idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
|---|---|---|
16,400 | def from_section ( cls , stream , section_name = '.pic' ) : binary = Executable ( stream ) section_data = binary . get_section_data ( section_name ) return cls ( section_data , binary . system ) | Construct a Converter object from the specified section of the specified binary stream . |
16,401 | def to_esc ( self ) : chunks = chunked ( self . stream , 2 ) return '' . join ( r'\x' + '' . join ( pair ) for pair in chunks ) | Convert to escape string . |
16,402 | def get_percentage_relative_to ( val , other ) : val = float ( val ) other = float ( other ) ratio = val / other - 1 return ratio * 100.0 | Finds percentage between 2 numbers |
16,403 | def setup_ui ( self , ) : self . main_vbox = QtGui . QVBoxLayout ( self ) self . import_all_references_cb = QtGui . QCheckBox ( "Import references" ) self . main_vbox . addWidget ( self . import_all_references_cb ) | Create all ui elements and layouts |
16,404 | def get_cleanups ( self , ) : cleanups = [ ] open_unit = ActionUnit ( name = "Open" , description = "Open the maya scene." , actionfunc = open_scene ) cleanups . append ( open_unit ) if self . _option_widget . import_references ( ) : import_unit = ActionUnit ( name = "Import references" , description = "Import all references in the scene." , actionfunc = import_all_references , depsuccess = [ open_unit ] ) cleanups . append ( import_unit ) update_scenenode_unit = ActionUnit ( name = "Update Scene Node" , description = "Change the id from the jbscene node from work to releasefile." , actionfunc = update_scenenode , depsuccess = [ open_unit ] ) cleanups . append ( update_scenenode_unit ) save_unit = ActionUnit ( name = "Save" , description = "Save the scene." , actionfunc = save_scene , depsuccess = [ update_scenenode_unit ] ) cleanups . append ( save_unit ) return ActionCollection ( cleanups ) | Get the cleanup actions for a releaes depending on the selected options |
16,405 | def epcr_primer_file ( self , formattedprimers ) : logging . info ( 'Creating re-PCR-compatible primer file' ) with open ( formattedprimers , 'w' ) as formatted : for basename in sorted ( self . forward_dict ) : for forward_index , forward_primer in enumerate ( self . forward_dict [ basename ] ) : for reverse_index , reverse_primer in enumerate ( self . reverse_dict [ basename ] ) : primer_name = '{bn}_{fi}_{ri}' . format ( bn = basename , fi = forward_index , ri = reverse_index ) output_string = '{pn}\t{fp}\t{rp}\n' . format ( pn = primer_name , fp = forward_primer , rp = reverse_primer ) formatted . write ( output_string ) | Create the ePCR - compatible primer file from the dictionaries of primer combinations |
16,406 | def epcr_threads ( self , formattedprimers , ampliconsize = 10000 ) : for sample in self . metadata : if sample . general . bestassemblyfile != 'NA' : threads = Thread ( target = self . epcr , args = ( ) ) threads . setDaemon ( True ) threads . start ( ) logging . info ( 'Running ePCR analyses' ) for sample in self . metadata : if sample . general . bestassemblyfile != 'NA' : setattr ( sample , self . analysistype , GenObject ( ) ) sample [ self . analysistype ] . primers = formattedprimers sample [ self . analysistype ] . reportdir = os . path . join ( sample . general . outputdirectory , self . analysistype ) make_path ( sample [ self . analysistype ] . reportdir ) outfile = os . path . join ( sample [ self . analysistype ] . reportdir , sample . name ) sample . commands . famap = '{famap} -b {outfile}.famap {fasta}' . format ( famap = os . path . join ( self . homepath , 'ePCR' , 'famap' ) , outfile = outfile , fasta = sample . general . bestassemblyfile ) sample . commands . fahash = '{fahash} -b {outfile}.hash {outfile}.famap' . format ( fahash = os . path . join ( self . homepath , 'ePCR' , 'fahash' ) , outfile = outfile ) sample . commands . epcr = '{rePCR} -S {outfile}.hash -r + -d 1-{ampsize} -n {mismatches} -g 0 -G -q ' '-o {outfile}.txt {primers}' . format ( rePCR = os . path . join ( self . homepath , 'ePCR' , 're-PCR' ) , outfile = outfile , ampsize = ampliconsize , mismatches = self . mismatches , primers = sample [ self . analysistype ] . primers ) sample [ self . analysistype ] . resultsfile = '{of}.txt' . format ( of = outfile ) self . epcrqueue . put ( ( sample , outfile ) ) self . epcrqueue . join ( ) | Run ePCR in a multi - threaded fashion |
16,407 | def epcr_parse ( self ) : logging . info ( 'Parsing ePCR outputs' ) for sample in self . metadata : if sample . general . bestassemblyfile != 'NA' : toxin_set = set ( ) if os . path . isfile ( sample [ self . analysistype ] . resultsfile ) : with open ( sample [ self . analysistype ] . resultsfile ) as epcrresults : for result in epcrresults : if "#" not in result : data = result . split ( '\t' ) vttype = data [ 0 ] . split ( '_' ) [ 0 ] toxin_set . add ( vttype ) sample [ self . analysistype ] . toxinprofile = ";" . join ( sorted ( list ( toxin_set ) ) ) if toxin_set else 'ND' else : setattr ( sample , self . analysistype , GenObject ( ) ) sample [ self . analysistype ] . toxinprofile = 'NA' | Parse the ePCR outputs |
16,408 | def epcr_report ( self ) : logging . info ( 'Creating {at} report' . format ( at = self . analysistype ) ) with open ( os . path . join ( self . reportpath , '{at}.csv' . format ( at = self . analysistype ) ) , 'w' ) as report : data = 'Strain,ToxinProfile\n' for sample in self . metadata : data += '{sn},{tp}\n' . format ( sn = sample . name , tp = sample [ self . analysistype ] . toxinprofile ) report . write ( data ) | Create a report of the ePCR - calculated toxin profiles |
16,409 | def parse_epcr ( self ) : for sample in self . vtyper_object . metadata : sample [ self . analysistype ] . result_dict = dict ( ) with open ( sample [ self . analysistype ] . resultsfile ) as epcrresults : for result in epcrresults : if "#" not in result : primer_set , contig , strand , start , stop , total_mismatches , indels , amplicon_combo = result . rstrip ( ) . split ( '\t' ) total_mismatches = int ( total_mismatches ) genome_pos = '{min}-{max}' . format ( min = min ( [ int ( start ) , int ( stop ) ] ) , max = max ( [ int ( start ) , int ( stop ) ] ) ) gene_re = re . search ( r'([\w-]+)_(\d{1,3})_(\d{1,3})' , primer_set ) gene = gene_re . groups ( ) [ 0 ] amplicon_length = amplicon_combo . split ( '/' ) [ 0 ] try : if total_mismatches < sample [ self . analysistype ] . result_dict [ gene ] [ 'total_mismatches' ] : self . populate_results_dict ( sample = sample , gene = gene , total_mismatches = total_mismatches , genome_pos = genome_pos , amplicon_length = amplicon_length , contig = contig , primer_set = primer_set ) except KeyError : self . populate_results_dict ( sample = sample , gene = gene , total_mismatches = total_mismatches , genome_pos = genome_pos , amplicon_length = amplicon_length , contig = contig , primer_set = primer_set ) | Parse the ePCR output file . Populate dictionary of resutls . For alleles find the best result based on the number of mismatches before populating dictionary |
