
embeddings /= np.sqrt(np.sum(embeddings ** 2, axis=1, keepdims=True) + 1e-12)
num_embeddings = embeddings.shape[0]
if num_embeddings > max_num_embeddings:
# Downsample the embeddings and labels
step = num_embeddings /... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def compute_EER(self, FAR, FRR):\r\n print('Computing EER')\r\n distance = abs(FAR - FRR)\r\n min_distance = min(distance)\r\n idx = np.where(distance == min_distance)\r\n return np.mean((FAR[idx] + FRR[idx]) / 2)",
"def similarity(self, e1, e2):\n\t\tpass",
"def E(q, r0, x, ... | [
"0.61746013",
"0.58410585",
"0.56296",
"0.55749977",
"0.55027765",
"0.545726",
"0.5402459",
"0.5398751",
"0.5388317",
"0.5339811",
"0.533653",
"0.5312333",
"0.5311478",
"0.52783436",
"0.5232789",
"0.522407",
"0.52214503",
"0.52191997",
"0.5212163",
"0.52099633",
"0.52089626",... | 0.5987465 | 1 |
Check whether part of the string s appears in the list. | def substring_in_list(s, varlist):
if varlist is None:
return False
is_sub = False
for v in varlist:
if v in s:
is_sub = True
break
return is_sub | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def check_string(s, strings):\n for string in strings:\n if string not in s:\n return False\n return True",
"def check(s,l):\n if len(s)==1:\n if s[0] in l:\n return False\n else:\n return True\n else:\n if s[0] in l:\n return Fa... | [
"0.72143257",
"0.71113634",
"0.7025717",
"0.6971482",
"0.6968255",
"0.6905735",
"0.6830441",
"0.68250275",
"0.6770632",
"0.6740407",
"0.67399365",
"0.66369486",
"0.6623817",
"0.65804917",
"0.657662",
"0.6519753",
"0.64646107",
"0.6462173",
"0.6444658",
"0.6384393",
"0.6381318... | 0.72698176 | 0 |
Create a summary for activations given the endpoints. | def activation_summaries(endpoints):
sum = []
with tf.name_scope('summaries'):
for act in endpoints.values():
tensor_name = act.op.name
sum.append(tf.summary.histogram(tensor_name + '/activations', act))
# sum.append(tf.summary.scalar(tensor_name + '/sparsity', tf.nn.... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _activation_summary(x):\n tensor_name = re.sub('%s_[0-9]*/' % TOWER_NAME, '', x.op.name)\n tf.summary.histogram(tensor_name + '/activations', x)\n tf.summary.scalar(tensor_name + '/sparsity', tf.nn.zero_fraction(x))",
"def _activation_summary(x):\n # Remove 'tower_[0-9]/' from the name in case th... | [
"0.59474593",
"0.5940539",
"0.59343994",
"0.59330446",
"0.5931891",
"0.59268993",
"0.5921793",
"0.59189427",
"0.58822054",
"0.56461763",
"0.5312166",
"0.5241216",
"0.51119596",
"0.51063263",
"0.50800484",
"0.50588953",
"0.50553143",
"0.5045727",
"0.5015067",
"0.501194",
"0.49... | 0.7658504 | 0 |
Compute the restricted attention using kaldi position encoding. | def compute_kaldi_restricted_attention(endpoints, params):
# Use a basic for loop
value = endpoints["value"]
key = endpoints["key"]
query = endpoints["query"]
batch_size, length, total_dim = value.shape
num_heads = params.sann_num_heads
context_size = params.sann_restricted_context_size
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_attention(self, X):\n if self.bn:\n layer = 16\n else:\n layer = 14\n inputs = [K.learning_phase()] + [self.model.inputs[0]]\n _attention_f = K.function(inputs, [\n self.model.layers[layer].output])\n \n return _attention_f([0] + [X... | [
"0.6223233",
"0.6138006",
"0.6051119",
"0.60232174",
"0.60205334",
"0.5843146",
"0.5834027",
"0.57716316",
"0.57679117",
"0.56381214",
"0.5616626",
"0.5609945",
"0.5591088",
"0.5589141",
"0.5581806",
"0.5557133",
"0.55491656",
"0.553368",
"0.5524424",
"0.551581",
"0.55075306"... | 0.5936036 | 5 |
Get agents id according to task id for frontend display | def get_common_food(cls):
objs = cls.objects
return objs | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getAgentID(self):\n\t\treturn self.agentID",
"def agent_id(self) -> pulumi.Output[int]:\n return pulumi.get(self, \"agent_id\")",
"def get_task_id(self):\n if self.task_id:\n return self.task_id\n return (f'{self.task_type}_{self.get_source_system().lower()}'\n ... | [
"0.6345138",
"0.62534577",
"0.6244555",
"0.621085",
"0.61262393",
"0.6091852",
"0.6032438",
"0.5948106",
"0.58429515",
"0.5799198",
"0.5767654",
"0.5767654",
"0.5767654",
"0.5767654",
"0.5675799",
"0.56328017",
"0.56262046",
"0.5620824",
"0.5587475",
"0.55463105",
"0.5515732"... | 0.0 | -1 |
Get agents id according to task id for frontend display | def search_food(cls, name):
obj = cls.objects(name=name).first()
return obj | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getAgentID(self):\n\t\treturn self.agentID",
"def agent_id(self) -> pulumi.Output[int]:\n return pulumi.get(self, \"agent_id\")",
"def get_task_id(self):\n if self.task_id:\n return self.task_id\n return (f'{self.task_type}_{self.get_source_system().lower()}'\n ... | [
"0.6345138",
"0.62534577",
"0.6244555",
"0.621085",
"0.61262393",
"0.6091852",
"0.6032438",
"0.5948106",
"0.58429515",
"0.5799198",
"0.5767654",
"0.5767654",
"0.5767654",
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"0.5675799",
"0.56328017",
"0.56262046",
"0.5620824",
"0.5587475",
"0.55463105",
"0.5515732"... | 0.0 | -1 |
Get agents id according to task id for frontend display | def get_food_with_id(cls, food_id):
obj = cls.objects(food_id=food_id).first()
return obj | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getAgentID(self):\n\t\treturn self.agentID",
"def agent_id(self) -> pulumi.Output[int]:\n return pulumi.get(self, \"agent_id\")",
"def get_task_id(self):\n if self.task_id:\n return self.task_id\n return (f'{self.task_type}_{self.get_source_system().lower()}'\n ... | [
"0.63489664",
"0.6257465",
"0.62421757",
"0.62146336",
"0.6130093",
"0.60894895",
"0.6033828",
"0.5952367",
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"0.56785834",
"0.5629973",
"0.56234723",
"0.5619558",
"0.55869734",
"0.5543945",
"0.5513756... | 0.0 | -1 |
Executes SSM document for given document name and input parameters. | def execute(self, document_name, input_params):
if self._document_exists(document_name):
self.logger.info("Executing SSM document [%s] with parameters: [%s]", document_name, input_params)
# Executing SSM document
execution_id = self.ssm_client.start_automation_execution(
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def runQuery(cred, structuredQuery):\n url = cred.base_url + \"documents:runQuery\"\n\n makeRequest(cred, url, 'POST', structuredQuery)",
"def _send_command_to_nodes(self, document_name, parameters, node_ids):\n logger.debug(\"Sending SSM command to {} node(s). Document name: {}. \"\n ... | [
"0.5480394",
"0.5434591",
"0.5376649",
"0.52243423",
"0.5214718",
"0.52023363",
"0.5189893",
"0.5051979",
"0.5050216",
"0.49367806",
"0.49262178",
"0.49162",
"0.4915455",
"0.48682842",
"0.48337287",
"0.4806876",
"0.48034984",
"0.47985923",
"0.47829112",
"0.47478285",
"0.47474... | 0.8131812 | 0 |
Returns SSM document final execution status, if status is in PROGRESS/PENDING it will wait till SSM document execution will be completed. | def wait_for_execution_completion(self, execution_id, document_name=None):
# Fetch ssm execution status
status = self._get_execution_status(execution_id, document_name)
# Wait for execution to be completed
while status == 'InProgress' or status == 'Pending' or status == 'Cancelling' or ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_execution_status(self, execution_id, document_name=None):\n execution = self.ssm_client.get_automation_execution(\n AutomationExecutionId=execution_id\n )\n # TODO(semiond): we can remove document name as parameter, can take it by execution id.\n document_name = docu... | [
"0.68110305",
"0.6518064",
"0.65054107",
"0.6139724",
"0.6080517",
"0.6051617",
"0.59565747",
"0.59161776",
"0.58984363",
"0.586592",
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"0.5753716",
"0.5740925",
"0.5731959",
"0.57306814",
"0.57306814",
"0.5700119",
"0.5700... | 0.6551534 | 1 |
Returns execution step final status or WAITING, if step is in PROGRESS/PENDING status it will wait till step execution will be completed starts waiting for approval. | def wait_for_execution_step_status_is_terminal_or_waiting(self, execution_id, document_name,
step_name, time_to_wait):
start_time = time.time()
step_status = self._get_execution_step_status(execution_id, step_name)
elapsed_time = time... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_execution_step_status(self, execution_id, step_name):\n execution = self.ssm_client.get_automation_execution(\n AutomationExecutionId=execution_id\n )\n step_executions = execution['AutomationExecution']['StepExecutions']\n step = self._get_step_by_name(step_executio... | [
