1:\n print 'warning: inkonsistente Kopfdaten in AFK00: FKRGNR = %s' % rechnungsnr\n print kopf\n kopf = kopf[0]\n # TODO: der code schient nciht zu klappen, wenn gar keine Auftragstexte vorhanden sind.\n postmp = get_connection().query(['AFU00', 'AAT00'],\n condition=\"FURGNR=%s AND FUAUFN=ATAUFN AND FUAUPO=ATAUPO AND ATTART=8\" % sql_escape(rechnungsnr))\n\n # wenn eine Rechnungsposition mehr als einen Rechnungstext hat, ist sie jetzt mehrfach in positionen\n # dedupen und spezial felder auseinanderklamuesern\n positionen = {}\n texte = {}\n for line in postmp:\n positionen.setdefault(line['auftragsposition'], {}).update(line)\n text = line['text'].strip()\n if not text.startswith('#:'):\n texte.setdefault(line['auftragsposition'], []).append(line['text'])\n if text.startswith('#:guid:'):\n positionen[line['auftragsposition']]['guid'] = text[7:]\n for posnr, textlines in texte.items():\n positionen[posnr]['text'] = ' '.join(textlines)\n\n return kopf, positionen.values()","def getJournal(self):\n if 'journal' in self.extras: \n return self.extras['journal']\n #--Default \n self.extras['journal'] = _('[No Journal Record Found.]')\n #--Open save file and look for journal entry\n inPath = os.path.join(self.dir,self.name)\n ins = Tes3Reader(self.name,file(inPath,'rb'))\n #--Raw data read\n while not ins.atEnd():\n #--Get record info and handle it\n (name,size,delFlag,recFlag) = ins.unpackRecHeader()\n if name != 'JOUR':\n ins.seek(size,1,name)\n #--Journal\n else:\n (subName,subSize) = ins.unpackSubHeader('JOUR')\n if subName != 'NAME':\n self.extras['journal'] == _('[Error reading file.]')\n else:\n reDate = re.compile(r'<FONT COLOR=\"9F0000\">(.+?)</FONT><BR>')\n reTopic = re.compile(r'@(.*?)#')\n data = ins.read(subSize)\n data = reDate.sub(ReplJournalDate(),data)\n data = reTopic.sub(r'\\1',data)\n self.extras['journal'] = cstrip(data)\n break\n #--Done\n ins.close()\n print self.extras['journal']\n return self.extras['journal']","def get_article(doi, output='txt'):\n xml = download_article(doi)\n if xml is None:\n return None\n et = ET.fromstring(xml)\n full_text = et.find('article:originalText', elsevier_ns)\n if full_text is None:\n logging.info('Could not find full text for %s.' % doi)\n return None\n main_body = full_text.find('xocs:doc/xocs:serial-item/ja:article/ja:body',\n elsevier_ns)\n if main_body is None:\n return None\n if output == 'xml':\n return main_body\n elif output == 'txt':\n sections = main_body.findall('common:sections/common:section',\n elsevier_ns)\n full_txt = ''\n for s in sections:\n # Paragraphs that are directly under the section\n pars = s.findall('common:para', elsevier_ns)\n # Paragraphs that are under a section within the section\n pars += s.findall('common:section/common:para', elsevier_ns)\n for p in pars:\n # Get the initial string inside the paragraph\n if p.text is not None:\n full_txt += p.text\n # When there are tags inside the paragraph (for instance\n # references), we need to take those child elements one by one\n # and get the corresponding tail strings and join these. \n full_txt += ''.join([c.tail if c.tail is not None \n else '' for c in p.getchildren()])\n full_txt += '\\n'\n else:\n logging.error('Unknown output format %s.' % output)\n return None\n return full_txt","def _backup_ligand_extraction(self, pdb, resname):\n from rdkit import Chem\n ligand_lines = []\n\n with open(pdb, \"r\") as f:\n lines = f.readlines()\n for line in lines:\n if (line.startswith(\"ATOM\") or line.startswith(\"HETATM\")) and line[17:20].strip() == resname:\n ligand_lines.append(line)\n ligand_block = \"\".join(ligand_lines)\n ligand = Chem.MolFromPDBBlock(ligand_block)\n return ligand","def get_paper_by_id(paper_id):\n dblp_key = paper_id.replace(\"/\", \"_\")\n if local.paper_exists(dblp_key):\n return dblp_key\n\n print(\"getting information from dblp about paper {}\".format(paper_id))\n data = get(\"https://dblp.org/rec/\" + paper_id + \".xml\")[\"dblp\"]\n return get_paper(data)","def find_rent(self, id):\n allR=self.__loadFromFile()\n for bk in allR:\n if bk.getId()==id:\n return bk","def get_by_id(dataobj_id):\n results = list(get_data_dir().rglob(f\"{dataobj_id}-*.md\"))\n return results[0] if results else None","def get_observation(observation_id: str):\n pass","def get_bom_by_name(request):\n if not request.user.is_authenticated:\n return JsonResponse({\"success\": False}, status=401)\n if request.method == \"GET\" and request.is_ajax():\n bom_name = request.GET.get(\"searchTerm\")\n try:\n boms = BillOfMaterial.objects.filter(\n bom_name__icontains=bom_name\n )\n data = [\n {\"id\": bom.bom_name,\n \"text\": bom.bom_name, }\n for bom in boms\n ]\n except Exception:\n return JsonResponse({\"success\": False}, status=400)\n return JsonResponse(data, safe=False, status=200)\n return JsonResponse({\"success\": False}, status=405)","def identify_dvd(job):\n # Added from pull 366\n \"\"\" Manipulates the DVD title and calls OMDB to try and \t\n lookup the title \"\"\"\n\n # Safe way of dealing with log files if the users need to post it online\n # cleanlog = makecleanlogfile(job)\n # logging.debug(\"#### --- job ----\" + str(cleanlog))\n\n # Added from #338\n # Some older DVDs aren't actually labelled\n if not job.label or job.label == \"\":\n job.label = \"not identified\"\n\n dvd_info_xml = False\n dvd_release_date = \"\"\n\n # TODO: remove this because its pointless keeping when it can never work\n try:\n crc64 = pydvdid.compute(str(job.mountpoint))\n fallback_title = \"{0}_{1}\".format(str(job.label), str(crc64))\n dvd_title = str(fallback_title)\n except pydvdid.exceptions.PydvdidException as e:\n logging.error(\"Pydvdid failed with the error: \" + str(e))\n dvd_title = fallback_title = str(job.label)\n crc64 = \"\"\n\n logging.info(\"DVD CRC64 hash is: \" + str(crc64))\n job.crc_id = str(crc64)\n\n # Dead needs removing\n urlstring = \"http://metaservices.windowsmedia.com/pas_dvd_B/template/GetMDRDVDByCRC.xml?CRC={0}\".format(str(crc64))\n logging.debug(urlstring)\n\n dvd_title = job.label\n logging.debug(\"dvd_title_label= \" + str(dvd_title))\n # strip all non-numeric chars and use that for year\n year = re.sub(\"[^0-9]\", \"\", str(job.year))\n # next line is not really needed, but we dont want to leave an x somewhere\n dvd_title = job.label.replace(\"16x9\", \"\")\n # Rip out any not alpha chars replace with\n dvd_title = re.sub(\"[^a-zA-Z ]\", \" \", dvd_title)\n logging.debug(\"dvd_title ^a-z= \" + str(dvd_title))\n # rip out any SKU's at the end of the line\n dvd_title = re.sub(\"SKU$\", \" \", dvd_title)\n logging.debug(\"dvd_title SKU$= \" + str(dvd_title))\n\n # try to contact omdb\n try:\n dvd_info_xml = callwebservice(job, job.config.OMDB_API_KEY, dvd_title, year)\n logging.debug(\"DVD_INFO_XML: \" + str(dvd_info_xml))\n except OSError as e:\n # we couldnt reach omdb\n logging.error(\"Failed to reach OMDB\")\n return False\n\n job.year = year\n job.title = dvd_title\n db.session.commit()\n return True","def get_prediction_judgement(id):\n for line in open('working/sick.run'):\n if line.split()[0] is str(id):\n return line.split()[2]\n print line.split()[2]\n\n return 2.5","def getMaterialIndex(gltf, idname):\n if idname is None:\n return -1\n\n if gltf.get('materials') is None:\n return -1\n\n index = 0\n for material in gltf['materials']:\n key = 'id' if material.get('id') != None else 'name'\n if material.get(key) == idname:\n return index\n\n index += 1\n\n return -1","def find_one_byflexibleid(cls, stringfieldname, nameorid):\n if (isinstance(nameorid,(int,long)) or nameorid.isnumeric()):\n return cls.find_one_byprimaryid(nameorid)\n return cls.find_one_bykey({stringfieldname:nameorid})","def get_material(material):\n for libn,tdict in liblist:\n if material in tdict:\n return tdict[material]\n print (material, \" not found\")\n raise KeyError","def get_ols_link(prefix: str, identifier: str) -> Optional[str]:\n ols_prefix = get_ols_prefix(prefix)\n obo_link = get_obofoundry_link(prefix, identifier)\n if ols_prefix is None or obo_link is None:\n return None\n return f\"https://www.ebi.ac.uk/ols/ontologies/{ols_prefix}/terms?iri={obo_link}\"","def fetch_arxiv_bibtex(fp, info=None):\n info = info if info else is_arxiv(fp)\n\n if info:\n cat, num = info\n\n # Successful. Now fetch the BiBTeX.\n page = urlopen('http://adsabs.harvard.edu/cgi-bin/bib_query?'\n 'arXiv:{}{}'.format(cat + '/' if cat else '',\n num)).read()\n soup = BeautifulSoup(page, 'html5lib')\n el = soup.find('a', text='Bibtex entry for this abstract', href=True)\n href = urlopen(el['href']).read().decode()\n\n # Skip until the first '@', which should mark the beginning of the\n # BiBTeX.\n return '@' + '@'.join(href.split('@')[1:])\n return None","def select_calib_from_database(index_file, dateobs):\n\n # get instrument name\n mobj = re.match('wlcalib_(\\S*)\\.dat$', os.path.basename(index_file))\n instrument = mobj.group(1)\n\n calibtable = Table.read(index_file, format='ascii.fixed_width_two_line')\n\n input_date = dateutil.parser.parse(dateobs)\n\n # select the closest ThAr\n timediff = [(dateutil.parser.parse(t)-input_date).total_seconds()\n for t in calibtable['obsdate']]\n irow = np.abs(timediff).argmin()\n row = calibtable[irow]\n fileid = row['fileid'] # selected fileid\n md5 = row['md5']\n\n message = 'Select {} from database index as ThAr reference'.format(fileid)\n logger.info(message)\n\n filepath = os.path.join('instruments/{}'.format(instrument),\n 'wlcalib_{}.fits'.format(fileid))\n filename = get_file(filepath, md5)\n\n # load spec, calib, and aperset from selected FITS file\n hdu_lst = fits.open(filename)\n head = hdu_lst[0].header\n spec = hdu_lst[1].data\n hdu_lst.close()\n\n calib = get_calib_from_header(head)\n\n return spec, calib","def fetch(bibcode, filename=None, replace=None):\n arxiv = False\n print('Fetching PDF file from Journal website:')\n req = request_ads(bibcode, source='journal')\n if req is None:\n return\n\n if req.status_code != 200:\n print('Fetching PDF file from ADS website:')\n req = request_ads(bibcode, source='ads')\n if req is None:\n return\n\n if req.status_code != 200:\n print('Fetching PDF file from ArXiv website:')\n req = request_ads(bibcode, source='arxiv')\n arxiv = True\n if replace is None:\n replace = False\n if req is None:\n return\n if replace is None:\n replace = True\n\n if req.status_code == 200:\n if bm.find(bibcode=bibcode) is None:\n if filename is None:\n filename = f'{bibcode}.pdf'\n with builtin_open(filename, 'wb') as f:\n f.write(req.content)\n print(f\"Saved PDF to: '{filename}'.\\n\"\n \"(Note that BibTex entry is not in the Bibmanager database)\")\n else:\n filename = set_pdf(\n bibcode, bin_pdf=req.content, filename=filename, arxiv=arxiv,\n replace=replace)\n return filename\n\n print('Could not fetch PDF from any source.')","def GetJ(self, *args):\n return _table.Table_GetJ(self, *args)","def get_term(self, idx):\n try:\n return self.id2term[idx]\n except KeyError:\n return self.unk_term","def _eidnamelookup(eid):\n\n url = b64decode('aHR0cDovL20uZXNwbi5nby5jb20vbmZsL3BsYXllcmluZm8/cGxheWVySWQ9') + eid + '&wjb='\n req = urllib2.Request(url)\n r = urllib2.urlopen(req)\n html = r.read()\n try:\n soup = BeautifulSoup(html)\n team = soup.find('td', attrs={'class':'teamHeader'}).find('b')\n name = soup.find('div', attrs={'class':'sub bold'})\n return \"{0} {1}\".format(team.getText(), name.getText())\n except Exception, e:\n print \"ERROR: _eidnamelookup :: {0}\".format(e)\n return None","def get_arxiv_report_nr(text):\n return text.lower().lstrip(\"arxiv:\").strip(\"/\")","def get_basis_element_from_ccRepo(element,\n program='Gaussian',\n basis='cc-pVDZ'):\n\n # Check main page element list\n with req.get(\"http://www.grant-hill.group.shef.ac.uk/ccrepo/\") as resp:\n element_list = []\n for m in re.finditer('class=\"sym\" href=', resp.text):\n # print(resp.text[m.end():m.end()+50].split('\"')[1] )\n element_list.append(resp.text[m.end():m.end()+50].split('\"')[1])\n\n element_dict = {atom[1]: atom[2].lower() for atom in atom_data[1:]}\n\n try:\n resp = req.get(\"http://www.grant-hill.group.shef.ac.uk/ccrepo/{}\".format(element_dict[element]))\n except KeyError as e:\n raise Exception('Atom label {} not recognized'.format(e.args[0]))\n\n n_ini = resp.text.find('form-inline')\n\n # determinte the php web address for particular element\n php_site = resp.text[n_ini:n_ini+100].split('\"')[2]\n\n # print('http://www.grant-hill.group.shef.ac.uk/ccrepo/{}/{}'.format(element, php_site))\n # r = req.post(url = 'http://www.grant-hill.group.shef.ac.uk/ccrepo/titanium/tibasis.php', data = data)\n r = req.post(url='http://www.grant-hill.group.shef.ac.uk/ccrepo/{}/{}'.format(element_dict[element], php_site),\n data={'basis': basis, 'program': program})\n\n # parse the data\n tree = html.fromstring(r.content)\n r.close()\n\n header = tree.xpath('//div[@class=\"container\"]/text()')\n citation = unicodedata.normalize('NFC', six.text_type(header[1])).strip()\n description = unicodedata.normalize('NFC', header[2]).strip()\n\n\n basis_data = tree.xpath('/html/body/div/nobr/text()')\n basis_clean = [unicodedata.normalize('NFKC', six.text_type(line)).strip() for line in basis_data]\n # basis_name = basis_clean[1].split('\"')[1]\n\n return citation, description, basis_clean[2:]","def get_ontology_version(name):\n if isinstance(name, str) == False:\n name = name.version\n\n return name.replace(\".\", \"_\")","def get_model(branch, internet):\n\n url = 'https://raw.githubusercontent.com/sot/chandra_models/master/chandra_models/xija/'\n local_dir = '/AXAFLIB/chandra_models/chandra_models/xija/'\n\n if internet:\n model_spec_url = url + branch # aca/aca_spec.json'\n with urlopen(model_spec_url) as url:\n response = url.read()\n f = response.decode('utf-8')\n else:\n with open(home + local_dir + branch) as fid: # 'aca/aca_spec.json', 'rb') as fid:\n f = fid.read()\n return json.loads(f)","def term_from_uri(uri):\n if uri is None:\n return None\n # This insures that if we get a Literal with an integer value (as we\n # do for modification positions), it will get converted to a string,\n # not an integer.\n if isinstance(uri, rdflib.Literal):\n uri = str(uri.toPython())\n # This is to handle URIs like\n # http://www.openbel.org/bel/namespace//MAPK%20Erk1/3%20Family\n # or\n # http://www.openbel.org/bel/namespace/MAPK%20Erk1/3%20Family\n # In the current implementation, the order of the patterns\n # matters.\n patterns = ['http://www.openbel.org/bel/namespace//(.*)',\n 'http://www.openbel.org/vocabulary//(.*)',\n 'http://www.openbel.org/bel//(.*)',\n 'http://www.openbel.org/bel/namespace/(.*)',\n 'http://www.openbel.org/vocabulary/(.*)',\n 'http://www.openbel.org/bel/(.*)']\n for pr in patterns:\n match = re.match(pr, uri)\n if match is not None:\n term = match.groups()[0]\n term = unquote(term)\n return term\n # If none of the patterns match then the URI is actually a simple term\n # for instance a site: \"341\" or a substitution: \"sub(V,600,E)\"\n return uri","def compatible_firmware_version(self):\n identifier = self.firmware_version.split('compiled')[0]\n buf_size = self.MAX_BUF_SIZE\n buf = (ctypes.c_char * buf_size)()\n res = self._dll.JLINKARM_GetEmbeddedFWString(identifier.encode(), buf, buf_size)\n if res < 0:\n raise errors.JLinkException(res)\n\n return ctypes.string_at(buf).decode()","def author(self):\n\t\tauthor = re.search(r\"([Ff]rom\\s)(.+) ([tT]\\s*o)([^,]+),\",self.raw_text()[:150])\n\t\treport = re.search(r\".*[Rr]eport of ([^,]+),\",self.raw_text()[:150])\n\t\torder = re.search(r\".*[Oo]rder of ([^,]+)[,.]* to\",self.raw_text()[:250])\n\t\torder2 = re.search(r\".*[Oo]rder of ([^,]+),\",self.raw_text()[:250])\n\t\tlogbook = re.search(r\".*[lL]og of ([^,]+)[,.]\",self.raw_text()[:250])\n\t\tif order:\n\t\t\torder = order.group(1)\n\t\t\treturn order\n\t\tif order2:\n\t\t\torder2 = order2.group(1)\n\t\t\treturn order2\n\t\tif logbook:\n\t\t\tlogbook = logbook.group(1)\n\t\t\treturn logbook\n\t\tif report:\n\t\t\treport = report.group(1)\n\t\t\treturn report\n\t\tif author: \t\n\t\t\tauthor = author.group(2) \n\t\t\tauthor = re.sub(r\"([^,]*),.*\",r\"\\1\",author)\t \n\t\t\treturn author\n\t\t\n\t\treturn \"Unknown\"","def _get_version(self, identifier: Identifier,\n version: Optional[int] = None) -> DocMetadata:\n parent_path = self._get_parent_path(identifier=identifier,\n version=version)\n path = os.path.join(parent_path,\n (f'{identifier.filename}.abs' if not version\n else f'{identifier.filename}v{version}.abs'))\n return self.parse_abs_file(filename=path)","def getTerm(vocabulary_id, term_id):\n if term_id is None:\n return None\n vocabulary = getVocabulary(vocabulary_id)\n for term in vocabulary:\n if term['id'] == term_id:\n return term\n return None","def _get_target_version_by_name(jira, conf, name):\n versions = jira.project_versions(conf.JIRA['project'])\n for version in versions:\n if getattr(version, 'name') == name:\n return version\n\n return None","def getVersion(self,fileName):\n if not fileName in self.data or not self.data[fileName].tes3:\n return ''\n maVersion = reVersion.search(self.data[fileName].tes3.hedr.description)\n return (maVersion and maVersion.group(2)) or ''","def sparql_compare_ont(obj):\n if not 'ontology_purl' in obj:\n return\n purl = obj['ontology_purl']\n id = obj['id']\n # this could be made more declarative, or driven by the context.jsonld mapping;\n # however, for now this is relatively simple and easy to understand:\n license = obj['license']['url'] if 'license' in obj else ''\n run_sparql(obj, 'license', license, \"SELECT DISTINCT ?license WHERE {<\"+purl+\"> <http://purl.org/dc/elements/1.1/license> ?license}\")\n run_sparql(obj, 'title', obj['title'] if 'title' in obj else '', \"SELECT DISTINCT ?title WHERE {<\"+purl+\"> <http://purl.org/dc/elements/1.1/title> ?title}\")\n run_sparql(obj, 'description', obj['description'] if 'description' in obj else '', \"SELECT DISTINCT ?description WHERE {<\"+purl+\"> <http://purl.org/dc/elements/1.1/description> ?description}\")\n run_sparql(obj, 'homepage', obj['homepage'] if 'homepage' in obj else '', \"SELECT DISTINCT ?homepage WHERE {<\"+purl+\"> <http://xmlns.com/foaf/0.1/homepage> ?homepage}\")","def findBorehole(strg, fld_name, bh_name):\r\n\r\n #print(fld_name, bh_name)\r\n\r\n reg_fld = strg.getRegHelper().getFieldRegistry()\r\n fld = reg_fld.findByName(fld_name)\r\n if fld is None:\r\n return None\r\n\r\n reg_bh = strg.getRegHelper().getBoreholeRegistry()\r\n bh = reg_bh.findByNameAndField(fld.getID(), bh_name)\r\n\r\n return bh","def longestorf(args):\n p = OptionParser(longestorf.__doc__)\n p.add_option(\"--ids\", action=\"store_true\", help=\"Generate table with ORF info\")\n opts, args = p.parse_args(args)\n\n if len(args) != 1:\n sys.exit(not p.print_help())\n\n (fastafile,) = args\n pf = fastafile.rsplit(\".\", 1)[0]\n orffile = pf + \".orf.fasta\"\n idsfile = None\n if opts.ids:\n idsfile = pf + \".orf.ids\"\n fwids = open(idsfile, \"w\")\n\n f = Fasta(fastafile, lazy=True)\n fw = must_open(orffile, \"w\")\n before, after = 0, 0\n for name, rec in f.iteritems_ordered():\n cds = rec.seq\n before += len(cds)\n # Try all six frames\n orf = ORFFinder(cds)\n lorf = orf.get_longest_orf()\n newcds = Seq(lorf)\n after += len(newcds)\n newrec = SeqRecord(newcds, id=name, description=rec.description)\n SeqIO.write([newrec], fw, \"fasta\")\n if idsfile:\n print(\"\\t\".join((name, orf.info)), file=fwids)\n\n fw.close()\n if idsfile:\n fwids.close()\n\n logging.debug(\n \"Longest ORFs written to `{0}` ({1}).\".format(\n orffile, percentage(after, before)\n )\n )\n\n return orffile","def orfFinder(data):\n\t\n\tORFile = getORFs(data.seqFile, \n\t\t\t\t\t data.queryName, \n\t\t\t\t\t data.o)\n\tsetattr(data, \"ORFs\", ORFile)","def get_instance(string):\n row = string.split(\".\")\n\n # handles \"f.eid\" case\n if len(row) < 4:\n return \"0\"\n\n # the number is somewhat arbitrary... \n # it is determined by Joeri's UK Phenotypes script.\n # (which is \"get_UKphenotypes.r\" --- thanks Joeri!)\n return row[2]","def get_software_by_id(self, id_code):\r\n malware_return = self.fs.query([\r\n Filter('type', '=', 'malware'),\r\n Filter('external_references.external_id', '=', id_code)\r\n ])\r\n\r\n tool_return = self.fs.query([\r\n Filter('type', '=', 'tool'),\r\n Filter('external_references.external_id', '=', id_code)\r\n ])\r\n\r\n if malware_return:\r\n return malware_return\r\n elif tool_return:\r\n return tool_return","def get_scn_unq_name(self, unq_id):\n logger.debug(\"Creating Database Engine and Session.\")\n db_engine = sqlalchemy.create_engine(self.db_info_obj.dbConn)\n session_sqlalc = sqlalchemy.orm.sessionmaker(bind=db_engine)\n ses = session_sqlalc()\n logger.debug(\"Perform query to find scene.\")\n query_result = ses.query(EDDSentinel1ASF).filter(EDDSentinel1ASF.PID == unq_id).one_or_none()\n if query_result is None:\n raise EODataDownException(\"Scene ('{}') could not be found in database\".format(unq_id))\n unq_name = \"{}_{}\".format(query_result.Product_File_ID, query_result.PID)\n ses.close()\n logger.debug(\"Closed the database session.\")\n return unq_name","def get_wdetJ(self, etype: str, *, elm: int, nds: list = None) -> np.ndarray:\n if etype == \"area\":\n cod = self._coords[:, np.array(self._connectivity[elm])[nds]][: self._n_dof]\n else:\n cod = self._coords[:, self._connectivity[elm]][: self._n_dof]\n\n return self._shapef[self._element_name[elm]][etype].get_wdetJ(cod)","def match_doi_or_arxiv(text, only=[\"DOI\", \"arXiv\"]):\n text = text.lower()\n # Try to extract DOI\n if \"DOI\" in only:\n extractID = regex.doi.search(text.replace('Œ', '-'))\n if not extractID:\n # PNAS fix\n extractID = regex.doi_pnas.search(text.\n replace('pnas', '/pnas'))\n if not extractID:\n # JSB fix\n extractID = regex.doi_jsb.search(text)\n if extractID:\n # If DOI extracted, clean it and return it\n cleanDOI = False\n cleanDOI = extractID.group(0).replace(':', '').replace(' ', '')\n if regex.clean_doi.search(cleanDOI):\n cleanDOI = cleanDOI[1:]\n # FABSE J fix\n if regex.clean_doi_fabse.search(cleanDOI):\n cleanDOI = cleanDOI[:20]\n # Second JCB fix\n if regex.clean_doi_jcb.search(cleanDOI):\n cleanDOI = cleanDOI[:21]\n if len(cleanDOI) > 40:\n cleanDOItemp = regex.clean_doi_len.sub('000', cleanDOI)\n reps = {'.': 'A', '-': '0'}\n cleanDOItemp = tools.replaceAll(cleanDOItemp[8:], reps)\n digitStart = 0\n for i in range(len(cleanDOItemp)):\n if cleanDOItemp[i].isdigit():\n digitStart = 1\n if cleanDOItemp[i].isalpha() and digitStart:\n break\n cleanDOI = cleanDOI[0:(8+i)]\n return (\"DOI\", cleanDOI)\n # Else, try to extract arXiv\n if \"arXiv\" in only:\n extractID = regex.arXiv.search(text)\n if extractID:\n return (\"arXiv\", extractID.group(1))\n return None","def jid_jname(jnid):\n jails = jails_list()\n try:\n int(jnid) == True\n testid = 0\n except ValueError:\n testid = 1\n\n if testid == 0:\n if jnid in jails[2]:\n j = jails[2].index(jnid)\n jnid = jails[1][j]\n else:\n print \" Jail with ID '%s' not found!\" % (jnid)\n return False\n\n return jnid","def get_party_name_by_id(party_id: int) -> str:\n # Open a new connection\n db, cursor = db_connector.cursor()\n query = \"select name from party where id = '{}';\".format(party_id)\n cursor.execute(query)\n data = cursor.fetchall()\n db.disconnect()\n return data[0][0]","def get_sf (pdb_id):\n pdb_ftp_link = \"https://ftp.rcsb.org/pub/pdb/data/structures/all/structure_factors/\"\n url = pdb_ftp_link + \"r{}sf.ent.gz\".format(pdb_id)\n r = requests.get(url)\n with open(sf_path + \"r{}sf.cif.gz\".format(pdb_id), 'wb') as f:\n f.write(r.content)\n #unzips the downloaded file\n os.system(\"gunzip \"+sf_path + \"r{}sf.cif.gz\".format(pdb_id))\n return \"r{}sf.cif\".format(pdb_id)","def onto(disgenet, edam):\n disgenet = disgenet.replace(' ', '+').replace(\"'\", \"%27\")\n edam = edam.replace(' ', '+').replace(\"'\", \"%27\")\n disid = subprocess.Popen(\n [\"curl -s -k http://127.0.0.1:3030/ds/query -X POST --data \" +\n \"'query=PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0A\" +\n \"PREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A\" +\n \"PREFIX+ncit%3A+%3Chttp%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23%3E%0A\" +\n \"SELECT+DISTINCT+%0A%09%3Fdisease+%0AFROM+%3Chttp%3A%2F%2Frdf.disgenet.org%3E+%0AWHERE+%7B%0A++\" +\n \"SERVICE+%3Chttp%3A%2F%2Frdf.disgenet.org%2Fsparql%2F%3E+%7B%0A++++\" +\n \"%3Fdisease+rdf%3Atype+ncit%3AC7057+%3B%0A++++%09dcterms%3Atitle+%22\" + disgenet +\n \"%22%40en+.%0A%7D%0A%7D' -H 'Accept: application/sparql-results+json,*/*;q=0.9'\"],\n stdout=subprocess.PIPE, shell=True).communicate()[0]\n edam_id = subprocess.Popen([\"curl -s 'http://www.ebi.ac.uk/ols/api/search?q=\" + edam + \"&ontology=edam' 'Accept: application/json'\"],\n stdout=subprocess.PIPE, shell=True).communicate()[0]\n try:\n jdisease = json.loads(disid)\n umllist = []\n umls = jdisease['results']['bindings'][0]['disease']['value']\n except (IndexError, ValueError):\n umls = \"No disgenet record\"\n try:\n jedam = json.loads(edam_id)\n eid = jedam['response']['docs'][0]['iri']\n except (IndexError, ValueError):\n eid = \"No EDAM record\"\n return umls, eid","def get_movie(self, identifier: int) -> Movie:\n result = list(filter(lambda x: x.identifier == identifier, self.items))\n if result:\n return result[0]\n\n return None","def getFencerByAskfredId(table_conn=None, fencer_id=None):\n\n if table_conn is None or fencer_id is None:\n return None\n\n table_conn.execute('SELECT * FROM fencers WHERE fencer_id=?', fencer_id) \n\n row = table_conn.fetchall()\n if len(row) > 1:\n print((\"Duplicate fencer record:\", row[0][1], \" \", row[0][2]))\n\n if len(row) == 0:\n return None\n\n return Fencer(row[0][0], row[0][1], row[0][2], row[0][3], row[0][4])","def get_object(id):","def get_bsp_from_jpl(identifier, initial_date, final_date, email, directory):\n import pathlib\n import shutil\n from datetime import datetime as dt\n\n import requests\n import spiceypy as spice\n\n date1 = dt.strptime(initial_date, \"%Y-%m-%d\")\n date2 = dt.strptime(final_date, \"%Y-%m-%d\")\n diff = date2 - date1\n\n if diff.days <= 32:\n raise ValueError(\n \"The [final_date] must be more than 32 days later than [initial_date]\"\n )\n\n urlJPL = \"https://ssd.jpl.nasa.gov/x/smb_spk.cgi?OPTION=Make+SPK\"\n\n path = pathlib.Path(directory)\n if not path.exists():\n raise ValueError(\"The directory {} does not exist!