16,410 | def create_epr_report ( self ) : with open ( os . path . join ( self . reportpath , 'ePCR_report.csv' ) , 'w' ) as report : results = 'Sample,Gene,GenomeLocation,AmpliconSize,Contig,TotalMismatches,PrimerSet\n' for sample in self . vtyper_object . metadata : if sample [ self . analysistype ] . result_dict : for gene , result_dict in sample [ self . analysistype ] . result_dict . items ( ) : results += '{sn},{gene},{genomelocation},{ampliconsize},{contig},{nm},{ps}\n' . format ( sn = sample . name , gene = gene , genomelocation = result_dict [ 'genome_pos' ] , ampliconsize = result_dict [ 'amplicon_length' ] , contig = result_dict [ 'contig' ] , nm = result_dict [ 'total_mismatches' ] , ps = result_dict [ 'primer_set' ] ) if self . export_amplicons : self . ampliconfile ( sample = sample , contig = result_dict [ 'contig' ] , amplicon_range = result_dict [ 'genome_pos' ] . split ( '-' ) , primer_set = result_dict [ 'primer_set' ] ) else : results += '{sn}\n' . format ( sn = sample . name ) report . write ( results ) | Parse the results dictionaries and create a final report |
16,411 | def samplesheet ( self ) : if self . demultiplex : make_path ( self . samplesheetpath ) self . customsamplesheet = os . path . join ( self . samplesheetpath , 'SampleSheet.csv' ) header = [ 'Sample_ID' , 'Sample_Name' , 'Sample_Plate' , 'Sample_Well' , 'I7_Index_ID' , 'index' , 'I5_Index_ID' , 'index2' , 'Sample_Project' , 'Description' ] with open ( self . customsamplesheet , 'w' ) as samplesheet : lines = str ( ) lines += '[Header]\n' lines += 'IEMFileVersion,{}\n' . format ( self . header . IEMFileVersion ) lines += 'Investigator Name,{}\n' . format ( self . header . InvestigatorName ) lines += 'Experiment Name,{}\n' . format ( self . header . ExperimentName ) lines += 'Date,{}\n' . format ( self . header . Date ) lines += 'Workflow,{}\n' . format ( self . header . Workflow ) lines += 'Application,{}\n' . format ( self . header . Application ) lines += 'Assay,{}\n' . format ( self . header . Assay ) lines += 'Description,{}\n' . format ( self . header . Description ) lines += 'Chemistry,{}\n' . format ( self . header . Chemistry ) lines += '\n' lines += '[Reads]\n' lines += str ( self . forward ) + '\n' lines += str ( self . reverse ) + '\n' lines += '\n' lines += '[Settings]\n' lines += 'ReverseComplement,{}\n' . format ( self . header . ReverseComplement ) lines += 'Adapter,{}\n' . format ( self . header . Adapter ) lines += '\n' lines += '[Data]\n' lines += ',' . join ( header ) lines += '\n' for incomplete in self . incomplete : for sample in self . rundata : if incomplete == sample [ 'SampleID' ] : for data in header : result = sample [ data . replace ( '_' , '' ) ] if data != 'Description' : lines += '{},' . format ( result . replace ( 'NA' , '' ) ) else : lines += '{}\n' . format ( result . replace ( 'NA' , '' ) ) samplesheet . write ( lines ) | Create a custom sample sheet based on the original sample sheet for the run but only including the samples that did not pass the quality threshold on the previous iteration |
16,412 | def update ( connection = None , silent = False , hgnc_file_path = None , hcop_file_path = None , low_memory = False ) : database = DbManager ( connection ) database . db_import ( silent = silent , hgnc_file_path = hgnc_file_path , hcop_file_path = hcop_file_path , low_memory = low_memory ) database . session . close ( ) | Update the database with current version of HGNC |
16,413 | def set_connection ( connection = defaults . sqlalchemy_connection_string_default ) : config_path = defaults . config_file_path config = RawConfigParser ( ) if not os . path . exists ( config_path ) : with open ( config_path , 'w' ) as config_file : config [ 'database' ] = { 'sqlalchemy_connection_string' : connection } config . write ( config_file ) log . info ( 'create configuration file {}' . format ( config_path ) ) else : config . read ( config_path ) config . set ( 'database' , 'sqlalchemy_connection_string' , connection ) with open ( config_path , 'w' ) as configfile : config . write ( configfile ) | Set the connection string for sqlalchemy and write it to the config file . |
16,414 | def set_mysql_connection ( host = 'localhost' , user = 'pyhgnc_user' , passwd = 'pyhgnc_passwd' , db = 'pyhgnc' , charset = 'utf8' ) : connection_string = 'mysql+pymysql://{user}:{passwd}@{host}/{db}?charset={charset}' . format ( host = host , user = user , passwd = passwd , db = db , charset = charset ) set_connection ( connection_string ) return connection_string | Method to set a MySQL connection |
16,415 | def relocate ( self , destination ) : for activate in self . bin . activates : activate . vpath = destination for binfile in self . bin . files : if binfile . shebang and ( 'python' in binfile . shebang or 'pypy' in binfile . shebang ) : binfile . shebang = '#!{0}' . format ( os . path . join ( destination , 'bin' , 'python' ) ) | Configure the virtual environment for another path . |
16,416 | def move ( self , destination ) : self . relocate ( destination ) shutil . move ( self . path , destination ) self . _path = destination | Reconfigure and move the virtual environment to another path . |
16,417 | def aggregate ( self ) : for report in self . reportset : printtime ( 'Processing {}' . format ( report . split ( '.' ) [ 0 ] ) , self . start ) header = '' if report != 'mlst.csv' else 'Strain,Genus,SequenceType,Matches,1,2,3,4,5,6,7\n' data = '' with open ( os . path . join ( self . reportpath , report ) , 'w' ) as aggregate : for sample in self . runmetadata . samples : try : with open ( os . path . join ( sample . general . reportpath , report ) , 'r' ) as runreport : if not header : header = runreport . readline ( ) else : for row in runreport : if not row . endswith ( '\n' ) : row += '\n' if row . split ( ',' ) [ 0 ] != header . split ( ',' ) [ 0 ] : data += row except IOError : pass aggregate . write ( header ) aggregate . write ( data ) | Aggregate all reports of the same type into a master report |
16,418 | def _parse_blocks ( instream ) : ilines = sugar . unblank ( instream ) for line in ilines : if line . startswith ( '[' ) : level , one , name , seqcount , params = _parse_block_header ( line ) qlen , qchars = _parse_block_postheader ( next ( ilines ) ) sequences = list ( _parse_sequences ( ilines , qlen ) ) if not len ( sequences ) == seqcount : logging . warn ( "Expected %d sequences in block %s, found %d" , seqcount , name , len ( sequences ) ) yield { 'level' : level , 'one' : one , 'name' : name , 'params' : params , 'query_length' : qlen , 'query_chars' : qchars , 'sequences' : sequences , } | Parse an alignment block from the given file handle . |