"0.7485493",
"0.70891434",
"0.6701339",
"0.66645974",
"0.6656338",
"0.6454856",
"0.6294289",
"0.6240593",
"0.6126569",
"0.59519774",
"0.59398484",
"0.58865476",
"0.5874422",
"0.58664155",
"0.5823973",
"0.5785563",
"0.57727575",
"0.5757077",
"0.5743372",
"0.5742786",
"0.571064... | 0.7079293 | 2 |
Returns when execution step is IN PROGRESS | def wait_for_execution_step_status_is_in_progress(self, execution_id, document_name, step_name, time_to_wait):
start_time = time.time()
step_status = self._get_execution_step_status(execution_id, step_name)
elapsed_time = time.time() - start_time
# Wait for execution step to resolve in ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def status(self):\n if self.num_steps >= self.timeout:\n return Status.TIMEOUT\n\n return Status.IN_PROGRESS",
"def wait_progress(self):\n pass",
"def wait_progress(self):\n pass",
"def query_job_progress():\n pass",
"def progress(self):\n return self.runPro... | [
"0.71910757",
"0.68339044",
"0.68339044",
"0.6804736",
"0.6747416",
"0.6747416",
"0.6707005",
"0.6707005",
"0.6707005",
"0.6707005",
"0.6684109",
"0.65764314",
"0.65122974",
"0.65017164",
"0.6432889",
"0.6429691",
"0.64150727",
"0.639098",
"0.63840777",
"0.6276231",
"0.616246... | 0.5902694 | 41 |
Returns SSM document step output for given execution id, step name and output key. | def get_step_output(self, execution_id, step_name, output_key):
execution = self.ssm_client.get_automation_execution(
AutomationExecutionId=execution_id
)
step_executions = execution['AutomationExecution']['StepExecutions']
step = self._get_step_by_name(step_executions, step_... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_step_output_uri(self, step):\n # parse in reverse order, in case there are multiple -output args\n args = step.args()\n for i, arg in reversed(list(enumerate(args[:-1]))):\n if arg == '-output':\n return args[i + 1]\n else:\n return None",
... | [
"0.59275943",
"0.5889858",
"0.58484614",
"0.57326436",
"0.56344503",
"0.55983704",
"0.55777663",
"0.5569992",
"0.5539353",
"0.5533122",
"0.54646003",
"0.54497415",
"0.5416543",
"0.5371535",
"0.53153986",
"0.5273433",
"0.52668524",
"0.522895",
"0.5222754",
"0.5222012",
"0.5202... | 0.79215145 | 0 |
Cancels SSM document execution in waits till 'TriggerRollback' step triggered SSM execution is completed. | def cancel_execution_with_rollback(self, execution_id: str):
execution_url = self.get_execution_url(execution_id)
try:
self.logger.info("Canceling SSM execution: {}".format(execution_url))
self.ssm_client.stop_automation_execution(AutomationExecutionId=execution_id, Type='Cancel'... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def cancel(self):\n self.session.rollback()",
"def rollback(self) -> None:\n with self.lock:\n self.wait(self._rollback_gen())",
"def test_cancel(self) -> None:\n context: Dict[str,ArtifactDescriptor] = dict()\n cmd = pycell.python_cell(\n source='import time\\... | [
"0.60639095",
"0.5988455",
"0.581982",
"0.5772934",
"0.5643513",
"0.56363535",
"0.56363535",
"0.56363535",
"0.56363535",
"0.5620277",
"0.56076694",
"0.5583796",
"0.55767006",
"0.5570505",
"0.55680966",
"0.5564965",
"0.5541141",
"0.5533509",
"0.55272144",
"0.54791105",
"0.5477... | 0.62550855 | 0 |
Returns SSM document execution status for given execution id. | def _get_execution_status(self, execution_id, document_name=None):
execution = self.ssm_client.get_automation_execution(
AutomationExecutionId=execution_id
)
# TODO(semiond): we can remove document name as parameter, can take it by execution id.
document_name = document_name ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def wait_for_execution_completion(self, execution_id, document_name=None):\n # Fetch ssm execution status\n status = self._get_execution_status(execution_id, document_name)\n\n # Wait for execution to be completed\n while status == 'InProgress' or status == 'Pending' or status == 'Cance... | [
"0.6311759",
"0.62737817",
"0.624106",
"0.6151789",
"0.61108553",
"0.6006403",
"0.59510785",
"0.5879625",
"0.585945",
"0.56999177",
"0.56882",
"0.5642697",
"0.5611689",
"0.5606932",
"0.55757666",
"0.5573651",
"0.5539164",
"0.5529198",
"0.5528047",
"0.5503078",
"0.5492322",
... | 0.7906296 | 0 |
Returns execution step status for given execution id and step name. | def _get_execution_step_status(self, execution_id, step_name):
execution = self.ssm_client.get_automation_execution(
AutomationExecutionId=execution_id
)
step_executions = execution['AutomationExecution']['StepExecutions']
step = self._get_step_by_name(step_executions, step_n... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_successfully_executed_steps_by_order(self, execution_id):\n execution = self.ssm_client.get_automation_execution(\n AutomationExecutionId=execution_id\n )\n step_executions = execution['AutomationExecution']['StepExecutions']\n step_names: List = []\n if step_e... | [
"0.6936771",
"0.6909824",
"0.6842648",
"0.6689437",
"0.65554833",
"0.6498717",
"0.6436358",
"0.63689363",
"0.62805057",
"0.6166205",
"0.61314565",
"0.5980744",
"0.5944853",
"0.58768517",
"0.5850708",
"0.58459425",
"0.5805325",
"0.57995373",
"0.5733456",
"0.5710865",
"0.569416... | 0.85641456 | 0 |
Returns successfully executed steps by order of their execution | def get_successfully_executed_steps_by_order(self, execution_id):
execution = self.ssm_client.get_automation_execution(
AutomationExecutionId=execution_id
)
step_executions = execution['AutomationExecution']['StepExecutions']
step_names: List = []
if step_executions:
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getSteps():",
"def test_by_order(self):\n # addon_executor = AddonExecutor(execute_order, stop_order)\n # self.assertEqual(expected, addon_executor.execute_with_order(addon, execute_order, stop_order))\n self.run_mgr.by_order(self.cli_inst, ['execute', 'start'], ['stop'])\n output... | [
"0.6670046",
"0.6322163",
"0.6297291",
"0.6226086",
"0.619969",
"0.6090397",
"0.6030043",
"0.6016758",
"0.6015137",
"0.59943765",
"0.5981895",
"0.5952482",
"0.5910737",
"0.5910737",
"0.5741957",
"0.57394445",
"0.57195204",
"0.5695635",
"0.5670944",
"0.5652498",
"0.56230104",
... | 0.6954507 | 0 |
Returns SSM document step by given status. | def _get_step_by_status(self, steps, status):
if steps:
for s in steps:
if s['StepStatus'] == status:
return s | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def select_step_with_status(status, steps):\n for step in steps:\n assert isinstance(step, model.Step), \"TYPE-MISMATCH: \"+\\\n \"step.class={0}\".format(step.__class__.__name__)\n if step.status == status:\n return step\n # -- OTHERWISE: No step with the give... | [
"0.6839485",
"0.6071293",
"0.55562955",
"0.5460878",
"0.53241044",
"0.5310991",
"0.53065586",
"0.52873224",
"0.5144956",
"0.5040669",
"0.503265",
"0.503265",
"0.5010804",
"0.49962842",
"0.49321508",
"0.48371494",
"0.4831955",
"0.4813281",
"0.48044667",
"0.47959918",
"0.479289... | 0.7587236 | 0 |
Returns SSM document step by a given name. | def _get_step_by_name(self, steps, step_name):
if steps:
for s in steps:
if s['StepName'] == step_name:
return s | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_step_by_name(self, name):\n self._validate_step_name(name)\n name = str(name)\n try:\n return self.all_upstream_steps[name]\n except KeyError as e:\n msg = 'No Step with name \"{}\" found. ' \\\n 'You have following Steps: {}'.format(name, ... | [
"0.69454134",
"0.6490663",
"0.61872965",
"0.6077294",
"0.6018053",
"0.58520585",
"0.57159656",
"0.5648309",
"0.5618685",
"0.5614397",
"0.5590065",
"0.54544705",
"0.5426001",
"0.54098606",
"0.5397997",
"0.5348861",
"0.53418255",
"0.5339116",
"0.5339116",
"0.53089184",
"0.52940... | 0.7589914 | 0 |
Returns True if SSM document for given name exist, False otherwise. | def _document_exists(self, document_name):
return len(self.ssm_client.list_document_versions(Name=document_name)['DocumentVersions']) >= 1 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def object_exists(self, name: str):\n file_path = self.__get_file_path(name)\n return os.path.exists(file_path)",
"def exists(self) -> bool:\n doc_ref = self.doc_ref\n if isinstance(doc_ref, DocumentReference):\n return doc_ref.get().exists\n return False",
"def do... | [
"0.6926537",
"0.67250514",
"0.6712991",
"0.67112947",
"0.6679739",
"0.6626868",
"0.6602372",
"0.65388644",
"0.6513464",
"0.65095633",
"0.650585",
"0.649972",
"0.64888805",
"0.6445123",
"0.64327896",
"0.6388695",
"0.6188683",
"0.61496204",
"0.61428565",
"0.6134926",
"0.6089026... | 0.7727576 | 0 |
Returns ssm document execution URL. | def get_execution_url(self, execution_id: str) -> str:
return f'https://{self.region}.console.aws.amazon.com/systems-manager/automation/execution/{execution_id}' | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def prog_url(self):\n # type: () -> string_types\n return self._prog_url",
"def invoke_url(self) -> pulumi.Output[str]:\n return self.stage.invoke_url # type: ignore[no-any-return]",
"def runbook_url(self) -> pulumi.Output[Optional[str]]:\n return pulumi.get(self, \"runbook_url\")"... | [
"0.64966375",
"0.64278257",
"0.63142085",
"0.6183461",
"0.6183461",
"0.6183461",
"0.6183461",
"0.6183461",
"0.6183461",
"0.6183461",
"0.6118322",
"0.6099205",
"0.6099205",
"0.6086366",
"0.6022877",
"0.598758",
"0.5956474",
"0.59558874",
"0.59377545",
"0.59377545",
"0.59377545... | 0.6347872 | 2 |
Return ssm document execution step URL. | def get_execution_step_url(self, execution_id: str, step_name: str, steps: [] = None) -> str:
if not steps or len(steps) < 1:
execution = self.ssm_client.get_automation_execution(AutomationExecutionId=execution_id)
steps = execution['AutomationExecution']['StepExecutions']
step ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def invoke_url(self) -> pulumi.Output[str]:\n return self.stage.invoke_url # type: ignore[no-any-return]",
"def get_redirect_url(self, *args, **kwargs):\n return self.document.file.url",
"def runbook_url(self) -> pulumi.Output[Optional[str]]:\n return pulumi.get(self, \"runbook_url\")",
... | [
"0.6653019",
"0.6429969",
"0.6305271",
"0.6265999",
"0.6141591",
"0.60876673",
"0.60876673",
"0.60759395",
"0.6074171",
"0.597044",
"0.5946428",
"0.5923328",
"0.5830999",
"0.5830999",
"0.5830999",
"0.5830999",
"0.5830999",
"0.5830999",
"0.5830999",
"0.5813061",
"0.5805103",
... | 0.6712275 | 0 |
Returns SSM document step execution sequence index | def _get_step_execution_index(self, step_executions: [], step_name):
index = 1
for step_execution in step_executions:
if step_name == step_execution['StepName']:
return index
index += 1 | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_sequence_index(self):\n\t\treturn call_sdk_function('PrlBootDev_GetSequenceIndex', self.handle)",
"def step_index(self, step):\n return self.steps.index(step)",
"def get_step_idx(self, step_id: str) -> int:\n return self.step_id2idx.get(step_id, None)",
"def step_id(self) -> pulumi.Outp... | [
"0.68235666",
"0.6603684",
"0.6303389",
"0.63007843",
"0.627349",
"0.61597484",
"0.6039806",
"0.60359675",
"0.60088104",
"0.59596723",
"0.595375",
"0.5940087",
"0.5922751",
"0.59192324",
"0.5902262",
"0.5867469",
"0.5863946",
"0.58638436",
"0.58619946",
"0.58510906",
"0.58207... | 0.7016882 | 0 |
Given a sequence of string expression append them to the specified file. | def append_sequence_of_text(self, sequence):
file_name = self.file_name
with open(file_name, 'a+') as file:
file.write('\n\n')
for line in sequence:
file.write('\t{}\n'.format(line)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def appendToFile(strsToAppend,fileName):\n \n file=open(fileName,mode='r')\n fileText=file.read()\n file.close()\n for strToAppend in strsToAppend:\n fileText+=strToAppend\n file=open(fileName,mode='w')\n file.write(fileText)\n file.close()",
"def append_after(filename=\"\", search_string=\"\", new_st... | [
"0.6397394",
"0.61963135",
"0.5710745",
"0.5632932",
"0.55954385",
"0.5565831",
"0.5564826",
"0.5506781",
"0.5497444",
"0.5495759",
"0.54679596",
"0.5452065",
"0.5451475",
"0.54342514",
"0.5433327",
"0.5427626",
"0.5420789",
"0.54194903",
"0.5415856",
"0.54111415",
"0.5393554... | 0.5328022 | 26 |
Read C functions from functions_for_c.txt and write it to feature.c | def create_cfile_head(self):
head = """#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include "../init_array_lib/init_dyn_array.h"
#include "../pips_lib/define_script.h"
int main(int argc, const char* argv[])
{
srand(time(NULL));
"""
self.append_text_to_file(str(head)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def main():\n import argparse\n parser = argparse.ArgumentParser()\n parser.add_argument('-i', '--input', help='Input .py file', nargs='+')\n args = parser.parse_args()\n\n mod_func = []\n\n for pyfile in args.input:\n tree = ast.parse(open(pyfile).read())\n\n methods = sorted({node... | [
"0.59324694",
"0.58911663",
"0.58243126",
"0.57736236",
"0.57395834",
"0.56943256",
"0.5641427",
"0.56040597",
"0.5594164",
"0.55703723",
"0.5558408",
"0.5429776",
"0.5418675",
"0.538488",
"0.53502434",
"0.5337874",
"0.5311122",
"0.5278216",
"0.5270166",
"0.52565664",
"0.5244... | 0.4812378 | 68 |
Append the end to the feature.c | def create_cfile_tail(self):
end_c = """
clock_t stop = clock();
double elapsed = ((double)(stop - start)) / CLOCKS_PER_SEC;
printf("%f", elapsed); """
self.append_text_to_file(str(end_c)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def new_end(self, end): \n self.last_words.append(end)",
"def _concatenate_features(features):\n pass",
"def _ends_with_op(spec):",
"def endow(self, struct):\n pass",
"def append_end(self, data):\r\n with open(self.file_name, 'a', encoding='utf-8') as self.file:\r\n ... | [
"0.63034153",
"0.58832604",
"0.5827753",
"0.57650805",
"0.5743487",
"0.5646226",
"0.5572082",
"0.55490077",
"0.5458949",
"0.54464453",
"0.5430893",
"0.54125154",
"0.53740317",
"0.5346468",
"0.5325698",
"0.53060746",
"0.530568",
"0.5292237",
"0.5266684",
"0.5266067",
"0.525623... | 0.54177976 | 11 |
Write an array of shape (bands, width, heigth) to file. | def create_test_file(filename, array):
array = np.ma.asanyarray(array)
crs = rasterio.crs.CRS(init='epsg:4326')
transform = from_origin(52, 4, 10, 10)
with rasterio.open(
filename,
mode='w',
driver='GTiff',
width=array.shape[1],
height=array.sh... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def writeArray(fname,arr):\n fh = open(fname,'w')\n fh.write('%d\\n' % arr.shape[0])\n fh.write('%d\\n' % arr.shape[1])\n for x in range(arr.shape[0]):\n for y in range(arr.shape[1]):\n if arr.dtype == np.complex:\n fh.write('%.7e %.7e\\n' % (arr[x,y].real, arr[x,y].ima... | [
"0.71242523",
"0.6744671",
"0.66219556",
"0.63390946",
"0.630486",
"0.6265362",
"0.6262193",
"0.6123394",
"0.60802317",
"0.60766524",
"0.60740805",
"0.6067983",
"0.60587114",
"0.60536265",
"0.6040121",
"0.597492",
"0.5973886",
"0.5965214",
"0.59603775",
"0.59558237",
"0.59542... | 0.6307405 | 4 |
Create a test Image instance. | def create_test_image(dirname, array, normalization=None):
filename = str(dirname / 'tmp.tif')
create_test_file(filename, array)
satellite = 'quickbird'
image = Image(filename, satellite, normalization_parameters=normalization)
return image | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_create_image(self):\n pass",
"def maketestimage(self, *args, **kwargs):\n return _image.image_maketestimage(self, *args, **kwargs)",
"def new_test_image():\n warnings.warn(DeprecationWarning(\n \"new_test_image() is deprecated in favour of the get_sample_image() \"\n \"c... | [
"0.83210063",
"0.7775136",
"0.73910016",
"0.7141617",
"0.6988279",
"0.68101066",
"0.6806548",
"0.6761812",
"0.6656161",
"0.66465604",
"0.6600724",
"0.65849966",
"0.65514433",
"0.64627105",
"0.64578843",
"0.63991606",
"0.63800454",
"0.637194",
"0.6369904",
"0.6350396",
"0.6344... | 0.6682606 | 8 |
Computes the total evictions filed | def total(evictiondata):
total = 0
for index, row in evictiondata.iterrows():
total += row['filings_2020'] | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __calc_empirical_counts__(self):\n self.empirical_counts = np.zeros(self._features_vector_length, dtype=float)\n for feature, freq in self.features_dict.items():\n for index in feature:\n self.empirical_counts[index] += freq\n assert len(self.empirical_counts) == ... | [
"0.6445968",
"0.6362767",
"0.60137343",
"0.60097814",
"0.5861046",
"0.5823471",
"0.5804749",
"0.5785384",
"0.5758527",
"0.57364535",
"0.5653729",
"0.563426",
"0.56016433",
"0.559297",
"0.55897456",
"0.5586372",
"0.5580745",
"0.55679435",
"0.5510253",
"0.5509895",
"0.5496174",... | 0.59621006 | 4 |
Eviction filings broken down into a weekbyweek basis | def weekly(evictiondata):
evictions_per_week = {}
for index, row in evictiondata.iterrows():
if row['week_date'] not in evictions_per_week.keys():
evictions_per_week[row['week_date']] = row['filings_2020']
else:
evictions_per_week[row['week_date']] += row['filings_2... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def weekly():",
"def weekly():\n\n response = {}\n\n # 0..6 => Sunday..Saturday\n for i in range(7):\n hours = []\n interactions = 0\n\n for j in range(25):\n try:\n wfile = open(common.stats_path + '/weekly-average/' + str(i) + '/' + str(j))\n ... | [