\".format(path))\n\n filename = identifier.replace(\" \", \"\") + \".bsp\"\n\n parameters = {\n \"OBJECT\": identifier,\n \"START\": date1.strftime(\"%Y-%b-%d\"),\n \"STOP\": date2.strftime(\"%Y-%b-%d\"),\n \"EMAIL\": email,\n \"TYPE\": \"-B\",\n }\n\n r = requests.get(urlJPL, params=parameters, stream=True)\n bspFormat = r.headers[\"Content-Type\"]\n if r.status_code == requests.codes.ok and bspFormat == \"application/download\":\n file_path = path.joinpath(filename)\n with open(file_path, \"wb\") as f:\n r.raw.decode_content = True\n shutil.copyfileobj(r.raw, f)\n\n return file_path\n else:\n # TODO: Add a Debug\n raise Exception(\"It was not able to download the bsp file for object.\")","async def matchStrandToClass(pdbid:str, strand_id:str)->Union[str, None]:\n CYPHER=\"\"\"match (r:RibosomeStructure{{_rcsb_id: \"{}\"}})-[]-(rp:RibosomalProtein{{entity_poly_strand_id:\"{}\"}})-[]-(n:NomenclatureClass)\n return n.class_id\"\"\".format(pdbid.upper(), strand_id)\n resp = _neoget(CYPHER)\n if len(resp) > 0:\n return resp[0]\n else:\n return None","def get_id(self, refobj):\n return cmds.getAttr(\"%s.identifier\" % refobj)","def fetch(\n self,\n search_method: str,\n objective_function: str,\n weight: int,\n ):\n if os.path.isfile(self.filename):\n with open(self.filename, 'r+') as f:\n table = pandas.io.json.read_json(f)\n try:\n table = table[(table[\"objective\"] == objective_function)\n & (table[\"weight\"] == weight)\n & (table[\"search\"] == search_method)]\n best = table.loc[table['cost'].idxmax()]\n self.best_cost = best[\"cost\"]\n return best[\"code\"], best[\"cost\"], best[\"progress\"]\n except (ValueError, KeyError):\n pass\n return None, -np.inf, 0","def get_revision(filing_id, business_id):\n business = Business.find_by_internal_id(business_id)\n filing = Filing.find_by_id(filing_id)\n\n revision_json = {}\n revision_json['filing'] = {}\n if filing.filing_type == 'incorporationApplication':\n revision_json['filing'] = \\\n VersionedBusinessDetailsService.get_ia_revision(filing, business)\n elif filing.filing_type == 'changeOfDirectors':\n revision_json['filing'] = \\\n VersionedBusinessDetailsService.get_cod_revision(filing, business)\n elif filing.filing_type == 'changeOfAddress':\n revision_json['filing'] = \\\n VersionedBusinessDetailsService.get_coa_revision(filing, business)\n elif filing.filing_type == 'annualReport':\n revision_json['filing'] = \\\n VersionedBusinessDetailsService.get_ar_revision(filing, business)\n elif filing.filing_type == 'correction':\n revision_json = filing.json\n\n # This is required to find diff\n for party in revision_json.get('filing', {}).get('incorporationApplication', {}).get('parties', []):\n party['id'] = party.get('officer', {}).get('id', None)\n for party_role in party['roles']:\n party_role['id'] = party_role['roleType']\n\n # filing_type's yet to be handled alteration, changeOfName, specialResolution, voluntaryDissolution\n if not revision_json['filing']:\n revision_json = filing.json\n revision_json['filing']['business'] = \\\n VersionedBusinessDetailsService.get_business_revision(filing.transaction_id, business)\n\n revision_json['filing']['header'] = VersionedBusinessDetailsService.get_header_revision(filing)\n\n return revision_json","def get_orfs(gtf, args, config, is_annotated=False, is_de_novo=False):\n\n call = not args.do_not_call\n chr_name_file = os.path.join(config[\"star_index\"], \"chrName.txt\")\n chr_name_str = \"--chr-name-file {}\".format(chr_name_file)\n\n logging_str = logging_utils.get_logging_options_string(args)\n cpus_str = \"--num-cpus {}\".format(args.num_cpus)\n\n # extract a BED12 of the annotated ORFs\n transcript_bed = filenames.get_bed(\n config[\"genome_base_path\"],\n config[\"genome_name\"],\n is_annotated=is_annotated,\n is_de_novo=is_de_novo,\n )\n\n cmd = \"gtf-to-bed12 {} {} {} {} {}\".format(\n gtf, transcript_bed, chr_name_str, cpus_str, logging_str\n )\n in_files = [gtf]\n out_files = [transcript_bed]\n shell_utils.call_if_not_exists(\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\n )\n\n # extract the transcript fasta\n transcript_fasta = filenames.get_transcript_fasta(\n config[\"genome_base_path\"],\n config[\"genome_name\"],\n is_annotated=is_annotated,\n is_de_novo=is_de_novo,\n )\n\n cmd = \"extract-bed-sequences {} {} {} {}\".format(\n transcript_bed, config[\"fasta\"], transcript_fasta, logging_str\n )\n in_files = [transcript_bed, config[\"fasta\"]]\n out_files = [transcript_fasta]\n shell_utils.call_if_not_exists(\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\n )\n\n # extract ORFs from the transcripts using genomic coordinates\n orfs_genomic = filenames.get_orfs(\n config[\"genome_base_path\"],\n config[\"genome_name\"],\n note=config.get(\"orf_note\"),\n is_annotated=is_annotated,\n is_de_novo=is_de_novo,\n )\n\n start_codons_str = utils.get_config_argument(\n config, \"start_codons\", default=default_start_codons\n )\n\n stop_codons_str = utils.get_config_argument(\n config, \"stop_codons\", default=default_stop_codons\n )\n\n cmd = \"extract-orf-coordinates {} {} {} {} {} {} {}\".format(\n transcript_bed,\n transcript_fasta,\n orfs_genomic,\n cpus_str,\n start_codons_str,\n stop_codons_str,\n logging_str,\n )\n in_files = [transcript_fasta, transcript_bed]\n out_files = [orfs_genomic]\n shell_utils.call_if_not_exists(\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\n )\n\n # write the ORF exons, used to label the ORFs\n exons_file = filenames.get_exons(\n config[\"genome_base_path\"],\n config[\"genome_name\"],\n note=config.get(\"orf_note\"),\n is_annotated=is_annotated,\n is_de_novo=is_de_novo,\n )\n\n cmd = \"split-bed12-blocks {} {} --num-cpus {} {}\".format(\n orfs_genomic, exons_file, args.num_cpus, logging_str\n )\n in_files = [orfs_genomic]\n out_files = [exons_file]\n shell_utils.call_if_not_exists(\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\n )\n\n # label the ORFs\n labeled_orfs = filenames.get_labels(\n config[\"genome_base_path\"],\n config[\"genome_name\"],\n note=config.get(\"orf_note\"),\n is_annotated=is_annotated,\n is_de_novo=is_de_novo,\n )\n\n annotated_bed = filenames.get_bed(\n config[\"genome_base_path\"],\n config[\"genome_name\"],\n is_annotated=True,\n )\n\n orf_exons_str = \"--orf-exons {}\".format(exons_file)\n\n de_novo_str = \"\"\n if is_de_novo:\n de_novo_str = '--label-prefix \"novel_\" --filter --nonoverlapping-label \"novel\"'\n\n cmd = \"label-orfs {} {} {} {} {} {} {}\".format(\n annotated_bed,\n orfs_genomic,\n labeled_orfs,\n orf_exons_str,\n de_novo_str,\n logging_str,\n cpus_str,\n )\n in_files = [annotated_bed, orfs_genomic, exons_file]\n # ** this function overwrites the input file `orfs_genomic`\n out_files = [labeled_orfs]\n shell_utils.call_if_not_exists(\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\n )","def lookup(name):","def lookup(name):","def download_document(self,model,field,id,filename=None, **kw):\n Model = request.registry[model]\n cr, uid, context = request.cr, request.uid, request.context\n fields = [field]\n res = Model.read(cr, uid, [int(id)], fields, context)[0]\n filecontent = base64.b64decode(res.get(field) or '')\n if not filecontent:\n return request.not_found()\n else:\n if not filename:\n filename = '%s_%s' % (model.replace('.', '_'), id)\n return request.make_response(filecontent,\n [('Content-Type', 'application/octet-stream'),\n ('Content-Disposition', content_disposition(filename))])","def get_review(self, id_):\n cursor = self._connection.cursor()\n select_command = make_select_command(\"reviews\")\n select_command += \" WHERE id_ = ?\"\n cursor.execute(select_command, (id_,))\n for row in cursor:\n return expandable_from_tuple(row, FIELD_DESCRIPTIONS) \n return None","def get_date(bfo):\n from invenio.bibformat_elements.bfe_INSPIRE_arxiv import get_arxiv\n\n #true date\n date = bfo.fields('269__c')\n if date:\n datestruct=parse_date(date[0])\n if datestruct[0]:\n return(datestruct)\n\n\n #arxiv date\n arxiv = get_arxiv(bfo,category=\"no\")\n if arxiv:\n date=re.search('(\\d+)',arxiv[0]).groups()[0]\n if len(date) >=4:\n year = date[0:2]\n if year > '90':\n year='19'+year\n else:\n year='20'+year\n date = year+date[2:4]+'00'\n date=parse_date(date)\n if date[1]: return(date)\n\n\n\n #journal year\n if bfo.fields('773__y'):\n date= parse_date(bfo.fields('773__y')[0]+'0000')\n if date[0]:\n return date\n\n #date added\n if bfo.fields('961__x'):\n date= parse_date(bfo.fields('961__x')[0])\n if date[0]:\n return date\n\n\n return None","def fetch_sequence(sequence_id, database='uniprot'):\n if sequence_id.startswith('UPI'):\n database = 'uniparc'\n url_template = 'http://www.uniprot.org/uniparc/{}.fasta'\n elif sequence_id.startswith('UniRef'):\n database = 'uniref'\n url_template = 'http://www.uniprot.org/uniref/{}.fasta'\n else:\n database = 'uniprot'\n url_template = 'http://www.uniprot.org/uniprot/{}.fasta'\n\n url = url_template.format(sequence_id)\n logger.debug('Downloading sequence {} from {}...'.format(sequence_id, url))\n\n r = requests.get(url)\n if r.status_code != 200:\n raise Exception(\"Failed to fetch sequence with return code: {}\".format(r.status_code))\n\n seq = Bio.SeqIO.read(io.StringIO(r.text), 'fasta')\n if database == 'uniprot':\n seq.annotations['db'], seq.id, seq.name = re.split('[\\| ]', seq.id)\n return seq","def get_johans_features(modsizedif, prediction, id):\n data = []\n \n prover_output = 0\n if modsizedif == None:\n print id\n return ['1','1','1','1','1','1','1']\n \n if modsizedif[0].split()[0] == 'contradiction.':\n prover_output = 0.0\n if modsizedif[0].split()[0] == 'unknown.':\n prover_output = 0.5\n if modsizedif[0].split()[0] == 'proof.':\n prover_output = 1.0\n\n data.append(prover_output) # prover output\n data.append(float(modsizedif[1].split()[0][:-1])) # domain novelty\n data.append(float(modsizedif[2].split()[0][:-1])) # relation novelty\n data.append(float(modsizedif[3].split()[0][:-1])) # wordnet novelty\n data.append(float(modsizedif[4].split()[0][:-1])) # model novelty\n data.append(float(modsizedif[5].split()[0][:-1])) # word overlap\n \n if prediction[0].split()[0] == 'informative': # prediction.txt\n data.append(0)\n else:\n data.append(1)\n\n return data","def get_truck_by_driver_id(identifier):\n key = 'name'\n if identifier.isdigit():\n key = 'id'\n\n truck_to_return = {}\n driver = utils.get_dict_by_key_value_from_list(\n key, identifier, drivers)\n truck_to_return = utils.get_dict_by_key_value_from_list(\n 'id', driver.get('id'), trucks)\n return jsonify(truck_to_return)","def getObject(language=None):","def get(self, name_or_id):\n \n r = self.library.database.get_name(name_or_id)\n\n if not r[0]:\n r = self.library.database.get_id(name_or_id)\n \n return r","def _select_kinase_structure_by_pdb_id(\n self,\n pdb_id: str,\n klifs_kinase_id: int,\n chain_id: Union[str, None] = None,\n alternate_location: Union[str, None] = None,\n ) -> pd.Series:\n import pandas as pd\n\n from ..utils import LocalFileStorage\n\n logging.debug(\"Searching kinase structures from KLIFS matching the pdb of interest ...\")\n klifs_structures = pd.read_csv(LocalFileStorage.klifs_structure_db(self.cache_dir))\n structures = klifs_structures[\n klifs_structures[\"structure.pdb_id\"] == pdb_id\n ]\n structures = structures[\n structures[\"kinase.klifs_id\"] == klifs_kinase_id\n ]\n if alternate_location:\n structures = structures[\n structures[\"structure.alternate_model\"] == alternate_location\n ]\n if chain_id:\n structures = structures[\n structures[\"structure.chain\"] == chain_id\n ]\n\n if len(structures) == 0:\n text = (\n f\"No structure found for PDB ID {pdb_id}, chain {chain_id} and alternate location \"\n f\"{alternate_location}.\"\n )\n logging.debug(\"Exception: \" + text)\n raise NotImplementedError(text)\n else:\n logging.debug(\"Picking structure with highest KLIFS quality score ...\")\n structures = structures.sort_values(\n by=[\n \"structure.qualityscore\",\n \"structure.resolution\",\n \"structure.chain\",\n \"structure.alternate_model\"\n ],\n ascending=[False, True, True, True]\n )\n kinase_structure = structures.iloc[0]\n\n return kinase_structure","def retrieve(document_id: str) -> Fulltext:\n return current_session().retrieve(document_id)","def _cookIdCore(self, ref, **kwargs):\n\n # AUTHORS\n namepart='nobody'\n if self._refHasAuthorNames(ref):\n lastnames = []\n for each in ref['authors']:\n if each.get('lastname', None):\n lastnames.append(each['lastname'])\n\n if len(lastnames) > 1:\n namepart = '%s' % ''.join([ lastname[0] for lastname in lastnames ])\n elif len(lastnames) == 1:\n namepart = lastnames[0][:3]\n else:\n pass\n\n # PUBLICATION YEAR\n if ref.get('publication_year', None):\n yearpart = str(ref['publication_year'])\n else:\n yearpart = \"1000\"\n\n return namepart + yearpart","def identifier_version(self):\n return next(self.graph[self.identifier_bound:owl.versionIRI])","def get_jnt_index(self, jnt_name):\n return self.wrapper.get_jnt_index(self.instance, jnt_name.encode('utf-8'))","def _find_recife_editions(self, text):\n return (\n edition\n for edition in text.split(\"&\")\n if re.search(\"prefeituradorecife\", edition, re.IGNORECASE)\n )","def feature_to_open511_element(feature):\n\n # Using a hash of the geometry for an ID. For proper production use,\n # there'll probably have to be some code in the importer\n # that compares to existing entries in the DB to determine whether\n # this is new or modified...\n geom_hash = hashlib.md5(feature.geom.wkt).hexdigest()\n id = JURISDICTION + ':' + geom_hash\n while id in ids_seen:\n id += 'x'\n ids_seen.add(id)\n\n elem = E.RoadEvent(id=id)\n\n def set_val(tag, val):\n if val not in (None, ''):\n e = etree.Element(tag)\n e.text = unicode(val)\n elem.append(e)\n\n set_val('Title', feature.get('Name').decode('utf8'))\n\n blob = lxml.html.fragment_fromstring(feature.get('Description').decode('utf8'),\n create_parent='content')\n\n description_label = blob.xpath('//strong[text()=\"Description\"]')\n if description_label:\n description_bits = []\n el = description_label[0].getnext()\n while el.tag == 'p':\n description_bits.append(_get_el_text(el))\n el = el.getnext()\n set_val('Description', '\\n\\n'.join(description_bits))\n\n localisation = blob.cssselect('div#localisation p')\n if localisation:\n set_val('AffectedRoads', '\\n\\n'.join(_get_el_text(el) for el in localisation))\n\n try:\n set_val('ExternalURL', blob.cssselect('#avis_residants a, #en_savoir_plus a')[0].get('href'))\n except IndexError:\n pass\n\n facultatif = blob.cssselect('div#itineraire_facult p')\n if facultatif:\n set_val('Detour', '\\n\\n'.join(_get_el_text(el) for el in facultatif))\n\n if blob.cssselect('div#dates strong'):\n try:\n start_date = blob.xpath(u'div[@id=\"dates\"]/strong[text()=\"Date de d\\xe9but\"]')[0].tail\n end_date = blob.xpath(u'div[@id=\"dates\"]/strong[text()=\"Date de fin\"]')[0].tail\n if start_date and end_date:\n set_val('StartDate', _fr_string_to_date(start_date))\n set_val('EndDate', _fr_string_to_date(end_date))\n except IndexError:\n pass\n\n elem.append(E.Geometry(\n geom_to_xml_element(feature.geom)\n ))\n\n return elem","def j_jal(byte_string):\n\n opcode = int(byte_string[:6], 2)\n target = int(byte_string[6:], 2)\n if opcode == 2:\n target = target << 2\n print(OPCODES[opcode] + '\\t' + str(target))","def getGenomeName(recordID, filename):\n global FILENAMES\n global GENOMENAMES\n recordID = str(recordID)\n\n\n #Look for lcl followed by the possible genome name\n if re.search('lcl\\|([\\w-]*)', recordID):\n match = re.search('lcl\\|([\\w-]*)', recordID)\n match = str(match.group())\n genome_name = match.split('|')[1]\n\n #Look for a possible genome name at the beginning of the record ID\n elif re.search('(^[a-zA-Z][a-zA-Z]\\w{6}\\.\\d)',recordID):\n match = re.search('(\\w{8}\\.\\d)',recordID)\n genome_name = str(match.group())\n\n #Look for ref, gb, emb or dbj followed by the possible genome name\n elif re.search('(ref\\|\\w{2}_\\w{6}|gb\\|\\w{8}|emb\\|\\w{8}|dbj\\|\\w{8})',recordID):\n match = re.search('(ref\\|\\w{2}_\\w{6}|gb\\|\\w{8}|emb\\|\\w{8}|dbj\\|\\w{8})',recordID)\n match = str(match.group())\n genome_name = match.split('|')[1]\n\n #Look for gi followed by the possible genome name\n elif re.search('gi\\|\\d{8}', recordID):\n match = re.search('gi\\|\\d{8}', recordID)\n match = str(match.group())\n genome_name = match.split('|')[1]\n #Assign the file name as genome name\n else:\n genome_name = filename\n\n if recordID not in FILENAMES:\n FILENAMES[recordID] = filename\n if filename not in GENOMENAMES:\n GENOMENAMES[filename] = recordID\n\n return genome_name","def id(text):\n url = \"https://bio.torre.co/api/bios/{}\".format(text)\n request = get(url)\n print(request.status_code)\n if request.status_code != 200:\n abort(404, 'Not Found')\n return request.json()","def computeRjb(self, lon, lat, depth, var=False):\n cdir, tmp = os.path.split(__file__)\n origin = self._origin\n\n # -------------------\n # Sort out file names\n # -------------------\n mech = origin.mech\n if not hasattr(origin, '_tectonic_region'):\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechA_ar1p0_seis0_20_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechA_ar1p0_seis0_20_Var.csv\")\n elif origin._tectonic_region == 'Active Shallow Crust':\n if mech == 'ALL':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechA_ar1p7_seis0_20_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechA_ar1p7_seis0_20_Var.csv\")\n elif mech == 'RS':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechR_ar1p7_seis0_20_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechR_ar1p7_seis0_20_Var.csv\")\n elif mech == 'NM':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechN_ar1p7_seis0_20_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechN_ar1p7_seis0_20_Var.csv\")\n elif mech == 'SS':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechSS_ar1p7_seis0_20_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechSS_ar1p7_seis0_20_Var.csv\")\n elif origin._tectonic_region == 'Stable Shallow Crust':\n if mech == 'ALL':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechA_ar1p0_seis0_15_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechA_ar1p0_seis0_15_Var.csv\")\n elif mech == 'RS':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechR_ar1p0_seis0_15_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechR_ar1p0_seis0_15_Var.csv\")\n elif mech == 'NM':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechN_ar1p0_seis0_15_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechN_ar1p0_seis0_15_Var.csv\")\n elif mech == 'SS':\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechSS_ar1p0_seis0_15_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_S14_mechSS_ar1p0_seis0_15_Var.csv\")\n else:\n warnings.warn(\n 'Unsupported tectonic region; using coefficients for unknown'\n 'tectonic region.')\n rf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechA_ar1p0_seis0_20_Ratios.csv\")\n vf = os.path.join(\n cdir, \"data\", \"ps2ff\",\n \"Rjb_WC94_mechA_ar1p0_seis0_20_Var.csv\")\n\n # -----------------\n # Start with ratios\n # -----------------\n repi2rjb_ratios_tbl = pd.read_csv(rf, comment='#')\n r2rrt_cols = repi2rjb_ratios_tbl.columns[1:]\n mag_list = []\n for column in (r2rrt_cols):\n if re.search('R\\d+\\.*\\d*', column):\n magnitude = float(re.findall(\n 'R(\\d+\\.*\\d*)', column)[0])\n mag_list.append(magnitude)\n mag_list = np.array(mag_list)\n dist_list = np.log(np.array(repi2rjb_ratios_tbl['Repi_km']))\n repi2rjb_grid = repi2rjb_ratios_tbl.values[:, 1:]\n repi2rjb_obj = spint.RectBivariateSpline(\n dist_list, mag_list, repi2rjb_grid, kx=1, ky=1)\n\n def repi2rjb_tbl(repi, M):\n ratio = repi2rjb_obj.ev(np.log(repi), M)\n rjb = repi * ratio\n return rjb\n\n repis = self.computeRepi(lon, lat, depth)\n mags = np.ones_like(repis) * origin.mag\n rjb_hat = repi2rjb_tbl(repis, mags)\n\n # -------------------\n # Additional Variance\n # -------------------\n repi2rjbvar_ratios_tbl = pd.read_csv(vf, comment='#')\n repi2rjbvar_grid = repi2rjbvar_ratios_tbl.values[:, 1:]\n repi2rjbvar_obj = spint.RectBivariateSpline(\n dist_list, mag_list, repi2rjbvar_grid, kx=1, ky=1)\n rjbvar = repi2rjbvar_obj.ev(np.log(repis), mags)\n\n if var is True:\n return (rjb_hat, rjbvar)\n else:\n return rjb_hat","def searchTerm(self, resource, search, mode='default'):\n\n search = urlparse_quote(search)\n if mode == 'exact':\n url = self.fullUrl(resource) + '?$filter=Term%20eq%20%27{0}%27'.format(search)\n else:\n url = self.fullUrl(resource) + '?$filter=startswith(Term,%27{0}%27)%20eq%20true'.format(search)\n\n req = self.getRequest(url)\n return req\n #return req.json()","def getobj(*args, **kw):\n # 2008-07-30 16:56 IJC: Created\n # 2010-03-07 22:24 IJC: Updated w/new exoplanets.org data table! \n # 2010-03-11 10:01 IJC: If planet name not found, return list of\n # planet names. Restructured input format.\n # 2010-11-01 13:30 IJC: Added \"import os\"\n # 2011-05-19 15:56 IJC: Modified documentation.\n\n import os\n\n if kw.has_key('datafile'):\n datafile=kw['datafile']\n else:\n datafile=os.path.expanduser('~/python/exoplanets.csv')\n if kw.has_key('verbose'):\n verbose = kw['verbose']\n else:\n verbose=False\n\n if len(args)==0:\n inp = 'noplanetname'\n else:\n inp = args[0]\n\n if verbose: print \"datafile>>\" + datafile\n f = open(datafile, 'r')\n data = f.readlines()\n f.close()\n data = data[1::] # remove header line\n names = array([line.split(',')[0] for line in data])\n\n foundobj = (names==inp)\n if (not foundobj.any()):\n if verbose: print \"could not find desired planet; returning names of known planets\"\n return names\n else:\n planetind = int(find(foundobj))\n pinfo = data[planetind].strip().split(',')\n myplanet = planet(*pinfo)\n \n return myplanet","def get_kuali_award_id (self, award_id):\n # print '\\nget_kuali_award_id: award_id = {}'.format(award_id)\n info = self.get_kuali_award_info(award_id)\n # print 'info is a {}'.format(type(info))\n # print json.dumps(info, indent=3)\n\n \"\"\"\n if info is not None:\n # on a total whiff, the fainId field is none\n if info['fainId'] == 'none':\n print 'MISS'\n return None\n\n for field in ['sponsorAwardId', 'fainId']:\n if info[field] is None:\n continue\n sought_id = self.sanitize_id(info[field])\n test_id = self.sanitize_id(award_id)\n\n # kludge for when the ids only differ but a 3-char prefix\n if three_letter_start_pat.match(test_id[:3]):\n test_id = test_id[3:]\n\n\n # print 'sought: \"{}\" test: \"{}\"'.format(sought_id,test_id)\n if sought_id.endswith (test_id):\n return info[field]\n\n if test_id.endswith (sought_id):\n return info[field]\n\n # print 'not found'\n return None\n \"\"\"\n return self.find_kuali_id_in_result(award_id, info)"],"string":"[\n \"def get_element_from_id(self, identifier):\\n classification, org, rel, com = classify_id(identifier)\\n if classification == id_classification.org:\\n return self.get_org_question(org)\\n elif classification == id_classification.rel:\\n return self.get_rel_question(org, rel)\\n elif classification == id_classification.com:\\n return self.get_rel_comment(org, rel, com)\\n return None\",\n \"def getOntologyTermByID(self, oid, oType=0):\\n\\n url = \\\"ontologies/{0}/{1}\\\".format(oType, oid)\\n req = self.getRequest(url)\\n return req\",\n \"def which_obs_mjd(filename):\\n return None\",\n \"def get_library(self,identifier=None,version=None,filename=None):\\r\\n\\r\\n session = self.session\\r\\n if identifier is not None and identifier > \\\"\\\":\\r\\n libraries = session.query(LibraryRecord).filter(LibraryRecord.id_name==identifier).order_by(desc(LibraryRecord.version)).all()\\r\\n if len(libraries) == 0:\\r\\n raise Exception(f\\\"No library with identifier {identifier} found\\\")\\r\\n else:\\r\\n libraryListStr = \\\"\\\"\\r\\n for library in libraries:\\r\\n libraryListStr += library.version+\\\",\\\"\\r\\n if version is not None and version > \\\"\\\":\\r\\n if version == library.version:\\r\\n return(library)\\r\\n if version is not None and version > \\\"\\\":\\r\\n raise Exception(f\\\"Unable to find version {version} of library {identifier}\\\")\\r\\n if len(libraries) == 1:\\r\\n return(library)\\r\\n raise Exception(f\\\"There are several version of this library ({libraryListStr}). Please specify a version\\\")\\r\\n return()\\r\\n\\r\\n elif filename is not None and filename > \\\"\\\":\\r\\n raise Exception(\\\"Search by filename not implemented\\\")\\r\\n else:\\r\\n raise Exception(\\\"Not enough information to find library\\\")\\r\\n\\r\\n return()\",\n \"def fetch(\\n self,\\n L,\\n objective_function,\\n weight,\\n ):\\n W = str(weight) # must be a string otherwise dupicate entries\\n filename = os.path.join(self.output_dir, f\\\"{L}.json\\\")\\n if not os.path.isfile(filename):\\n raise NotInCatalogError(L, W, objective_function)\\n with open(filename, 'r') as f:\\n try:\\n data = json.load(f)\\n except json.decoder.JSONDecodeError:\\n logger.warning(f\\\"{filename} exists, \\\"\\n f\\\"but it is improperly formatted.