16,419 | def _parse_sequences ( ilines , expect_qlen ) : while True : first = next ( ilines ) if first . startswith ( '_' ) and first . endswith ( '].' ) : break try : index , this_len , query_len = _parse_seq_preheader ( first ) except ValueError : logging . warn ( 'Unparseable line (SKIPPING):\n%s' , first ) continue ( rec_id , dbxrefs , headlen , taillen , phylum , taxchar , description ) = _parse_seq_header ( next ( ilines ) ) try : headseq , molseq , tailseq = _parse_seq_body ( next ( ilines ) ) except ValueError : logging . warn ( 'Unparseable sequence: %s -- SKIPPING' , rec_id ) continue if expect_qlen != query_len : logging . warn ( "Query length in %s given as %d; expected %d" , rec_id , query_len , expect_qlen ) if not headseq and not headlen : headlen = 0 if not tailseq and not taillen : taillen = 0 if headseq : if headlen is None : headlen = len ( headseq ) elif headlen != len ( headseq ) : logging . warn ( "Conflicting head flank lengths in %s: %d, %d" , rec_id , headlen , len ( headseq ) ) if tailseq : if taillen is None : taillen = len ( tailseq ) elif taillen != len ( tailseq ) : logging . warn ( "Conflicting tail flank lengths in %s: %d, %d" , rec_id , taillen , len ( tailseq ) ) yield { 'index' : index , 'id' : rec_id , 'description' : description , 'dbxrefs' : dbxrefs , 'phylum' : phylum , 'taxchar' : taxchar , 'head_len' : headlen , 'tail_len' : taillen , 'head_seq' : headseq , 'tail_seq' : tailseq , 'length' : this_len , 'seq' : molseq , } | Parse the sequences in the current block . |
16,420 | def realign_seqs ( block , gap_char = '.' , align_indels = False ) : all_chars = [ list ( sq [ 'seq' ] ) for sq in block [ 'sequences' ] ] nrows = len ( all_chars ) i = 0 while i < len ( all_chars [ 0 ] ) : rows_need_gaps = [ r for r in all_chars if not r [ i ] . islower ( ) ] if len ( rows_need_gaps ) != nrows : for row in rows_need_gaps : row . insert ( i , gap_char ) i += 1 return [ '' . join ( row ) for row in all_chars ] | Add gaps to a block so all residues in a column are equivalent . |
16,421 | def collapse_to_consensus ( seqrecords , strict = False , do_iron = True ) : level = 0 name = seqrecords [ 0 ] . id if hasattr ( seqrecords , '_records' ) : if hasattr ( seqrecords , 'level' ) : level = seqrecords . level if hasattr ( seqrecords , 'name' ) : name = seqrecords . name seqrecords = seqrecords . _records consensus = seqrecords . pop ( 0 ) cons_length = len ( consensus ) for i , s in enumerate ( seqrecords ) : if len ( s ) != cons_length : raise ValueError ( "Sequence #%d has length %d, consensus is %d" % ( i + 2 , len ( s ) , cons_length ) ) if '.' in str ( consensus . seq ) : if '-' in str ( consensus . seq ) : if strict : raise ValueError ( "Consensus contains '-' gap characters" ) logging . warn ( "Consensus sequence contains both '.' and '-' gap " "characters -- is it really the consensus?" ) aligned_cols = [ ( c not in '.-' ) for c in str ( consensus . seq ) ] else : aligned_cols = [ c != '.' for c in str ( consensus . seq ) ] else : aligned_cols = [ c != '-' for c in str ( consensus . seq ) ] consensus . seq = replace_asterisks ( consensus . seq , 'consensus' ) block = consensus2block ( consensus , level = level , name = name ) qlen = block [ 'query_length' ] for index , rec in zip ( xrange ( 2 , len ( seqrecords ) + 2 ) , seqrecords ) : new_mol_seq = [ ] is_beginning = True for aligned_col , char in zip ( aligned_cols , replace_asterisks ( rec . seq , index ) ) : if aligned_col : is_beginning = False if char in '-.' : new_mol_seq . append ( '-' ) else : new_mol_seq . append ( char . upper ( ) ) else : if char not in '-.' and not is_beginning : new_mol_seq . append ( char . lower ( ) ) rec . seq = '' . join ( new_mol_seq ) if do_iron : rec . seq = iron ( rec . seq ) block [ 'sequences' ] . append ( seqrecord2sequence ( rec , qlen , index ) ) return block | Opposite of realign_seqs . |
16,422 | def iron ( sequence ) : r_indel = re . compile ( r'(-[a-y]|[a-y]-)' ) orig_sequence = sequence while r_indel . search ( sequence ) : in_insert = False in_gap = False seen_gaps = 0 inserts = [ ] outchars = [ ] for char in sequence : if in_insert : if char . islower ( ) : inserts . append ( char ) elif char . isupper ( ) : in_insert = False outchars . extend ( inserts ) inserts = [ ] outchars . append ( '-' * seen_gaps ) seen_gaps = 0 outchars . append ( char ) else : assert char == '-' if not inserts : in_insert = False in_gap = True seen_gaps += 1 else : outchars . append ( inserts . pop ( 0 ) . upper ( ) ) if not inserts : in_insert = False in_gap = True elif in_gap : if char . islower ( ) : in_insert = True in_gap = False if inserts : outchars . extend ( inserts ) outchars . append ( '-' * seen_gaps ) seen_gaps = 0 inserts = [ char ] elif char . isupper ( ) : in_gap = False if inserts : outchars . extend ( inserts ) inserts = [ ] outchars . append ( '-' * seen_gaps ) seen_gaps = 0 outchars . append ( char ) else : assert char == '-' seen_gaps += 1 else : assert not inserts and not seen_gaps , ( "Inserts: %s, gaps: %s, seq: %s, in_ins=%s, in_gap=%s" % ( inserts , seen_gaps , sequence , in_insert , in_gap ) ) if char . isupper ( ) : outchars . append ( char ) elif char . islower ( ) : inserts . append ( char ) in_insert = True else : assert char == '-' seen_gaps += 1 in_gap = True if inserts : outchars . extend ( inserts ) if seen_gaps : outchars . append ( '-' * seen_gaps ) sequence = '' . join ( outchars ) assert ( sequence . replace ( '-' , '' ) . upper ( ) == orig_sequence . replace ( '-' , '' ) . upper ( ) ) , '\nOrig: ' + orig_sequence + '\nIron: ' + sequence return sequence | Iron out indel regions in the aligned sequence . |
16,423 | def get_github_content ( repo , path , auth = None ) : request = requests . get ( file_url . format ( repo = repo , path = path ) , auth = auth ) if not request . ok : print ( "There is a problem with the request" ) print ( file_url . format ( repo = repo , path = path ) ) print ( request . json ( ) ) exit ( 1 ) if not request . json ( ) [ 'encoding' ] == 'base64' : raise RuntimeError ( "Unknown Encoding encountered when fetching {} from repo {}: {}" . format ( path , repo , request . json ( ) [ 'encoding' ] ) ) return request . json ( ) [ 'content' ] . decode ( 'base64' ) . decode ( 'utf8' ) | Retrieve text files from a github repo |