"0.7323955",
"0.62316436",
"0.6126304",
"0.6112387",
"0.6050204",
"0.6010439",
"0.5954555",
"0.59421486",
"0.5924618",
"0.59082824",
"0.5864308",
"0.5844851",
"0.5800671",
"0.57960045",
"0.57312167",
"0.5713384",
"0.5708791",
"0.568154",
"0.5680631",
"0.56350195",
"0.56308794... | 0.7517364 | 0 |
Visualizes the week by week eviction data into a graph | def graphify(evictions_per_week):
weeks = []
for week in evictions_per_week.keys():
if '2020' in week:
weeks.append(week)
evictions_filed = []
for week in weeks:
evictions_filed.append(evictions_per_week[week])
plt.figure(figsize=(50, 10))
plt.plot(weeks, evi... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def graph_baseline(evictiondata, weeks):\r\n base_evictions_per_week = {}\r\n for index, row in evictiondata.iterrows():\r\n if row['week_date'] not in base_evictions_per_week.keys():\r\n base_evictions_per_week[row['week_date']] = row['filings_avg']\r\n elif row['GEOID'] != 'sealed'... | [
"0.7287062",
"0.7240408",
"0.7095925",
"0.67528796",
"0.6648603",
"0.6480761",
"0.62646145",
"0.62237006",
"0.6187958",
"0.6187809",
"0.613508",
"0.60985005",
"0.60869294",
"0.6011801",
"0.59913427",
"0.59690994",
"0.59242606",
"0.59085816",
"0.5906574",
"0.5892883",
"0.58743... | 0.81232464 | 0 |
Graphs the baseline eviction data of 20152016 in the same format | def graph_baseline(evictiondata, weeks):
base_evictions_per_week = {}
for index, row in evictiondata.iterrows():
if row['week_date'] not in base_evictions_per_week.keys():
base_evictions_per_week[row['week_date']] = row['filings_avg']
elif row['GEOID'] != 'sealed':
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def cross_analyze(evictions_filed, base_evictions_filed, weeks):\r\n plt.figure(figsize=(50, 10))\r\n plt.plot(weeks, evictions_filed, label = '2020')\r\n plt.plot(weeks, base_evictions_filed, label = '2015-2016')\r\n plt.xlabel('Date', fontsize = 25)\r\n plt.ylabel('Evictions filed', fontsize = 25)... | [
"0.61644155",
"0.6124098",
"0.6031411",
"0.5979967",
"0.59787333",
"0.5971069",
"0.5943029",
"0.59208447",
"0.58984315",
"0.58976746",
"0.5869825",
"0.5843553",
"0.5836322",
"0.5829148",
"0.5803515",
"0.57898813",
"0.5787882",
"0.5771819",
"0.57714844",
"0.57601196",
"0.57472... | 0.73401976 | 0 |
Cross analyzes the baseline with 2020's eviction data. NOTE Requires you to run the above functions | def cross_analyze(evictions_filed, base_evictions_filed, weeks):
plt.figure(figsize=(50, 10))
plt.plot(weeks, evictions_filed, label = '2020')
plt.plot(weeks, base_evictions_filed, label = '2015-2016')
plt.xlabel('Date', fontsize = 25)
plt.ylabel('Evictions filed', fontsize = 25)
plt.title... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def CrossCheck(dataloader):",
"def do_crossval():\n df = read_df()\n # X = df['review'].apply(remove_html_lower)\n\n X = df['review']\n y = df['sentiment']\n X_train, X_holdout, y_train, y_holdout = train_test_split(X, y, test_size=0.3, shuffle=True, stratify=y, random_state=222 )\n\n tfidf = T... | [
"0.5959022",
"0.5762439",
"0.57529324",
"0.5593366",
"0.55377454",
"0.5520248",
"0.5454742",
"0.5441111",
"0.53812",
"0.53765136",
"0.5361948",
"0.5333665",
"0.5293056",
"0.5286",
"0.52654094",
"0.52570784",
"0.52462506",
"0.523822",
"0.5229423",
"0.52216583",
"0.5211983",
... | 0.6554467 | 0 |
Return User IP address. | def index():
if request.environ.get('HTTP_X_FORWARDED_FOR') is None:
print('here')
return request.environ['REMOTE_ADDR']
else:
print('there')
return request.environ['HTTP_X_FORWARDED_FOR'] | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_user_ip(request):\n x_forwarded_for = request.META.get(\"HTTP_X_FORWARDED_FOR\")\n if x_forwarded_for:\n ip = x_forwarded_for.split(\",\")[0]\n else:\n ip = request.META.get(\"REMOTE_ADDR\")\n return ip",
"def _get_user_ip(request):\n x_forwarded_for ... | [
"0.8345858",
"0.82466626",
"0.7922481",
"0.7832889",
"0.7778117",
"0.7757266",
"0.7738831",
"0.7738831",
"0.7738804",
"0.7711175",
"0.7705773",
"0.76555246",
"0.76353395",
"0.7631577",
"0.757635",
"0.7562413",
"0.75591487",
"0.75566554",
"0.754953",
"0.75480884",
"0.75266033"... | 0.0 | -1 |
prints how many games left | def __str__(self):
if self.number == 0:
return 'info'
elif self.number == 1:
return '1 game left!'
else:
return f'{self.number} games left!' | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def count_left_players(definition):\n return int(parse_player_definition(definition)[1]['left_players'])",
"def count_games(self) -> int:\n return len(self.rating_history) - 1",
"def print_game_stats(games_won=games_won):\n for k,v in games_won.items():\n print(k)\n print(v)\n i... | [
"0.6974114",
"0.6791024",
"0.6751497",
"0.6710043",
"0.65938455",
"0.6576891",
"0.65446955",
"0.6521832",
"0.6435398",
"0.6420975",
"0.6311479",
"0.630272",
"0.6236893",
"0.62334865",
"0.6208109",
"0.6105158",
"0.60977644",
"0.6067719",
"0.60583055",
"0.60553783",
"0.60514903... | 0.6323121 | 10 |
prints end of round information | def round_end_screen(self, board, p1, ai):
if self.number == 0:
if p1.score > ai.score:
print(f'Round {self.last_game} {p1.score}:{ai.score}\n{board}\n\nYou Won! ', end='')
elif ai.score > p1.score:
print(f'Round {self.last_game} {p1.score}:{ai.score}\n{bo... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def print_end_of_round_rankings(self):\n print('\\nFINAL SCORES')\n print('-'*12)\n for k, v in enumerate(self.ranking_dict):\n print(f\"{k+1} {v[0]}: {v[1]}\")\n print('\\n')",
"def display_end(self, nsep):\n\n if self.opt['Verbose'] and self.opt['StatusHeader']:\n ... | [
"0.74614024",
"0.65657973",
"0.6424565",
"0.6388435",
"0.63060915",
"0.62910116",
"0.6192829",
"0.6159963",
"0.61290896",
"0.6064716",
"0.6061334",
"0.6057542",
"0.6036575",
"0.59916383",
"0.5950914",
"0.5948961",
"0.5936187",
"0.5924599",
"0.5921035",
"0.5875291",
"0.5866037... | 0.61398834 | 8 |
Overwritten setter functions to convert the time_struct into a real timestamp. | def set_startTime(self, startTime):
self.startTime = mktime(startTime) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def UpdateStructTime(self, t):\n self.date.UpdateStructTime(t)\n self.time.UpdateStructTime(t)",
"def timestamp(self, value):\n value = util.parse_valid_date(value)\n self._set_attr('timestamp', value)",
"def UpdateStructTime(self, t):\n if not self.Complete():\n r... | [
"0.66382796",
"0.65591556",
"0.64815944",
"0.6390295",
"0.6382825",
"0.63617474",
"0.6329803",
"0.63273144",
"0.63211745",
"0.63090664",
"0.6307001",
"0.6288048",
"0.62831414",
"0.62622255",
"0.6251193",
"0.62397015",
"0.6201132",
"0.61923033",
"0.618849",
"0.61747265",
"0.61... | 0.0 | -1 |
Overwritten setter functions to convert the time_struct into a real timestamp. | def set_stopTime(self, stopTime):
self.stopTime = mktime(stopTime) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def UpdateStructTime(self, t):\n self.date.UpdateStructTime(t)\n self.time.UpdateStructTime(t)",
"def timestamp(self, value):\n value = util.parse_valid_date(value)\n self._set_attr('timestamp', value)",
"def UpdateStructTime(self, t):\n if not self.Complete():\n r... | [
"0.66382796",
"0.65591556",
"0.64815944",
"0.6390295",
"0.6382825",
"0.63617474",
"0.6329803",
"0.63273144",
"0.63211745",
"0.63090664",
"0.6307001",
"0.6288048",
"0.62831414",
"0.62622255",
"0.6251193",
"0.62397015",
"0.6201132",
"0.61923033",
"0.618849",
"0.61747265",
"0.61... | 0.0 | -1 |
Check if a switch exist for device. | def _switch_exist(lge_device: LGEDevice, switch_desc: ThinQSwitchEntityDescription) -> bool:
if switch_desc.value_fn is not None:
return True
feature = switch_desc.key
if feature in lge_device.available_features:
return True
return False | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_switch(self):\n\n svc = \"urn:upnp-org:serviceId:SwitchPower1\"\n if not svc in self.services:\n raise RuntimeError, \"Device doesn't support the service\"\n \n status = self.get_variable(svc, \"Status\")\n return status == 1",
"def _verify_switch_created(sel... | [
"0.6747511",
"0.6441467",
"0.6203834",
"0.6106376",
"0.60789245",
"0.60287935",
"0.59896916",
"0.58936965",
"0.58648187",
"0.58274436",
"0.5758467",
"0.5728313",
"0.57069063",
"0.5637247",
"0.56260467",
"0.56259376",
"0.56258166",
"0.5610697",
"0.55567384",
"0.55409193",
"0.5... | 0.7844338 | 0 |
Set up the LGE switch. | async def async_setup_entry(
hass: HomeAssistant, entry: ConfigEntry, async_add_entities: AddEntitiesCallback
) -> None:
entry_config = hass.data[DOMAIN]
lge_devices = entry_config.get(LGE_DEVICES)
if not lge_devices:
return
_LOGGER.debug("Starting LGE ThinQ switch setup...")