\\\")\\n raise\\n if (W in data and objective_function in data[W]\\n and 'code' in data[W][objective_function]):\\n return data[W][objective_function]\\n else:\\n raise NotInCatalogError(L, W, objective_function)\",\n \"def get_person_text(self, uid):\\n words = \\\"\\\"\\n\\n query = \\\"\\\"\\\"\\nSELECT ?overview ?researchO ?label\\nWHERE\\n{\\n <%s> <http://vivoweb.org/ontology/core#overview> ?overview .\\n <%s> <http://vivoweb.org/ontology/core#researchOverview> ?researchO .\\n <%s> <http://www.w3.org/2000/01/rdf-schema#label> ?label .\\n}\\n \\\"\\\"\\\" % (uid, uid, uid)\\n self.setQuery(query)\\n try:\\n rval = self.query()\\n try:\\n g = rval.convert()\\n except:\\n pass\\n words = \\\"%s %s %s\\\" % (g['results']['bindings'][0]['overview']['value'], g['results']['bindings'][0]['researchO']['value'], g['results']['bindings'][0]['label']['value'])\\n except:\\n print \\\"Select failed: %s\\\" % query\\n\\n self.setQuery(\\\"\\\"\\\"\\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\nPREFIX vivo: <http://vivoweb.org/ontology/core#>\\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\\nSELECT ?name\\nWHERE\\n{\\n ?auth vivo:relates <%s> .\\n ?auth rdf:type vivo:Authorship .\\n ?auth vivo:relates ?art .\\n filter (?art!=<%s>) .\\n ?art <http://vivoweb.org/ontology/core#dateTimeValue> ?date .\\n ?date <http://vivoweb.org/ontology/core#dateTime> ?year .\\n filter (?year>\\\"2009-01-01T00:00:00Z\\\"^^xsd:dateTime) .\\n ?art rdfs:label ?name .\\n}\\nLIMIT 20\\n\\\"\\\"\\\" % (uid, uid))\\n try:\\n rval = self.query()\\n try:\\n g = rval.convert()\\n except:\\n pass\\n for t in g['results']['bindings']:\\n words = words + \\\" \\\" + t['name']['value']\\n\\n except:\\n print \\\"Select failed\\\"\\n traceback.print_exc(file=sys.stdout)\\n\\n self.setQuery(\\\"\\\"\\\"\\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\nPREFIX vivo: <http://vivoweb.org/ontology/core#>\\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\\n\\nSELECT ?name\\nWHERE\\n{\\n ?grant vivo:relates <%s> .\\n ?grant rdf:type vivo:Grant .\\n ?grant <http://vivoweb.org/ontology/core#dateTimeInterval> ?date .\\n ?date <http://vivoweb.org/ontology/core#end> ?end .\\n ?end <http://vivoweb.org/ontology/core#dateTime> ?year .\\n filter (?year>\\\"2009-01-01T00:00:00Z\\\"^^xsd:dateTime) .\\n ?grant rdfs:label ?name .\\n}\\n\\n \\\"\\\"\\\" % (uid))\\n try:\\n rval = self.query()\\n try:\\n g = rval.convert()\\n except:\\n pass\\n\\n for t in g['results']['bindings']:\\n words = words + \\\" \\\" + t['name']['value']\\n\\n except:\\n print \\\"Select failed\\\"\\n traceback.print_exc(file=sys.stdout)\\n\\n\\n\\n\\n return words\",\n \"def getKOI(KeplerID):\\n \\n if inKEPPC(KeplerID):\\n db = MySQLdb.connect(host='tddb.astro.washington.edu', user='tddb', passwd='tddb', db='Kepler')\\n cursor = db.cursor()\\n foo1 = 'select KOI from KEPPC where (KID = %s)' % (KeplerID)\\n cursor.execute(foo1)\\n results = cursor.fetchall()\\n elif inKEPFP(KeplerID):\\n db = MySQLdb.connect(host='tddb.astro.washington.edu', user='tddb', passwd='tddb', db='Kepler')\\n cursor = db.cursor()\\n foo1 = 'select KOI from KEPFP where (KID = %s)' % (KeplerID)\\n cursor.execute(foo1)\\n results = cursor.fetchall()\\n else:\\n results = None\\n \\n return results\",\n \"def getIdentifier(_session, _el, _language):\\n # get identification set\\n caption = None\\n idtf_set = searchOneShotBinPairAttrToNode(_session, _el, keynodes.common.nrel_identification, sc.SC_CONST)\\n if idtf_set is not None:\\n return getLocalizedTextFromSet(_session, idtf_set, _language)\\n \\n return None\",\n \"def index_by_rev_id(s):\\n return (json.loads(s)['rev_id'], s)\",\n \"def _eidnamefetch(eid):\\n\\n try:\\n url = 'http://api.espn.com/v1/sports/football/nfl/athletes/%s?apikey=dha4fmjhb6q36zffzkech2zn' % str(eid)\\n req = urllib2.Request(url)\\n req.add_header(\\\"User-Agent\\\",\\\"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:17.0) Gecko/17.0 Firefox/17.0\\\")\\n r = urllib2.urlopen(req)\\n data = json.loads(r.read())\\n data = data['sports'][0]['leagues'][0]['athletes'][0]\\n fn = data['fullName']\\n return fn\\n except Exception, e:\\n print \\\"ERROR: _eidnamefetch :: {0}\\\".format(e)\\n return None\",\n \"def searchAltId(name):\\n # Make sure user passed a string as parameter\\n if not isinstance(name, str):\\n raise TypeError('Wrong type as parameter. A string type was expected.')\\n\\n # Extract catalog name and object number to make sure we search the name in correct form\\n nameParts = re.match(r'(LBN|M|MWSC|PGC|UGC)\\\\s?(\\\\d+)',name.upper())\\n if nameParts is None :\\n raise ValueError('Wrong object name. Search can be performed for Messier, PGC, LBN, MWSC or UGC catalogs.')\\n\\n selectWhat = 'objects.name'\\n fromWhere = 'objects'\\n if nameParts[1] == 'M':\\n # M102 == M101\\n if nameParts[2] == \\\"102\\\":\\n constraint = 'messier=\\\"101\\\"'\\n else:\\n constraint = 'messier=\\\"' + nameParts[2] + '\\\"'\\n elif nameParts[1] == 'PGC': # 6 digits format\\n constraint = 'identifiers LIKE \\\"%PGC ' + \\\"{:0>6}\\\".format(nameParts[2]) + '%\\\"'\\n elif nameParts[1] == 'UGC': # 5 digits format\\n constraint = 'identifiers LIKE \\\"%UGC ' + \\\"{:0>5}\\\".format(nameParts[2]) + '%\\\"'\\n elif nameParts[1] == 'MWSC': # 4 digits format\\n constraint = 'identifiers LIKE \\\"%MWSC ' + \\\"{:0>4}\\\".format(nameParts[2]) + '%\\\"'\\n elif nameParts[1] == 'LBN': # 3 digits format\\n constraint = 'identifiers LIKE \\\"%LBN ' + \\\"{:0>3}\\\".format(nameParts[2]) + '%\\\"'\\n objectData = _queryFetchOne(selectWhat, fromWhere, constraint)\\n\\n if objectData is not None:\\n return Dso(objectData[0])\\n else:\\n return \\\"Object not found.\\\"\",\n \"def get_agent_from_rdl_filename(rdlfile):\\n b, e = os.path.splitext(os.path.basename(rdlfile))\\n parts = b.split(\\\"_\\\")\\n for p in parts:\\n if p[0] == \\\"r\\\":\\n try:\\n return int(p[1:])\\n except:\\n pass\\n return 0\",\n \"def obliquity(jd, algorithm=2006):\\n if algorithm == 2006:\\n return np.rad2deg(erfa.obl06(jd, 0))\\n elif algorithm == 2000:\\n return np.rad2deg(erfa.obl80(jd, 0) + erfa.pr00(jd, 0)[1])\\n elif algorithm == 1980:\\n return np.rad2deg(erfa.obl80(jd, 0))\\n else:\\n raise ValueError(\\\"invalid algorithm year for computing obliquity\\\")\",\n \"def searchOntologyTerm(self, search, oType='0', mode='default'):\\n search = urlparse_quote(search)\\n\\n if mode == 'exact':\\n url = self.url + \\\"ontologies/{0}?$filter=Term%20eq%20%27{1}%27\\\".format(oType, search)\\n else:\\n url = self.url + \\\"ontologies/{0}?$filter=startswith(Term,%27{1}%27)%20eq%20true\\\".format(oType, search)\\n\\n res = list(self.getAllPaginated(url))\\n\\n itemlist = list()\\n\\n if len(res) > 0:\\n for item in res:\\n itemlist.append(vsdModels.OntologyItem(**item))\\n return itemlist\\n else:\\n return None\",\n \"def eidr_identifier(title):\\n pass\",\n \"def get_info_for_identifier(identifier):\\n\\n page = requests.get(f\\\"https://www.drugbank.ca/drugs/{identifier}\\\")\\n parsed_drug_doc = BeautifulSoup(page.text, 'html.parser')\\n\\n smiles = get_smiles(parsed_drug_doc)\\n gene_action_pairs = get_gene_action_pairs(parsed_drug_doc)\\n external_links = get_external_links(parsed_drug_doc)\\n\\n # print(\\\"identifier\\\", identifier)\\n # print(\\\"smiles\\\", smiles)\\n # print(\\\"gene actions\\\", gene_action_pairs)\\n # print(\\\"external links\\\", external_links)\\n\\n return {\\n \\\"identifier\\\": identifier,\\n \\\"smiles\\\": smiles,\\n \\\"gene_action_pairs\\\": gene_action_pairs,\\n \\\"external_links\\\": external_links\\n }\",\n \"def geef_rij_omschrijving(self, code):\\n return self._rij_codelijst.geef_omschrijving(code)\",\n \"def extract_journal(name):\\n match = re.search(\\\"\\\\d+\\\", name)\\n if match != None: \\n return name[:match.start()], int(name[match.start(): match.end()])\\n else: \\n return \\\"\\\", 0\",\n \"def parse_rdf_version(rdf_data):\\n m = re.match('([A-Z]+)_([A-Z0-9]+)_(\\\\d+Q\\\\d)(.*)', rdf_data, re.IGNORECASE)\\n if m:\\n is_level0 = m.group(4).upper().strip('_') == Util.LEVEL0_FLAG\\n return m.group(2).upper(), m.group(1).upper(), m.group(3).upper(), is_level0\\n else:\\n return None, None, None, None\",\n \"def id2term(var, key, return_key, json_blob):\\n result = var\\n for obj in json_blob:\\n if obj[key] == var:\\n result = obj[return_key]\\n return result\",\n \"def which_obs_mjd(filename):\\n if not is_galex_file(filename):\\n return None\\n h_ = pf.getheader(filename)\\n return time.Time(h_[\\\"OBS-DATE\\\"]+\\\"T\\\"+h_[\\\"TIME-OBS\\\"]).mjd\",\n \"def _fetch_idjj_data(year=None):\\n try:\\n if year is None:\\n year = _get_max_year([11, 12, 34, 35]) + 1\\n\\n database = 'PrisonMain'\\n tbl_admit = 'IDJJ_Admissions'\\n tbl_exit = 'IDJJ_exits'\\n cols = 'Age, SFY, County, sex, race, admtypo, OFFTYPE9, hclass'\\n condition = f'SFY = {year}'\\n\\n df_a = _fetch_from_ms_sql_server(database, tbl_admit, cols, condition)\\n df_e = _fetch_from_ms_sql_server(database, tbl_exit, 'Exit'+cols, condition)\\n\\n return (\\n pd.DataFrame()\\n .append(_tranform_idjj(df_a))\\n .append(_tranform_idjj(df_a, age1720=True))\\n .append(_tranform_idjj(df_e, exit=True))\\n .append(_tranform_idjj(df_e, age1720=True, exit=True))\\n )\\n except:\\n raise\",\n \"def get_rechnung(rechnungsnr):\\n\\n if str(rechnungsnr).startswith('RG'):\\n rechnungsnr = str(rechnungsnr)[2:]\\n kopf = get_connection().query(['AFK00'],\\n condition=\\\"FKRGNR = %s\\\" % sql_escape(rechnungsnr))\\n if len(kopf) < 1:\\n raise RuntimeError('inkonsistente Kopfdaten in AFK00: %r' % kopf)\\n if len(kopf) > 1:\\n print 'warning: inkonsistente Kopfdaten in AFK00: FKRGNR = %s' % rechnungsnr\\n print kopf\\n kopf = kopf[0]\\n # TODO: der code schient nciht zu klappen, wenn gar keine Auftragstexte vorhanden sind.\\n postmp = get_connection().query(['AFU00', 'AAT00'],\\n condition=\\\"FURGNR=%s AND FUAUFN=ATAUFN AND FUAUPO=ATAUPO AND ATTART=8\\\" % sql_escape(rechnungsnr))\\n\\n # wenn eine Rechnungsposition mehr als einen Rechnungstext hat, ist sie jetzt mehrfach in positionen\\n # dedupen und spezial felder auseinanderklamuesern\\n positionen = {}\\n texte = {}\\n for line in postmp:\\n positionen.setdefault(line['auftragsposition'], {}).update(line)\\n text = line['text'].strip()\\n if not text.startswith('#:'):\\n texte.setdefault(line['auftragsposition'], []).append(line['text'])\\n if text.startswith('#:guid:'):\\n positionen[line['auftragsposition']]['guid'] = text[7:]\\n for posnr, textlines in texte.items():\\n positionen[posnr]['text'] = ' '.join(textlines)\\n\\n return kopf, positionen.values()\",\n \"def getJournal(self):\\n if 'journal' in self.extras: \\n return self.extras['journal']\\n #--Default \\n self.extras['journal'] = _('[No Journal Record Found.]')\\n #--Open save file and look for journal entry\\n inPath = os.path.join(self.dir,self.name)\\n ins = Tes3Reader(self.name,file(inPath,'rb'))\\n #--Raw data read\\n while not ins.atEnd():\\n #--Get record info and handle it\\n (name,size,delFlag,recFlag) = ins.unpackRecHeader()\\n if name != 'JOUR':\\n ins.seek(size,1,name)\\n #--Journal\\n else:\\n (subName,subSize) = ins.unpackSubHeader('JOUR')\\n if subName != 'NAME':\\n self.extras['journal'] == _('[Error reading file.]')\\n else:\\n reDate = re.compile(r'<FONT COLOR=\\\"9F0000\\\">(.+?)</FONT><BR>')\\n reTopic = re.compile(r'@(.*?)#')\\n data = ins.read(subSize)\\n data = reDate.sub(ReplJournalDate(),data)\\n data = reTopic.sub(r'\\\\1',data)\\n self.extras['journal'] = cstrip(data)\\n break\\n #--Done\\n ins.close()\\n print self.extras['journal']\\n return self.extras['journal']\",\n \"def get_article(doi, output='txt'):\\n xml = download_article(doi)\\n if xml is None:\\n return None\\n et = ET.fromstring(xml)\\n full_text = et.find('article:originalText', elsevier_ns)\\n if full_text is None:\\n logging.info('Could not find full text for %s.' % doi)\\n return None\\n main_body = full_text.find('xocs:doc/xocs:serial-item/ja:article/ja:body',\\n elsevier_ns)\\n if main_body is None:\\n return None\\n if output == 'xml':\\n return main_body\\n elif output == 'txt':\\n sections = main_body.findall('common:sections/common:section',\\n elsevier_ns)\\n full_txt = ''\\n for s in sections:\\n # Paragraphs that are directly under the section\\n pars = s.findall('common:para', elsevier_ns)\\n # Paragraphs that are under a section within the section\\n pars += s.findall('common:section/common:para', elsevier_ns)\\n for p in pars:\\n # Get the initial string inside the paragraph\\n if p.text is not None:\\n full_txt += p.text\\n # When there are tags inside the paragraph (for instance\\n # references), we need to take those child elements one by one\\n # and get the corresponding tail strings and join these. \\n full_txt += ''.join([c.tail if c.tail is not None \\n else '' for c in p.getchildren()])\\n full_txt += '\\\\n'\\n else:\\n logging.error('Unknown output format %s.' % output)\\n return None\\n return full_txt\",\n \"def _backup_ligand_extraction(self, pdb, resname):\\n from rdkit import Chem\\n ligand_lines = []\\n\\n with open(pdb, \\\"r\\\") as f:\\n lines = f.readlines()\\n for line in lines:\\n if (line.startswith(\\\"ATOM\\\") or line.startswith(\\\"HETATM\\\")) and line[17:20].strip() == resname:\\n ligand_lines.append(line)\\n ligand_block = \\\"\\\".join(ligand_lines)\\n ligand = Chem.MolFromPDBBlock(ligand_block)\\n return ligand\",\n \"def get_paper_by_id(paper_id):\\n dblp_key = paper_id.replace(\\\"/\\\", \\\"_\\\")\\n if local.paper_exists(dblp_key):\\n return dblp_key\\n\\n print(\\\"getting information from dblp about paper {}\\\".format(paper_id))\\n data = get(\\\"https://dblp.org/rec/\\\" + paper_id + \\\".xml\\\")[\\\"dblp\\\"]\\n return get_paper(data)\",\n \"def find_rent(self, id):\\n allR=self.__loadFromFile()\\n for bk in allR:\\n if bk.getId()==id:\\n return bk\",\n \"def get_by_id(dataobj_id):\\n results = list(get_data_dir().rglob(f\\\"{dataobj_id}-*.md\\\"))\\n return results[0] if results else None\",\n \"def get_observation(observation_id: str):\\n pass\",\n \"def get_bom_by_name(request):\\n if not request.user.is_authenticated:\\n return JsonResponse({\\\"success\\\": False}, status=401)\\n if request.method == \\\"GET\\\" and request.is_ajax():\\n bom_name = request.GET.get(\\\"searchTerm\\\")\\n try:\\n boms = BillOfMaterial.objects.filter(\\n bom_name__icontains=bom_name\\n )\\n data = [\\n {\\\"id\\\": bom.bom_name,\\n \\\"text\\\": bom.bom_name, }\\n for bom in boms\\n ]\\n except Exception:\\n return JsonResponse({\\\"success\\\": False}, status=400)\\n return JsonResponse(data, safe=False, status=200)\\n return JsonResponse({\\\"success\\\": False}, status=405)\",\n \"def identify_dvd(job):\\n # Added from pull 366\\n \\\"\\\"\\\" Manipulates the DVD title and calls OMDB to try and \\t\\n lookup the title \\\"\\\"\\\"\\n\\n # Safe way of dealing with log files if the users need to post it online\\n # cleanlog = makecleanlogfile(job)\\n # logging.debug(\\\"#### --- job ----\\\" + str(cleanlog))\\n\\n # Added from #338\\n # Some older DVDs aren't actually labelled\\n if not job.label or job.label == \\\"\\\":\\n job.label = \\\"not identified\\\"\\n\\n dvd_info_xml = False\\n dvd_release_date = \\\"\\\"\\n\\n # TODO: remove this because its pointless keeping when it can never work\\n try:\\n crc64 = pydvdid.compute(str(job.mountpoint))\\n fallback_title = \\\"{0}_{1}\\\".format(str(job.label), str(crc64))\\n dvd_title = str(fallback_title)\\n except pydvdid.exceptions.PydvdidException as e:\\n logging.error(\\\"Pydvdid failed with the error: \\\" + str(e))\\n dvd_title = fallback_title = str(job.label)\\n crc64 = \\\"\\\"\\n\\n logging.info(\\\"DVD CRC64 hash is: \\\" + str(crc64))\\n job.crc_id = str(crc64)\\n\\n # Dead needs removing\\n urlstring = \\\"http://metaservices.windowsmedia.com/pas_dvd_B/template/GetMDRDVDByCRC.xml?CRC={0}\\\".format(str(crc64))\\n logging.debug(urlstring)\\n\\n dvd_title = job.label\\n logging.debug(\\\"dvd_title_label= \\\" + str(dvd_title))\\n # strip all non-numeric chars and use that for year\\n year = re.sub(\\\"[^0-9]\\\", \\\"\\\", str(job.year))\\n # next line is not really needed, but we dont want to leave an x somewhere\\n dvd_title = job.label.replace(\\\"16x9\\\", \\\"\\\")\\n # Rip out any not alpha chars replace with\\n dvd_title = re.sub(\\\"[^a-zA-Z ]\\\", \\\" \\\", dvd_title)\\n logging.debug(\\\"dvd_title ^a-z= \\\" + str(dvd_title))\\n # rip out any SKU's at the end of the line\\n dvd_title = re.sub(\\\"SKU$\\\", \\\" \\\", dvd_title)\\n logging.debug(\\\"dvd_title SKU$= \\\" + str(dvd_title))\\n\\n # try to contact omdb\\n try:\\n dvd_info_xml = callwebservice(job, job.config.OMDB_API_KEY, dvd_title, year)\\n logging.debug(\\\"DVD_INFO_XML: \\\" + str(dvd_info_xml))\\n except OSError as e:\\n # we couldnt reach omdb\\n logging.error(\\\"Failed to reach OMDB\\\")\\n return False\\n\\n job.year = year\\n job.title = dvd_title\\n db.session.commit()\\n return True\",\n \"def get_prediction_judgement(id):\\n for line in open('working/sick.run'):\\n if line.split()[0] is str(id):\\n return line.split()[2]\\n print line.split()[2]\\n\\n return 2.5\",\n \"def getMaterialIndex(gltf, idname):\\n if idname is None:\\n return -1\\n\\n if gltf.get('materials') is None:\\n return -1\\n\\n index = 0\\n for material in gltf['materials']:\\n key = 'id' if material.get('id') != None else 'name'\\n if material.get(key) == idname:\\n return index\\n\\n index += 1\\n\\n return -1\",\n \"def find_one_byflexibleid(cls, stringfieldname, nameorid):\\n if (isinstance(nameorid,(int,long)) or nameorid.isnumeric()):\\n return cls.find_one_byprimaryid(nameorid)\\n return cls.find_one_bykey({stringfieldname:nameorid})\",\n \"def get_material(material):\\n for libn,tdict in liblist:\\n if material in tdict:\\n return tdict[material]\\n print (material, \\\" not found\\\")\\n raise KeyError\",\n \"def get_ols_link(prefix: str, identifier: str) -> Optional[str]:\\n ols_prefix = get_ols_prefix(prefix)\\n obo_link = get_obofoundry_link(prefix, identifier)\\n if ols_prefix is None or obo_link is None:\\n return None\\n return f\\\"https://www.ebi.ac.uk/ols/ontologies/{ols_prefix}/terms?iri={obo_link}\\\"\",\n \"def fetch_arxiv_bibtex(fp, info=None):\\n info = info if info else is_arxiv(fp)\\n\\n if info:\\n cat, num = info\\n\\n # Successful. Now fetch the BiBTeX.\\n page = urlopen('http://adsabs.harvard.edu/cgi-bin/bib_query?'\\n 'arXiv:{}{}'.format(cat + '/' if cat else '',\\n num)).read()\\n soup = BeautifulSoup(page, 'html5lib')\\n el = soup.find('a', text='Bibtex entry for this abstract', href=True)\\n href = urlopen(el['href']).read().decode()\\n\\n # Skip until the first '@', which should mark the beginning of the\\n # BiBTeX.\\n return '@' + '@'.join(href.split('@')[1:])\\n return None\",\n \"def select_calib_from_database(index_file, dateobs):\\n\\n # get instrument name\\n mobj = re.match('wlcalib_(\\\\S*)\\\\.dat$', os.path.basename(index_file))\\n instrument = mobj.group(1)\\n\\n calibtable = Table.read(index_file, format='ascii.fixed_width_two_line')\\n\\n input_date = dateutil.parser.parse(dateobs)\\n\\n # select the closest ThAr\\n timediff = [(dateutil.parser.parse(t)-input_date).total_seconds()\\n for t in calibtable['obsdate']]\\n irow = np.abs(timediff).argmin()\\n row = calibtable[irow]\\n fileid = row['fileid'] # selected fileid\\n md5 = row['md5']\\n\\n message = 'Select {} from database index as ThAr reference'.format(fileid)\\n logger.info(message)\\n\\n filepath = os.path.join('instruments/{}'.format(instrument),\\n 'wlcalib_{}.fits'.format(fileid))\\n filename = get_file(filepath, md5)\\n\\n # load spec, calib, and aperset from selected FITS file\\n hdu_lst = fits.open(filename)\\n head = hdu_lst[0].header\\n spec = hdu_lst[1].data\\n hdu_lst.close()\\n\\n calib = get_calib_from_header(head)\\n\\n return spec, calib\",\n \"def fetch(bibcode, filename=None, replace=None):\\n arxiv = False\\n print('Fetching PDF file from Journal website:')\\n req = request_ads(bibcode, source='journal')\\n if req is None:\\n return\\n\\n if req.status_code != 200:\\n print('Fetching PDF file from ADS website:')\\n req = request_ads(bibcode, source='ads')\\n if req is None:\\n return\\n\\n if req.status_code != 200:\\n print('Fetching PDF file from ArXiv website:')\\n req = request_ads(bibcode, source='arxiv')\\n arxiv = True\\n if replace is None:\\n replace = False\\n if req is None:\\n return\\n if replace is None:\\n replace = True\\n\\n if req.status_code == 200:\\n if bm.find(bibcode=bibcode) is None:\\n if filename is None:\\n filename = f'{bibcode}.pdf'\\n with builtin_open(filename, 'wb') as f:\\n f.write(req.content)\\n print(f\\\"Saved PDF to: '{filename}'.\\\\n\\\"\\n \\\"(Note that BibTex entry is not in the Bibmanager database)\\\")\\n else:\\n filename = set_pdf(\\n bibcode, bin_pdf=req.content, filename=filename, arxiv=arxiv,\\n replace=replace)\\n return filename\\n\\n print('Could not fetch PDF from any source.')\",\n \"def GetJ(self, *args):\\n return _table.Table_GetJ(self, *args)\",\n \"def get_term(self, idx):\\n try:\\n return self.id2term[idx]\\n except KeyError:\\n return self.unk_term\",\n \"def _eidnamelookup(eid):\\n\\n url = b64decode('aHR0cDovL20uZXNwbi5nby5jb20vbmZsL3BsYXllcmluZm8/cGxheWVySWQ9') + eid + '&wjb='\\n req = urllib2.Request(url)\\n r = urllib2.urlopen(req)\\n html = r.read()\\n try:\\n soup = BeautifulSoup(html)\\n team = soup.find('td', attrs={'class':'teamHeader'}).find('b')\\n name = soup.find('div', attrs={'class':'sub bold'})\\n return \\\"{0} {1}\\\".format(team.getText(), name.getText())\\n except Exception, e:\\n print \\\"ERROR: _eidnamelookup :: {0}\\\".format(e)\\n return None\",\n \"def get_arxiv_report_nr(text):\\n return text.lower().lstrip(\\\"arxiv:\\\").strip(\\\"/\\\")\",\n \"def get_basis_element_from_ccRepo(element,\\n program='Gaussian',\\n basis='cc-pVDZ'):\\n\\n # Check main page element list\\n with req.get(\\\"http://www.grant-hill.group.shef.ac.uk/ccrepo/\\\") as resp:\\n element_list = []\\n for m in re.finditer('class=\\\"sym\\\" href=', resp.text):\\n # print(resp.text[m.end():m.end()+50].split('\\\"')[1] )\\n element_list.append(resp.text[m.end():m.end()+50].split('\\\"')[1])\\n\\n element_dict = {atom[1]: atom[2].lower() for atom in atom_data[1:]}\\n\\n try:\\n resp = req.get(\\\"http://www.grant-hill.group.shef.ac.uk/ccrepo/{}\\\".format(element_dict[element]))\\n except KeyError as e:\\n raise Exception('Atom label {} not recognized'.format(e.args[0]))\\n\\n n_ini = resp.text.find('form-inline')\\n\\n # determinte the php web address for particular element\\n php_site = resp.text[n_ini:n_ini+100].split('\\\"')[2]\\n\\n # print('http://www.grant-hill.group.shef.ac.uk/ccrepo/{}/{}'.format(element, php_site))\\n # r = req.post(url = 'http://www.grant-hill.group.shef.ac.uk/ccrepo/titanium/tibasis.php', data = data)\\n r = req.post(url='http://www.grant-hill.group.shef.ac.uk/ccrepo/{}/{}'.format(element_dict[element], php_site),\\n data={'basis': basis, 'program': program})\\n\\n # parse the data\\n tree = html.fromstring(r.content)\\n r.close()\\n\\n header = tree.xpath('//div[@class=\\\"container\\\"]/text()')\\n citation = unicodedata.normalize('NFC', six.text_type(header[1])).strip()\\n description = unicodedata.normalize('NFC', header[2]).strip()\\n\\n\\n basis_data = tree.xpath('/html/body/div/nobr/text()')\\n basis_clean = [unicodedata.normalize('NFKC', six.text_type(line)).strip() for line in basis_data]\\n # basis_name = basis_clean[1].split('\\\"')[1]\\n\\n return citation, description, basis_clean[2:]\",\n \"def get_ontology_version(name):\\n if isinstance(name, str) == False:\\n name = name.version\\n\\n return name.replace(\\\".\\\", \\\"_\\\")\",\n \"def get_model(branch, internet):\\n\\n url = 'https://raw.githubusercontent.com/sot/chandra_models/master/chandra_models/xija/'\\n local_dir = '/AXAFLIB/chandra_models/chandra_models/xija/'\\n\\n if internet:\\n model_spec_url = url + branch # aca/aca_spec.json'\\n with urlopen(model_spec_url) as url:\\n response = url.read()\\n f = response.decode('utf-8')\\n else:\\n with open(home + local_dir + branch) as fid: # 'aca/aca_spec.json', 'rb') as fid:\\n f = fid.read()\\n return json.loads(f)\",\n \"def term_from_uri(uri):\\n if uri is None:\\n return None\\n # This insures that if we get a Literal with an integer value (as we\\n # do for modification positions), it will get converted to a string,\\n # not an integer.\\n if isinstance(uri, rdflib.Literal):\\n uri = str(uri.toPython())\\n # This is to handle URIs like\\n # http://www.openbel.org/bel/namespace//MAPK%20Erk1/3%20Family\\n # or\\n # http://www.openbel.org/bel/namespace/MAPK%20Erk1/3%20Family\\n # In the current implementation, the order of the patterns\\n # matters.\\n patterns = ['http://www.openbel.org/bel/namespace//(.*)',\\n 'http://www.openbel.org/vocabulary//(.*)',\\n 'http://www.openbel.org/bel//(.*)',\\n 'http://www.openbel.org/bel/namespace/(.*)',\\n 'http://www.openbel.org/vocabulary/(.