16,424 | def collect_reponames ( ) : reponames = [ ] try : with open ( os . devnull ) as devnull : remote_data = subprocess . check_output ( [ "git" , "remote" , "-v" , "show" ] , stderr = devnull ) branches = { } for line in remote_data . decode ( 'utf-8' ) . split ( "\n" ) : if line . strip ( ) == "" : continue remote_match = re_mote . match ( line ) if not remote_match is None : branches [ remote_match . group ( 1 ) ] = remote_match . group ( 5 ) if len ( branches ) > 0 : if "origin" in branches : reponames . append ( branches [ "origin" ] ) else : reponames . append ( branches . values ( ) [ 0 ] ) except OSError : pass except subprocess . CalledProcessError : pass for fname in glob . iglob ( "*.html" ) : fid = open ( fname , "r" , "utf8" ) fid . readline ( ) line = fid . readline ( ) match = re . match ( repo_marker_re , line ) if not match is None : reponames . append ( match . group ( 1 ) ) reponames = list ( set ( reponames ) ) return reponames | Try to figure out a list of repos to consider by default from the contents of the working directory . |
16,425 | def collect_github_config ( ) : github_config = { } for field in [ "user" , "token" ] : try : github_config [ field ] = subprocess . check_output ( [ "git" , "config" , "github.{}" . format ( field ) ] ) . decode ( 'utf-8' ) . strip ( ) except ( OSError , subprocess . CalledProcessError ) : pass return github_config | Try load Github configuration such as usernames from the local or global git config |
16,426 | def setCurveModel ( self , model ) : self . stimModel = model self . ui . curveWidget . setModel ( model ) | Sets the stimulus model for the calibration curve test |
16,427 | def addOption ( self , stim ) : self . ui . calTypeCmbbx . insertItem ( 0 , stim . name ) editor = stim . showEditor ( ) durInput = editor . durationInputWidget ( ) self . durationWidgets . append ( durInput ) durInput . setEnabled ( False ) self . ui . caleditorStack . insertWidget ( 0 , editor ) self . ui . calTypeCmbbx . setCurrentIndex ( 0 ) | Adds a stimulus to the list of stims to use for testing calibration |
16,428 | def saveToObject ( self ) : for i in range ( self . ui . caleditorStack . count ( ) ) : try : self . ui . caleditorStack . widget ( i ) . saveToObject ( ) except AttributeError : logger = logging . getLogger ( 'main' ) logger . debug ( 'index {} does not have method saveToObject' . format ( i ) ) | Saves the current UI setting to the model |
16,429 | def isToneCal ( self ) : return self . ui . calTypeCmbbx . currentIndex ( ) == self . ui . calTypeCmbbx . count ( ) - 1 | Whether the currently selected calibration stimulus type is the calibration curve |
16,430 | def reset_generation ( self , trigger ) : self . tone_lock . acquire ( ) npts = self . stim . size try : self . aotask = AOTaskFinite ( self . aochan , self . fs , npts , trigsrc = trigger ) self . aotask . write ( self . stim ) if self . attenuator is not None : self . attenuator . SetAtten ( self . atten ) else : pass self . ngenerated += 1 if self . stim_changed : new_gen = self . stim else : new_gen = None self . stim_changed = False except : print u'ERROR! TERMINATE!' self . tone_lock . release ( ) raise self . tone_lock . release ( ) return new_gen | Re - arms the analog output according to current settings |
16,431 | def set_stim ( self , signal , fs , attenuation = 0 ) : self . tone_lock . acquire ( ) self . stim = signal self . fs = fs self . atten = attenuation self . stim_changed = True self . tone_lock . release ( ) | Sets any vector as the next stimulus to be output . Does not call write to hardware |
16,432 | def connect_attenuator ( self , connect = True ) : if connect : try : pa5 = win32com . client . Dispatch ( "PA5.x" ) success = pa5 . ConnectPA5 ( 'GB' , 1 ) if success == 1 : print 'Connection to PA5 attenuator established' pass else : print 'Connection to PA5 attenuator failed' errmsg = pa5 . GetError ( ) print u"Error: " , errmsg raise Exception ( u"Attenuator connection failed" ) except : print "Error connecting to attenuator" pa5 = None self . attenuator = pa5 else : if self . attenuator : self . attenuator . setAtten ( 0 ) self . attenuator = None return self . attenuator | Establish a connection to the TDT PA5 attenuator |
16,433 | def start_timer ( self , reprate ) : print 'starting digital output at rate {} Hz' . format ( reprate ) self . trigger_task = DigitalOutTask ( self . trigger_src , reprate ) self . trigger_task . start ( ) | Start the digital output task that serves as the acquistion trigger |
16,434 | def start ( self ) : if self . aitask is not None : self . stop ( ) raise Exception ( "FIX ME : NESTED START OPERATIONS ALLOWED" ) self . daq_lock . acquire ( ) self . ngenerated = 0 self . nacquired = 0 return self . reset ( ) | Writes output buffer and settings to device |
16,435 | def stop ( self ) : try : self . aitask . stop ( ) self . aotask . stop ( ) pass except : print u"No task running" self . aitask = None self . aotask = None | Halts the acquisition this must be called before resetting acquisition |
16,436 | def start_continuous ( self , aichans , update_hz = 10 ) : self . daq_lock . acquire ( ) self . ngenerated = 0 npts = int ( self . aifs / update_hz ) nchans = len ( aichans ) self . aitask = AITask ( aichans , self . aifs , npts * 5 * nchans ) self . aitask . register_callback ( self . _read_continuous , npts ) self . aitask . start ( ) | Begins a continuous analog generation calling a provided function at a rate of 10Hz |
16,437 | def run ( self ) : self . aotask . StartTask ( ) self . aotask . wait ( ) self . aotask . stop ( ) self . aotask = None | Executes the stimulus generation and returns when completed |
16,438 | def stop_all ( self ) : if self . aotask is not None : self . aotask . stop ( ) self . aitask . stop ( ) self . daq_lock . release ( ) self . aitask = None self . aotask = None | Halts both the analog output and input tasks |
16,439 | def get ( self , url , params = None , raw = False , stream = False , ** request_kwargs ) : full_url = self . build_url ( url ) params = params or { } if self . _token : params . setdefault ( 'token' , self . _token ) response = requests . get ( full_url , params = params , stream = stream , ** request_kwargs ) self . check_for_errors ( response ) if stream : return response if raw or not response . content : return response . content return json . loads ( response . text ) | GET request to AmigoCloud endpoint . |
16,440 | def post ( self , url , data = None , files = None , headers = None , raw = False , send_as_json = True , content_type = None , ** request_kwargs ) : return self . _secure_request ( url , 'post' , data = data , files = files , headers = headers , raw = raw , send_as_json = send_as_json , content_type = content_type , ** request_kwargs ) | POST request to AmigoCloud endpoint . |