lge_switch... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def setupLL_Enhanced(self):\n self.LLE_Selector = slicer.qMRMLNodeComboBox()\n self.LLE_Selector.nodeTypes = ['vtkMRMLMultiVolumeNode']\n self.LLE_Selector.noneEnabled = True\n self.LLE_Selector.setMRMLScene(slicer.mrmlScene)\n self.LLE_Selector.addEnabled = 0\n self.LLE_SelectorLabel = qt.QLabel... | [
"0.5947192",
"0.5850148",
"0.56737316",
"0.5606522",
"0.5558895",
"0.55538154",
"0.5521745",
"0.54545707",
"0.5443126",
"0.54028803",
"0.53712314",
"0.53409106",
"0.53184915",
"0.5313045",
"0.52870697",
"0.52844626",
"0.52780974",
"0.52673054",
"0.5264901",
"0.52587765",
"0.5... | 0.5751763 | 2 |
Return True if entity has to be polled for state. We overwrite coordinator property default setting because we need to poll to avoid the effect that after changing switch state it is immediately set to prev state. The async_update method here do nothing because the real update is performed by coordinator. | def should_poll(self) -> bool:
return True | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def is_on(self):\n if self.is_update_locked():\n return self.graceful_state\n if self._state['action'] == 1 and self._state['state'] == 2:\n return True\n return False",
"async def async_update(self) -> None:\n all_states = [self.hass.states.get(x) for x in self.... | [
"0.6846774",
"0.6731269",
"0.66712904",
"0.66300744",
"0.6437781",
"0.6404045",
"0.6392167",
"0.6353482",
"0.63164604",
"0.6313499",
"0.6303177",
"0.6263767",
"0.62205803",
"0.6157645",
"0.61570364",
"0.6144633",
"0.61069655",
"0.61067325",
"0.6105299",
"0.61030585",
"0.60936... | 0.60423785 | 66 |
Update the entity. This is a fake update, real update is done by coordinator. | async def async_update(self) -> None:
return | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_otoroshi_controllers_adminapi_tcp_service_api_controller_update_entity_action(self):\n pass",
"def update(self) -> None:\n self._api.update()\n if self.available:\n self._attr_native_value = self._api.data[self.entity_description.key]\n else:\n self._att... | [
"0.7222287",
"0.70166487",
"0.69060814",
"0.6806648",
"0.6790305",
"0.67849994",
"0.6726298",
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"0.6582124",
"0.6562766",
"0.6562766",
"0.6562766",
"0.65472424",
"0.6530599",
"0.6529737... | 0.0 | -1 |
Return the state of the switch. | def is_on(self):
ret_val = self._get_switch_state()
if ret_val is None:
return False
if isinstance(ret_val, bool):
return ret_val
if ret_val == STATE_ON:
return True
state = STATE_LOOKUP.get(ret_val, STATE_OFF)
return state == STATE_ON | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_switch_state(self):\n if self.entity_description.value_fn is not None:\n return self.entity_description.value_fn(self._wrap_device)\n\n if self._api.state:\n feature = self.entity_description.key\n return self._api.state.device_features.get(feature)\n\n ... | [
"0.7842734",
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"0.72651184",
"0.72400886",
"0.7129502",
"0.71215",
"0.70571035",
"0.7047622"... | 0.0 | -1 |
Return True if entity is available. | def available(self) -> bool:
is_avail = True
if self.entity_description.available_fn is not None:
is_avail = self.entity_description.available_fn(self._wrap_device)
return self._api.available and is_avail | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def available(self) -> bool:\n return super().available and (\n self.coordinator.data.get(self.entity_description.key) is not None\n )",
"def available(self) -> bool:\n if self.entity_description.always_available:\n return True\n return self.knx.xknx.connection_m... | [
"0.8291221",
"0.8025913",
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"0.7093814",
"0.7093814",
"0.70866835",
"0.7074035",
"0.70578057",... | 0.8099782 | 1 |
Turn the entity off. | async def async_turn_off(self, **kwargs):
if self.entity_description.turn_off_fn is None:
raise NotImplementedError()
if self.is_on:
await self.entity_description.turn_off_fn(self._wrap_device) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def turn_off(self, **kwargs):\n self._is_on = False",
"def turn_off(self, **kwargs):\n setattr(self.resource, self.variable, False)",
"def turn_off(self, **kwargs):\n set_sonoff_state(self._host, \"off\")\n self._state = False",
"def turn_off(self):\n self.handleCommand(1)\... | [
"0.7907074",
"0.78206724",
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"0.73854035",
"0.737846",
"0.7305533",
"0.72589344",
"0.72304344",
"0.723010... | 0.69814616 | 38 |
Turn the entity on. | async def async_turn_on(self, **kwargs):
if self.entity_description.turn_on_fn is None:
raise NotImplementedError()
if not self.is_on:
await self.entity_description.turn_on_fn(self._wrap_device) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def turn_on(self, **kwargs):\n self._is_on = True",
"async def async_turn_on(self, **kwargs: Any) -> None:\n await self.entity_description.set_command(self, True)",
"def turn_on(self, **kwargs) -> None:\n self.heater.turn_on()",
"def turn_on(self, **kwargs):\n self._send_command(\... | [
"0.7749855",
"0.76333284",
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"0.7380775",
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"0.71320957",
"0.70755565",
"0.7069967",
"0.69911647",
"0.6968239",
"0.6960... | 0.68312943 | 29 |
Get current switch state | def _get_switch_state(self):
if self.entity_description.value_fn is not None:
return self.entity_description.value_fn(self._wrap_device)
if self._api.state:
feature = self.entity_description.key
return self._api.state.device_features.get(feature)
return None | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_state(self):\n return self.controller.get_state()",
"def get_current_state(self):\n return self._current_state",
"def get_current_state(self):\n return self.game.get_current_state()",
"def state(self) -> bool:\n return self.get_state(self.entity_ids[\"switch\"])",
"def r... | [
"0.74889183",
"0.73827314",
"0.73482925",
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"0.7095693",
"0.70940304",
"0.70775414",
"0.7067311",
"0.7067311",
"0.7... | 0.7429907 | 1 |
Return the state of the switch. | def is_on(self):
return self._wrap_device.device.get_duct_zone(self._zone) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_switch_state(self):\n if self.entity_description.value_fn is not None:\n return self.entity_description.value_fn(self._wrap_device)\n\n if self._api.state:\n feature = self.entity_description.key\n return self._api.state.device_features.get(feature)\n\n ... | [
"0.784124",
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"0.78202283",
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"0.7267481",
"0.7242181",
"0.71317464",
"0.7118259",
"0.7058468",
"0.704671",
... | 0.0 | -1 |
Return True if entity is available. | def available(self) -> bool:
return (
self._wrap_device.device.is_duct_zone_enabled(self._zone)
and self._wrap_device.is_power_on
) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def available(self) -> bool:\n return super().available and (\n self.coordinator.data.get(self.entity_description.key) is not None\n )",
"def available(self) -> bool:\n is_avail = True\n if self.entity_description.available_fn is not None:\n is_avail = self.entit... | [
"0.8290694",
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"0.7099363",
"0.70918226",
"0.70918226",
"0.70918226",
"0.7083896",
"0.7070601",... | 0.0 | -1 |
Turn the entity off. | async def async_turn_off(self, **kwargs):
self._wrap_device.device.set_duct_zone(self._zone, False) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def turn_off(self, **kwargs):\n self._is_on = False",
"def turn_off(self, **kwargs):\n setattr(self.resource, self.variable, False)",
"def turn_off(self, **kwargs):\n set_sonoff_state(self._host, \"off\")\n self._state = False",
"def turn_off(self):\n self.handleCommand(1)\... | [
"0.7907074",
"0.78206724",
"0.7738741",
"0.7726449",
"0.7717234",
"0.7699036",
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"0.73854035",
"0.737846",
"0.7305533",
"0.72589344",
"0.72304344",
"0.723010... | 0.6796552 | 56 |
Turn the entity on. | async def async_turn_on(self, **kwargs):
self._wrap_device.device.set_duct_zone(self._zone, True) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def turn_on(self, **kwargs):\n self._is_on = True",
"async def async_turn_on(self, **kwargs: Any) -> None:\n await self.entity_description.set_command(self, True)",
"def turn_on(self, **kwargs) -> None:\n self.heater.turn_on()",