*)',\\n 'http://www.openbel.org/bel/(.*)']\\n for pr in patterns:\\n match = re.match(pr, uri)\\n if match is not None:\\n term = match.groups()[0]\\n term = unquote(term)\\n return term\\n # If none of the patterns match then the URI is actually a simple term\\n # for instance a site: \\\"341\\\" or a substitution: \\\"sub(V,600,E)\\\"\\n return uri\",\n \"def compatible_firmware_version(self):\\n identifier = self.firmware_version.split('compiled')[0]\\n buf_size = self.MAX_BUF_SIZE\\n buf = (ctypes.c_char * buf_size)()\\n res = self._dll.JLINKARM_GetEmbeddedFWString(identifier.encode(), buf, buf_size)\\n if res < 0:\\n raise errors.JLinkException(res)\\n\\n return ctypes.string_at(buf).decode()\",\n \"def author(self):\\n\\t\\tauthor = re.search(r\\\"([Ff]rom\\\\s)(.+) ([tT]\\\\s*o)([^,]+),\\\",self.raw_text()[:150])\\n\\t\\treport = re.search(r\\\".*[Rr]eport of ([^,]+),\\\",self.raw_text()[:150])\\n\\t\\torder = re.search(r\\\".*[Oo]rder of ([^,]+)[,.]* to\\\",self.raw_text()[:250])\\n\\t\\torder2 = re.search(r\\\".*[Oo]rder of ([^,]+),\\\",self.raw_text()[:250])\\n\\t\\tlogbook = re.search(r\\\".*[lL]og of ([^,]+)[,.]\\\",self.raw_text()[:250])\\n\\t\\tif order:\\n\\t\\t\\torder = order.group(1)\\n\\t\\t\\treturn order\\n\\t\\tif order2:\\n\\t\\t\\torder2 = order2.group(1)\\n\\t\\t\\treturn order2\\n\\t\\tif logbook:\\n\\t\\t\\tlogbook = logbook.group(1)\\n\\t\\t\\treturn logbook\\n\\t\\tif report:\\n\\t\\t\\treport = report.group(1)\\n\\t\\t\\treturn report\\n\\t\\tif author: \\t\\n\\t\\t\\tauthor = author.group(2) \\n\\t\\t\\tauthor = re.sub(r\\\"([^,]*),.*\\\",r\\\"\\\\1\\\",author)\\t \\n\\t\\t\\treturn author\\n\\t\\t\\n\\t\\treturn \\\"Unknown\\\"\",\n \"def _get_version(self, identifier: Identifier,\\n version: Optional[int] = None) -> DocMetadata:\\n parent_path = self._get_parent_path(identifier=identifier,\\n version=version)\\n path = os.path.join(parent_path,\\n (f'{identifier.filename}.abs' if not version\\n else f'{identifier.filename}v{version}.abs'))\\n return self.parse_abs_file(filename=path)\",\n \"def getTerm(vocabulary_id, term_id):\\n if term_id is None:\\n return None\\n vocabulary = getVocabulary(vocabulary_id)\\n for term in vocabulary:\\n if term['id'] == term_id:\\n return term\\n return None\",\n \"def _get_target_version_by_name(jira, conf, name):\\n versions = jira.project_versions(conf.JIRA['project'])\\n for version in versions:\\n if getattr(version, 'name') == name:\\n return version\\n\\n return None\",\n \"def getVersion(self,fileName):\\n if not fileName in self.data or not self.data[fileName].tes3:\\n return ''\\n maVersion = reVersion.search(self.data[fileName].tes3.hedr.description)\\n return (maVersion and maVersion.group(2)) or ''\",\n \"def sparql_compare_ont(obj):\\n if not 'ontology_purl' in obj:\\n return\\n purl = obj['ontology_purl']\\n id = obj['id']\\n # this could be made more declarative, or driven by the context.jsonld mapping;\\n # however, for now this is relatively simple and easy to understand:\\n license = obj['license']['url'] if 'license' in obj else ''\\n run_sparql(obj, 'license', license, \\\"SELECT DISTINCT ?license WHERE {<\\\"+purl+\\\"> <http://purl.org/dc/elements/1.1/license> ?license}\\\")\\n run_sparql(obj, 'title', obj['title'] if 'title' in obj else '', \\\"SELECT DISTINCT ?title WHERE {<\\\"+purl+\\\"> <http://purl.org/dc/elements/1.1/title> ?title}\\\")\\n run_sparql(obj, 'description', obj['description'] if 'description' in obj else '', \\\"SELECT DISTINCT ?description WHERE {<\\\"+purl+\\\"> <http://purl.org/dc/elements/1.1/description> ?description}\\\")\\n run_sparql(obj, 'homepage', obj['homepage'] if 'homepage' in obj else '', \\\"SELECT DISTINCT ?homepage WHERE {<\\\"+purl+\\\"> <http://xmlns.com/foaf/0.1/homepage> ?homepage}\\\")\",\n \"def findBorehole(strg, fld_name, bh_name):\\r\\n\\r\\n #print(fld_name, bh_name)\\r\\n\\r\\n reg_fld = strg.getRegHelper().getFieldRegistry()\\r\\n fld = reg_fld.findByName(fld_name)\\r\\n if fld is None:\\r\\n return None\\r\\n\\r\\n reg_bh = strg.getRegHelper().getBoreholeRegistry()\\r\\n bh = reg_bh.findByNameAndField(fld.getID(), bh_name)\\r\\n\\r\\n return bh\",\n \"def longestorf(args):\\n p = OptionParser(longestorf.__doc__)\\n p.add_option(\\\"--ids\\\", action=\\\"store_true\\\", help=\\\"Generate table with ORF info\\\")\\n opts, args = p.parse_args(args)\\n\\n if len(args) != 1:\\n sys.exit(not p.print_help())\\n\\n (fastafile,) = args\\n pf = fastafile.rsplit(\\\".\\\", 1)[0]\\n orffile = pf + \\\".orf.fasta\\\"\\n idsfile = None\\n if opts.ids:\\n idsfile = pf + \\\".orf.ids\\\"\\n fwids = open(idsfile, \\\"w\\\")\\n\\n f = Fasta(fastafile, lazy=True)\\n fw = must_open(orffile, \\\"w\\\")\\n before, after = 0, 0\\n for name, rec in f.iteritems_ordered():\\n cds = rec.seq\\n before += len(cds)\\n # Try all six frames\\n orf = ORFFinder(cds)\\n lorf = orf.get_longest_orf()\\n newcds = Seq(lorf)\\n after += len(newcds)\\n newrec = SeqRecord(newcds, id=name, description=rec.description)\\n SeqIO.write([newrec], fw, \\\"fasta\\\")\\n if idsfile:\\n print(\\\"\\\\t\\\".join((name, orf.info)), file=fwids)\\n\\n fw.close()\\n if idsfile:\\n fwids.close()\\n\\n logging.debug(\\n \\\"Longest ORFs written to `{0}` ({1}).\\\".format(\\n orffile, percentage(after, before)\\n )\\n )\\n\\n return orffile\",\n \"def orfFinder(data):\\n\\t\\n\\tORFile = getORFs(data.seqFile, \\n\\t\\t\\t\\t\\t data.queryName, \\n\\t\\t\\t\\t\\t data.o)\\n\\tsetattr(data, \\\"ORFs\\\", ORFile)\",\n \"def get_instance(string):\\n row = string.split(\\\".\\\")\\n\\n # handles \\\"f.eid\\\" case\\n if len(row) < 4:\\n return \\\"0\\\"\\n\\n # the number is somewhat arbitrary... \\n # it is determined by Joeri's UK Phenotypes script.\\n # (which is \\\"get_UKphenotypes.r\\\" --- thanks Joeri!)\\n return row[2]\",\n \"def get_software_by_id(self, id_code):\\r\\n malware_return = self.fs.query([\\r\\n Filter('type', '=', 'malware'),\\r\\n Filter('external_references.external_id', '=', id_code)\\r\\n ])\\r\\n\\r\\n tool_return = self.fs.query([\\r\\n Filter('type', '=', 'tool'),\\r\\n Filter('external_references.external_id', '=', id_code)\\r\\n ])\\r\\n\\r\\n if malware_return:\\r\\n return malware_return\\r\\n elif tool_return:\\r\\n return tool_return\",\n \"def get_scn_unq_name(self, unq_id):\\n logger.debug(\\\"Creating Database Engine and Session.\\\")\\n db_engine = sqlalchemy.create_engine(self.db_info_obj.dbConn)\\n session_sqlalc = sqlalchemy.orm.sessionmaker(bind=db_engine)\\n ses = session_sqlalc()\\n logger.debug(\\\"Perform query to find scene.\\\")\\n query_result = ses.query(EDDSentinel1ASF).filter(EDDSentinel1ASF.PID == unq_id).one_or_none()\\n if query_result is None:\\n raise EODataDownException(\\\"Scene ('{}') could not be found in database\\\".format(unq_id))\\n unq_name = \\\"{}_{}\\\".format(query_result.Product_File_ID, query_result.PID)\\n ses.close()\\n logger.debug(\\\"Closed the database session.\\\")\\n return unq_name\",\n \"def get_wdetJ(self, etype: str, *, elm: int, nds: list = None) -> np.ndarray:\\n if etype == \\\"area\\\":\\n cod = self._coords[:, np.array(self._connectivity[elm])[nds]][: self._n_dof]\\n else:\\n cod = self._coords[:, self._connectivity[elm]][: self._n_dof]\\n\\n return self._shapef[self._element_name[elm]][etype].get_wdetJ(cod)\",\n \"def match_doi_or_arxiv(text, only=[\\\"DOI\\\", \\\"arXiv\\\"]):\\n text = text.lower()\\n # Try to extract DOI\\n if \\\"DOI\\\" in only:\\n extractID = regex.doi.search(text.replace('Œ', '-'))\\n if not extractID:\\n # PNAS fix\\n extractID = regex.doi_pnas.search(text.\\n replace('pnas', '/pnas'))\\n if not extractID:\\n # JSB fix\\n extractID = regex.doi_jsb.search(text)\\n if extractID:\\n # If DOI extracted, clean it and return it\\n cleanDOI = False\\n cleanDOI = extractID.group(0).replace(':', '').replace(' ', '')\\n if regex.clean_doi.search(cleanDOI):\\n cleanDOI = cleanDOI[1:]\\n # FABSE J fix\\n if regex.clean_doi_fabse.search(cleanDOI):\\n cleanDOI = cleanDOI[:20]\\n # Second JCB fix\\n if regex.clean_doi_jcb.search(cleanDOI):\\n cleanDOI = cleanDOI[:21]\\n if len(cleanDOI) > 40:\\n cleanDOItemp = regex.clean_doi_len.sub('000', cleanDOI)\\n reps = {'.': 'A', '-': '0'}\\n cleanDOItemp = tools.replaceAll(cleanDOItemp[8:], reps)\\n digitStart = 0\\n for i in range(len(cleanDOItemp)):\\n if cleanDOItemp[i].isdigit():\\n digitStart = 1\\n if cleanDOItemp[i].isalpha() and digitStart:\\n break\\n cleanDOI = cleanDOI[0:(8+i)]\\n return (\\\"DOI\\\", cleanDOI)\\n # Else, try to extract arXiv\\n if \\\"arXiv\\\" in only:\\n extractID = regex.arXiv.search(text)\\n if extractID:\\n return (\\\"arXiv\\\", extractID.group(1))\\n return None\",\n \"def jid_jname(jnid):\\n jails = jails_list()\\n try:\\n int(jnid) == True\\n testid = 0\\n except ValueError:\\n testid = 1\\n\\n if testid == 0:\\n if jnid in jails[2]:\\n j = jails[2].index(jnid)\\n jnid = jails[1][j]\\n else:\\n print \\\" Jail with ID '%s' not found!\\\" % (jnid)\\n return False\\n\\n return jnid\",\n \"def get_party_name_by_id(party_id: int) -> str:\\n # Open a new connection\\n db, cursor = db_connector.cursor()\\n query = \\\"select name from party where id = '{}';\\\".format(party_id)\\n cursor.execute(query)\\n data = cursor.fetchall()\\n db.disconnect()\\n return data[0][0]\",\n \"def get_sf (pdb_id):\\n pdb_ftp_link = \\\"https://ftp.rcsb.org/pub/pdb/data/structures/all/structure_factors/\\\"\\n url = pdb_ftp_link + \\\"r{}sf.ent.gz\\\".format(pdb_id)\\n r = requests.get(url)\\n with open(sf_path + \\\"r{}sf.cif.gz\\\".format(pdb_id), 'wb') as f:\\n f.write(r.content)\\n #unzips the downloaded file\\n os.system(\\\"gunzip \\\"+sf_path + \\\"r{}sf.cif.gz\\\".format(pdb_id))\\n return \\\"r{}sf.cif\\\".format(pdb_id)\",\n \"def onto(disgenet, edam):\\n disgenet = disgenet.replace(' ', '+').replace(\\\"'\\\", \\\"%27\\\")\\n edam = edam.replace(' ', '+').replace(\\\"'\\\", \\\"%27\\\")\\n disid = subprocess.Popen(\\n [\\\"curl -s -k http://127.0.0.1:3030/ds/query -X POST --data \\\" +\\n \\\"'query=PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0A\\\" +\\n \\\"PREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A\\\" +\\n \\\"PREFIX+ncit%3A+%3Chttp%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23%3E%0A\\\" +\\n \\\"SELECT+DISTINCT+%0A%09%3Fdisease+%0AFROM+%3Chttp%3A%2F%2Frdf.disgenet.org%3E+%0AWHERE+%7B%0A++\\\" +\\n \\\"SERVICE+%3Chttp%3A%2F%2Frdf.disgenet.org%2Fsparql%2F%3E+%7B%0A++++\\\" +\\n \\\"%3Fdisease+rdf%3Atype+ncit%3AC7057+%3B%0A++++%09dcterms%3Atitle+%22\\\" + disgenet +\\n \\\"%22%40en+.%0A%7D%0A%7D' -H 'Accept: application/sparql-results+json,*/*;q=0.9'\\\"],\\n stdout=subprocess.PIPE, shell=True).communicate()[0]\\n edam_id = subprocess.Popen([\\\"curl -s 'http://www.ebi.ac.uk/ols/api/search?q=\\\" + edam + \\\"&ontology=edam' 'Accept: application/json'\\\"],\\n stdout=subprocess.PIPE, shell=True).communicate()[0]\\n try:\\n jdisease = json.loads(disid)\\n umllist = []\\n umls = jdisease['results']['bindings'][0]['disease']['value']\\n except (IndexError, ValueError):\\n umls = \\\"No disgenet record\\\"\\n try:\\n jedam = json.loads(edam_id)\\n eid = jedam['response']['docs'][0]['iri']\\n except (IndexError, ValueError):\\n eid = \\\"No EDAM record\\\"\\n return umls, eid\",\n \"def get_movie(self, identifier: int) -> Movie:\\n result = list(filter(lambda x: x.identifier == identifier, self.items))\\n if result:\\n return result[0]\\n\\n return None\",\n \"def getFencerByAskfredId(table_conn=None, fencer_id=None):\\n\\n if table_conn is None or fencer_id is None:\\n return None\\n\\n table_conn.execute('SELECT * FROM fencers WHERE fencer_id=?', fencer_id) \\n\\n row = table_conn.fetchall()\\n if len(row) > 1:\\n print((\\\"Duplicate fencer record:\\\", row[0][1], \\\" \\\", row[0][2]))\\n\\n if len(row) == 0:\\n return None\\n\\n return Fencer(row[0][0], row[0][1], row[0][2], row[0][3], row[0][4])\",\n \"def get_object(id):\",\n \"def get_bsp_from_jpl(identifier, initial_date, final_date, email, directory):\\n import pathlib\\n import shutil\\n from datetime import datetime as dt\\n\\n import requests\\n import spiceypy as spice\\n\\n date1 = dt.strptime(initial_date, \\\"%Y-%m-%d\\\")\\n date2 = dt.strptime(final_date, \\\"%Y-%m-%d\\\")\\n diff = date2 - date1\\n\\n if diff.days <= 32:\\n raise ValueError(\\n \\\"The [final_date] must be more than 32 days later than [initial_date]\\\"\\n )\\n\\n urlJPL = \\\"https://ssd.jpl.nasa.gov/x/smb_spk.cgi?OPTION=Make+SPK\\\"\\n\\n path = pathlib.Path(directory)\\n if not path.exists():\\n raise ValueError(\\\"The directory {} does not exist!\\\".format(path))\\n\\n filename = identifier.replace(\\\" \\\", \\\"\\\") + \\\".bsp\\\"\\n\\n parameters = {\\n \\\"OBJECT\\\": identifier,\\n \\\"START\\\": date1.strftime(\\\"%Y-%b-%d\\\"),\\n \\\"STOP\\\": date2.strftime(\\\"%Y-%b-%d\\\"),\\n \\\"EMAIL\\\": email,\\n \\\"TYPE\\\": \\\"-B\\\",\\n }\\n\\n r = requests.get(urlJPL, params=parameters, stream=True)\\n bspFormat = r.headers[\\\"Content-Type\\\"]\\n if r.status_code == requests.codes.ok and bspFormat == \\\"application/download\\\":\\n file_path = path.joinpath(filename)\\n with open(file_path, \\\"wb\\\") as f:\\n r.raw.decode_content = True\\n shutil.copyfileobj(r.raw, f)\\n\\n return file_path\\n else:\\n # TODO: Add a Debug\\n raise Exception(\\\"It was not able to download the bsp file for object.\\\")\",\n \"async def matchStrandToClass(pdbid:str, strand_id:str)->Union[str, None]:\\n CYPHER=\\\"\\\"\\\"match (r:RibosomeStructure{{_rcsb_id: \\\"{}\\\"}})-[]-(rp:RibosomalProtein{{entity_poly_strand_id:\\\"{}\\\"}})-[]-(n:NomenclatureClass)\\n return n.class_id\\\"\\\"\\\".format(pdbid.upper(), strand_id)\\n resp = _neoget(CYPHER)\\n if len(resp) > 0:\\n return resp[0]\\n else:\\n return None\",\n \"def get_id(self, refobj):\\n return cmds.getAttr(\\\"%s.identifier\\\" % refobj)\",\n \"def fetch(\\n self,\\n search_method: str,\\n objective_function: str,\\n weight: int,\\n ):\\n if os.path.isfile(self.filename):\\n with open(self.filename, 'r+') as f:\\n table = pandas.io.json.read_json(f)\\n try:\\n table = table[(table[\\\"objective\\\"] == objective_function)\\n & (table[\\\"weight\\\"] == weight)\\n & (table[\\\"search\\\"] == search_method)]\\n best = table.loc[table['cost'].idxmax()]\\n self.best_cost = best[\\\"cost\\\"]\\n return best[\\\"code\\\"], best[\\\"cost\\\"], best[\\\"progress\\\"]\\n except (ValueError, KeyError):\\n pass\\n return None, -np.inf, 0\",\n \"def get_revision(filing_id, business_id):\\n business = Business.find_by_internal_id(business_id)\\n filing = Filing.find_by_id(filing_id)\\n\\n revision_json = {}\\n revision_json['filing'] = {}\\n if filing.filing_type == 'incorporationApplication':\\n revision_json['filing'] = \\\\\\n VersionedBusinessDetailsService.get_ia_revision(filing, business)\\n elif filing.filing_type == 'changeOfDirectors':\\n revision_json['filing'] = \\\\\\n VersionedBusinessDetailsService.get_cod_revision(filing, business)\\n elif filing.filing_type == 'changeOfAddress':\\n revision_json['filing'] = \\\\\\n VersionedBusinessDetailsService.get_coa_revision(filing, business)\\n elif filing.filing_type == 'annualReport':\\n revision_json['filing'] = \\\\\\n VersionedBusinessDetailsService.get_ar_revision(filing, business)\\n elif filing.filing_type == 'correction':\\n revision_json = filing.json\\n\\n # This is required to find diff\\n for party in revision_json.get('filing', {}).get('incorporationApplication', {}).get('parties', []):\\n party['id'] = party.get('officer', {}).get('id', None)\\n for party_role in party['roles']:\\n party_role['id'] = party_role['roleType']\\n\\n # filing_type's yet to be handled alteration, changeOfName, specialResolution, voluntaryDissolution\\n if not revision_json['filing']:\\n revision_json = filing.json\\n revision_json['filing']['business'] = \\\\\\n VersionedBusinessDetailsService.get_business_revision(filing.transaction_id, business)\\n\\n revision_json['filing']['header'] = VersionedBusinessDetailsService.get_header_revision(filing)\\n\\n return revision_json\",\n \"def get_orfs(gtf, args, config, is_annotated=False, is_de_novo=False):\\n\\n call = not args.do_not_call\\n chr_name_file = os.path.join(config[\\\"star_index\\\"], \\\"chrName.txt\\\")\\n chr_name_str = \\\"--chr-name-file {}\\\".format(chr_name_file)\\n\\n logging_str = logging_utils.get_logging_options_string(args)\\n cpus_str = \\\"--num-cpus {}\\\".format(args.num_cpus)\\n\\n # extract a BED12 of the annotated ORFs\\n transcript_bed = filenames.get_bed(\\n config[\\\"genome_base_path\\\"],\\n config[\\\"genome_name\\\"],\\n is_annotated=is_annotated,\\n is_de_novo=is_de_novo,\\n )\\n\\n cmd = \\\"gtf-to-bed12 {} {} {} {} {}\\\".format(\\n gtf, transcript_bed, chr_name_str, cpus_str, logging_str\\n )\\n in_files = [gtf]\\n out_files = [transcript_bed]\\n shell_utils.call_if_not_exists(\\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\\n )\\n\\n # extract the transcript fasta\\n transcript_fasta = filenames.get_transcript_fasta(\\n config[\\\"genome_base_path\\\"],\\n config[\\\"genome_name\\\"],\\n is_annotated=is_annotated,\\n is_de_novo=is_de_novo,\\n )\\n\\n cmd = \\\"extract-bed-sequences {} {} {} {}\\\".format(\\n transcript_bed, config[\\\"fasta\\\"], transcript_fasta, logging_str\\n )\\n in_files = [transcript_bed, config[\\\"fasta\\\"]]\\n out_files = [transcript_fasta]\\n shell_utils.call_if_not_exists(\\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\\n )\\n\\n # extract ORFs from the transcripts using genomic coordinates\\n orfs_genomic = filenames.get_orfs(\\n config[\\\"genome_base_path\\\"],\\n config[\\\"genome_name\\\"],\\n note=config.get(\\\"orf_note\\\"),\\n is_annotated=is_annotated,\\n is_de_novo=is_de_novo,\\n )\\n\\n start_codons_str = utils.get_config_argument(\\n config, \\\"start_codons\\\", default=default_start_codons\\n )\\n\\n stop_codons_str = utils.get_config_argument(\\n config, \\\"stop_codons\\\", default=default_stop_codons\\n )\\n\\n cmd = \\\"extract-orf-coordinates {} {} {} {} {} {} {}\\\".format(\\n transcript_bed,\\n transcript_fasta,\\n orfs_genomic,\\n cpus_str,\\n start_codons_str,\\n stop_codons_str,\\n logging_str,\\n )\\n in_files = [transcript_fasta, transcript_bed]\\n out_files = [orfs_genomic]\\n shell_utils.call_if_not_exists(\\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\\n )\\n\\n # write the ORF exons, used to label the ORFs\\n exons_file = filenames.get_exons(\\n config[\\\"genome_base_path\\\"],\\n config[\\\"genome_name\\\"],\\n note=config.get(\\\"orf_note\\\"),\\n is_annotated=is_annotated,\\n is_de_novo=is_de_novo,\\n )\\n\\n cmd = \\\"split-bed12-blocks {} {} --num-cpus {} {}\\\".format(\\n orfs_genomic, exons_file, args.num_cpus, logging_str\\n )\\n in_files = [orfs_genomic]\\n out_files = [exons_file]\\n shell_utils.call_if_not_exists(\\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\\n )\\n\\n # label the ORFs\\n labeled_orfs = filenames.get_labels(\\n config[\\\"genome_base_path\\\"],\\n config[\\\"genome_name\\\"],\\n note=config.get(\\\"orf_note\\\"),\\n is_annotated=is_annotated,\\n is_de_novo=is_de_novo,\\n )\\n\\n annotated_bed = filenames.get_bed(\\n config[\\\"genome_base_path\\\"],\\n config[\\\"genome_name\\\"],\\n is_annotated=True,\\n )\\n\\n orf_exons_str = \\\"--orf-exons {}\\\".format(exons_file)\\n\\n de_novo_str = \\\"\\\"\\n if is_de_novo:\\n de_novo_str = '--label-prefix \\\"novel_\\\" --filter --nonoverlapping-label \\\"novel\\\"'\\n\\n cmd = \\\"label-orfs {} {} {} {} {} {} {}\\\".format(\\n annotated_bed,\\n orfs_genomic,\\n labeled_orfs,\\n orf_exons_str,\\n de_novo_str,\\n logging_str,\\n cpus_str,\\n )\\n in_files = [annotated_bed, orfs_genomic, exons_file]\\n # ** this function overwrites the input file `orfs_genomic`\\n out_files = [labeled_orfs]\\n shell_utils.call_if_not_exists(\\n cmd, out_files, in_files=in_files, overwrite=args.overwrite, call=call\\n )\",\n \"def lookup(name):\",\n \"def lookup(name):\",\n \"def download_document(self,model,field,id,filename=None, **kw):\\n Model = request.registry[model]\\n cr, uid, context = request.cr, request.uid, request.context\\n fields = [field]\\n res = Model.read(cr, uid, [int(id)], fields, context)[0]\\n filecontent = base64.b64decode(res.get(field) or '')\\n if not filecontent:\\n return request.not_found()\\n else:\\n if not filename:\\n filename = '%s_%s' % (model.replace('.', '_'), id)\\n return request.make_response(filecontent,\\n [('Content-Type', 'application/octet-stream'),\\n ('Content-Disposition', content_disposition(filename))])\",\n \"def get_review(self, id_):\\n cursor = self._connection.cursor()\\n select_command = make_select_command(\\\"reviews\\\")\\n select_command += \\\" WHERE id_ = ?\\\"\\n cursor.execute(select_command, (id_,))\\n for row in cursor:\\n return expandable_from_tuple(row, FIELD_DESCRIPTIONS) \\n return None\",\n \"def get_date(bfo):\\n from invenio.bibformat_elements.bfe_INSPIRE_arxiv import get_arxiv\\n\\n #true date\\n date = bfo.fields('269__c')\\n if date:\\n datestruct=parse_date(date[0])\\n if datestruct[0]:\\n return(datestruct)\\n\\n\\n #arxiv date\\n arxiv = get_arxiv(bfo,category=\\\"no\\\")\\n if arxiv:\\n date=re.search('(\\\\d+)',arxiv[0]).groups()[0]\\n if len(date) >=4:\\n year = date[0:2]\\n if year > '90':\\n year='19'+year\\n else:\\n year='20'+year\\n date = year+date[2:4]+'00'\\n date=parse_date(date)\\n if date[1]: return(date)\\n\\n\\n\\n #journal year\\n if bfo.fields('773__y'):\\n date= parse_date(bfo.fields('773__y')[0]+'0000')\\n if date[0]:\\n return date\\n\\n #date added\\n if bfo.fields('961__x'):\\n date= parse_date(bfo.fields('961__x')[0])\\n if date[0]:\\n return date\\n\\n\\n return None\",\n \"def fetch_sequence(sequence_id, database='uniprot'):\\n if sequence_id.startswith('UPI'):\\n database = 'uniparc'\\n url_template = 'http://www.uniprot.org/uniparc/{}.fasta'\\n elif sequence_id.startswith('UniRef'):\\n database = 'uniref'\\n url_template = 'http://www.uniprot.org/uniref/{}.fasta'\\n else:\\n database = 'uniprot'\\n url_template = 'http://www.uniprot.org/uniprot/{}.fasta'\\n\\n url = url_template.format(sequence_id)\\n logger.debug('Downloading sequence {} from {}...'.format(sequence_id, url))\\n\\n r = requests.get(url)\\n if r.status_code != 200:\\n raise Exception(\\\"Failed to fetch sequence with return code: {}\\\".format(r.status_code))\\n\\n seq = Bio.SeqIO.read(io.StringIO(r.text), 'fasta')\\n if database == 'uniprot':\\n seq.annotations['db'], seq.id, seq.name = re.split('[\\\\| ]', seq.id)\\n return seq\",\n \"def get_johans_features(modsizedif, prediction, id):\\n data = []\\n \\n prover_output = 0\\n if modsizedif == None:\\n print id\\n return ['1','1','1','1','1','1','1']\\n \\n if modsizedif[0].split()[0] == 'contradiction.':\\n prover_output = 0.0\\n if modsizedif[0].split()[0] == 'unknown.':\\n prover_output = 0.5\\n if modsizedif[0].split()[0] == 'proof.':\\n prover_output = 1.0\\n\\n data.append(prover_output) # prover output\\n data.append(float(modsizedif[1].split()[0][:-1])) # domain novelty\\n data.append(float(modsizedif[2].split()[0][:-1])) # relation novelty\\n data.append(float(modsizedif[3].split()[0][:-1])) # wordnet novelty\\n data.append(float(modsizedif[4].split()[0][:-1])) # model novelty\\n data.append(float(modsizedif[5].split()[0][:-1])) # word overlap\\n \\n if prediction[0].split()[0] == 'informative': # prediction.txt\\n data.append(0)\\n else:\\n data.append(1)\\n\\n return data\",\n \"def get_truck_by_driver_id(identifier):\\n key = 'name'\\n if identifier.isdigit():\\n key = 'id'\\n\\n truck_to_return = {}\\n driver = utils.get_dict_by_key_value_from_list(\\n key, identifier, drivers)\\n truck_to_return = utils.get_dict_by_key_value_from_list(\\n 'id', driver.get('id'), trucks)\\n return jsonify(truck_to_return)\",\n \"def getObject(language=None):\",\n \"def get(self, name_or_id):\\n \\n r = self.library.database.get_name(name_or_id)\\n\\n if not r[0]:\\n r = self.library.database.get_id(name_or_id)\\n \\n return r\",\n \"def _select_kinase_structure_by_pdb_id(\\n self,\\n pdb_id: str,\\n klifs_kinase_id: int,\\n chain_id: Union[str, None] = None,\\n alternate_location: Union[str, None] = None,\\n ) -> pd.Series:\\n import pandas as pd\\n\\n from ..utils import LocalFileStorage\\n\\n logging.debug(\\\"Searching kinase structures from KLIFS matching the pdb of interest ...\\\")\\n klifs_structures = pd.read_csv(LocalFileStorage.klifs_structure_db(self.cache_dir))\\n structures = klifs_structures[\\n klifs_structures[\\\"structure.pdb_id\\\"] == pdb_id\\n ]\\n structures = structures[\\n structures[\\\"kinase.klifs_id\\\"] == klifs_kinase_id\\n ]\\n if alternate_location:\\n structures = structures[\\n structures[\\\"structure.alternate_model\\\"] == alternate_location\\n ]\\n if chain_id:\\n structures = structures[\\n structures[\\\"structure.chain\\\"] == chain_id\\n ]\\n\\n if len(structures) == 0:\\n text = (\\n f\\\"No structure found for PDB ID {pdb_id}, chain {chain_id} and alternate location \\\"\\n f\\\"{alternate_location}.\\\"\\n )\\n logging.debug(\\\"Exception: \\\" + text)\\n raise NotImplementedError(text)\\n else:\\n logging.debug(\\\"Picking structure with highest KLIFS quality score ...