16,441 | def upload_gallery_photo ( self , gallery_id , source_amigo_id , file_obj , chunk_size = CHUNK_SIZE , force_chunked = False , metadata = None ) : simple_upload_url = 'related_tables/%s/upload' % gallery_id chunked_upload_url = 'related_tables/%s/chunked_upload' % gallery_id data = { 'source_amigo_id' : source_amigo_id } if isinstance ( file_obj , basestring ) : data [ 'filename' ] = os . path . basename ( file_obj ) else : data [ 'filename' ] = os . path . basename ( file_obj . name ) if metadata : data . update ( metadata ) return self . upload_file ( simple_upload_url , chunked_upload_url , file_obj , chunk_size = chunk_size , force_chunked = force_chunked , extra_data = data ) | Upload a photo to a dataset s gallery . |
16,442 | def listen_user_events ( self ) : if not self . _user_id : raise AmigoCloudError ( self . error_msg [ 'logged_in_websockets' ] ) response = self . get ( '/me/start_websocket_session' ) websocket_session = response [ 'websocket_session' ] auth_data = { 'userid' : self . _user_id , 'websocket_session' : websocket_session } self . amigosocket . emit ( 'authenticate' , auth_data ) | Authenticate to start listening to user events . |
16,443 | def listen_dataset_events ( self , owner_id , project_id , dataset_id ) : if not self . _user_id : raise AmigoCloudError ( self . error_msg [ 'logged_in_websockets' ] ) url = '/users/%s/projects/%s/datasets/%s/start_websocket_session' response = self . get ( url % ( owner_id , project_id , dataset_id ) ) websocket_session = response [ 'websocket_session' ] auth_data = { 'userid' : self . _user_id , 'datasetid' : dataset_id , 'websocket_session' : websocket_session } self . amigosocket . emit ( 'authenticate' , auth_data ) | Authenticate to start using dataset events . |
16,444 | def build_markdown_table ( headers , rows , row_keys = None ) : row_maxes = _find_row_maxes ( headers , rows ) row_keys = row_keys or [ key for key , value in headers . items ( ) ] table = [ _build_row ( headers , row_maxes , row_keys ) , _build_separator ( row_maxes , row_keys ) ] for row in rows : table . append ( _build_row ( row , row_maxes , row_keys ) ) return '\n' . join ( table ) + '\n' | Build a lined up markdown table . |
16,445 | def write_to_path ( self , path , suffix = '' , format = 'png' , overwrite = False ) : if os . path . exists ( path ) and overwrite is False : raise ValueError ( "Error: use ovewrite=True to overwrite images" ) if not os . path . exists ( path ) : os . makedirs ( path ) for i , r in self . iterrows ( ) : spath = os . path . join ( path , r [ 'project_name' ] , r [ 'sample_name' ] ) if not os . path . exists ( spath ) : os . makedirs ( spath ) if suffix == '' : fname = os . path . join ( spath , r [ 'frame_name' ] + '.' + format ) else : fname = os . path . join ( spath , r [ 'frame_name' ] + '_' + suffix + '.' + format ) imageio . imwrite ( fname , r [ 'image' ] , format = format ) | Output the data the dataframe s image column to a directory structured by project - > sample and named by frame |
16,446 | def build_segmentation_image ( self , schema , background = ( 0 , 0 , 0 , 0 ) ) : cummulative = self . copy ( ) def _set_blank ( img , blank ) : img [ : ] [ : ] = blank return img cummulative [ 'merged' ] = cummulative . apply ( lambda x : _set_blank ( np . zeros ( list ( x [ 'shape' ] ) + [ 4 ] ) , background ) , 1 ) for layer in schema : if self . verbose : sys . stderr . write ( "Calculating layer " + str ( layer ) + "\n" ) images = self . get_outline_images ( subset_logic = layer [ 'subset_logic' ] , edge_color = layer [ 'edge_color' ] , watershed_steps = layer [ 'watershed_steps' ] , fill_color = layer [ 'fill_color' ] ) cummulative = cummulative . rename ( columns = { 'merged' : 'old' } ) cummulative = cummulative . merge ( images , on = list ( self . columns ) ) cummulative [ 'new' ] = cummulative . apply ( lambda x : _merge_images ( x [ 'merged' ] , x [ 'old' ] ) , 1 ) cummulative = cummulative . drop ( columns = [ 'old' , 'merged' ] ) . rename ( columns = { 'new' : 'merged' } ) cummulative = cummulative . rename ( columns = { 'merged' : 'image' } ) return SegmentationImageOutput ( cummulative ) | Put together an image . Defined by a list of layers with RGBA colors |
16,447 | def valid ( number ) : checksum = 0 number_len = len ( number ) offset = ord ( '0' ) i = number_len - 1 while i >= 0 : n = ord ( number [ i ] ) - offset checksum += n i -= 2 i = number_len - 2 while i >= 0 : n = ord ( number [ i ] ) - offset n *= 2 if n > 9 : n -= 9 checksum += n i -= 2 return checksum % 10 == 0 | Returns true if the number string is luhn valid and false otherwise . The number string passed to the function must contain only numeric characters otherwise behavior is undefined . |
16,448 | def create_publication_assistant ( self , ** args ) : logdebug ( LOGGER , 'Creating publication assistant..' ) mandatory_args = [ 'drs_id' , 'version_number' , 'is_replica' ] esgfpid . utils . check_presence_of_mandatory_args ( args , mandatory_args ) if self . __thredds_service_path is None : msg = 'No thredds_service_path given (but it is mandatory for publication)' logwarn ( LOGGER , msg ) raise esgfpid . exceptions . ArgumentError ( msg ) if self . __data_node is None : msg = 'No data_node given (but it is mandatory for publication)' logwarn ( LOGGER , msg ) raise esgfpid . exceptions . ArgumentError ( msg ) if self . __coupler . is_solr_switched_off ( ) : pass assistant = esgfpid . assistant . publish . DatasetPublicationAssistant ( drs_id = args [ 'drs_id' ] , version_number = args [ 'version_number' ] , thredds_service_path = self . __thredds_service_path , data_node = self . __data_node , prefix = self . prefix , coupler = self . __coupler , is_replica = args [ 'is_replica' ] , consumer_solr_url = self . __consumer_solr_url ) logdebug ( LOGGER , 'Creating publication assistant.. done' ) return assistant | Create an assistant for a dataset that allows to make PID requests for the dataset and all of its files . |
16,449 | def unpublish_one_version ( self , ** args ) : optional_args = [ 'handle' , 'drs_id' , 'version_number' ] esgfpid . utils . add_missing_optional_args_with_value_none ( args , optional_args ) if self . __data_node is None : msg = 'No data_node given (but it is mandatory for unpublication)' logwarn ( LOGGER , msg ) raise esgfpid . exceptions . ArgumentError ( msg ) assistant = esgfpid . assistant . unpublish . AssistantOneVersion ( drs_id = args [ 'drs_id' ] , data_node = self . __data_node , prefix = self . prefix , coupler = self . __coupler , message_timestamp = esgfpid . utils . get_now_utc_as_formatted_string ( ) ) assistant . unpublish_one_dataset_version ( handle = args [ 'handle' ] , version_number = args [ 'version_number' ] ) | Sends a PID update request for the unpublication of one version of a dataset currently published at the given data node . |