"def turn_on(self, **kwargs):\n self._send_command(\... | [
"0.7749855",
"0.76333284",
"0.740764",
"0.7400453",
"0.7380775",
"0.7380276",
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"0.7311529",
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"0.71320957",
"0.70755565",
"0.7069967",
"0.69911647",
"0.6968239",
"0.6960... | 0.6249411 | 68 |
saves image into src | def save_img(arr):
png = BytesIO()
io.imsave(png, arr)
png_url = blobs.createBlob(date, png.getvalue())
row = Src(data_url = png_url,\
type = 3)
session.add(row)
session.commit()
return row.id
# TODO: Save image and data into src table an... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def save_image(self):\n img = self.driver.find_element_by_xpath(web_map[self.region][img_path]).get_attribute(\"src\")\n img = requests.get(img, stream=True)\n self.search_results.export_image(self.region, img)",
"def save_image(self):\n self.save()",
"def save_image_action(self):\n ... | [
"0.7691621",
"0.7572592",
"0.7285594",
"0.71995753",
"0.69788265",
"0.6970801",
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"0.65806913",
"0.6570882",
"0.6566736",
"0.6561037",
"0.65172124",
"0.6489499... | 0.6599078 | 12 |
Takes a List of Tensors and returns a List of mask Tensor with 1 if the input was all zeros (on dimension 2) and 0 otherwise. This is used in the Attention layer to mask the padding observations. | def get_zero_entities_mask(entities: List[torch.Tensor]) -> List[torch.Tensor]:
with torch.no_grad():
if exporting_to_onnx.is_exporting():
with warnings.catch_warnings():
# We ignore a TracerWarning from PyTorch that warns that doing
# shape[n].item() will cause ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def build_attention_mask(input_ids): \n attention_masks = [] \n\n # 1 for input and 0 for pad\n for seq in input_ids: \n attention_masks.append([float(i>0) for i in seq])\n\n return attention_masks",
"def get_padding_mask(inputs, padding_value=0):\n mask = tf.cast(tf.equal(inputs, padding_val... | [
"0.7192867",
"0.68340164",
"0.6609743",
"0.651477",
"0.64316094",
"0.63892573",
"0.62922674",
"0.6264108",
"0.6230588",
"0.62144625",
"0.61776084",
"0.61677283",
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"0.61276275",
"0.611358",
"0.6040983",
"0.6023705",
"0.6021974",
"0.60033125",
"0.59760505... | 0.684822 | 1 |
Multi Head Attention module. We do not use the regular Torch implementation since Barracuda does not support some operators it uses. | def __init__(self, embedding_size: int, num_heads: int):
super().__init__()
self.n_heads = num_heads
self.head_size: int = embedding_size // self.n_heads
self.embedding_size: int = self.head_size * self.n_heads | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, nheads, d_model):\n super(MultiheadAttention, self).__init__()\n assert d_model % nheads == 0\n self.d_head = d_model // nheads\n self.nheads = nheads\n self.Q_fc = nn.Linear(d_model, d_model, bias=False)\n self.K_fc = nn.Linear(d_model, d_model, bias=Fa... | [
"0.70109355",
"0.690106",
"0.62428415",
"0.6242478",
"0.6139386",
"0.61331534",
"0.6070684",
"0.5960381",
"0.5922543",
"0.5858437",
"0.57944554",
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"0.56587964",
"0.56468225",
"0.56435096",
"0.5608189",
"0.56068873",
"0.5573652",
"0.553277... | 0.0 | -1 |
Constructs an EntityEmbedding module. | def __init__(
self,
entity_size: int,
entity_num_max_elements: Optional[int],
embedding_size: int,
):
super().__init__()
self.self_size: int = 0
self.entity_size: int = entity_size
self.entity_num_max_elements: int = -1
if entity_num_max_elemen... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, heropool_size, embedding_dim):\r\n super().__init__()\r\n self.embedding_dim = embedding_dim\r\n self.embeddings = nn.Embedding(heropool_size, embedding_dim)\r\n self.affine = nn.Linear(embedding_dim, heropool_size)\r\n self.init_emb()",
"def __init__(self, i... | [
"0.6292023",
"0.60847014",
"0.60154206",
"0.59721136",
"0.59668916",
"0.5889968",
"0.5888461",
"0.58747995",
"0.58164847",
"0.58022374",
"0.57965434",
"0.5796521",
"0.57831573",
"0.5779244",
"0.5756787",
"0.57168114",
"0.57117504",
"0.57061046",
"0.5703201",
"0.5696537",
"0.5... | 0.57668835 | 14 |
Constructs a ResidualSelfAttention module. | def __init__(
self,
embedding_size: int,
entity_num_max_elements: Optional[int] = None,
num_heads: int = 4,
):
super().__init__()
self.max_num_ent: Optional[int] = None
if entity_num_max_elements is not None:
self.max_num_ent = entity_num_max_eleme... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, pretrained=True, freeze_weights=True):\n super(RaisinNet34, self).__init__()\n # Define the model's name for it's output files\n # Load a pre-trained ResNet-34 model and turn off autograd\n # so its weights won't change.\n architecture = resnet34(pretrained=pre... | [
"0.5621225",
"0.544435",
"0.53626496",
"0.5334829",
"0.5327962",
"0.5268676",
"0.523798",
"0.5227105",
"0.5201277",
"0.5181055",
"0.5148044",
"0.51474625",
"0.5142541",
"0.5127878",
"0.5121603",
"0.51125926",
"0.5108721",
"0.5103974",
"0.50641334",
"0.50507617",
"0.50487804",... | 0.0 | -1 |
Load the configuration file that manage raw data. conf is a dictionary | def load_config_raw_data(conf):
path = Path(conf["conf_raw_data"])
with open(path) as f:
txt = f.read()
conf = json.loads(txt)
return conf | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_from_conf(self):\r\n raise NotImplementedError",
"def load_from_conf(self):\n raise NotImplementedError",
"def loadConf(self):\n\n with open(self.configFile) as f:\n self.config = json.load(f)",
"def load_conf(self):\n self._read_uconf()",
"def _load_conf(sel... | [
"0.7817127",
"0.77862626",
"0.7596874",
"0.74215615",
"0.73315775",
"0.7204006",
"0.7175266",
"0.71260387",
"0.6957915",
"0.6763186",
"0.6753021",
"0.6738471",
"0.6700064",
"0.6662929",
"0.6654338",
"0.6623613",
"0.66206634",
"0.66160893",
"0.6608538",
"0.66063255",
"0.655592... | 0.80604255 | 0 |
Load as a pandas Dataframe the table specified by the name 'table' (string). Must match one of the keys in the \ conf raw data file | def load_raw_table(conf, table):
confrd = load_config_raw_data(conf)
path_table = Path(confrd[table]["path"])
sep = confrd[table]["sep"]
encoding = confrd[table]["encoding"]
df = pd.read_csv(path_table, sep=sep, encoding=encoding)
return df | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_table(**kargs):\n from transformer import dehyphenate\n sep = LoincMTRT.delimit # kargs.get('sep', ',')\n input_dir = kargs.get('input_dir', 'data')\n dehyphen = kargs.get('dehyphenate', True)\n deq = kargs.get('dequote', True)\n one_to_one = kargs.get('one_to_one... | [
"0.68337256",
"0.66754687",
"0.6670916",
"0.6593603",
"0.65836316",
"0.65808636",
"0.6576015",
"0.65135646",
"0.64685476",
"0.6413054",
"0.6406398",
"0.6404005",
"0.6317207",
"0.6181754",
"0.6180371",
"0.6171104",
"0.61608464",
"0.615348",
"0.6132976",
"0.6097652",
"0.6096849... | 0.8200111 | 0 |
Return slice of a, keeping only those values that are furthest away from 0 along axis | def maxabs(a, axis=None):
maxa = a.max(axis=axis)
mina = a.min(axis=axis)
p = abs(maxa) > abs(mina) # bool, or indices where +ve values win
n = abs(mina) > abs(maxa) # bool, or indices where -ve values win
if axis == None:
if p: return maxa
else: return mina
shape = list(a.shape)... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def trim_zeros(array):\n multislice = []\n for i in range(array.ndim):\n sum_axes = tuple(j for j in range(array.ndim) if j is not i)\n edges = np.where(np.sum(array, axis=sum_axes) > 0)\n if edges[0].size == 0:\n return np.array([], dtype=array.dtype)\n low = edges[0][... | [
"0.69114363",
"0.6314677",
"0.6179363",
"0.6159046",
"0.6158749",
"0.60858554",
"0.59848356",
"0.591753",
"0.5856637",
"0.575877",
"0.5749622",
"0.5729806",
"0.57214385",
"0.5714138",
"0.5689817",
"0.5685795",
"0.56851953",
"0.56598985",
"0.56490386",
"0.5639668",
"0.5613493"... | 0.5415767 | 30 |
Return cell volume in angstroms^3. | def volume_from_rs(rs,Nel):
a0 = 0.5291772 # Bohr radius (angstroms/bohr)
volume = (4.0*pi/3.0)*Nel * (rs*a0)**3
return volume | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_unitcell_volume(self):\n \n reduced_volume = sqrt( 1 - (cos(self.alpha))**2 - (cos(self.beta))**2 - (cos(self.gamma))**2 + 2*cos(self.alpha)*cos(self.beta)*cos(self.gamma) )\n volume = reduced_volume*self.lattice_spacing_a*self.lattice_spacing_b*self.lattice_spacing_c\n \n ... | [
"0.77642494",
"0.7538697",
"0.74564636",
"0.7429672",
"0.74056345",
"0.7332025",
"0.7079599",
"0.69186044",
"0.68799436",