\\\")\\n structures = structures.sort_values(\\n by=[\\n \\\"structure.qualityscore\\\",\\n \\\"structure.resolution\\\",\\n \\\"structure.chain\\\",\\n \\\"structure.alternate_model\\\"\\n ],\\n ascending=[False, True, True, True]\\n )\\n kinase_structure = structures.iloc[0]\\n\\n return kinase_structure\",\n \"def retrieve(document_id: str) -> Fulltext:\\n return current_session().retrieve(document_id)\",\n \"def _cookIdCore(self, ref, **kwargs):\\n\\n # AUTHORS\\n namepart='nobody'\\n if self._refHasAuthorNames(ref):\\n lastnames = []\\n for each in ref['authors']:\\n if each.get('lastname', None):\\n lastnames.append(each['lastname'])\\n\\n if len(lastnames) > 1:\\n namepart = '%s' % ''.join([ lastname[0] for lastname in lastnames ])\\n elif len(lastnames) == 1:\\n namepart = lastnames[0][:3]\\n else:\\n pass\\n\\n # PUBLICATION YEAR\\n if ref.get('publication_year', None):\\n yearpart = str(ref['publication_year'])\\n else:\\n yearpart = \\\"1000\\\"\\n\\n return namepart + yearpart\",\n \"def identifier_version(self):\\n return next(self.graph[self.identifier_bound:owl.versionIRI])\",\n \"def get_jnt_index(self, jnt_name):\\n return self.wrapper.get_jnt_index(self.instance, jnt_name.encode('utf-8'))\",\n \"def _find_recife_editions(self, text):\\n return (\\n edition\\n for edition in text.split(\\\"&\\\")\\n if re.search(\\\"prefeituradorecife\\\", edition, re.IGNORECASE)\\n )\",\n \"def feature_to_open511_element(feature):\\n\\n # Using a hash of the geometry for an ID. For proper production use,\\n # there'll probably have to be some code in the importer\\n # that compares to existing entries in the DB to determine whether\\n # this is new or modified...\\n geom_hash = hashlib.md5(feature.geom.wkt).hexdigest()\\n id = JURISDICTION + ':' + geom_hash\\n while id in ids_seen:\\n id += 'x'\\n ids_seen.add(id)\\n\\n elem = E.RoadEvent(id=id)\\n\\n def set_val(tag, val):\\n if val not in (None, ''):\\n e = etree.Element(tag)\\n e.text = unicode(val)\\n elem.append(e)\\n\\n set_val('Title', feature.get('Name').decode('utf8'))\\n\\n blob = lxml.html.fragment_fromstring(feature.get('Description').decode('utf8'),\\n create_parent='content')\\n\\n description_label = blob.xpath('//strong[text()=\\\"Description\\\"]')\\n if description_label:\\n description_bits = []\\n el = description_label[0].getnext()\\n while el.tag == 'p':\\n description_bits.append(_get_el_text(el))\\n el = el.getnext()\\n set_val('Description', '\\\\n\\\\n'.join(description_bits))\\n\\n localisation = blob.cssselect('div#localisation p')\\n if localisation:\\n set_val('AffectedRoads', '\\\\n\\\\n'.join(_get_el_text(el) for el in localisation))\\n\\n try:\\n set_val('ExternalURL', blob.cssselect('#avis_residants a, #en_savoir_plus a')[0].get('href'))\\n except IndexError:\\n pass\\n\\n facultatif = blob.cssselect('div#itineraire_facult p')\\n if facultatif:\\n set_val('Detour', '\\\\n\\\\n'.join(_get_el_text(el) for el in facultatif))\\n\\n if blob.cssselect('div#dates strong'):\\n try:\\n start_date = blob.xpath(u'div[@id=\\\"dates\\\"]/strong[text()=\\\"Date de d\\\\xe9but\\\"]')[0].tail\\n end_date = blob.xpath(u'div[@id=\\\"dates\\\"]/strong[text()=\\\"Date de fin\\\"]')[0].tail\\n if start_date and end_date:\\n set_val('StartDate', _fr_string_to_date(start_date))\\n set_val('EndDate', _fr_string_to_date(end_date))\\n except IndexError:\\n pass\\n\\n elem.append(E.Geometry(\\n geom_to_xml_element(feature.geom)\\n ))\\n\\n return elem\",\n \"def j_jal(byte_string):\\n\\n opcode = int(byte_string[:6], 2)\\n target = int(byte_string[6:], 2)\\n if opcode == 2:\\n target = target << 2\\n print(OPCODES[opcode] + '\\\\t' + str(target))\",\n \"def getGenomeName(recordID, filename):\\n global FILENAMES\\n global GENOMENAMES\\n recordID = str(recordID)\\n\\n\\n #Look for lcl followed by the possible genome name\\n if re.search('lcl\\\\|([\\\\w-]*)', recordID):\\n match = re.search('lcl\\\\|([\\\\w-]*)', recordID)\\n match = str(match.group())\\n genome_name = match.split('|')[1]\\n\\n #Look for a possible genome name at the beginning of the record ID\\n elif re.search('(^[a-zA-Z][a-zA-Z]\\\\w{6}\\\\.\\\\d)',recordID):\\n match = re.search('(\\\\w{8}\\\\.\\\\d)',recordID)\\n genome_name = str(match.group())\\n\\n #Look for ref, gb, emb or dbj followed by the possible genome name\\n elif re.search('(ref\\\\|\\\\w{2}_\\\\w{6}|gb\\\\|\\\\w{8}|emb\\\\|\\\\w{8}|dbj\\\\|\\\\w{8})',recordID):\\n match = re.search('(ref\\\\|\\\\w{2}_\\\\w{6}|gb\\\\|\\\\w{8}|emb\\\\|\\\\w{8}|dbj\\\\|\\\\w{8})',recordID)\\n match = str(match.group())\\n genome_name = match.split('|')[1]\\n\\n #Look for gi followed by the possible genome name\\n elif re.search('gi\\\\|\\\\d{8}', recordID):\\n match = re.search('gi\\\\|\\\\d{8}', recordID)\\n match = str(match.group())\\n genome_name = match.split('|')[1]\\n #Assign the file name as genome name\\n else:\\n genome_name = filename\\n\\n if recordID not in FILENAMES:\\n FILENAMES[recordID] = filename\\n if filename not in GENOMENAMES:\\n GENOMENAMES[filename] = recordID\\n\\n return genome_name\",\n \"def id(text):\\n url = \\\"https://bio.torre.co/api/bios/{}\\\".format(text)\\n request = get(url)\\n print(request.status_code)\\n if request.status_code != 200:\\n abort(404, 'Not Found')\\n return request.json()\",\n \"def computeRjb(self, lon, lat, depth, var=False):\\n cdir, tmp = os.path.split(__file__)\\n origin = self._origin\\n\\n # -------------------\\n # Sort out file names\\n # -------------------\\n mech = origin.mech\\n if not hasattr(origin, '_tectonic_region'):\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechA_ar1p0_seis0_20_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechA_ar1p0_seis0_20_Var.csv\\\")\\n elif origin._tectonic_region == 'Active Shallow Crust':\\n if mech == 'ALL':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechA_ar1p7_seis0_20_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechA_ar1p7_seis0_20_Var.csv\\\")\\n elif mech == 'RS':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechR_ar1p7_seis0_20_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechR_ar1p7_seis0_20_Var.csv\\\")\\n elif mech == 'NM':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechN_ar1p7_seis0_20_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechN_ar1p7_seis0_20_Var.csv\\\")\\n elif mech == 'SS':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechSS_ar1p7_seis0_20_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechSS_ar1p7_seis0_20_Var.csv\\\")\\n elif origin._tectonic_region == 'Stable Shallow Crust':\\n if mech == 'ALL':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechA_ar1p0_seis0_15_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechA_ar1p0_seis0_15_Var.csv\\\")\\n elif mech == 'RS':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechR_ar1p0_seis0_15_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechR_ar1p0_seis0_15_Var.csv\\\")\\n elif mech == 'NM':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechN_ar1p0_seis0_15_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechN_ar1p0_seis0_15_Var.csv\\\")\\n elif mech == 'SS':\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechSS_ar1p0_seis0_15_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_S14_mechSS_ar1p0_seis0_15_Var.csv\\\")\\n else:\\n warnings.warn(\\n 'Unsupported tectonic region; using coefficients for unknown'\\n 'tectonic region.')\\n rf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechA_ar1p0_seis0_20_Ratios.csv\\\")\\n vf = os.path.join(\\n cdir, \\\"data\\\", \\\"ps2ff\\\",\\n \\\"Rjb_WC94_mechA_ar1p0_seis0_20_Var.csv\\\")\\n\\n # -----------------\\n # Start with ratios\\n # -----------------\\n repi2rjb_ratios_tbl = pd.read_csv(rf, comment='#')\\n r2rrt_cols = repi2rjb_ratios_tbl.columns[1:]\\n mag_list = []\\n for column in (r2rrt_cols):\\n if re.search('R\\\\d+\\\\.*\\\\d*', column):\\n magnitude = float(re.findall(\\n 'R(\\\\d+\\\\.*\\\\d*)', column)[0])\\n mag_list.append(magnitude)\\n mag_list = np.array(mag_list)\\n dist_list = np.log(np.array(repi2rjb_ratios_tbl['Repi_km']))\\n repi2rjb_grid = repi2rjb_ratios_tbl.values[:, 1:]\\n repi2rjb_obj = spint.RectBivariateSpline(\\n dist_list, mag_list, repi2rjb_grid, kx=1, ky=1)\\n\\n def repi2rjb_tbl(repi, M):\\n ratio = repi2rjb_obj.ev(np.log(repi), M)\\n rjb = repi * ratio\\n return rjb\\n\\n repis = self.computeRepi(lon, lat, depth)\\n mags = np.ones_like(repis) * origin.mag\\n rjb_hat = repi2rjb_tbl(repis, mags)\\n\\n # -------------------\\n # Additional Variance\\n # -------------------\\n repi2rjbvar_ratios_tbl = pd.read_csv(vf, comment='#')\\n repi2rjbvar_grid = repi2rjbvar_ratios_tbl.values[:, 1:]\\n repi2rjbvar_obj = spint.RectBivariateSpline(\\n dist_list, mag_list, repi2rjbvar_grid, kx=1, ky=1)\\n rjbvar = repi2rjbvar_obj.ev(np.log(repis), mags)\\n\\n if var is True:\\n return (rjb_hat, rjbvar)\\n else:\\n return rjb_hat\",\n \"def searchTerm(self, resource, search, mode='default'):\\n\\n search = urlparse_quote(search)\\n if mode == 'exact':\\n url = self.fullUrl(resource) + '?$filter=Term%20eq%20%27{0}%27'.format(search)\\n else:\\n url = self.fullUrl(resource) + '?$filter=startswith(Term,%27{0}%27)%20eq%20true'.format(search)\\n\\n req = self.getRequest(url)\\n return req\\n #return req.json()\",\n \"def getobj(*args, **kw):\\n # 2008-07-30 16:56 IJC: Created\\n # 2010-03-07 22:24 IJC: Updated w/new exoplanets.org data table! \\n # 2010-03-11 10:01 IJC: If planet name not found, return list of\\n # planet names. Restructured input format.\\n # 2010-11-01 13:30 IJC: Added \\\"import os\\\"\\n # 2011-05-19 15:56 IJC: Modified documentation.\\n\\n import os\\n\\n if kw.has_key('datafile'):\\n datafile=kw['datafile']\\n else:\\n datafile=os.path.expanduser('~/python/exoplanets.csv')\\n if kw.has_key('verbose'):\\n verbose = kw['verbose']\\n else:\\n verbose=False\\n\\n if len(args)==0:\\n inp = 'noplanetname'\\n else:\\n inp = args[0]\\n\\n if verbose: print \\\"datafile>>\\\" + datafile\\n f = open(datafile, 'r')\\n data = f.readlines()\\n f.close()\\n data = data[1::] # remove header line\\n names = array([line.split(',')[0] for line in data])\\n\\n foundobj = (names==inp)\\n if (not foundobj.any()):\\n if verbose: print \\\"could not find desired planet; returning names of known planets\\\"\\n return names\\n else:\\n planetind = int(find(foundobj))\\n pinfo = data[planetind].strip().split(',')\\n myplanet = planet(*pinfo)\\n \\n return myplanet\",\n \"def get_kuali_award_id (self, award_id):\\n # print '\\\\nget_kuali_award_id: award_id = {}'.format(award_id)\\n info = self.get_kuali_award_info(award_id)\\n # print 'info is a {}'.format(type(info))\\n # print json.dumps(info, indent=3)\\n\\n \\\"\\\"\\\"\\n if info is not None:\\n # on a total whiff, the fainId field is none\\n if info['fainId'] == 'none':\\n print 'MISS'\\n return None\\n\\n for field in ['sponsorAwardId', 'fainId']:\\n if info[field] is None:\\n continue\\n sought_id = self.sanitize_id(info[field])\\n test_id = self.sanitize_id(award_id)\\n\\n # kludge for when the ids only differ but a 3-char prefix\\n if three_letter_start_pat.match(test_id[:3]):\\n test_id = test_id[3:]\\n\\n\\n # print 'sought: \\\"{}\\\" test: \\\"{}\\\"'.format(sought_id,test_id)\\n if sought_id.endswith (test_id):\\n return info[field]\\n\\n if test_id.endswith (sought_id):\\n return info[field]\\n\\n # print 'not found'\\n return None\\n \\\"\\\"\\\"\\n return self.find_kuali_id_in_result(award_id, info)\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.49641275","0.46501428","0.4630191","0.45927075","0.4589712","0.4521436","0.44825307","0.44575438","0.44496873","0.44368324","0.43593493","0.43212026","0.43087837","0.42987674","0.42854863","0.42817187","0.42626467","0.4260149","0.4252432","0.4248289","0.42374262","0.42306983","0.4226469","0.42214328","0.42117286","0.42115965","0.42003205","0.42001492","0.41925964","0.4190527","0.41795334","0.4175817","0.41675955","0.41594297","0.41544315","0.41507003","0.41499525","0.41445118","0.41401425","0.41217753","0.4116407","0.41118035","0.41060454","0.40999588","0.40890005","0.40825447","0.4082466","0.4076177","0.40758613","0.40739217","0.40718752","0.4065545","0.40642026","0.40594307","0.40592062","0.40575925","0.40564486","0.4050519","0.4050294","0.40463412","0.40453607","0.4043023","0.40348238","0.4029534","0.4026058","0.40209413","0.4020557","0.40138605","0.40108562","0.40102977","0.40009725","0.4000552","0.39975756","0.39965996","0.39873007","0.39871818","0.39850986","0.39850986","0.39846936","0.39845258","0.39790308","0.39771637","0.39761278","0.39753085","0.39712214","0.39667162","0.3966384","0.39662698","0.39659414","0.39594364","0.39586794","0.39527363","0.39512923","0.39463174","0.39427748","0.39396483","0.393689","0.39352256","0.3933268","0.39320394"],"string":"[\n \"0.49641275\",\n \"0.46501428\",\n \"0.4630191\",\n \"0.45927075\",\n \"0.4589712\",\n \"0.4521436\",\n \"0.44825307\",\n \"0.44575438\",\n \"0.44496873\",\n \"0.44368324\",\n \"0.43593493\",\n \"0.43212026\",\n \"0.43087837\",\n \"0.42987674\",\n \"0.42854863\",\n \"0.42817187\",\n \"0.42626467\",\n \"0.4260149\",\n \"0.4252432\",\n \"0.4248289\",\n \"0.42374262\",\n \"0.42306983\",\n \"0.4226469\",\n \"0.42214328\",\n \"0.42117286\",\n \"0.42115965\",\n \"0.42003205\",\n \"0.42001492\",\n \"0.41925964\",\n \"0.4190527\",\n \"0.41795334\",\n \"0.4175817\",\n \"0.41675955\",\n \"0.41594297\",\n \"0.41544315\",\n \"0.41507003\",\n \"0.41499525\",\n \"0.41445118\",\n \"0.41401425\",\n \"0.41217753\",\n \"0.4116407\",\n \"0.41118035\",\n \"0.41060454\",\n \"0.40999588\",\n \"0.40890005\",\n \"0.40825447\",\n \"0.4082466\",\n \"0.4076177\",\n \"0.40758613\",\n \"0.40739217\",\n \"0.40718752\",\n \"0.4065545\",\n \"0.40642026\",\n \"0.40594307\",\n \"0.40592062\",\n \"0.40575925\",\n \"0.40564486\",\n \"0.4050519\",\n \"0.4050294\",\n \"0.40463412\",\n \"0.40453607\",\n \"0.4043023\",\n \"0.40348238\",\n \"0.4029534\",\n \"0.4026058\",\n \"0.40209413\",\n \"0.4020557\",\n \"0.40138605\",\n \"0.40108562\",\n \"0.40102977\",\n \"0.40009725\",\n \"0.4000552\",\n \"0.39975756\",\n \"0.39965996\",\n \"0.39873007\",\n \"0.39871818\",\n \"0.39850986\",\n \"0.39850986\",\n \"0.39846936\",\n \"0.39845258\",\n \"0.39790308\",\n \"0.39771637\",\n \"0.39761278\",\n \"0.39753085\",\n \"0.39712214\",\n \"0.39667162\",\n \"0.3966384\",\n \"0.39662698\",\n \"0.39659414\",\n \"0.39594364\",\n \"0.39586794\",\n \"0.39527363\",\n \"0.39512923\",\n \"0.39463174\",\n \"0.39427748\",\n \"0.39396483\",\n \"0.393689\",\n \"0.39352256\",\n \"0.3933268\",\n \"0.39320394\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.5531085"},"document_rank":{"kind":"string","value":"0"}}},{"rowIdx":80698,"cells":{"query":{"kind":"string","value":"Fetches article by id"},"document":{"kind":"string","value":"def consult_article(self, article_id: str) -> Dict[str, Any]:\n self._update_client_if_necessary()\n return _article_by_id(article_id, self._client)"},"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 article_by_id(self, id):\n return self.es.get(index=self.index, doc_type=self.doc_type, id=id)","def get_article_by_id(article_id):\n return Article.query.get(article_id)","def get_article(db:Session, article_id:int):\n return db.query(ArticleModel).filter(ArticleModel.id==article_id).first()","def articles_id (_id = None):\n\n with current_app.config.dba.engine.begin () as conn:\n res = execute (conn, r\"\"\"\n SELECT no\n FROM article\n WHERE no = :id\n \"\"\", { 'id' : _id })\n\n return make_articles_response (res)","def get(self, request, article_id):\n article = get_object_or_404(Article.objects.all(), pk=article_id)\n article_serializer = ArticleSerializer(article)\n return Response(article_serializer.data)","def article_detail(request, id):\n try:\n logger.info('Calling the api' + APIURL + '/articles/' + id + '/?format=json')\n response = requests.get(APIURL + '/articles/' + id + '/?format=json')\n parser = json.loads(response.content)\n images = article_images(id)\n next_read = read_next()\n return render_to_response('article/details.html', {'article':parser, 'next_read': next_read, 'related_images': images}, RequestContext(request))\n except:\n logger.error('Calling the api error in article_detail')\n raise Http404(\"Article does not exist\")","def get_object(self, article_id):\n try:\n comments = Comment.objects.all()\n #filter to only contain comments for specified article (article_id)\n comments = list(filter(lambda x: x.article_id == article_id , comments))\n return comments\n except Comment.DoesNotExist:\n raise Http404","def article(request, id, slug=None):\n article = get_object_or_404(Article, id=id)\n\n context = {\n 'article': article,\n }\n return render(request, 'article.html', context)","def article(self, article_id):\r\n return articles.Article(self, article_id)","def article(request, article_id):\n article = get_object_or_404(Article, pk=article_id)\n context = {'article': article}\n return render(request, 'sacms/article.html', context)","def articles(self, id):\n response = self._connection.session.get(\n self._connection.url + \"ticket_articles/by_ticket/%s?expand=true\" % id\n )\n return self._raise_or_return_json(response)","def articles(id):\n articles = get_articles(id)\n return render_template('article.html', articles = articles)","def get_entity_by_id(self, id):\n # url = '{}/ngsi-ld/v1/entities?type={}&offset={}&limit={}'.format(self.url, type, offset, limit)\n url = '{}/ngsi-ld/v1/entities/{}'.format(self.url, id)\n r = requests.get(url, headers=self.headers_ld)\n return r.json()","def test_get_article_by_id():\n article = Article(\n author = 'jane@doe.com',\n title = 'New Article',\n content = 'Super extra awesome article'\n ).save()\n\n query = GetArticleByIDQuery(\n id = article.id\n )\n\n assert query.execute().id == article.id","def get_article(request, article_id):\n try:\n article = Article.objects.get(pk=article_id)\n increment_articles_views(article_id)\n return format_ajax_response(True, \"Knowledgebase article retrieved successfully.\", {\"article\": article.dump_to_dict()})\n except Exception as ex:\n logger.error(\"Failed to get_article: %s\" % ex)\n return format_ajax_response(False, \"There was an error retrieving the knowledgebase article.\")","def view_article(request, id_article):\n article = get_object_or_404(Article, id=id_article)\n return render(request, 'core/view_article.html', {'article': article})","def get_article(article_id):\n article = db_session.query(Article)\\\n .filter_by(id=article_id).one()\n return jsonify(article.serialize)","def article(self, article_id):\r\n return contents.Article(self, article_id)","def article(self, article_id):\n return articles.Article(self, article_id)","def get(self, story_id):","def article(article_id):\n\tarticle = models.Article.query.get(article_id)\n\tif not article:\n\t\tabort(404)\n\treturn jsonify(article.dictionary())","def get(self, request, slug, id):\n article = ArticleInst.fetch(slug)\n\n try:\n comment = Comment.objects.get(pk=id, article=article)\n except Comment.DoesNotExist:\n data = {\n 'error': f'Comment of ID {id} nonexistent'\n }\n status_ = status.HTTP_404_NOT_FOUND\n else:\n serializer = self.serializer_class(comment)\n status_ = status.HTTP_200_OK\n data = serializer.data\n return Response(\n data=data,\n status=status_)","def fetch(cls, slug):\n try:\n article = Article.objects.get(slug=slug)\n except Article.DoesNotExist:\n raise exceptions.NotFound(f'Article of slug {slug} nonexistent')\n else:\n return article","def fetch(cls, slug):\n try:\n article = Article.objects.get(slug=slug)\n except Article.DoesNotExist:\n raise exceptions.NotFound(f'Article with slug {slug} nonexistent')\n else:\n return article","def get(self, _id):","def download(self, id, article_id, ticket_id):\n response = self._connection.session.get(\n self.url + f\"/{ticket_id}/{article_id}/{id}\"\n )\n return self._raise_or_return_json(response)","def getbyid(self, id):\n\n return esd.retrieve(id)","def articles(id):\n articles = get_articles(id)\n print(articles)\n\n\n return render_template('article.html', id = id,articles= articles)","def get_by_id(self, id):\n return Entry.all().filter('entry_id = ', id).get()","def get_by_id(self, id: int):\n\n\t\traise NotImplemented","def get_by_id(cls, id):\n e = api.get([key.Key(cls.__name__, id)])\n if e:\n return cls.from_entity(e[0])\n raise ObjectDoesNotExist","def news_article(id):\n articles = get_articles(id)\n return render_template('news_article.html', articles = articles)","def get_object(self, id):\n try:\n return Comment.objects.get(id=id)\n except Comment.DoesNotExist:\n raise Http404","def detail(request, article_id):\n try:\n article = Article.objects.get(pk=article_id)\n except Member.DoesNotExist:\n raise Http404(\"Article does not exist\")\n #article_list = Article.objects.order_by('-released_at')[:5]\n login = request.user and request.user.is_authenticated()\n article_list = get_article_list('-released_at',login)[:5]\n auth_form = AuthenticationForm(None, request.POST or None)\n return render(request, 'app/article_detail.html', { \n 'title':'ニュースの詳細',\n 'year':datetime.now().year,\n 'articles':article_list,\n 'blogs':EntryView.get_entry_list('-posted_at',-1, -1 if not login else request.user.pk )[:5],\n 'article': article,\n 'auth_form':auth_form,\n 'current_user':request.user,\n }\n )","def get_article(uuid):\n return Article.get(Article.uuid == uuid)","def news(id):\n\tarticle = data.get_article(id)\n\tif not article:\n\t\treturn \"article not found\", 404\n\treturn render_template(\"article.html\", article=article)","async def read(articleid=True, uid=False):\n\n # Load Settings\n settings = await fetch_settings()\n table = settings[\"table\"]\n\n if uid:\n connection = await connect()\n row = await connection.fetch(f\"\"\"\n SELECT * FROM \"{table}\" WHERE \"UID\" = $1;\n \"\"\", str(uid))\n await connection.close()\n return row\n try:\n articleid = int(articleid)\n except ValueError:\n return []\n connection = await connect()\n rows = await connection.fetch(f\"\"\"\n SELECT * FROM \"{table}\" WHERE \"ID\" = $1;\n \"\"\", articleid)\n await connection.close()\n\n result = []\n for row in rows:\n row_dict = dict(row)\n row_dict[\"dateReleased\"] = row[\"dateReleased\"].replace(year=(row[\"dateReleased\"].year + GAME_YEAR_OFFSET))\n\n result.append(row_dict)\n\n return result","def detail(request, article_id):\n return render(request, 'knowledgebase/detail.html', {'article_id': article_id})","def get_object(id):","def edit(id):\n r = requests.get(API_ROUTE + '/' + str(id), headers={'Auth': _auth()})\n if r.status_code != requests.codes.ok:\n return r.text, r.status_code\n\n return render_template('editor.html', article=r.json())","def article_exists(self, article_id):\n try:\n Article.objects.get(pk=article_id)\n return True\n except Article.DoesNotExist:\n raise Http404","def get_by_id(cls, id):\n return cls.query().get(id)","def update_article(id):\n # get and check article author against current_user\n the_article = models.Article.get_by_id(id)\n if current_user.id == the_article.author.id or current_user.role == 'admin':\n # get payload\n payload = request.get_json()\n # run update\n query = models.Article.update(**payload).where(models.Article.id==id)\n query.execute()\n return jsonify(\n data=model_to_dict(models.Article.get_by_id(id)),\n status={\"code\": 200, \"message\": \"Article updated successfully\"}\n ), 200\n else:\n return jsonify(data={}, status={\"code\": 403, \"message\": \"Not authorized\"})","def load_article(paper_id):\n s3 = boto3.client('s3')\n key = 'json/%s.json' % paper_id\n LOGGER.info('bucket=%s, key=%s', ARTICLE_BUCKET_NAME, key)\n obj = s3.get_object(\n Bucket=ARTICLE_BUCKET_NAME,\n Key=key)\n body = obj['Body']\n article = json.loads(body.read())\n body.close()\n return article","def get_object(self, id):\n try:\n return Post.objects.get(id=id)\n except Post.DoesNotExist:\n raise Http404","def get(cls, id):\n\n return cls.query.get(id)","def get(cls, id):\n\n return cls.query.get(id)","def get(id=None):\n return requests.get(\"/{}\".format(id))","def article_one(request, article_id):\n if request.method == \"GET\":\n article = Article.objects.get(pk=article_id)\n title = article.title\n author = article.author\n content = article.content\n phrases = list(\n map(\n lambda phrase: {\n \"content\": phrase.content,\n \"keyword\": phrase.word.content,\n },\n article.phrases.all(),\n )\n )\n return JsonResponse(\n {\n \"title\": title,\n \"author\": author,\n \"content\": content,\n \"phrases\": phrases,\n },\n safe=False,\n status=200,\n )\n else:\n return HttpResponseNotAllowed([\"GET\"])","def retrieve(self, request, slug=None):\n article = get_object_or_404(self.queryset, slug=slug)\n serializer = self.serializer_class(article)\n if request.user and not isinstance(request.user, AnonymousUser):\n self.update_read(article)\n return Response(serializer.data, status=status.HTTP_200_OK)","def get_article(self, slug):\n try:\n return Article.objects.get(slug=slug)\n except User.DoesNotExist:\n raise Http404","def get(self, id):\n return self.