16,450 | def unpublish_all_versions ( self , ** args ) : mandatory_args = [ 'drs_id' ] esgfpid . utils . check_presence_of_mandatory_args ( args , mandatory_args ) if self . __data_node is None : msg = 'No data_node given (but it is mandatory for publication)' logwarn ( LOGGER , msg ) raise esgfpid . exceptions . ArgumentError ( msg ) if self . __coupler . is_solr_switched_off ( ) : msg = 'Unpublication of all versions. Without solr access, we cannot identify the versions, so the consumer will have to take care of this.' logdebug ( LOGGER , msg ) assistant = esgfpid . assistant . unpublish . AssistantAllVersions ( drs_id = args [ 'drs_id' ] , data_node = self . __data_node , prefix = self . prefix , coupler = self . __coupler , message_timestamp = esgfpid . utils . get_now_utc_as_formatted_string ( ) , consumer_solr_url = self . __consumer_solr_url ) assistant . unpublish_all_dataset_versions ( ) | Sends a PID update request for the unpublication of all versions of a dataset currently published at the given data node . |
16,451 | def add_errata_ids ( self , ** args ) : mandatory_args = [ 'drs_id' , 'version_number' , 'errata_ids' ] esgfpid . utils . check_presence_of_mandatory_args ( args , mandatory_args ) esgfpid . utils . check_noneness_of_mandatory_args ( args , mandatory_args ) assistant = esgfpid . assistant . errata . ErrataAssistant ( coupler = self . __coupler , prefix = self . prefix ) assistant . add_errata_ids ( drs_id = args [ 'drs_id' ] , version_number = args [ 'version_number' ] , errata_ids = args [ 'errata_ids' ] ) | Add errata ids to a dataset handle record . |
16,452 | def make_handle_from_drsid_and_versionnumber ( self , ** args ) : args [ 'prefix' ] = self . prefix return esgfpid . utils . make_handle_from_drsid_and_versionnumber ( ** args ) | Create a handle string for a specific dataset based on its dataset id and version number and the prefix passed to the library at initializing . |
16,453 | def mousePressEvent ( self , event ) : super ( AbstractDragView , self ) . mousePressEvent ( event ) self . dragStartPosition = event . pos ( ) | saves the drag position so we know when a drag should be initiated |
16,454 | def dragLeaveEvent ( self , event ) : super ( AbstractDragView , self ) . dragLeaveEvent ( event ) self . dragline = None self . viewport ( ) . update ( ) event . accept ( ) | Clears drop cursor line |
16,455 | def childEvent ( self , event ) : super ( AbstractDragView , self ) . childEvent ( event ) if event . type ( ) == QtCore . QEvent . ChildRemoved : if self . originalPos is not None : selected = self . limbo_component self . model ( ) . insertItem ( self . originalPos , selected ) self . originalPos = None self . dragStartPosition = None self . viewport ( ) . update ( ) | Catches items dropped off edge of view reinserts at original position |
16,456 | def mouseReleaseEvent ( self , event ) : super ( AbstractDragView , self ) . mouseReleaseEvent ( event ) self . dragStartPosition = None | Resets the drag start position |
16,457 | async def setup ( self ) : try : db = await self . db collections = await db . list_collection_names ( ) created = False if self . table_name not in collections : logger . info ( "Creating MongoDB collection [{}]" . format ( self . table_name ) ) await db . create_collection ( self . table_name ) await db [ self . table_name ] . create_index ( [ ( "target_id" , DESCENDING ) , ( "post_id" , DESCENDING ) ] ) created = True if self . control_table_name and self . control_table_name not in collections : logger . info ( "Creating MongoDB control data collection [{}]" . format ( self . control_table_name ) ) await db . create_collection ( self . control_table_name ) created = True return created except Exception as exc : logger . error ( "[DB] Error when setting up MongoDB collections: {}" . format ( exc ) ) return False | Setting up MongoDB collections if they not exist . |
16,458 | def setDoc ( self , docs ) : docs = sorted ( docs , key = lambda k : k [ 'start_s' ] ) for doc in docs : stim_type = doc [ 'stim_type' ] if not stim_type in self . displayTable : continue if not stim_type in self . displayTable [ stim_type ] : continue display_attributes = self . displayTable . get ( stim_type , self . defaultAttributes ) self . lyt . addWidget ( ComponentDetailFrame ( doc , display_attributes ) ) | Sets the documentation to display |
16,459 | def setComponents ( self , components ) : layout = self . layout ( ) for comp in components : attrWidget = ComponentAttributerChecker ( comp ) layout . addWidget ( attrWidget ) | Clears and sets the components contained in this widget |
16,460 | def setCheckedDetails ( self , checked ) : layout = self . layout ( ) for i in range ( layout . count ( ) ) : w = layout . itemAt ( i ) . widget ( ) if w . stimType in checked : w . setChecked ( checked [ w . stimType ] ) | Sets which components are checked |
16,461 | def getCheckedDetails ( self ) : attrs = { } layout = self . layout ( ) for i in range ( layout . count ( ) ) : w = layout . itemAt ( i ) . widget ( ) attrs [ w . stimType ] = w . getChecked ( ) return attrs | Gets the currently checked components and checked attributes |
16,462 | def getChecked ( self ) : attrs = [ ] layout = self . layout ( ) for i in range ( layout . count ( ) ) : w = layout . itemAt ( i ) . widget ( ) if w . isChecked ( ) : attrs . append ( str ( w . text ( ) ) ) return attrs | Gets the checked attributes |
16,463 | def headerData ( self , section , orientation , role ) : if role == QtCore . Qt . DisplayRole : if orientation == QtCore . Qt . Horizontal : return self . headers [ section ] | Get the Header for the columns in the table |
16,464 | def cursor ( self , pos ) : row = self . indexAt ( pos ) . row ( ) if row == - 1 : row = self . model ( ) . rowCount ( ) row_height = self . rowHeight ( 0 ) y = row_height * row x = self . width ( ) return QtCore . QLine ( 0 , y , x , y ) | Returns a line at the nearest row split between tests . |
16,465 | def mousePressEvent ( self , event ) : index = self . indexAt ( event . pos ( ) ) if index . isValid ( ) : if index . column ( ) == 0 : self . edit ( index , QtGui . QAbstractItemView . DoubleClicked , event ) else : super ( ProtocolView , self ) . mousePressEvent ( event ) | Launches edit of cell if first column clicked otherwise passes to super class |