"0.68330055",
"0.67884755",
"0.6783145",
"0.6772365",
"0.67689323",
"0.67625916",
"0.6737969",
"0.67258954",
"0.67070013",
"0.670095",
"0.67007643",
"0.66... | 0.6428115 | 28 |
initializes the icommands for an irods userzone | def iinit(self):
# remove old irods settings if they exist
if os.path.exists(self.ienv):
os.remove(self.ienv)
if os.path.exists(self.iauth):
os.remove(self.iauth)
self._init_icommands()
pass | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def initGui(self):\n\n icon_path = ':/plugins/PluginChoucas/img/loaddata.png'\n self.add_action(\n icon_path,\n text=self.tr(u'Chargement de données de montagne'),\n callback=self.run,\n parent=self.iface.mainWindow())\n \n icon_path = ':/plug... | [
"0.62643325",
"0.62293196",
"0.6199269",
"0.60921407",
"0.60914946",
"0.6089207",
"0.6083126",
"0.60564566",
"0.60542786",
"0.60514116",
"0.6041391",
"0.5982728",
"0.5969388",
"0.5960284",
"0.59464496",
"0.5934442",
"0.5928464",
"0.59121406",
"0.5886387",
"0.5881636",
"0.5859... | 0.54540724 | 44 |
lists contents of hydroshare irods userspace | def ils(self):
cmd = Popen(['ils'], stdout=PIPE, stderr=STDOUT, shell=True)
stdout = cmd.communicate()[0].decode('ascii')
if cmd.returncode != 0:
print('Failed to fetch irods file list: %s' % stdout)
return []
return [s.replace('C-', '').strip() for s in
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def list():\n rino.remote.list()",
"def list_data(self):\n with self.read():\n keys = self.handle.keys()\n return [i.lstrip('/') for i in keys]",
"def list():",
"def list():",
"def list(self):",
"def list():\n data = getInstaData()\n return render_template(\"list.htm... | [
"0.6433237",
"0.6131444",
"0.6028496",
"0.6028496",
"0.60075146",
"0.5948483",
"0.5939381",
"0.591174",
"0.58719695",
"0.5800662",
"0.5770601",
"0.56504005",
"0.5648978",
"0.5616612",
"0.55690056",
"0.5552401",
"0.5549238",
"0.55253196",
"0.54935414",
"0.5482844",
"0.5472509"... | 0.6275398 | 1 |
gets a file from the hydroshare irods userspace | def iget(self, filename, destination=None, unzip=True):
# build the destination
if destination is None:
destination = os.environ['DATA']
irods_cmd = 'iget -f -r %s %s' % (filename, destination)
cmd = Popen([irods_cmd], stdout=PIPE, stderr=STDOUT, shell=True... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_file(self, sys_id):\n url = \"{}/file\".format(self._target(sys_id))\n r = self._client.session.get(url, stream=True)\n return r",
"def get_file():\n fname = get_var(request, \"fname\")\n return open(fname).read()",
"def get_file(self, path):\n file = self.get('data_re... | [
"0.6181166",
"0.58981305",
"0.5823172",
"0.56751233",
"0.56499076",
"0.56092876",
"0.5596054",
"0.5592535",
"0.55464715",
"0.5544626",
"0.5531637",
"0.5511701",
"0.54973",
"0.5472415",
"0.54524964",
"0.5451512",
"0.54413545",
"0.5437654",
"0.54289883",
"0.5412935",
"0.5410079... | 0.0 | -1 |
sync files between Jupyter and iRODs | def irsync(self, source, target, source_irods=False, target_irods=True,
dryrun=False):
liverun = True
source = 'i:%s' % source if source_irods else source
target = 'i:%s' % target if target_irods else target
irods_cmd = 'irsync -r %s %s' % (source, target)
if dryr... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def sync(self, notebook):\n raise NotImplementedError(\"The function sync has not been \"\\\n \"implemented.\")",
"def task_sync():\n target = 'analysis.ipynb'\n dep = 'analysis.md'\n return {\n 'file_dep': [dep],\n 'targets': [target],\n 'act... | [
"0.66149557",
"0.649017",
"0.63795453",
"0.5787912",
"0.5727001",
"0.5634277",
"0.55603755",
"0.5512296",
"0.5494928",
"0.548126",
"0.54650515",
"0.54617155",
"0.5455434",
"0.5448497",
"0.54231524",
"0.53581405",
"0.53554475",
"0.53354084",
"0.5319489",
"0.5262123",
"0.526039... | 0.53802687 | 15 |
transfers a large file from hydroshare. | def getResourceFromHydroshare(self, resid, destination=None):
print('Not Implemented') | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def transfer(file_obj):",
"def peer_server_upload(self, conn, data_received):\n try:\n file_size = os.path.getsize(SHARED_DIR+'/'+data_received['file_name'])\n f = open(SHARED_DIR+'/'+data_received['file_name'], 'rb')\n #print \"Hosting File: %s for download\" % data_recei... | [
"0.71689564",
"0.63118",
"0.61202866",
"0.5992885",
"0.5918774",
"0.58268136",
"0.5826182",
"0.5798397",
"0.5767912",
"0.5700033",
"0.56148034",
"0.55912936",
"0.5553005",
"0.5547394",
"0.5540036",
"0.55270714",
"0.5510804",
"0.5509437",
"0.55006397",
"0.5494637",
"0.545897",... | 0.0 | -1 |
This is the exposed Event keyword to toby/Robot | def run_event(self, event, *args, **kwargs):
if not self.events_registered:
# get the BuiltIn list of events
self.events_registered = self.register_event()
iteration = int(kwargs.get('iteration', 1))
device = kwargs.get('device', None)
#interface = kwargs.get('i... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def on_event(self, event):",
"def on_event(self, event):\r\n pass",
"def trigger(self, type, event):",
"def __call__(self, trigger, type, event):",
"def on_event(self, event):\n pass",
"def handle_event(self, event):",
"def events(self):",
"def visit_event(self, event):",
"def handleE... | [
"0.74635714",
"0.74540436",
"0.7425531",
"0.7424931",
"0.73351365",
"0.71755356",
"0.7141372",
"0.71365786",
"0.6942784",
"0.69211715",
"0.6871382",
"0.68416166",
"0.6831906",
"0.68172306",
"0.67804134",
"0.6772497",
"0.67365015",
"0.6691763",
"0.66311324",
"0.6611874",
"0.65... | 0.0 | -1 |
Parses help function related command line arguments | def parse_help_command(args):
if len(args) < 2:
print_generic_help()
elif len(args) == 2:
print_specific_help(args[1])
else:
print 'Error! Found too many arguments for --help! Use --help with ' \
'0 arguments to print generic help or type --help <tool_name> ' \
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def help_args():\n pass",
"def cmd_help(args):",
"def help():",
"def parse_help(func):\n # Grab the raw doc\n doc = func.__doc__\n\n # Check for non-existent documentation and return a 404 message of sorts\n if not doc:\n return 'Woops, there isn\\'t any documentation for this comma... | [
"0.7847874",
"0.77260983",
"0.70513254",
"0.69754887",
"0.69650877",
"0.6873133",
"0.68621254",
"0.68289644",
"0.68287694",
"0.6820131",
"0.6775463",
"0.6759491",
"0.67532665",
"0.6748584",
"0.6723732",
"0.6722001",
"0.67210186",
"0.67115545",
"0.6693269",
"0.66598135",
"0.65... | 0.7642248 | 2 |
Prints basic info and help. | def print_generic_help():
print ART_NAME
print 'Version {1}\nby {2}'.format(NAME, VERSION, AUTHOR)
print DESCRIPTION
tools = sorted(AvailableCommands.commands.keys(), key=lambda v: v.upper())
# Do not show CUSTOM command in the help
tools.remove('CUSTOM')
tools.remove('CUSTOM_NO_OUTPU... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def printhelp():",
"def print_help(self):\n print self.get_help()",
"def print_help():\n\tprint(\"Help text\")",
"def print_help():\n parser = parsersetup()\n parser.print_help()",
"def printHelp(self,):\n print man\n return 0",
"def print_help(self):\n self.parser.print... | [
"0.8107689",
"0.80103046",
"0.80062634",
"0.79572546",
"0.78228676",
"0.7787149",
"0.77444273",
"0.7615102",
"0.75675267",
"0.75575185",
"0.74872893",
"0.7475385",
"0.745855",
"0.7442314",
"0.73533386",
"0.7345682",
"0.73190933",
"0.7296384",
"0.7265832",
"0.7260435",
"0.7245... | 0.7423533 | 14 |
Prints help for a specified tool. | def print_specific_help(tool_name):
if tool_name not in AvailableCommands.commands:
print 'Command is not supported: {0}'.format(tool_name)
return
cmd = AvailableCommands.commands[tool_name]
print 'Usage of {0}:'.format(cmd.name)
print '\nAccepted input types:\n{0}'.format(str(li... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def print_generic_help():\r\n print ART_NAME\r\n print 'Version {1}\\nby {2}'.format(NAME, VERSION, AUTHOR)\r\n print DESCRIPTION\r\n tools = sorted(AvailableCommands.commands.keys(), key=lambda v: v.upper())\r\n # Do not show CUSTOM command in the help\r\n tools.remove('CUSTOM')\r\n tools.rem... | [
"0.7634922",
"0.72920835",
"0.72188467",
"0.71694416",
"0.7161719",
"0.71323955",
"0.70277065",
"0.7019475",
"0.7019475",
"0.7019475",
"0.69998395",
"0.69744694",
"0.6969143",
"0.6901238",
"0.6899467",
"0.6888493",
"0.68664163",
"0.6864778",
"0.68607914",
"0.6853852",
"0.6775... | 0.83063513 | 0 |
Reads through the config.txt file and reports any issues | def validate_config_file(args):
# Validate arguments
if len(args) > 2:
print 'Error! --validate_config does not take any arguments.'