__model__.query.get(id)","def get_object(self, id, **args):\n return self.request(\"{0}/{1}\".format(self.version, id), args)","def get_story(self, id):\n url = self.base_url + 'stories/{story}'\n\n req = requests.get(headers=self.headers, url=url.format(story=id))\n\n return req.json()","def get_object(self, id_):\n return self._objects.get(id_, None)","def find(self, id):\n response = self._connection.session.get(self.url + \"/%s\" % id)\n return self._raise_or_return_json(response)","def get_article_by_key(cls, key):\n db_key = \"article:\" + str(key)\n result = cls.db.hgetall(db_key)\n return (Article.build(result) if type(result) is dict else None)","def getAuthorByID(id: int) -> Author:\n if not id:\n abort(400)\n author = Author.query.get(id)\n if not author:\n abort(404, \"Author is not found\")\n return author.serialize()","def find_by_id(id):\n query = \"SELECT * FROM parcels WHERE id=%s\"\n return db.find_one(query, (id,))","def get(self,id):\r\n person = get_one(id=id)\r\n if not person:\r\n api.abort(404)\r\n else:\r\n return person","def edit_news(id):\n\n\tarticle = data.get_article(id)\n\treturn render_template(\"admin/edit_article.html\", article=article)","def get(self, id):\n resultado = EmployeeModel.query.filter_by(employee_id=id).first()\n if resultado:\n return resultado\n api.abort(404)","def read_item(id: str, request: Request):\n obj = db.get(id, kind=endpoint_model)\n return obj","def get_content_by_id_get(self, head, id, locale):\n # TODO: Assuming first server is good - need to make fallback logic\n return self.session.get_any(\"{base}{request_url}\".format(base=self.servers[0],\n request_url=F\"/Content/GetContentById/{id}/{locale}/\"))","def get_entry_by_id(model, id):\n print(model, id)\n return db.session.query(model).filter_by(id=id).first()","def fetch_obj(type, id, error=404, new_id=False):\n if id is None:\n abort(error)\n obj_q = Session.query(type)\n obj = obj_q.get(int(id))\n #else:\n # obj = obj_q.filter(type.ID==int(id)).first()\n\n if obj is None:\n abort(error)\n return obj","def fetch_comment(self, comment_id, **args):\n return self.fetch(\"/comment/\" + comment_id, **args)","def get_by_id(cls, id):\n try:\n return cls.objects.get(id=id)\n except(IntegrityError, OperationalError):\n return None","def load_post_by_id(self, id):\n post = None\n posts = self.session.query(Post).filter(Post.id == id).all()\n if len(posts) > 0:\n post = posts[0]\n return post","def articles(news_id):\n #get news based on source id\n articles = get_articles(news_id)\n print(articles)\n title = f'{news_id}'\n return render_template(\"articles.html\", articles = articles, title = title)","def find_by_id(id: int):\n exercise = Exercise.try_find_by_id(id)\n if not exercise:\n raise NotFound(EXERCISE_NOT_FOUND_MSG)\n return exercise","def delete_article(id):\n # get and check article author against current_user\n the_article = models.Article.get_by_id(id)\n if current_user.id == the_article.author.id or current_user.role == 'admin':\n # delete article\n query = models.Article.delete().where(models.Article.id==id)\n query.execute()\n return jsonify(\n data='Article successfully deleted',\n status={\"code\": 200, \"message\": \"Article deleted successfully\"}\n ), 200\n else:\n return jsonify(data={}, status={\"code\": 403, \"message\": \"Not authorized\"})","def fetch_entry(self, entry_id, **args):\n return self.fetch(\"/entry/\" + entry_id, **args)","def fetch_article(self):\n dl = download(self.url, max_content_length=settings.PYPO_MAX_CONTENT_LENGTH)\n self.title, self.readable_article = parse(self, content_type=dl.content_type,\n text=dl.text, content=dl.content)","def get(self,id):\r\n person = get_one_by_persons_id(id=id)\r\n if not person:\r\n api.abort(404)\r\n else:\r\n return person","def read_by_id(self, id, fields=None):\n assert id is not None, \"id can not be None\"\n return self.read_many_by_id([id], fields)[0]","async def read_maintenance_record_by_id(id: int, conn: Database = Depends(get_db)):\n\n item = await get(conn=conn, id=id)\n if not item:\n raise HTTPException(status_code=400, detail=\"Item not found\")\n return item","def fetch_feed(self, feed_id, **args):\n return self.fetch(\"/feed/\" + feed_id, **args)","def getItem(self, id):\n path = 'item/' + id\n return self.sendRestRequest('GET', path)","def articles_id_formats (_id):\n\n canonical_url = app.config['APPLICATION_MAIN_URL'] + 'search?article_id='\n\n with current_app.config.dba.engine.begin () as conn:\n res = execute (conn, r\"\"\"\n SELECT webtext FROM article WHERE no=:no\n \"\"\", { 'no' : _id })\n return make_json_response ([\n {\n 'mimetype' : 'text/x-html-literal',\n 'lang' : LANG,\n 'embeddable' : True,\n 'text' : normalize_iso ('<div>%s</div>' % res.fetchone ()[0]),\n },\n {\n 'mimetype' : 'text/html',\n 'lang' : LANG,\n 'canonical' : True,\n 'urls' : [ canonical_url + str (_id) ],\n }\n ])","def article_details(request, pk):\n try:\n article = Article.objects.get(pk=pk)\n except Article.DoesNotExist:\n return HttpResponse(status='404')\n\n if request.method == 'GET':\n serializer = ArticleSerializer(article)\n return JsonResponse(serializer.data)\n\n elif request.method == 'PUT':\n data = JSONParser().parse(request)\n serializer = ArticleSerializer(article, data=data)\n\n if serializer.is_valid():\n serializer.save()\n return JsonResponse(serializer.data)\n return JsonResponse(serializer.errors, status=400)\n elif request.method == 'DELETE':\n article.delete()\n return HttpResponse(status='204')","def get(self, id):\n return {'id': id}","def get_object(self, id, **args):\n return self.request(id, args)","def edit_article(article_id):\n \n if 'username' in session: \n article = mongo.db.articles.find_one_or_404(\n {'_id': ObjectId(article_id)})\n form=BlogForm()\n form.title.data = article['title']\n form.content.data = article['content']\n return render_template('pages/editarticle.html',\n form=form, \n article=article, \n legend='Edit your Blog Article'\n )","def query_by_id(_id: int) -> dict:\n post = Posts.query.filter_by(id=_id).first()\n if post is None:\n return {\"status\": 404, \"message\": \"No id Available\"}\n return {\n \"title\": post.title,\n \"body\": markdown.markdown(post.body),\n \"timestamp\": post.timestamp,\n \"id\": post.id,\n \"url\": make_url_from_title(post.title),\n }","def find(self, id):\n return self._select_one('''\n select\n *\n from\n {table}\n where\n {primary_key} = %s\n '''.format(table=self.__class__._table,\n primary_key=self.__class__._primary_key), [id])","def get_by_id(cls, id):\n return db.session.query(cls).get(id)","def test_otoroshi_controllers_adminapi_tcp_service_api_controller_find_entity_by_id_action(self):\n pass","async def get(self, ctx, id : int):\n response = await self.api.get(id)\n await ctx.send(embed=self._build_embed(response))\n return True","def fetch_author(author_id, alternatives):\n if author_id:\n req = AUTHOR_API.format(author_id=author_id)\n try:\n response = requests.get(req)\n response.raise_for_status()\n author_data = response.json()\n save_author(author_data)\n\n except requests.exceptions.HTTPError as error:\n if len(alternatives) and alternatives[0].get('href'):\n try:\n response = requests.get(alternatives[0].get('href'))\n author_data = response.json()\n author_data['id'] = author_id\n save_author(author_data)\n except Exception as e:\n raise Reject(error)","def read_item(id):\n\n username = login_session.get('username', None)\n item = session.query(Item).filter_by(id=id).one()\n item_display = {'id': item.id, 'title': item.title, 'desc': item.desc}\n return render_template(\n 'read_item.html',\n item_display=item_display,\n username=username)","def _fetch_news(self, docid):\n detail_link = Fetch163.detail_link % docid\n try:\n resp = urllib2.urlopen(detail_link)\n except urllib2.URLError as e:\n urllib_error(e)\n else:\n try:\n doc_json = json.load(resp)\n content = doc_json[docid]\n title = content['title']\n except KeyError:\n print \"Error while Fetching docid: %s\" % docid\n except ValueError:\n print \"No JSON obj could be decoded\", resp.read()\n else:\n if self._filter_test(title):\n #print title\n c_num = content['replyCount']\n ptime = content['ptime']\n img_list = content['img']\n if img_list:\n list_pic = img_list[0]['src']\n else:\n list_pic = ''\n body = content['body']\n abstract = self._retrieve_abstract(body)\n body = convert_163(body, img_list)\n return abstract, body, c_num, ptime, list_pic\n return '', '', '', '', list_pic","def fetch_recipe(*, recipe_id: int) -> Any:\n\n result = [recipe for recipe in RECIPES if recipe[\"id\"] == recipe_id]\n if not result:\n # the exception is raised, not returned - you will get a validation\n # error otherwise.\n raise HTTPException(\n status_code=404, detail=f\"Recipe with ID {recipe_id} not found\"\n )\n\n return result[0]","def get_topics_article(topic_id, article_id):\n article = db_session.query(Article)\\\n .filter_by(topic_id=topic_id, id=article_id).one()\n return jsonify(article.serialize)","def get(self, cls, id):\n pass","def get_image_by_id(id):\n return Image.objects.get(id=id)","def update_article(db:Session, article_id:int, article: ArticleCreate):\n the_article:Article = db.query(ArticleModel).filter(ArticleModel.id==article_id).first()\n\n if the_article is None:\n raise HTTPException(status_code=404, detail=\"The article does not exist\")\n\n the_article.title = article.title\n the_article.description = article.description\n the_article.author = article.author\n db.commit()\n return the_article","def get(self, predicate, successHandler, failHandler=None):\n querySelect = \\\n \"SELECT `article_id`, `title`, `date`, `ip` \" \\\n \"FROM `article_article` \" \\\n \"WHERE `{}` {} %s \" \\\n \"LIMIT 1; \".format(\n predicate[0],\n predicate[1]\n )\n\n querySelectParams = []\n if isinstance(predicate[2], datetime):\n querySelectParams.append(predicate[2].strftime(\"%Y-%m-%d %H:%M:%S\"))\n else:\n querySelectParams.append(predicate[2])\n\n def failCallback(error):\n errorMessage = str(error)\n if isinstance(error, Failure):\n errorMessage = error.getErrorMessage()\n\n self.log.error(\n \"[Default.Article] get() database error: {errorMessage}\",\n errorMessage=errorMessage\n )\n\n if failHandler is not None:\n reactor.callInThread(failHandler, [\"DatabaseError\"])\n\n def successCallback(results):\n if len(results) == 0 and failHandler is not None:\n reactor.callInThread(failHandler, [\"ArticleNotFound\"])\n return\n\n reactor.callInThread(successHandler, {\n \"article_id\": results[0][0],\n \"title\": results[0][1],\n \"date\": results[0][2],\n \"ip\": results[0][3]\n })\n\n operation = self.dbService.runQuery(\n querySelect,\n tuple(querySelectParams)\n )\n operation.addCallbacks(successCallback, failCallback)","def detail(request, article_id):\n article = get_object_or_404(Article, pk=article_id)\n form = PartialCommentForm() #blank form\n return render_to_response('article/detail.html', locals(),\n context_instance=RequestContext(request))","def get_question_by_id(self, id, params={}):\n\n try:\n url = BASE_URL + 'api/v1/questions/' + str(int(id))\n data = self.request('get', url, '_parse_question_json', params)\n return data\n except Exception as e:\n Utils.log(traceback.format_exc())\n Utils.send('question.error')\n Utils.error(e.args[0])"],"string":"[\n \"def article_by_id(self, id):\\n return self.es.get(index=self.index, doc_type=self.doc_type, id=id)\",\n \"def get_article_by_id(article_id):\\n return Article.query.get(article_id)\",\n \"def get_article(db:Session, article_id:int):\\n return db.query(ArticleModel).filter(ArticleModel.id==article_id).first()\",\n \"def articles_id (_id = None):\\n\\n with current_app.config.dba.engine.begin () as conn:\\n res = execute (conn, r\\\"\\\"\\\"\\n SELECT no\\n FROM article\\n WHERE no = :id\\n \\\"\\\"\\\", { 'id' : _id })\\n\\n return make_articles_response (res)\",\n \"def get(self, request, article_id):\\n article = get_object_or_404(Article.objects.all(), pk=article_id)\\n article_serializer = ArticleSerializer(article)\\n return Response(article_serializer.data)\",\n \"def article_detail(request, id):\\n try:\\n logger.info('Calling the api' + APIURL + '/articles/' + id + '/?format=json')\\n response = requests.get(APIURL + '/articles/' + id + '/?format=json')\\n parser = json.loads(response.content)\\n images = article_images(id)\\n next_read = read_next()\\n return render_to_response('article/details.html', {'article':parser, 'next_read': next_read, 'related_images': images}, RequestContext(request))\\n except:\\n logger.error('Calling the api error in article_detail')\\n raise Http404(\\\"Article does not exist\\\")\",\n \"def get_object(self, article_id):\\n try:\\n comments = Comment.objects.all()\\n #filter to only contain comments for specified article (article_id)\\n comments = list(filter(lambda x: x.article_id == article_id , comments))\\n return comments\\n except Comment.DoesNotExist:\\n raise Http404\",\n \"def article(request, id, slug=None):\\n article = get_object_or_404(Article, id=id)\\n\\n context = {\\n 'article': article,\\n }\\n return render(request, 'article.html', context)\",\n \"def article(self, article_id):\\r\\n return articles.Article(self, article_id)\",\n \"def article(request, article_id):\\n article = get_object_or_404(Article, pk=article_id)\\n context = {'article': article}\\n return render(request, 'sacms/article.html', context)\",\n \"def articles(self, id):\\n response = self._connection.session.get(\\n self._connection.url + \\\"ticket_articles/by_ticket/%s?expand=true\\\" % id\\n )\\n return self._raise_or_return_json(response)\",\n \"def articles(id):\\n articles = get_articles(id)\\n return render_template('article.html', articles = articles)\",\n \"def get_entity_by_id(self, id):\\n # url = '{}/ngsi-ld/v1/entities?type={}&offset={}&limit={}'.format(self.url, type, offset, limit)\\n url = '{}/ngsi-ld/v1/entities/{}'.format(self.url, id)\\n r = requests.get(url, headers=self.headers_ld)\\n return r.json()\",\n \"def test_get_article_by_id():\\n article = Article(\\n author = 'jane@doe.com',\\n title = 'New Article',\\n content = 'Super extra awesome article'\\n ).save()\\n\\n query = GetArticleByIDQuery(\\n id = article.id\\n )\\n\\n assert query.execute().id == article.id\",\n \"def get_article(request, article_id):\\n try:\\n article = Article.objects.get(pk=article_id)\\n increment_articles_views(article_id)\\n return format_ajax_response(True, \\\"Knowledgebase article retrieved successfully.\\\", {\\\"article\\\": article.dump_to_dict()})\\n except Exception as ex:\\n logger.error(\\\"Failed to get_article: %s\\\" % ex)\\n return format_ajax_response(False, \\\"There was an error retrieving the knowledgebase article.\\\")\",\n \"def view_article(request, id_article):\\n article = get_object_or_404(Article, id=id_article)\\n return render(request, 'core/view_article.html', {'article': article})\",\n \"def get_article(article_id):\\n article = db_session.query(Article)\\\\\\n .filter_by(id=article_id).one()\\n return jsonify(article.serialize)\",\n \"def article(self, article_id):\\r\\n return contents.Article(self, article_id)\",\n \"def article(self, article_id):\\n return articles.Article(self, article_id)\",\n \"def get(self, story_id):\",\n \"def article(article_id):\\n\\tarticle = models.Article.query.get(article_id)\\n\\tif not article:\\n\\t\\tabort(404)\\n\\treturn jsonify(article.dictionary())\",\n \"def get(self, request, slug, id):\\n article = ArticleInst.fetch(slug)\\n\\n try:\\n comment = Comment.objects.get(pk=id, article=article)\\n except Comment.DoesNotExist:\\n data = {\\n 'error': f'Comment of ID {id} nonexistent'\\n }\\n status_ = status.HTTP_404_NOT_FOUND\\n else:\\n serializer = self.serializer_class(comment)\\n status_ = status.HTTP_200_OK\\n data = serializer.data\\n return Response(\\n data=data,\\n status=status_)\",\n \"def fetch(cls, slug):\\n try:\\n article = Article.objects.get(slug=slug)\\n except Article.DoesNotExist:\\n raise exceptions.NotFound(f'Article of slug {slug} nonexistent')\\n else:\\n return article\",\n \"def fetch(cls, slug):\\n try:\\n article = Article.objects.get(slug=slug)\\n except Article.DoesNotExist:\\n raise exceptions.NotFound(f'Article with slug {slug} nonexistent')\\n else:\\n return article\",\n \"def get(self, _id):\",\n \"def download(self, id, article_id, ticket_id):\\n response = self._connection.session.get(\\n self.url + f\\\"/{ticket_id}/{article_id}/{id}\\\"\\n )\\n return self._raise_or_return_json(response)\",\n \"def getbyid(self, id):\\n\\n return esd.retrieve(id)\",\n \"def articles(id):\\n articles = get_articles(id)\\n print(articles)\\n\\n\\n return render_template('article.html', id = id,articles= articles)\",\n \"def get_by_id(self, id):\\n return Entry.all().filter('entry_id = ', id).get()\",\n \"def get_by_id(self, id: int):\\n\\n\\t\\traise NotImplemented\",\n \"def get_by_id(cls, id):\\n e = api.get([key.Key(cls.__name__, id)])\\n if e:\\n return cls.from_entity(e[0])\\n raise ObjectDoesNotExist\",\n \"def news_article(id):\\n articles = get_articles(id)\\n return render_template('news_article.html', articles = articles)\",\n \"def get_object(self, id):\\n try:\\n return Comment.objects.get(id=id)\\n except Comment.DoesNotExist:\\n raise Http404\",\n \"def detail(request, article_id):\\n try:\\n article = Article.objects.get(pk=article_id)\\n except Member.DoesNotExist:\\n raise Http404(\\\"Article does not exist\\\")\\n #article_list = Article.objects.order_by('-released_at')[:5]\\n login = request.user and request.user.is_authenticated()\\n article_list = get_article_list('-released_at',login)[:5]\\n auth_form = AuthenticationForm(None, request.POST or None)\\n return render(request, 'app/article_detail.html', { \\n 'title':'ニュースの詳細',\\n 'year':datetime.now().year,\\n 'articles':article_list,\\n 'blogs':EntryView.get_entry_list('-posted_at',-1, -1 if not login else request.user.pk )[:5],\\n 'article': article,\\n 'auth_form':auth_form,\\n 'current_user':request.user,\\n }\\n )\",\n \"def get_article(uuid):\\n return Article.get(Article.uuid == uuid)\",\n \"def news(id):\\n\\tarticle = data.get_article(id)\\n\\tif not article:\\n\\t\\treturn \\\"article not found\\\", 404\\n\\treturn render_template(\\\"article.html\\\", article=article)\",\n \"async def read(articleid=True, uid=False):\\n\\n # Load Settings\\n settings = await fetch_settings()\\n table = settings[\\\"table\\\"]\\n\\n if uid:\\n connection = await connect()\\n row = await connection.fetch(f\\\"\\\"\\\"\\n SELECT * FROM \\\"{table}\\\" WHERE \\\"UID\\\" = $1;\\n \\\"\\\"\\\", str(uid))\\n await connection.close()\\n return row\\n try:\\n articleid = int(articleid)\\n except ValueError:\\n return []\\n connection = await connect()\\n rows = await connection.fetch(f\\\"\\\"\\\"\\n SELECT * FROM \\\"{table}\\\" WHERE \\\"ID\\\" = $1;\\n \\\"\\\"\\\", articleid)\\n await connection.close()\\n\\n result = []\\n for row in rows:\\n row_dict = dict(row)\\n row_dict[\\\"dateReleased\\\"] = row[\\\"dateReleased\\\"].replace(year=(row[\\\"dateReleased\\\"].year + GAME_YEAR_OFFSET))\\n\\n result.append(row_dict)\\n\\n return result\",\n \"def detail(request, article_id):\\n return render(request, 'knowledgebase/detail.html', {'article_id': article_id})\",\n \"def get_object(id):\",\n \"def edit(id):\\n r = requests.get(API_ROUTE + '/' + str(id), headers={'Auth': _auth()})\\n if r.status_code != requests.codes.ok:\\n return r.text, r.status_code\\n\\n return render_template('editor.html', article=r.json())\",\n \"def article_exists(self, article_id):\\n try:\\n Article.objects.get(pk=article_id)\\n return True\\n except Article.DoesNotExist:\\n raise Http404\",\n \"def get_by_id(cls, id):\\n return cls.query().get(id)\",\n \"def update_article(id):\\n # get and check article author against current_user\\n the_article = models.Article.get_by_id(id)\\n if current_user.id == the_article.author.id or current_user.role == 'admin':\\n # get payload\\n payload = request.get_json()\\n # run update\\n query = models.Article.update(**payload).where(models.Article.id==id)\\n query.execute()\\n return jsonify(\\n data=model_to_dict(models.Article.get_by_id(id)),\\n status={\\\"code\\\": 200, \\\"message\\\": \\\"Article updated successfully\\\"}\\n ), 200\\n else:\\n return jsonify(data={}, status={\\\"code\\\": 403, \\\"message\\\": \\\"Not authorized\\\"})\",\n \"def load_article(paper_id):\\n s3 = boto3.client('s3')\\n key = 'json/%s.json' % paper_id\\n LOGGER.info('bucket=%s, key=%s', ARTICLE_BUCKET_NAME, key)\\n obj = s3.get_object(\\n Bucket=ARTICLE_BUCKET_NAME,\\n Key=key)\\n body = obj['Body']\\n article = json.loads(body.read())\\n body.close()\\n return article\",\n \"def get_object(self, id):\\n try:\\n return Post.objects.get(id=id)\\n except Post.DoesNotExist:\\n raise Http404\",\n \"def get(cls, id):\\n\\n return cls.query.get(id)\",\n \"def get(cls, id):\\n\\n return cls.query.get(id)\",\n \"def get(id=None):\\n return requests.get(\\\"/{}\\\".format(id))\",\n \"def article_one(request, article_id):\\n if request.method == \\\"GET\\\":\\n article = Article.objects.get(pk=article_id)\\n title = article.title\\n author = article.author\\n content = article.content\\n phrases = list(\\n map(\\n lambda phrase: {\\n \\\"content\\\": phrase.content,\\n \\\"keyword\\\": phrase.word.content,\\n },\\n article.phrases.all(),\\n )\\n )\\n return JsonResponse(\\n {\\n \\\"title\\\": title,\\n \\\"author\\\": author,\\n \\\"content\\\": content,\\n \\\"phrases\\\": phrases,\\n },\\n safe=False,\\n status=200,\\n )\\n else:\\n return HttpResponseNotAllowed([\\\"GET\\\"])\",\n \"def retrieve(self, request, slug=None):\\n article = get_object_or_404(self.queryset, slug=slug)\\n serializer = self.serializer_class(article)\\n if request.user and not isinstance(request.user, AnonymousUser):\\n self.update_read(article)\\n return Response(serializer.data, status=status.HTTP_200_OK)\",\n \"def get_article(self, slug):\\n try:\\n return Article.objects.get(slug=slug)\\n except User.DoesNotExist:\\n raise Http404\",\n \"def get(self, id):\\n return self.__model__.query.get(id)\",\n \"def get_object(self, id, **args):\\n return self.request(\\\"{0}/{1}\\\".format(self.version, id), args)\",\n \"def get_story(self, id):\\n url = self.base_url + 'stories/{story}'\\n\\n req = requests.get(headers=self.headers, url=url.format(story=id))\\n\\n return req.json()\",\n \"def get_object(self, id_):\\n return self._objects.get(id_, None)\",\n \"def find(self, id):\\n response = self._connection.session.get(self.url + \\\"/%s\\\" % id)\\n return self._raise_or_return_json(response)\",\n \"def get_article_by_key(cls, key):\\n db_key = \\\"article:\\\" + str(key)\\n result = cls.db.hgetall(db_key)\\n return (Article.build(result) if type(result) is dict else None)\",\n \"def getAuthorByID(id: int) -> Author:\\n if not id:\\n abort(400)\\n author = Author.query.get(id)\\n if not author:\\n abort(404, \\\"Author is not found\\\")\\n return author.serialize()\",\n \"def find_by_id(id):\\n query = \\\"SELECT * FROM parcels WHERE id=%s\\\"\\n return db.find_one(query, (id,))\",\n \"def get(self,id):\\r\\n person = get_one(id=id)\\r\\n if not person:\\r\\n api.abort(404)\\r\\n else:\\r\\n return person\",\n \"def edit_news(id):\\n\\n\\tarticle = data.get_article(id)\\n\\treturn render_template(\\\"admin/edit_article.html\\\", article=article)\",\n \"def get(self, id):\\n resultado = EmployeeModel.query.filter_by(employee_id=id).first()\\n if resultado:\\n return resultado\\n api.abort(404)\",\n \"def read_item(id: str, request: Request):\\n obj = db.get(id, kind=endpoint_model)\\n return obj\",\n \"def get_content_by_id_get(self, head, id, locale):\\n # TODO: Assuming first server is good - need to make fallback logic\\n return self.session.get_any(\\\"{base}{request_url}\\\".format(base=self.servers[0],\\n request_url=F\\\"/Content/GetContentById/{id}/{locale}/\\\"))\",\n \"def get_entry_by_id(model, id):\\n print(model, id)\\n return db.session.query(model).filter_by(id=id).first()\",\n \"def fetch_obj(type, id, error=404, new_id=False):\\n if id is None:\\n abort(error)\\n obj_q = Session.query(type)\\n obj = obj_q.get(int(id))\\n #else:\\n # obj = obj_q.filter(type.ID==int(id)).first()\\n\\n if obj is None:\\n abort(error)\\n return obj\",\n \"def fetch_comment(self, comment_id, **args):\\n return self.fetch(\\\"/comment/\\\" + comment_id, **args)\",\n \"def get_by_id(cls, id):\\n try:\\n return cls.objects.get(id=id)\\n except(IntegrityError, OperationalError):\\n return None\",\n \"def load_post_by_id(self, id):\\n post = None\\n posts = self.session.query(Post).filter(Post.id == id).all()\\n if len(posts) > 0:\\n post = posts[0]\\n return post\",\n \"def articles(news_id):\\n #get news based on source id\\n articles = get_articles(news_id)\\n print(articles)\\n title = f'{news_id}'\\n return render_template(\\\"articles.html\\\", articles = articles, title = title)\",\n \"def find_by_id(id: int):\\n exercise = Exercise.try_find_by_id(id)\\n if not exercise:\\n raise NotFound(EXERCISE_NOT_FOUND_MSG)\\n return exercise\",\n \"def delete_article(id):\\n # get and check article author against current_user\\n the_article = models.Article.get_by_id(id)\\n if current_user.id == the_article.author.id or current_user.role == 'admin':\\n # delete article\\n query = models.Article.delete().where(models.Article.id==id)\\n query.execute()\\n return jsonify(\\n data='Article successfully deleted',\\n status={\\\"code\\\": 200, \\\"message\\\": \\\"Article deleted successfully\\\"}\\n ), 200\\n else:\\n return jsonify(data={}, status={\\\"code\\\": 403, \\\"message\\\": \\\"Not authorized\\\"})\",\n \"def fetch_entry(self, entry_id, **args):\\n return self.fetch(\\\"/entry/\\\" + entry_id, **args)\",\n \"def fetch_article(self):\\n dl = download(self.url, max_content_length=settings.PYPO_MAX_CONTENT_LENGTH)\\n self.title, self.readable_article = parse(self, content_type=dl.content_type,\\n text=dl.text, content=dl.content)\",\n \"def get(self,id):\\r\\n person = get_one_by_persons_id(id=id)\\r\\n if not person:\\r\\n api.abort(404)\\r\\n else:\\r\\n return person\",\n \"def read_by_id(self, id, fields=None):\\n assert id is not None, \\\"id can not be None\\\"\\n return self.read_many_by_id([id], fields)[0]\",\n \"async def read_maintenance_record_by_id(id: int, conn: Database = Depends(get_db)):\\n\\n item = await get(conn=conn, id=id)\\n if not item:\\n raise HTTPException(status_code=400, detail=\\\"Item not found\\\")\\n return item\",\n \"def fetch_feed(self, feed_id, **args):\\n return self.fetch(\\\"/feed/\\\" + feed_id, **args)\",\n \"def getItem(self, id):\\n path = 'item/' + id\\n return self.sendRestRequest('GET', path)\",\n \"def articles_id_formats (_id):\\n\\n canonical_url = app.config['APPLICATION_MAIN_URL'] + 'search?article_id='\\n\\n with current_app.config.dba.engine.begin () as conn:\\n res = execute (conn, r\\\"\\\"\\\"\\n SELECT webtext FROM article WHERE no=:no\\n \\\"\\\"\\\", { 'no' : _id })\\n return make_json_response ([\\n {\\n 'mimetype' : 'text/x-html-literal',\\n 'lang' : LANG,\\n 'embeddable' : True,\\n 'text' : normalize_iso ('<div>%s</div>' % res.fetchone ()[0]),\\n },\\n {\\n 'mimetype' : 'text/html',\\n 'lang' : LANG,\\n 'canonical' : True,\\n 'urls' : [ canonical_url + str (_id) ],\\n }\\n ])\",\n \"def article_details(request, pk):\\n try:\\n article = Article.objects.get(pk=pk)\\n except Article.DoesNotExist:\\n return HttpResponse(status='404')\\n\\n if request.method == 'GET':\\n serializer = ArticleSerializer(article)\\n return JsonResponse(serializer.data)\\n\\n elif request.method == 'PUT':\\n data = JSONParser().parse(request)\\n serializer = ArticleSerializer(article, data=data)\\n\\n if serializer.is_valid():\\n serializer.save()\\n return JsonResponse(serializer.data)\\n return JsonResponse(serializer.errors, status=400)\\n elif request.method == 'DELETE':\\n article.delete()\\n return HttpResponse(status='204')\",\n \"def get(self, id):\\n return {'id': id}\",\n \"def get_object(self, id, **args):\\n return self.request(id, args)\",\n \"def edit_article(article_id):\\n \\n if 'username' in session: \\n article = mongo.db.articles.find_one_or_404(\\n {'_id': ObjectId(article_id)})\\n form=BlogForm()\\n form.title.data = article['title']\\n form.content.data = article['content']\\n return render_template('pages/editarticle.html',\\n form=form, \\n article=article, \\n legend='Edit your Blog Article'\\n )\",\n \"def query_by_id(_id: int) -> dict:\\n post = Posts.query.filter_by(id=_id).first()\\n if post is None:\\n return {\\\"status\\\": 404, \\\"message\\\": \\\"No id Available\\\"}\\n return {\\n \\\"title\\\": post.title,\\n \\\"body\\\": markdown.markdown(post.body),\\n \\\"timestamp\\\": post.timestamp,\\n \\\"id\\\": post.id,\\n \\\"url\\\": make_url_from_title(post.title),\\n }\",\n \"def find(self, id):\\n return self._select_one('''\\n select\\n *\\n from\\n {table}\\n where\\n {primary_key} = %s\\n '''.format(table=self.