16,466 | def run ( ) : args = parse_args ( ) codetools . setup_logging ( args . debug ) global g g = pygithub . login_github ( token_path = args . token_path , token = args . token ) if not args . hide : args . hide = [ ] org = g . get_organization ( args . organization ) try : repos = list ( org . get_repos ( ) ) except github . RateLimitExceededException : raise except github . GithubException as e : msg = 'error getting repos' raise pygithub . CaughtOrganizationError ( org , e , msg ) from None for r in repos : try : teamnames = [ t . name for t in r . get_teams ( ) if t . name not in args . hide ] except github . RateLimitExceededException : raise except github . GithubException as e : msg = 'error getting teams' raise pygithub . CaughtRepositoryError ( r , e , msg ) from None maxt = args . maxt if ( args . maxt is not None and args . maxt >= 0 ) else len ( teamnames ) if args . debug : print ( "MAXT=" , maxt ) if args . mint <= len ( teamnames ) <= maxt : print ( r . name . ljust ( 40 ) + args . delimiter . join ( teamnames ) ) | List repos and teams |
16,467 | def create_bar_chart ( self , x_labels , y_values , y_label ) : self . setup ( 0.25 ) ax1 = self . get_ax ( ) ax1 . set_xticks ( list ( range ( len ( x_labels ) ) ) ) ax1 . set_xticklabels ( [ x_labels [ i ] for i in range ( len ( x_labels ) ) ] , rotation = 90 ) plt . ylabel ( y_label ) x_pos = range ( len ( x_labels ) ) plt . bar ( x_pos , y_values , align = "center" ) return ax1 | Creates bar char |
16,468 | def create_multiple_bar_chart ( self , x_labels , mul_y_values , mul_y_labels , normalize = False ) : self . setup ( 0.25 ) ax1 = self . get_ax ( ) ax1 . set_xticks ( list ( range ( len ( x_labels ) ) ) ) ax1 . set_xticklabels ( [ x_labels [ i ] for i in range ( len ( x_labels ) ) ] , rotation = 90 ) y_counts = len ( mul_y_values ) colors = cm . rainbow ( np . linspace ( 0 , 1 , y_counts ) ) max_bar_width = 0.6 bar_width = max_bar_width / y_counts x_shifts = np . linspace ( 0 , max_bar_width , y_counts ) - max_bar_width * 0.5 ax_series = [ ] for i in range ( y_counts ) : x_pos = range ( len ( x_labels ) ) x_pos = np . array ( x_pos ) + x_shifts [ i ] if normalize : y_values = normalize_array ( mul_y_values [ i ] ) else : y_values = mul_y_values [ i ] ax_series . append ( ax1 . bar ( x_pos , y_values , width = bar_width , align = "center" , color = colors [ i ] ) ) ax1 . legend ( ax_series , mul_y_labels ) return ax1 | Creates bar chart with multiple lines |
16,469 | def file_parts ( self ) : file_parts = [ ] for part in self . parts : try : for sub_part in part : if isinstance ( sub_part , FileToken ) : file_parts . append ( sub_part ) except TypeError : if isinstance ( part , FileToken ) : file_parts . append ( part ) return file_parts | Returns a list of the file tokens in the list of parts . |
16,470 | def update_dependent_files ( self , prev_commands = [ ] ) : for command in prev_commands : for my_input in self . input_parts : for their_output in command . output_parts : if their_output == my_input : my_input . filename = their_output . eval ( ) | Update the command s dependencies based on the evaluated input and output of previous commands . |
16,471 | def eval ( self ) : eval = [ ] for part in self . parts : try : result = part . eval ( ) except AttributeError : result = part if result [ - 1 ] != '\n' : result += ' ' eval . append ( result ) return '' . join ( eval ) . strip ( ) | Evaluate the given job and return a complete shell script to be run by the job manager . |
16,472 | def add_type ( cls , typ ) : if not isinstance ( typ , basestring ) : raise TypeError ( "The type should be a string. But is %s" % type ( typ ) ) cls . types . append ( typ ) | Register a type for jb_reftrack nodes . |
16,473 | def transform ( transform_func ) : def decorator ( func ) : @ wraps ( func ) def f ( * args , ** kwargs ) : return transform_func ( func ( * args , ** kwargs ) ) return f return decorator | Apply a transformation to a functions return value |
16,474 | def subkey ( dct , keys ) : key = keys [ 0 ] if len ( keys ) == 1 : return dct [ key ] return subkey ( dct [ key ] , keys [ 1 : ] ) | Get an entry from a dict of dicts by the list of keys to follow |
16,475 | def get_driver ( self , name , version ) : user_credentials = self . get_user_credentials ( ) return discovery . build ( name , version , http = self . authenticate ( user_credentials ) ) | Authenticates and creates new API driver to perform scope stuff |
16,476 | def start_chart ( self ) : self . current_dataset_name = self . chart_name self . datafile . init_data ( self . current_dataset_name , mode = 'continuous' ) self . chart_name = increment_title ( self . chart_name ) self . player . start_continuous ( [ self . aichan , u"PCI-6259/ai31" ] ) | Begin on - going chart style acqusition |
16,477 | def qtdoc_role ( name , rawtext , text , lineno , inliner , options = { } , content = [ ] ) : base = 'http://qt-project.org/doc/qt-4.8/' match = re . search ( '([^<]+)(<[^<>]+>)?' , text ) if match is None : raise ValueError label = match . group ( 1 ) if match . lastindex == 2 : clsmeth = match . group ( 2 ) [ 1 : - 1 ] cls , meth = clsmeth . split ( '.' ) ref = base + cls + '.html#' + meth else : ref = base + label . lower ( ) + '.html' node = nodes . reference ( rawtext , label , refuri = ref , ** options ) return [ node ] , [ ] | Links to a Qt class s doc |
16,478 | def update_func_body ( original , updater = None ) : updated = '' regex = r'([_\w][_\w\d]*)\s*\(.*\)\s*\{' match = re . search ( regex , original ) while match : name = match . group ( 1 ) logging . debug ( _ ( 'Found candidate: %s' ) , name ) start = match . end ( ) end = start + find_balance_index ( original [ start : ] ) body = original [ start : end ] if updater : body = updater ( body , name ) updated += original [ : start ] + '\n' + body + original [ end ] original = original [ end + 1 : ] match = re . search ( regex , original ) return updated | Update all function body using the updating function . |
16,479 | def find_balance_index ( source , start = '{' , end = '}' ) : state = 1 for index , char in enumerate ( source ) : if char == start : state += 1 elif char == end : state -= 1 if state == 0 : return index raise RuntimeError ( 'This should not happen: Balance Not Found' ) | Get the first balance index . |
16,480 | def transform_sources ( self , sources , with_string = False ) : modules = { } updater = partial ( self . replace_source , modules = modules , prefix = 'string_' ) for filename in sources : updated = update_func_body ( sources [ filename ] , updater ) sources [ filename ] = EXTERN_AND_SEG + updated logging . debug ( 'modules: %s' , modules ) return sources , self . build_funcs ( modules ) | Get the defintions of needed strings and functions after replacement . |