return
# Check if the config.txt exists
if not os.path.exists(utils.CONFIG_FILE_PATH):
print 'Config file does not seem to exist. Do you w... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def read_config(self, config_filename):",
"def check_config_file(config_file_name, log_full_filename, log_file_path):\n try:\n if not os.path.isfile(config_file_name):\n # file not exist\n append_log_info(\"Config file not exists\", log_full_filename, log_file_path)\n r... | [
"0.7192984",
"0.67477554",
"0.6561265",
"0.6482356",
"0.6377692",
"0.63626087",
"0.6328165",
"0.6240044",
"0.62231106",
"0.61841595",
"0.618097",
"0.6171251",
"0.61445713",
"0.6141632",
"0.6137012",
"0.6134964",
"0.6129961",
"0.6128813",
"0.6123711",
"0.60856384",
"0.6077486"... | 0.6604901 | 2 |
Creates an updated version of current config.txt file If config.txt does not exist, it is created. | def update_config_file(commands_to_add, commands_to_remove):
# Parse the config.txt file contents
config_file_contents = {}
if os.path.exists(utils.CONFIG_FILE_PATH):
config_file_string = utils.get_config_file()
first_line = True
for line in config_file_string.split('\n'):
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def create():\n config_file = get_config_file()\n if os.path.isfile(config_file):\n logger.info(\"The config file already exists at '%s'\", config_file)\n return\n _create_config()\n logger.info(\"Created config file at '%s'\", config_file)",
"def configure_template_file(outName, CONFIG... | [
"0.70750207",
"0.7046834",
"0.67969155",
"0.6767401",
"0.6633",
"0.66246957",
"0.66090316",
"0.6598478",
"0.6496239",
"0.6465777",
"0.6396055",
"0.63894176",
"0.63544285",
"0.6312344",
"0.6298606",
"0.6227171",
"0.618552",
"0.6169344",
"0.6132309",
"0.61220276",
"0.6090062",
... | 0.59558344 | 32 |
Parses and validates command line arguments into a named tuple | def parse_command_line(args):
# Initial validity check of input command: each argument may be
# defined only once
for a in args:
if a.startswith('--'):
if args.count(a) > 1:
raise STAPLERerror.STAPLERerror('Each command line parameter can be '
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def parse_arguments(args):",
"def parseArgs ():\n independentBaseName = None\n dependentBaseName = None\n independentTSID = None\n dependentTSID = None\n statisticsFile = None\n nEquations = None\n logFile = None\n #\n # Loop through command line arguments\n for arg in sys.argv:\n ... | [
"0.73933643",
"0.7161926",
"0.71610683",
"0.694863",
"0.69094247",
"0.689724",
"0.6781782",
"0.67691696",
"0.6755849",
"0.6726755",
"0.67256963",
"0.6716309",
"0.6707882",
"0.6687657",
"0.6658016",
"0.6648027",
"0.6635262",
"0.6631878",
"0.6613462",
"0.6604489",
"0.6560422",
... | 0.61447746 | 73 |
Reads the user provided inputfile. | def parse_input_file(command_line_parameters):
try:
handle = open(command_line_parameters.staplerfile_path)
except IOError:
raise STAPLERerror.STAPLERerror(
'Unable to open input file: {0}'.format(command_line_parameters.staplerfile_path))
i = 0
staplefile = []
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _read_input_file(self):\n pass",
"def read_input_file(self):\n\n # Check if input file exists in current directory, if not kill process\n if not os.path.isfile('./visualise.inpt'):\n print('Cannot find input file \"visualise.inpt\" in current directory')\n sys.exit(... | [
"0.7806833",
"0.7186645",
"0.71339846",
"0.70758235",
"0.7059983",
"0.7019565",
"0.69860697",
"0.69175416",
"0.6860928",
"0.68346906",
"0.68346906",
"0.6793393",
"0.6735411",
"0.66906273",
"0.6640738",
"0.66247755",
"0.659747",
"0.65621734",
"0.6518654",
"0.64859736",
"0.6452... | 0.0 | -1 |
Deletes the directory tree (except input dir) and all contents. | def remove_workflow(input_file_parameters, dir_stack):
dirs_to_del = []
files_to_del = 0
for d in dir_stack[1:]:
if not os.path.exists(d.path): continue
dirs_to_del.append(d.path)
files_to_del += len(os.listdir(d.path))
if os.path.exists(input_file_parameters.output_dir):
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def DeleteFolderContents(dir):\n create_dir(dir)\n shutil.rmtree(dir)\n create_dir(dir)",
"def delete(self): # DirObj.delete\n self.deleted=True\n for name, d in self.subdirs.iteritems():\n d.delete()\n for name, f in self.files.iteritems... | [
"0.72931165",
"0.7170282",
"0.71510774",
"0.70483434",
"0.70209104",
"0.6979865",
"0.6977318",
"0.6941026",
"0.6845068",
"0.68373054",
"0.6833642",
"0.6824362",
"0.67982185",
"0.6728855",
"0.67046416",
"0.6693369",
"0.6665588",
"0.66357285",
"0.6628462",
"0.6615885",
"0.66041... | 0.0 | -1 |
Generates command line objects to compress/decompress a workflow. | def generate_compression_command_line_objects(dir_stack, command_line_parameters):
# Generate command lines
threads = []
thread_sizes = []
first_d = True
for d in dir_stack:
if first_d:
first_d = False
continue
if not os.path.isdir(d.path): continue... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def main():\n import argparse\n\n parser = argparse.ArgumentParser(\n description='Use the machine learning meta library shrynk to compress'\n )\n subparsers = parser.add_subparsers(dest=\"command\")\n compress = subparsers.add_parser('compress')\n compress.add_argument('file', help='file ... | [
"0.636741",
"0.61607385",
"0.6109988",
"0.5978106",
"0.5915388",
"0.58942014",
"0.58697283",
"0.58455306",
"0.5824884",
"0.58116597",
"0.5769307",
"0.5750805",
"0.57481354",
"0.5736904",
"0.57217336",
"0.5676748",
"0.5655071",
"0.5651055",
"0.5635633",
"0.5598006",
"0.5588914... | 0.65829694 | 0 |
Initiates the logging. NOTICE! This function has the side effect of changing the value of the class variable Current_log_path.path! | def init_logging(input_file_parameters, dir_stacks):
fl_name = '{0}_log_{1}_{2}.txt'.format(NAME,
START_TIME,
input_file_parameters.job_name)
#NOTICE! Current_log_path.path is changed here!
CurrentLogPath.path = os.pa... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, log_path, on=True):\n self.log_path = log_path\n self.on = on\n\n if self.on:\n while os.path.isfile(self.log_path):\n self.log_path += '+'",
"def setPath(logPath):\n GlobalLogger.logger.close()\n GlobalLogger.logger = FileLogger(log... | [
"0.73906374",
"0.71995836",
"0.71914166",
"0.7117808",
"0.70605886",
"0.6795082",
"0.668465",
"0.66670847",
"0.66334504",
"0.66144496",
"0.65918565",
"0.65881616",
"0.65418017",
"0.6516116",
"0.6497801",
"0.64702743",
"0.6458893",
"0.6458879",
"0.64564496",
"0.6424611",
"0.63... | 0.6691878 | 6 |
Infers the directory tree structure required for current workflows. | def infer_dir_stack(input_file_parameters, create_dirs, allow_existing_dirs = True):
dir_stack = [Directory(input_file_parameters.starting_point_directory,
create_dir=create_dirs)]
directory_name_index = 1
for i in xrange(len(input_file_parameters.commands)):
if input... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def tree(self) -> None:\n tree = Tree(self.root.path)\n self.root.walk_dir(tree)",
"def walker(self, path=None, base_folder=None):\n path = path or self.path\n base_folder = base_folder or self.base_folder\n # prevent trailing slashes and other inconsistencies on path.\n ... | [
"0.63796633",
"0.59604615",
"0.5903772",
"0.5750373",
"0.5714359",
"0.5682023",
"0.5665029",
"0.55971795",
"0.55720335",
"0.5561951",
"0.55350435",
"0.552684",
"0.5519678",
"0.54708374",
"0.54263985",
"0.5418281",
"0.54158896",
"0.5394255",
"0.53864056",
"0.5386263",
"0.53758... | 0.5606479 | 7 |
Generates commands to execute workflow for each input file. | def generate_command_line_objects(input_file_parameters, dir_stack, auto_split_workflows):
workflows = []
prev_number_of_ids_per_command = None
prev_command_had_output_dir = True
first_command = True
# Bools for splitting workflow. Separate values for automatically splitting workflow and
#... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def execute(self):\n for line in fileinput.input():\n line = line.rstrip()\n self._process_command(line)",
"def regenerate_command_line_objects(input_file_parameters, dir_stack,\r\n auto_split_workflows):\r\n workflows = []\r\n prev_number_of_i... | [
"0.65493697",
"0.61751366",
"0.61644983",
"0.6146389",
"0.58796287",
"0.58742994",
"0.5830146",
"0.5827008",
"0.5818108",
"0.5804637",
"0.57874596",
"0.5779958",
"0.5779178",
"0.57518756",
"0.571343",
"0.56952333",
"0.5652398",
"0.56454384",
"0.56206775",
"0.5620343",
"0.5577... | 0.6298623 | 1 |
Generates command lines that have not been successfully executed. | def regenerate_command_line_objects(input_file_parameters, dir_stack,
auto_split_workflows):
workflows = []
prev_number_of_ids_per_command = None
prev_command_had_output_dir = True
first_command = True
# Bools for splitting workflow. Separate values for autom... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def testEmptyCommands(self):\n pl = Pipeline(loadInitFile=False)\n repl = REPL(pl)\n\n repl.runCommandLine('4')\n self.assertEqual(4, pl.stdin)\n self.assertEqual(REPL.DEFAULT_PS1, repl.prompt)\n\n repl.runCommandLine('')\n self.assertEqual(4, pl.stdin)\n sel... | [
"0.5933541",
"0.58501595",
"0.5688975",
"0.56812465",
"0.55928385",
"0.5546314",
"0.55284",
"0.5519794",
"0.55064476",
"0.55031",
"0.54902095",
"0.5478368",
"0.547295",
"0.5469581",
"0.5469581",
"0.5469581",
"0.5469581",
"0.5458891",
"0.5446208",
"0.54371554",
"0.5420579",
... | 0.0 | -1 |
Analyzes output out and error files and reports putative errors. | def check_run_logs(input_file_parameters, dir_stack):
# Check resource manager produced .out and .err files for assumed error
# messages.
print 'Checking runtime log files for error messages...'
file_names = os.listdir(input_file_parameters.output_dir)
newest_fix_index = 0
files_to_check... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def error_analyze(\n self,\n data_dir: Path,\n processed_data_dir: Path,\n result_dir: Path,\n output_report_dir: Path,\n ) -> NoReturn:\n pass",
"def report_errors(clazz, output, max_lines):\n if COMPILE_ERR_PATC.search(output):\n # Comp... | [
"0.6987194",
"0.6444478",
"0.6306633",
"0.6203654",
"0.6200872",
"0.6159186",
"0.6075979",
"0.60607296",
"0.60173655",
"0.5971868",
"0.5959482",
"0.5884925",
"0.5875602",
"0.587055",
"0.5859751",
"0.5793299",
"0.5790206",
"0.5765882",
"0.5711678",
"0.5709301",
"0.57062423",
... | 0.54195714 | 52 |
Reports which commands have not been successfully run. Commands found in staplefile are compared with files found in directory stack to identify which commands have failed. | def validate_run_results(input_file_parameters, dir_stack):
prev_command_had_output_dir = True
dir_stack_index = -1
command_index = 0
for current_command in input_file_parameters.commands:
# Skip over SPLIT commands
if current_command == 'SPLIT':
continue
co... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def check_run_logs(input_file_parameters, dir_stack):\r\n # Check resource manager produced .out and .err files for assumed error\r\n # messages.\r\n print 'Checking runtime log files for error messages...'\r\n file_names = os.listdir(input_file_parameters.output_dir)\r\n\r\n newest_fix_index = 0\r\... | [
"0.6216581",
"0.5714732",
"0.56718695",
"0.56527007",
"0.5601208",
"0.55626947",
"0.5551729",
"0.5527082",
"0.5517359",
"0.54875124",
"0.5445772",
"0.5432267",
"0.54280514",
"0.54172146",
"0.5366206",
"0.5357607",
"0.5353905",
"0.5338872",
"0.5335011",
"0.5333496",
"0.5318811... | 0.67288995 | 0 |
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