__class__._table,\\n primary_key=self.__class__._primary_key), [id])\",\n \"def get_by_id(cls, id):\\n return db.session.query(cls).get(id)\",\n \"def test_otoroshi_controllers_adminapi_tcp_service_api_controller_find_entity_by_id_action(self):\\n pass\",\n \"async def get(self, ctx, id : int):\\n response = await self.api.get(id)\\n await ctx.send(embed=self._build_embed(response))\\n return True\",\n \"def fetch_author(author_id, alternatives):\\n if author_id:\\n req = AUTHOR_API.format(author_id=author_id)\\n try:\\n response = requests.get(req)\\n response.raise_for_status()\\n author_data = response.json()\\n save_author(author_data)\\n\\n except requests.exceptions.HTTPError as error:\\n if len(alternatives) and alternatives[0].get('href'):\\n try:\\n response = requests.get(alternatives[0].get('href'))\\n author_data = response.json()\\n author_data['id'] = author_id\\n save_author(author_data)\\n except Exception as e:\\n raise Reject(error)\",\n \"def read_item(id):\\n\\n username = login_session.get('username', None)\\n item = session.query(Item).filter_by(id=id).one()\\n item_display = {'id': item.id, 'title': item.title, 'desc': item.desc}\\n return render_template(\\n 'read_item.html',\\n item_display=item_display,\\n username=username)\",\n \"def _fetch_news(self, docid):\\n detail_link = Fetch163.detail_link % docid\\n try:\\n resp = urllib2.urlopen(detail_link)\\n except urllib2.URLError as e:\\n urllib_error(e)\\n else:\\n try:\\n doc_json = json.load(resp)\\n content = doc_json[docid]\\n title = content['title']\\n except KeyError:\\n print \\\"Error while Fetching docid: %s\\\" % docid\\n except ValueError:\\n print \\\"No JSON obj could be decoded\\\", resp.read()\\n else:\\n if self._filter_test(title):\\n #print title\\n c_num = content['replyCount']\\n ptime = content['ptime']\\n img_list = content['img']\\n if img_list:\\n list_pic = img_list[0]['src']\\n else:\\n list_pic = ''\\n body = content['body']\\n abstract = self._retrieve_abstract(body)\\n body = convert_163(body, img_list)\\n return abstract, body, c_num, ptime, list_pic\\n return '', '', '', '', list_pic\",\n \"def fetch_recipe(*, recipe_id: int) -> Any:\\n\\n result = [recipe for recipe in RECIPES if recipe[\\\"id\\\"] == recipe_id]\\n if not result:\\n # the exception is raised, not returned - you will get a validation\\n # error otherwise.\\n raise HTTPException(\\n status_code=404, detail=f\\\"Recipe with ID {recipe_id} not found\\\"\\n )\\n\\n return result[0]\",\n \"def get_topics_article(topic_id, article_id):\\n article = db_session.query(Article)\\\\\\n .filter_by(topic_id=topic_id, id=article_id).one()\\n return jsonify(article.serialize)\",\n \"def get(self, cls, id):\\n pass\",\n \"def get_image_by_id(id):\\n return Image.objects.get(id=id)\",\n \"def update_article(db:Session, article_id:int, article: ArticleCreate):\\n the_article:Article = db.query(ArticleModel).filter(ArticleModel.id==article_id).first()\\n\\n if the_article is None:\\n raise HTTPException(status_code=404, detail=\\\"The article does not exist\\\")\\n\\n the_article.title = article.title\\n the_article.description = article.description\\n the_article.author = article.author\\n db.commit()\\n return the_article\",\n \"def get(self, predicate, successHandler, failHandler=None):\\n querySelect = \\\\\\n \\\"SELECT `article_id`, `title`, `date`, `ip` \\\" \\\\\\n \\\"FROM `article_article` \\\" \\\\\\n \\\"WHERE `{}` {} %s \\\" \\\\\\n \\\"LIMIT 1; \\\".format(\\n predicate[0],\\n predicate[1]\\n )\\n\\n querySelectParams = []\\n if isinstance(predicate[2], datetime):\\n querySelectParams.append(predicate[2].strftime(\\\"%Y-%m-%d %H:%M:%S\\\"))\\n else:\\n querySelectParams.append(predicate[2])\\n\\n def failCallback(error):\\n errorMessage = str(error)\\n if isinstance(error, Failure):\\n errorMessage = error.getErrorMessage()\\n\\n self.log.error(\\n \\\"[Default.Article] get() database error: {errorMessage}\\\",\\n errorMessage=errorMessage\\n )\\n\\n if failHandler is not None:\\n reactor.callInThread(failHandler, [\\\"DatabaseError\\\"])\\n\\n def successCallback(results):\\n if len(results) == 0 and failHandler is not None:\\n reactor.callInThread(failHandler, [\\\"ArticleNotFound\\\"])\\n return\\n\\n reactor.callInThread(successHandler, {\\n \\\"article_id\\\": results[0][0],\\n \\\"title\\\": results[0][1],\\n \\\"date\\\": results[0][2],\\n \\\"ip\\\": results[0][3]\\n })\\n\\n operation = self.dbService.runQuery(\\n querySelect,\\n tuple(querySelectParams)\\n )\\n operation.addCallbacks(successCallback, failCallback)\",\n \"def detail(request, article_id):\\n article = get_object_or_404(Article, pk=article_id)\\n form = PartialCommentForm() #blank form\\n return render_to_response('article/detail.html', locals(),\\n context_instance=RequestContext(request))\",\n \"def get_question_by_id(self, id, params={}):\\n\\n try:\\n url = BASE_URL + 'api/v1/questions/' + str(int(id))\\n data = self.request('get', url, '_parse_question_json', params)\\n return data\\n except Exception as e:\\n Utils.log(traceback.format_exc())\\n Utils.send('question.error')\\n Utils.error(e.args[0])\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.78759176","0.7567833","0.71963876","0.71949047","0.70986164","0.69430614","0.6830546","0.6741828","0.6676814","0.6666822","0.6655588","0.6580953","0.6569796","0.65317386","0.65252817","0.65047145","0.64999455","0.64910865","0.6478443","0.64600855","0.64535636","0.6436058","0.64045674","0.6403972","0.6379147","0.637853","0.63696426","0.636629","0.63335526","0.62712765","0.62282974","0.6171434","0.6169395","0.6169116","0.6156419","0.61538255","0.6151461","0.61151975","0.6099184","0.6088951","0.60556376","0.60512966","0.6043655","0.6040509","0.6039715","0.60388345","0.60388345","0.6021333","0.60025626","0.59773016","0.5971457","0.5954626","0.59438944","0.5941895","0.5938812","0.59368235","0.59266776","0.5924626","0.59162414","0.5899476","0.589547","0.58858293","0.58745086","0.5871179","0.58682674","0.58580524","0.5845544","0.58270884","0.58167565","0.58124197","0.57986665","0.5785299","0.57832664","0.5781078","0.57686377","0.5756416","0.5754528","0.57528126","0.5748008","0.57351714","0.57300156","0.5711679","0.5705298","0.5700636","0.5693516","0.5687725","0.5686421","0.56788546","0.56727046","0.56703275","0.5651474","0.56454647","0.56424344","0.56355065","0.5634456","0.5630208","0.5623305","0.5614808","0.5609787","0.5599556"],"string":"[\n \"0.78759176\",\n \"0.7567833\",\n \"0.71963876\",\n \"0.71949047\",\n \"0.70986164\",\n \"0.69430614\",\n \"0.6830546\",\n \"0.6741828\",\n \"0.6676814\",\n \"0.6666822\",\n \"0.6655588\",\n \"0.6580953\",\n \"0.6569796\",\n \"0.65317386\",\n \"0.65252817\",\n \"0.65047145\",\n \"0.64999455\",\n \"0.64910865\",\n \"0.6478443\",\n \"0.64600855\",\n \"0.64535636\",\n \"0.6436058\",\n \"0.64045674\",\n \"0.6403972\",\n \"0.6379147\",\n \"0.637853\",\n \"0.63696426\",\n \"0.636629\",\n \"0.63335526\",\n \"0.62712765\",\n \"0.62282974\",\n \"0.6171434\",\n \"0.6169395\",\n \"0.6169116\",\n \"0.6156419\",\n \"0.61538255\",\n \"0.6151461\",\n \"0.61151975\",\n \"0.6099184\",\n \"0.6088951\",\n \"0.60556376\",\n \"0.60512966\",\n \"0.6043655\",\n \"0.6040509\",\n \"0.6039715\",\n \"0.60388345\",\n \"0.60388345\",\n \"0.6021333\",\n \"0.60025626\",\n \"0.59773016\",\n \"0.5971457\",\n \"0.5954626\",\n \"0.59438944\",\n \"0.5941895\",\n \"0.5938812\",\n \"0.59368235\",\n \"0.59266776\",\n \"0.5924626\",\n \"0.59162414\",\n \"0.5899476\",\n \"0.589547\",\n \"0.58858293\",\n \"0.58745086\",\n \"0.5871179\",\n \"0.58682674\",\n \"0.58580524\",\n \"0.5845544\",\n \"0.58270884\",\n \"0.58167565\",\n \"0.58124197\",\n \"0.57986665\",\n \"0.5785299\",\n \"0.57832664\",\n \"0.5781078\",\n \"0.57686377\",\n \"0.5756416\",\n \"0.5754528\",\n \"0.57528126\",\n \"0.5748008\",\n \"0.57351714\",\n \"0.57300156\",\n \"0.5711679\",\n \"0.5705298\",\n \"0.5700636\",\n \"0.5693516\",\n \"0.5687725\",\n \"0.5686421\",\n \"0.56788546\",\n \"0.56727046\",\n \"0.56703275\",\n \"0.5651474\",\n \"0.56454647\",\n \"0.56424344\",\n \"0.56355065\",\n \"0.5634456\",\n \"0.5630208\",\n \"0.5623305\",\n \"0.5614808\",\n \"0.5609787\",\n \"0.5599556\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.6894055"},"document_rank":{"kind":"string","value":"6"}}},{"rowIdx":80699,"cells":{"query":{"kind":"string","value":"Gets an object from S3."},"document":{"kind":"string","value":"def get(self, key):\n return s3.Object(self.bucket.name, key).get()['Body'].read()"},"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 _get_s3_object(self, s3_path):\n bucket_name, key = S3Util.get_bucket_and_key(s3_path)\n return self.s3_resource.Object(bucket_name, key)","def get_s3_object(self, key):\n try:\n bucket_name = app.config['S3_BUCKET_NAME']\n s3_client = app.config['S3']\n response = s3_client.get_object(Bucket=bucket_name, Key=key)\n return response['Body'].read()\n except Exception:\n return None","def get_object(self, key):\n r = self.s3client.get_object(Bucket = self.s3_bucket, Key = key)\n data = r['Body'].read()\n return data","def _aws_get_object(bucket, key, request_pays=True, client=None):\n if not client:\n session = boto3_session(region_name=REGION)\n client = session.client(\"s3\")\n\n params = {\"Bucket\": bucket, \"Key\": key}\n if request_pays:\n params[\"RequestPayer\"] = \"requester\"\n response = client.get_object(**params)\n return response[\"Body\"].read()","def getS3Object(self, bucket=None, s3Path=None, destPath=None):\n methodName = \"getS3Object\"\n \n if (not bucket):\n raise MissingArgumentException(\"An S3 bucket name (bucket) must be provided.\")\n #endIf\n \n if (not s3Path):\n raise MissingArgumentException(\"An S3 object key (s3Path) must be provided.\")\n #endIf\n \n if (not destPath):\n raise MissingArgumentException(\"A file destination path (destPath) must be provided.\")\n #endIf\n \n TR.info(methodName, \"STARTED download of object: %s from bucket: %s, to: %s\" % (s3Path,bucket,destPath))\n \n s3url = self.s3.generate_presigned_url(ClientMethod='get_object',Params={'Bucket': bucket, 'Key': s3Path},ExpiresIn=60)\n TR.fine(methodName,\"Getting S3 object with pre-signed URL: %s\" % s3url)\n #endIf\n \n destDir = os.path.dirname(destPath)\n if (not os.path.exists(destDir)):\n os.makedirs(destDir)\n TR.info(methodName,\"Created object destination directory: %s\" % destDir)\n #endIf\n \n r = requests.get(s3url, stream=True)\n with open(destPath, 'wb') as destFile:\n shutil.copyfileobj(r.raw, destFile)\n #endWith\n\n TR.info(methodName, \"COMPLETED download from bucket: %s, object: %s, to: %s\" % (bucket,s3Path,destPath))\n \n return destPath","def fetch(iid):\n if AWS_CLIENT_CONFIG and BUCKET_NAME:\n try:\n s3 = boto3.resource('s3', **AWS_CLIENT_CONFIG)\n obj = s3.Bucket(BUCKET_NAME).Object(iid).get()\n if obj:\n return obj.get('Body')\n except botocore.exceptions.ClientError as e:\n logger.error(e)\n else:\n # get locally from temp dir (tests, local development)\n return get_temp_file(iid)\n return None","def get_from_s3(s3_client, s3_url):\n url = urlparse(s3_url)\n\n # Split the bucket from the key\n bucket_name = urllib2.unquote(url.netloc).decode('utf8')\n key_name = urllib2.unquote(url.path[1:]).decode('utf8')\n\n # We're done parsing; start doing some S3 ops\n bucket = s3_client.get_bucket(bucket_name, validate=False)\n key = bucket.get_key(key_name)\n return key.get_contents_as_string()","def get_s3_object(self, remote_s3_url):\n try:\n _file = tempfile.mkstemp()[1]\n parsed_s3_path = remote_s3_url.split(\"/\", 3) # s3://bucket-name/key\n remote_bucket = parsed_s3_path[2] # Bucket name\n remote_key = parsed_s3_path[3] # Key\n self.download_file(remote_bucket, remote_key, _file)\n return _file\n except Exception as e:\n message = {'FILE': __file__.split('/')[-1],\n 'METHOD': inspect.stack()[0][3], 'EXCEPTION': str(e)}\n self.logger.exception(message)\n raise","def get_s3_object(bucket, key_name, local_file):\n\n tracer.put_metadata('object', f's3://{bucket}/{key_name}')\n\n try:\n s3_resource.Bucket(bucket).download_file(key_name, local_file)\n result = 'ok'\n tracer.put_annotation('OBJECT_DOWNLOAD', 'SUCCESS')\n except botocore.exceptions.ClientError as e:\n tracer.put_annotation('OBJECT_DOWNLOAD', 'FAILURE')\n if e.response['Error']['Code'] == '404':\n result = f'Error: s3://{bucket}/{key_name} does not exist'\n else:\n result = f'Error: {str(e)}'\n\n return(result)","def _read_s3_url(cls, s3_url):\n\n parsed_url = urllib.parse.urlparse(s3_url)\n return cls.s3.get_object(Bucket=parsed_url.netloc,\n Key=parsed_url.path.lstrip(\"/\"))[\"Body\"].read()","def get_s3_file(self, no_copy=False):\n return self.get_file(uri_type=URI_S3, no_copy=no_copy)","def _do_retrieve(bucket_name, key_path, number_retries=DEFAULT_S3_RETRIES):\n try:\n return conn.get_object(Bucket=bucket_name, Key=key_path, ResponseContentType='string')\n except Exception:\n if number_retries > 0:\n print(\"s3_retrieve failed with incomplete read, retrying on %s\" % key_path)\n return _do_retrieve(bucket_name, key_path, number_retries=number_retries - 1)\n raise","def get_object(Bucket=None, IfMatch=None, IfModifiedSince=None, IfNoneMatch=None, IfUnmodifiedSince=None, Key=None, Range=None, ResponseCacheControl=None, ResponseContentDisposition=None, ResponseContentEncoding=None, ResponseContentLanguage=None, ResponseContentType=None, ResponseExpires=None, VersionId=None, SSECustomerAlgorithm=None, SSECustomerKey=None, SSECustomerKeyMD5=None, RequestPayer=None, PartNumber=None):\n pass","def load_from_s3(filename):\n s3 = boto3.client('s3')\n obj = s3.get_object(Bucket=BUCKET_NAME, Key=S3_PATH.format(filename))\n return obj['Body'].read().decode()","def get_s3_content(bucket, key, access_id, access_secret):\n try:\n response = s3_client(access_id, access_secret).get_object(Bucket=bucket, Key=key)\n body = response['Body'].read()\n return body\n except ClientError as error:\n LOGGER.error(error)\n return None","def retrieve_s3_contents ( s3_conn, bucket_name, key_name, stored_filename = None ) :\n bucket = s3_conn.get_bucket( bucket_name )\n key = boto.s3.key.Key( bucket )\n key.key = key_name\n if key.exists( ) :\n if stored_filename :\n key.get_contents_to_filename( stored_filename )\n return stored_filename\n\n return key.get_contents_as_string( )\n\n return None","def test_s3_gets_object_content(self):\n mock_s3 = Mock()\n mock_s3_object = Mock()\n s3_response = {'Body': mock_s3_object}\n mock_s3_object.read.return_value = \"file content\"\n mock_s3.get_object.return_value = s3_response\n\n s3_bucket = S3Bucket('bucket_name', s3_client=mock_s3)\n assert s3_bucket.get_content('/file.text') == \\\n 'file content'","def _s3_get_file(url):\n try:\n return S3().get_contents_from_url(url)\n except Exception as e:\n raise ScrBaseException(\"Could not load file from {0}: {1}\".format(url, e))","def s3_read_data(self):\n\n self.k.open()\n self.k.read()","def s3resource(self):\n return self._s3resource","def get(self, bucket: str, object_name: str) -> bytes:\n raise NotImplementedError()","def read_key_s3(self, keyUrl='', bucket=None):\n \n if bucket is None:\n bucket = self.AWS_S3_BUCKET\n\n try:\n\n fileobj = self.get_s3_client().get_object(\n Bucket= bucket,\n Key= keyUrl\n )\n readKey = fileobj['Body'].read()\n # contentObj = readKey.decode('utf-8')\n\n return readKey\n\n except:\n time.sleep(1)\n pass","def get_s3_object_text(s3_resource: boto3.session.Session.resource, bucket_name: str, key: str) -> str:\n obj = s3_resource.Object(bucket_name, key)\n return obj.get()['Body'].read().decode('utf-8')","def get_object(self, bucket_name, key, stream=False, extra_get_args={}):\n url = self.__key_url(bucket_name, key)\n res = self.infinispan_client.get(url, headers=self.headers, auth=self.basicAuth)\n data = res.content\n return data","def get_object(uri):\n bucket_name, key = split_uri(uri)\n return get_client().get_object(bucket_name, key)","def from_s3(cls, bucket_name, mos_file_key):\n xml = s3.get_file_contents(bucket_name, mos_file_key)\n return cls.from_string(xml)","def get_file_s3(bucket, key):\n \n client = boto3.client('s3')\n return client.get_object(Bucket=bucket, Key=key)['Body'].read().decode('utf-8')","def s3_get(url, temp_file):\n s3_resource = boto3.resource(\"s3\")\n bucket_name, s3_path = split_s3_path(url)\n s3_resource.Bucket(bucket_name).download_fileobj(s3_path, temp_file)","def s3_get(url, temp_file):\n s3_resource = boto3.resource(\"s3\")\n bucket_name, s3_path = split_s3_path(url)\n s3_resource.Bucket(bucket_name).download_fileobj(s3_path, temp_file)","def _retrieve_blob(self, object_key):\n return self.s3_resource.Object(self.CVE_BUCKET, object_key).get()['Body'].read()","def boto_init_s3(bucket_name):\n c = boto.connect_s3(aws_access_key_id=settings.AWS_ACCESS_KEY_ID,\n aws_secret_access_key=settings.AWS_SECRET_ACCESS_KEY)\n b = c.get_bucket(bucket_name)\n\n return b","def get_object(self, key):\n try:\n return self.client.get_object(Bucket=self.bucket, Key=key)['Body'].read().decode('utf-8')\n except:\n return None","def s3_download(path):\n with s3_read(path):\n # Reading the file will cache the file locally.\n pass","def get_s3_client():\n return boto3.resource('s3')","def s3_get(url, temp_file, proxies=None):\n\ts3_resource = boto3.resource (\"s3\", config=Config (proxies=proxies))\n\tbucket_name, s3_path = split_s3_path (url)\n\ts3_resource.Bucket (bucket_name).download_fileobj (s3_path, temp_file)","def get_object(self, bucket_name, key, version_id=None):\n if version_id:\n return self._client.get_object(Bucket=bucket_name, Key=key, VersionId=version_id)\n return self._client.get_object(Bucket=bucket_name, Key=key)","def read_object(self, bucket_name, object_name, offset=0, size=0):\n\n data, done = h3lib.read_object(self._handle, bucket_name, object_name, offset, size, self._user_id)\n if data is None:\n data = b''\n return H3Bytes(data, done=done)","def __retrieve_from_bucket(fname):\n blob = BUCKET.blob(fname)\n json_data = json.loads(blob.download_as_string())\n return json_data","def get_blob(self, download_meta):\n bucket_name, key = self._get_bucket_key(download_meta)\n response = self.s3.get_object(Bucket=bucket_name,\n Key=key)\n return response['Body'].read().decode()","def download_file_from_s3_public_bucket(bucket, object, output_file):\n botocore_config = Config(signature_version=UNSIGNED)\n s3_client = boto3.client(\"s3\", config=botocore_config)\n s3_client.download_file(bucket, object, output_file)","def get_file_from_s3(bucket_name, file_name, json_parse=True):\n s3_client = boto3.client('s3')\n s3_file = s3_client.get_object(Bucket=bucket_name, Key=file_name)\n try:\n file_contents = s3_file['Body'].read()\n if json_parse:\n file_contents = json.loads(file_contents)\n except Exception as exc:\n LOGGER.error('Encountered error reading s3 file')\n raise exc\n return file_contents","def read_bucket_objects(bucket_name):\n s3 = boto3.resource('s3')\n bucket = s3.Bucket(bucket_name)\n for obj in bucket.objects.all():\n response = obj.get()\n body = response['Body'].read().decode('utf-8')\n print(body)","def read(path, bucket=None, show_progressbar=True,\n *args, **kwargs):\n path = s3_path_utils.clean_path(path)\n bucket = bucket or s3_path_utils.get_default_bucket()\n bucket = s3_path_utils.clean_bucket(bucket)\n\n filetype = s3_path_utils.get_filetype(path)\n read_fn = get_storage_fn(filetype, 'read')\n\n s3 = boto3.client('s3')\n s3_kwargs = get_s3_client_kwargs(path, bucket,\n operation='read',\n show_progressbar=show_progressbar)\n\n with NamedTemporaryFile(suffix='.' + filetype) as tmpfile:\n inform('Downloading from s3://{}/{}...'.format(bucket, path))\n s3.download_file(bucket, path, tmpfile.name, **s3_kwargs)\n inform('Reading from tempfile...')\n obj = read_fn(tmpfile, *args, **kwargs)\n return obj","def get_amazon_adj_cls_from_s3(s3_resource, bucket_name, prefix='') -> dict:\n amzn_filename = \"AMZN.json\"\n complete_path = os.path.join(prefix, amzn_filename)\n json_object = s3_resource.Object(bucket_name, complete_path)\n file_content = json_object.get()['Body'].read().decode('utf-8')\n json_content = json.loads(file_content)\n return json_content","def s3_retrieve(key_path, study_object_id, raw_path=False, number_retries=DEFAULT_S3_RETRIES):\n if not raw_path:\n key_path = study_object_id + \"/\" + key_path\n encrypted_data = _do_retrieve(S3_BUCKET, key_path, number_retries=number_retries)['Body'].read()\n return encryption.decrypt_server(encrypted_data, study_object_id)","def get_bytes(bucket: str, key: str) -> bytes:\n logger.debug(f'Reading from s3://{bucket}/{key}')\n response = client().get_object(Bucket=bucket, Key=key)\n return response['Body'].read()","def s3(self) -> Optional[pulumi.Input[str]]:\n return pulumi.get(self, \"s3\")","def download_object(object_location: ObjectLocation) -> io.BytesIO:\n s3 = boto3.client(\"s3\")\n stream = io.BytesIO()\n try:\n result = s3.download_fileobj(\n object_location.bucket.name, object_location.key, stream\n )\n except botocore.exceptions.ClientError as err:\n if err.response.get(\"Error\", {}).get(\"Message\", \"Unknown\") == \"Not Found\":\n log.debug(f\"S3 object {object_location} does not exist.\")\n raise KeyError(f\"S3 object {object_location} does not exist.