16,481 | def replace_source ( self , source , name , modules , prefix ) : needs_windll = False def _func_replacer ( match , modules , windll ) : matched = match . group ( 0 ) if matched in self . BLACKLIST : return matched module = self . database . query_func_module ( matched ) if module : try : modules [ module [ 0 ] ] += [ module [ 1 ] ] except KeyError : modules [ module [ 0 ] ] = [ module [ 1 ] ] if windll : return '{}->{}.{}' . format ( windll , * module ) return '{}->{}' . format ( * module ) return matched replacer = partial ( _func_replacer , modules = modules , windll = 'windll' ) replaced = re . sub ( r'[_\w][_\w\d]*(?=\s*\()' , replacer , source ) if source != replaced : needs_windll = True str_table = { } def _string_replacer ( match ) : matched = match . group ( ) [ 1 : - 1 ] try : number = str_table [ matched ] except KeyError : number = len ( str_table ) + 1 str_table . update ( { matched : number } ) return '{}{}' . format ( prefix , number ) replaced = re . sub ( r'".+?"' , _string_replacer , replaced ) strings , relocs = self . build_strings ( str_table , prefix ) strings = '' . join ( strings ) . strip ( ) windll32 = reloc_var ( 'windll' , 'reloc_delta' , True , 'windll_t' ) if needs_windll : relocs += [ windll32 ] if strings : strings = '\n' + strings if not needs_windll : relocs += [ windll32 ] needs_windll = True windll64 = '' if needs_windll : windll64 = '{0} *{1} = &_{1};\n' . format ( 'windll_t' , 'windll' ) relocs = reloc_both ( '' . join ( relocs ) , windll64 ) if name in [ 'main' ] : replaced = '\ninit();' + replaced return strings + relocs + replaced | Scan C source code for string literals as well as function calls and do replacement using the specified replacing function . Note that the regular expression currently used for strings is naive or quick and dirty . |
16,482 | def build_funcs ( modules ) : kernel32 = [ 'kernel32_' ] try : kernel32 += remove_dups ( modules [ 'kernel32' ] ) except KeyError : if len ( modules ) and 'LoadLibraryA' not in kernel32 : kernel32 . insert ( 1 , 'LoadLibraryA' ) if len ( modules ) > 1 and 'LoadLibraryA' not in kernel32 : kernel32 . insert ( 1 , 'LoadLibraryA' ) if 'GetProcAddress' not in kernel32 : kernel32 . insert ( 1 , 'GetProcAddress' ) logging . debug ( 'kernel32: %s' , kernel32 ) for module , funcs in modules . items ( ) : logging . debug ( '%s: %s' , module , funcs ) if module != 'kernel32' : kernel32 . extend ( [ module + '_' ] + remove_dups ( funcs ) ) return kernel32 | Build a used functions and modules list for later consumption . |
16,483 | def build_strings ( strings , prefix ) : strings = [ ( make_c_str ( prefix + str ( number ) , value ) , reloc_ptr ( prefix + str ( number ) , 'reloc_delta' , 'char *' ) ) for value , number in sort_values ( strings ) ] return [ i [ 0 ] for i in strings ] , [ i [ 1 ] for i in strings ] | Construct string definitions according to the previously maintained table . |
16,484 | def add_file ( self , ** args ) : self . __check_if_adding_files_allowed_right_now ( ) mandatory_args = [ 'file_name' , 'file_handle' , 'file_size' , 'checksum' , 'publish_path' , 'checksum_type' , 'file_version' ] utils . check_presence_of_mandatory_args ( args , mandatory_args ) self . __enforce_integer_file_size ( args ) self . __enforce_string_file_version ( args ) self . __check_and_correct_handle_syntax ( args ) self . __add_file ( ** args ) | Adds a file s information to the set of files to be published in this dataset . |
16,485 | def run_program ( program , * args ) : real_args = [ program ] real_args . extend ( args ) logging . debug ( _ ( 'check_output arguments: %s' ) , real_args ) check_output ( real_args , universal_newlines = True ) | Wrap subprocess . check_output to make life easier . |
16,486 | def get_parent_dir ( name ) : parent_dir = os . path . dirname ( os . path . dirname ( name ) ) if parent_dir : return parent_dir return os . path . abspath ( '.' ) | Get the parent directory of a filename . |
16,487 | def split_ext ( path , basename = True ) : if basename : path = os . path . basename ( path ) return os . path . splitext ( path ) | Wrap them to make life easier . |
16,488 | def ad_hoc_magic_from_file ( filename , ** kwargs ) : with open ( filename , 'rb' ) as stream : head = stream . read ( 16 ) if head [ : 4 ] == b'\x7fELF' : return b'application/x-executable' elif head [ : 2 ] == b'MZ' : return b'application/x-dosexec' else : raise NotImplementedError ( ) | Ad - hoc emulation of magic . from_file from python - magic . |
16,489 | def expand_path ( * paths ) : return os . path . join ( os . path . dirname ( os . path . realpath ( sys . argv [ 0 ] ) ) , * paths ) | Expand the path with the directory of the executed file . |
16,490 | def translate_filenames ( filenames ) : if is_windows ( ) : return filenames for index , filename in enumerate ( filenames ) : filenames [ index ] = vboxsf_to_windows ( filename ) | Convert filenames from Linux to Windows . |
16,491 | def vboxsf_to_windows ( filename , letter = 'f:' ) : home = os . path . expanduser ( '~' ) filename = os . path . abspath ( filename ) . replace ( home , letter ) return filename . replace ( '/' , '\\' ) | Convert the Linux path name to a Windows one . |
16,492 | def read_files ( filenames , with_name = False ) : text = [ read_file ( filename ) for filename in filenames ] if with_name : return dict ( zip ( filenames , text ) ) return text | Read many files . |
16,493 | def write_files ( text , where = '.' ) : for filename in text : target = os . path . join ( where , filename ) write_file ( target , text [ filename ] ) | Write many files . |
16,494 | def write_file ( filename , text ) : logging . debug ( _ ( 'Writing file: %s' ) , filename ) try : with open ( filename , 'w' ) as writable : writable . write ( text ) except ( PermissionError , NotADirectoryError ) : logging . error ( _ ( 'Error writing file: %s' ) , filename ) return False return True | Write text to a file . |
16,495 | def stylify_files ( text ) : for filename in text : text [ filename ] = stylify_code ( text [ filename ] ) return text | Stylify many files . |
16,496 | def stylify_code ( code ) : try : output = check_output ( [ 'astyle' , '--max-code-length=69' , '--indent=spaces=2' ] , universal_newlines = True , input = code ) except ( OSError , CalledProcessError , TypeError ) : logging . debug ( _ ( 'failed to stylify code' ) ) return code return output | Stylify the C source code using astyle . |
16,497 | def sort_item ( iterable , number , reverse = False ) : return sorted ( iterable , key = itemgetter ( number ) , reverse = reverse ) | Sort the itertable according to the given number item . |
16,498 | def remove_by ( keys , original ) : for i in [ original [ index ] for index , needed in enumerate ( keys ) if not needed ] : original . remove ( i ) | Remove items in a list according to another list . |
16,499 | def group_by ( iterable , key_func ) : groups = ( list ( sub ) for key , sub in groupby ( iterable , key_func ) ) return zip ( groups , groups ) | Wrap itertools . groupby to make life easier . |
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