\") from err\n raise\n\n stream.seek(0)\n log.debug(f\"Result of download from {object_location}: {result}\")\n return stream","def get_boto3(args=None, logger=None, stats=None):\n return Boto3(**__get_arguments(args, logger, stats))","def download(self, bucket_name=None,\n object_key=None,\n dest=None):\n\n if bucket_name == None or \\\n object_key == None or \\\n dest == None:\n u_print(\" Error - argument is missing\")\n\n u_print_d('S3.download() - bucket=[{}] key=[{}] dest=[{}]'.format(bucket_name,\n object_key,\n dest))\n return self.s3.Object(bucket_name, object_key).download_file(dest)","def read_data_from_s3(self, name, loc):\n try:\n filename = loc + name + \".json\"\n logger.info('Retrieving the data from the S3 file %s' % filename)\n return self._retrieve_dict(filename)\n except Exception as e:\n logger.error(e)\n return False","def download_object(self, path, dest):\n bucket, key = self.split_name(path)\n if os.path.isdir(dest):\n dest = os.path.join(dest, os.path.basename(key))\n assert os.path.exists(os.path.dirname(dest)), \\\n \"Destination directory does not exist: {}\".format(os.path.dirname(dest))\n try:\n self.s3_resource.Bucket(bucket).download_file(key, dest)\n except botocore.exceptions.ClientError as e:\n if e.response['Error']['Code'] == \"404\" or e.response['Error']['Code'] == \"403\" or \\\n e.response['Error']['Code'] == 'NoSuchKey':\n print(\"The object does not exist. {}\".format(path))\n dest = False\n elif e.response['Error']['Code'] == 'NoSuchBucket':\n print(\"The Bucket not exist. {}\".format(bucket))\n dest = False\n else:\n raise e\n return dest","async def read(self, size=-1):\n # read the object using the bucket and path already determined in\n # __init__, and using the connection object\n try:\n # get the file size first\n file_size = await self._getsize()\n if size== -1:\n range_start = 0\n range_end = file_size\n range_size = file_size\n else:\n range_start = self._seek_pos\n range_end = self._seek_pos+size-1\n if range_end > file_size:\n range_end = file_size-1\n range_size = range_end-range_start+1\n\n # if multipart download is not supported\n if not self._multipart_download:\n # get the full file\n s3_object = await self._conn_obj.conn.get_object(\n Bucket = self._bucket,\n Key = self._path,\n )\n body = s3_object['Body']\n data = await body.read()\n # if the file is smaller than the MAXIMUM_PART_SIZE\n elif (range_size < self._part_size):\n # the requested range is the full file, it is fastest to\n # not specify the range\n if (range_start == 0 and range_size == file_size):\n # get the full file\n s3_object = await self._conn_obj.conn.get_object(\n Bucket = self._bucket,\n Key = self._path,\n )\n # a portion of the file is requested\n else:\n s3_object = await self._conn_obj.conn.get_object(\n Bucket = self._bucket,\n Key = self._path,\n Range = 'bytes={}-{}'.format(\n range_start, range_end\n )\n )\n body = s3_object['Body']\n data = await body.read()\n # multipart download version\n else:\n \"\"\"Use range get to split up a file into the MAXIMUM_PART_SIZE\n and download each part asynchronously.\"\"\"\n # calculate the number of necessary parts\n n_parts = int(range_size / self._part_size + 1)\n # don't go above the maximum number downloadable\n if n_parts > self._max_parts:\n n_parts = self._max_parts\n # (re)calculate the download size\n part_size = float(range_size) / n_parts\n # create the tasks and assign the return data buffer\n tasks = []\n data_buf = io.BytesIO()\n\n for p in range(0, n_parts):\n event_loop = asyncio.get_event_loop()\n task = event_loop.create_task(self._read_partial_file(\n p, part_size\n ))\n tasks.append(task)\n # wait for all the tasks to finish\n results = await asyncio.gather(*tasks)\n # read each chunk of data and write into the global buffer\n for r in results:\n data_buf.write(r)\n r = None # indicate ready for garbage collection\n data_buf.seek(0)\n data = data_buf.read()\n\n except ClientError as e:\n raise IOException(\n \"Could not read from object {} {}\".format(self._path, e)\n )\n except AttributeError as e:\n self._handle_connection_exception(e)\n return data","def loadS3Blob(self, oid, serial):\n\n # Check if it's already in the cache\n cache_filename = self.fshelper.getBlobFilename(oid, serial)\n if os.path.exists(cache_filename):\n return ZEO.ClientStorage._accessed(cache_filename)\n\n # If not, download from S3...\n # First, we'll create the directory for this oid, if it doesn't exist.\n self.fshelper.createPathForOID(oid)\n\n # OK, it's not here and we (or someone) needs to get it. We\n # want to avoid getting it multiple times. We want to avoid\n # getting it multiple times even accross separate client\n # processes on the same machine. We'll use file locking.\n\n lock = ZEO.ClientStorage._lock_blob(cache_filename)\n try:\n # We got the lock, so it's our job to download it. First,\n # we'll double check that someone didn't download it while we\n # were getting the lock:\n\n if os.path.exists(cache_filename):\n return ZEO.ClientStorage._accessed(cache_filename)\n\n # Actually download the blob. When this function\n # returns, it will have been sent. (The receiving will\n # have been handled by the asyncore thread.)\n self.downloadBlob(oid, serial)\n\n if os.path.exists(cache_filename):\n return ZEO.ClientStorage._accessed(cache_filename)\n\n raise ZODB.POSException.POSKeyError(\"No blob file\", oid, serial)\n finally:\n lock.close()","def list_s3_content(bucket, access_id, access_secret, prefix=\"\"):\n try:\n response = s3_client(access_id, access_secret).list_objects(Bucket=bucket, Prefix=prefix)\n objects = []\n if response.get(\"Contents\"):\n for key in response['Contents']:\n objects.append(key['Key'])\n return objects\n except ClientError as error:\n LOGGER.error(error)\n return None","def make_s3(sitename):\n return s3.S3(sitename)","def load_archives_from_s3(self):\n s3_bucket = S3Backend(self.conf).bucket\n try:\n k = Key(s3_bucket)\n k.key = self.backup_key\n\n return json.loads(k.get_contents_as_string())\n except S3ResponseError, exc:\n log.error(exc)\n return {}","def get_google_adj_cls_from_s3(s3_resource, bucket_name, prefix='') -> dict:\n googl_filename = \"GOOGL.json\"\n complete_path = os.path.join(prefix, googl_filename)\n json_object = s3_resource.Object(bucket_name, complete_path)\n file_content = json_object.get()['Body'].read().decode('utf-8')\n json_content = json.loads(file_content)\n return json_content","def get_file(object_name: str, **kwargs) -> HTTPResponse:\n data = client.get_object(DATASETS_BUCKET, object_name, **kwargs)\n return data","def access_s3():\n try:\n s3helper = S3Helper()\n bucket = s3helper.get_bucket(get_archive_bucket())\n LOG.info('Access S3 bucket name: {0}'.format(bucket.name))\n except Exception:\n LOG.exception('check_database_connection')\n return False\n\n return True","def s3(self) -> Optional['outputs.DataRepositoryAssociationS3']:\n return pulumi.get(self, \"s3\")","def get_text(bucket, key):\n s3 = boto3.resource(\"s3\")\n\n ocr_obj = s3.Object(bucket, key)\n response = ocr_obj.get()\n data = response[\"Body\"].read()\n\n return data","def list_public_s3_objects(self):\n _response = urllib.urlopen(self.options.s3_bucket_url)\n _html = _response.read()\n\n if LOCAL_DEBUG:\n print _html\n\n try:\n assert \"AccessDenied\" not in _html\n assert \"NoSuchBucket\" not in _html\n except:\n print(\"ERROR: AccessDenied or NoSuchBucket for {}\".format(self.options.s3_bucket_url))\n raise","def downloadObject(bucket:str, object:str, region:str, path:Path) -> None:\n client = boto3.client('s3', region_name=region)\n try:\n with open(str(path), 'wb') as data:\n client.download_fileobj(Bucket=bucket, Object=object, Data=data)\n except Exception as e:\n raise ObjectDownloadError(e)","def download(self, key: str = None, tmp: str = '/tmp/') -> str:\n path = self._get_object_path(key)\n return s3.copy(path, dest=tmp, verbose=False)","def __get_s3_client(self):\n if self.AWS_ACCESS_KEY:\n s3_client = boto3.client(\n \"s3\",\n aws_access_key_id=self.AWS_ACCESS_KEY,\n aws_secret_access_key=self.AWS_SECRET_ACCESS_KEY,\n )\n else:\n s3_client = boto3.client(\"s3\")\n return s3_client","def get_s3_objects_from_dict(session, event, object_handler_function):\n\n objects = []\n s3 = session.client(\"s3\")\n # Get the object from the event and show its content type\n for record in event.get(\"Records\", []):\n bucket = record[\"s3\"][\"bucket\"][\"name\"]\n unprocessed_key = record[\"s3\"][\"object\"][\"key\"]\n # urllib changes structure and encoding is different\n # between python 2 and 3\n key = (\n urllib.parse.unquote_plus(unprocessed_key)\n # if sys.version_info[0] >= 3\n # else urllib.unquote_plus(unprocessed_key.encode(\"utf-8\"))\n )\n logging.info(\"Bucket: %s. Key: %s\", bucket, key)\n\n # get S3 object and add it to return list\n response = s3.get_object(Bucket=bucket, Key=key)\n objects.append(object_handler_function(response))\n return objects","def _get_resource(\n session: Optional[boto3.Session] = None, region: Optional[str] = None\n) -> S3ServiceResource:\n return (\n session.resource(\"s3\") if session else boto3.resource(\"s3\", region_name=region)\n )","def get_apple_adj_cls_from_s3(s3_resource, bucket_name, prefix='') -> dict:\n aapl_filename = \"AAPL.json\"\n complete_path = os.path.join(prefix, aapl_filename)\n json_object = s3_resource.Object(bucket_name, complete_path)\n file_content = json_object.get()['Body'].read().decode('utf-8')\n json_content = json.loads(file_content)\n return json_content","def s3_etag(url, proxies=None):\n\ts3_resource = boto3.resource (\"s3\", config=Config (proxies=proxies))\n\tbucket_name, s3_path = split_s3_path (url)\n\ts3_object = s3_resource.Object (bucket_name, s3_path)\n\treturn s3_object.e_tag","def load_pickle(self, bucket, key):\n\n with BytesIO() as obj_buffer:\n self._s3.Bucket(bucket).download_fileobj(key, obj_buffer)\n obj_buffer.seek(0)\n obj = pickle.load(obj_buffer)\n\n return obj","def read_s3_file(bucket, key):\r\n try:\r\n s_3 = boto3.client('s3')\r\n file = s_3.get_object(Bucket=bucket, Key=key)\r\n file_body = file['Body'].read().decode(\"utf-8\")\r\n return file_body\r\n\r\n except (FileNotFoundError, IndexError, SystemExit, OSError, IOError) as err:\r\n print(\"Error in reading file\", str(err))\r\n return \"\"","def openBucket(name):\n conn = boto.connect_s3() \n print \"Connecting to bucket: {}\".format(name)\n bucket = conn.get_bucket(name, validate=True)\n return bucket","def s3_resource(self):\n return boto3.resource('s3', \n aws_access_key_id=os.environ.get(\"MINIO_ACCESS_KEY\"),\n aws_secret_access_key=os.environ.get(\"MINIO_SECRET_KEY\"),\n endpoint_url=f'http://{os.environ.get(\"MINIO_SERVER\")}',\n config=Config(signature_version='s3v4')\n )","def get_s3_client(profile_name):\n try:\n session = boto3.session.Session(profile_name=profile_name)\n except ProfileNotFound as e:\n print(e, file=sys.stderr)\n raise FailureException from e\n return session.resource('s3')","def get_objects(self, bucket, s3_client=None):\n\n try:\n all_objects = s3_client.list_objects_v2(Bucket=bucket)\n except botocore.exceptions.EndpointConnectionError:\n logging.error(\"Couldn't connect to an S3 endpoint. If you're using an S3 compatible provider other than AWS, remember to set --s3-endpoint-url\")\n sys.exit(1)\n\n if 'Contents' in all_objects.keys():\n all_objects = [ k['Key'] for k in [ obj for obj in all_objects['Contents'] ]] # pylint: disable=unnecessary-comprehension\n else:\n all_objects = []\n\n return all_objects","def get_boto_client(self) -> S3Client:\n if self._boto_client is None:\n config = Config(signature_version=botocore.UNSIGNED)\n self._boto_client = self.session.client(\n \"s3\",\n region_name=settings.S3_REGION,\n endpoint_url=settings.S3_ENDPOINT_URL,\n config=config,\n )\n return self._boto_client","def download_keypair ( s3_infra_conn, aws_account_type, region_name, keypair_type ) :\n keypair_name = get_keypair_name( aws_account_type, region_name, keypair_type )\n keypair_bucket = get_admin_bucket_name( region_name = region_name )\n return retrieve_s3_contents( s3_conn = s3_infra_conn,\n bucket_name = keypair_bucket,\n key_name = get_keypair_keypath( aws_account_type ) + get_keypair_keyname( keypair_name ),\n stored_filename = keypair_name )","def s3_data_conn ( self ) :\n if not self.s3_data :\n self.s3_data = boto.s3.connection.S3Connection( self.access_key, self.access_key_secret )\n return self.s3_data","def head_object(self, bucket_name, object_name):\n try:\n return self._client.head_object(Bucket=bucket_name, Key=object_name)\n except ClientError as client_error:\n raise AWSClientError(\n function_name=\"head_object\",\n message=_process_s3_bucket_error(client_error, bucket_name),\n error_code=client_error.response[\"Error\"][\"Code\"],\n )","def s3_etag(url):\n s3_resource = boto3.resource(\"s3\")\n bucket_name, s3_path = split_s3_path(url)\n s3_object = s3_resource.Object(bucket_name, s3_path)\n return s3_object.e_tag","def s3_etag(url):\n s3_resource = boto3.resource(\"s3\")\n bucket_name, s3_path = split_s3_path(url)\n s3_object = s3_resource.Object(bucket_name, s3_path)\n return s3_object.e_tag","def read_file_from_s3(bucket, key, profile):\n s3_client = boto3.Session(profile_name=profile).client('s3')\n resp = s3_client.get_object(Bucket=bucket, Key=key)\n # Python 3.8/3.9 can't download files over 2GB via HTTP, so file is \n # streamed in chunks just in case\n content = ''.join([\n chunk.decode() for chunk in resp['Body'].iter_chunks()\n ])\n \n return content","def readFileFromS3(self, keyname, path):\n try:\n k = Key(self.BUCKET)\n k.key = keyname\n k.get_contents_to_filename(path)\n return True\n except IOError:\n return False","def get_pickle_from_s3(path):\n return load_pickle_from_s3(*load_bucket_and_path(path))","def _get_s3_bucket(bucket_name: str):\n s3 = getattr(_resources_for_thread, \"s3\", None)\n if s3 is None:\n # When multi-threaded, we can't use the default session. So keep one per thread.\n session = boto3.session.Session()\n s3 = session.resource(\"s3\")\n _resources_for_thread.s3 = s3\n return s3.Bucket(bucket_name)","def get(self, key):\n try:\n return self.resource.Object(self.bucketname, key).get()\n except botocore.exceptions.ClientError as error:\n if error.response['Error']['Code'] == 'NoSuchKey':\n # key does not exists\n raise KeyError(error.response['Error'])\n else:\n # unexpected error\n raise error","def test_get_object(self):\n err = None\n try:\n response = self.bos.put_object_from_string(self.BUCKET,\n self.KEY,\n \"This is a string.\",\n user_metadata={\"private\": \"private\"})\n except BceServerError as e:\n err = e\n finally:\n self.assertIsNone(err)\n self.check_headers(response)\n\n err = None\n try:\n response = self.bos.get_object(self.BUCKET, self.KEY)\n except BceServerError as e:\n err = e\n finally:\n self.assertIsNone(err)\n\n self.check_headers(response)\n self.assertEqual(response.metadata.etag, '13562b471182311b6eea8d241103e8f0')\n self.assertDictEqual(response.metadata.user_metadata, {u\"private\":u\"private\"})\n data = BytesIO(response.data.read())\n response.data.close()","def _get_aws_s3_connection(cls, access_key, secret_access_key):\n return boto.connect_s3(access_key, secret_access_key)","def s3client(self):\n return self._s3client","def load_pickle_from_s3(bucket, path):\n pkl = get_from_s3(bucket, path)\n try:\n return pickle.loads(pkl, encoding='utf-8') # python3\n except TypeError:\n return pickle.loads(pkl) # python2","def getBucket(self, name=None, create=True):\n try:\n return self.CONNECTION.get_bucket(name)\n except boto.exception.S3ResponseError:\n if create:\n bucket = self.CONNECTION.create_bucket(name)\n print 'created new bucket %s' % name\n return bucket\n return None","def s3_client(s3_url):\n with moto.mock_s3():\n with clients.S3Client(s3_url) as client:\n yield client","def s3_object_exists(s3_path: Path) -> bool:\n\n s3_args, unknown = get_s3_args().parse_known_args()\n s3_client = get_s3_client(s3_args)\n log = get_logger(\"s3_object_exists\")\n\n try:\n s3_client.get_object(Bucket=s3_args.s3_bucket, Key=str(s3_path))\n return True\n except s3_client.exceptions.NoSuchKey:\n return False","def get_blob(self, blob_name):\n return self.bucket.get_blob(blob_name)","def s3_client(self):\n return boto3.client('s3', \n aws_access_key_id=os.environ.get(\"MINIO_ACCESS_KEY\"),\n aws_secret_access_key=os.environ.get(\"MINIO_SECRET_KEY\"),\n endpoint_url=f'http://{os.environ.get(\"MINIO_SERVER\")}',\n config=Config(signature_version='s3v4')\n )","async def getStorJSONObj(app, key, bucket=None):\n\n client = _getStorageClient(app)\n if not bucket:\n bucket = app['bucket_name']\n if key[0] == '/':\n key = key[1:] # no leading slash\n log.info(f\"getStorJSONObj({bucket})/{key}\")\n\n data = await client.get_object(key, bucket=bucket)\n\n try:\n json_dict = json.loads(data.decode('utf8'))\n except UnicodeDecodeError:\n log.error(f\"Error loading JSON at key: {key}\")\n raise HTTPInternalServerError()\n\n log.debug(f\"storage key {key} returned: {json_dict}\")\n return json_dict","def stream_object(self, bucket, key) -> StreamingBody:\n return self.resource.Object(bucket, key).get()['Body']","def read_badpractice(path, bucket=None, filetype=None, show_progressbar=True,\n *args, **kwargs):\n logging.warning('You are using rivet\\'s read function that allows for '\n 'files stored with inadvisible S3 paths. It is highly '\n 'recommended that you use the standard \\'read\\' '\n 'function to ensure that good naming practices are '\n 'followed.')\n\n bucket = bucket or s3_path_utils.get_default_bucket()\n\n if filetype is None:\n filetype = s3_path_utils.get_filetype(path)\n\n read_fn = get_storage_fn(filetype, 'read')\n\n s3 = boto3.client('s3')\n s3_kwargs = get_s3_client_kwargs(path, bucket,\n operation='read',\n show_progressbar=show_progressbar)\n\n with NamedTemporaryFile(suffix='.' + filetype) as tmpfile:\n inform('Downloading from s3://{}/{}...'.format(bucket, path))\n s3.download_file(bucket, path, tmpfile.name, **s3_kwargs)\n inform('Reading object from tempfile...')\n obj = read_fn(tmpfile, *args, **kwargs)\n return obj","def authorizedClientCall(self):\n\t\tclient \t\t= boto3.client(\"s3\")\n\t\treturn(client)"],"string":"[\n \"def _get_s3_object(self, s3_path):\\n bucket_name, key = S3Util.get_bucket_and_key(s3_path)\\n return self.s3_resource.Object(bucket_name, key)\",\n \"def get_s3_object(self, key):\\n try:\\n bucket_name = app.config['S3_BUCKET_NAME']\\n s3_client = app.config['S3']\\n response = s3_client.get_object(Bucket=bucket_name, Key=key)\\n return response['Body'].read()\\n except Exception:\\n return None\",\n \"def get_object(self, key):\\n r = self.s3client.get_object(Bucket = self.s3_bucket, Key = key)\\n data = r['Body'].read()\\n return data\",\n \"def _aws_get_object(bucket, key, request_pays=True, client=None):\\n if not client:\\n session = boto3_session(region_name=REGION)\\n client = session.client(\\\"s3\\\")\\n\\n params = {\\\"Bucket\\\": bucket, \\\"Key\\\": key}\\n if request_pays:\\n params[\\\"RequestPayer\\\"] = \\\"requester\\\"\\n response = client.get_object(**params)\\n return response[\\\"Body\\\"].read()\",\n \"def getS3Object(self, bucket=None, s3Path=None, destPath=None):\\n methodName = \\\"getS3Object\\\"\\n \\n if (not bucket):\\n raise MissingArgumentException(\\\"An S3 bucket name (bucket) must be provided.\\\")\\n #endIf\\n \\n if (not s3Path):\\n raise MissingArgumentException(\\\"An S3 object key (s3Path) must be provided.\\\")\\n #endIf\\n \\n if (not destPath):\\n raise MissingArgumentException(\\\"A file destination path (destPath) must be provided.\\\")\\n #endIf\\n \\n TR.info(methodName, \\\"STARTED download of object: %s from bucket: %s, to: %s\\\" % (s3Path,bucket,destPath))\\n \\n s3url = self.s3.generate_presigned_url(ClientMethod='get_object',Params={'Bucket': bucket, 'Key': s3Path},ExpiresIn=60)\\n TR.fine(methodName,\\\"Getting S3 object with pre-signed URL: %s\\\" % s3url)\\n #endIf\\n \\n destDir = os.path.dirname(destPath)\\n if (not os.path.exists(destDir)):\\n os.makedirs(destDir)\\n TR.info(methodName,\\\"Created object destination directory: %s\\\" % destDir)\\n #endIf\\n \\n r = requests.get(s3url, stream=True)\\n with open(destPath, 'wb') as destFile:\\n shutil.copyfileobj(r.raw, destFile)\\n #endWith\\n\\n TR.info(methodName, \\\"COMPLETED download from bucket: %s, object: %s, to: %s\\\" % (bucket,s3Path,destPath))\\n \\n return destPath\",\n \"def fetch(iid):\\n if AWS_CLIENT_CONFIG and BUCKET_NAME:\\n try:\\n s3 = boto3.resource('s3', **AWS_CLIENT_CONFIG)\\n obj = s3.Bucket(BUCKET_NAME).Object(iid).get()\\n if obj:\\n return obj.get('Body')\\n except botocore.exceptions.ClientError as e:\\n logger.error(e)\\n else:\\n # get locally from temp dir (tests, local development)\\n return get_temp_file(iid)\\n return None\",\n \"def get_from_s3(s3_client, s3_url):\\n url = urlparse(s3_url)\\n\\n # Split the bucket from the key\\n bucket_name = urllib2.unquote(url.netloc).decode('utf8')\\n key_name = urllib2.unquote(url.path[1:]).decode('utf8')\\n\\n # We're done parsing; start doing some S3 ops\\n bucket = s3_client.get_bucket(bucket_name, validate=False)\\n key = bucket.get_key(key_name)\\n return key.get_contents_as_string()\",\n \"def get_s3_object(self, remote_s3_url):\\n try:\\n _file = tempfile.mkstemp()[1]\\n parsed_s3_path = remote_s3_url.split(\\\"/\\\", 3) # s3://bucket-name/key\\n remote_bucket = parsed_s3_path[2] # Bucket name\\n remote_key = parsed_s3_path[3] # Key\\n self.download_file(remote_bucket, remote_key, _file)\\n return _file\\n except Exception as e:\\n message = {'FILE': __file__.split('/')[-1],\\n 'METHOD': inspect.stack()[0][3], 'EXCEPTION': str(e)}\\n self.logger.exception(message)\\n raise\",\n \"def get_s3_object(bucket, key_name, local_file):\\n\\n tracer.put_metadata('object', f's3://{bucket}/{key_name}')\\n\\n try:\\n s3_resource.Bucket(bucket).download_file(key_name, local_file)\\n result = 'ok'\\n tracer.put_annotation('OBJECT_DOWNLOAD', 'SUCCESS')\\n except botocore.exceptions.ClientError as e:\\n tracer.put_annotation('OBJECT_DOWNLOAD', 'FAILURE')\\n if e.response['Error']['Code'] == '404':\\n result = f'Error: s3://{bucket}/{key_name} does not exist'\\n else:\\n result = f'Error: {str(e)}'\\n\\n return(result)\",\n \"def _read_s3_url(cls, s3_url):\\n\\n parsed_url = urllib.parse.urlparse(s3_url)\\n return cls.s3.get_object(Bucket=parsed_url.netloc,\\n Key=parsed_url.path.lstrip(\\\"/\\\"))[\\\"Body\\\"].read()\",\n \"def get_s3_file(self, no_copy=False):\\n return self.get_file(uri_type=URI_S3, no_copy=no_copy)\",\n \"def _do_retrieve(bucket_name, key_path, number_retries=DEFAULT_S3_RETRIES):\\n try:\\n return conn.get_object(Bucket=bucket_name, Key=key_path, ResponseContentType='string')\\n except Exception:\\n if number_retries > 0:\\n print(\\\"s3_retrieve failed with incomplete read, retrying on %s\\\" % key_path)\\n return _do_retrieve(bucket_name, key_path, number_retries=number_retries - 1)\\n raise\",\n \"def get_object(Bucket=None, IfMatch=None, IfModifiedSince=None, IfNoneMatch=None, IfUnmodifiedSince=None, Key=None, Range=None, ResponseCacheControl=None, ResponseContentDisposition=None, ResponseContentEncoding=None, ResponseContentLanguage=None, ResponseContentType=None, ResponseExpires=None, VersionId=None, SSECustomerAlgorithm=None, SSECustomerKey=None, SSECustomerKeyMD5=None, RequestPayer=None, PartNumber=None):\\n pass\",\n \"def load_from_s3(filename):\\n s3 = boto3.client('s3')\\n obj = s3.get_object(Bucket=BUCKET_NAME, Key=S3_PATH.format(filename))\\n return obj['Body'].read().decode()\",\n \"def get_s3_content(bucket, key, access_id, access_secret):\\n try:\\n response = s3_client(access_id, access_secret).get_object(Bucket=bucket, Key=key)\\n body = response['Body'].read()\\n return body\\n except ClientError as error:\\n LOGGER.error(error)\\n return None\",\n \"def retrieve_s3_contents ( s3_conn, bucket_name, key_name, stored_filename = None ) :\\n bucket = s3_conn.get_bucket( bucket_name )\\n key = boto.s3.key.Key( bucket )\\n key.key = key_name\\n if key.exists( ) :\\n if stored_filename :\\n key.get_contents_to_filename( stored_filename )\\n return stored_filename\\n\\n return key.get_contents_as_string( )\\n\\n return None\",\n \"def test_s3_gets_object_content(self):\\n mock_s3 = Mock()\\n mock_s3_object = Mock()\\n s3_response = {'Body': mock_s3_object}\\n mock_s3_object.read.return_value = \\\"file content\\\"\\n mock_s3.get_object.return_value = s3_response\\n\\n s3_bucket = S3Bucket('bucket_name', s3_client=mock_s3)\\n assert s3_bucket.get_content('/file.text') == \\\\\\n 'file content'\",\n \"def _s3_get_file(url):\\n try:\\n return S3().get_contents_from_url(url)\\n except Exception as e:\\n raise ScrBaseException(\\\"Could not load file from {0}: {1}\\\".format(url, e))\",\n \"def s3_read_data(self):\\n\\n self.k.open()\\n self.k.read()\",\n \"def s3resource(self):\\n return self._s3resource\",\n \"def get(self, bucket: str, object_name: str) -> bytes:\\n raise NotImplementedError()\",\n \"def read_key_s3(self, keyUrl='', bucket=None):\\n \\n if bucket is None:\\n bucket = self.AWS_S3_BUCKET\\n\\n try:\\n\\n fileobj = self.get_s3_client().get_object(\\n Bucket= bucket,\\n Key= keyUrl\\n )\\n readKey = fileobj['Body'].read()\\n # contentObj = readKey.decode('utf-8')\\n\\n return readKey\\n\\n except:\\n time.sleep(1)\\n pass\",\n \"def get_s3_object_text(s3_resource: boto3.session.Session.resource, bucket_name: str, key: str) -> str:\\n obj = s3_resource.Object(bucket_name, key)\\n return obj.get()['Body'].read().decode('utf-8')\",\n \"def get_object(self, bucket_name, key, stream=False, extra_get_args={}):\\n url = self.__key_url(bucket_name, key)\\n res = self.infinispan_client.get(url, headers=self.headers, auth=self.basicAuth)\\n data = res.content\\n return data\",\n \"def get_object(uri):\\n bucket_name, key = split_uri(uri)\\n return get_client().get_object(bucket_name, key)\",\n \"def from_s3(cls, bucket_name, mos_file_key):\\n xml = s3.get_file_contents(bucket_name, mos_file_key)\\n return cls.from_string(xml)\",\n \"def get_file_s3(bucket, key):\\n \\n client = boto3.client('s3')\\n return client.get_object(Bucket=bucket, Key=key)['Body'].read().decode('utf-8')\",\n \"def s3_get(url, temp_file):\\n s3_resource = boto3.resource(\\\"s3\\\")\\n bucket_name, s3_path = split_s3_path(url)\\n s3_resource.Bucket(bucket_name).download_fileobj(s3_path, temp_file)\",\n \"def s3_get(url, temp_file):\\n s3_resource = boto3.resource(\\\"s3\\\")\\n bucket_name, s3_path = split_s3_path(url)\\n s3_resource.Bucket(bucket_name).download_fileobj(s3_path, temp_file)\",\n \"def _retrieve_blob(self, object_key):\\n return self.s3_resource.Object(self.CVE_BUCKET, object_key).get()['Body'].read()\",\n \"def boto_init_s3(bucket_name):\\n c = boto.connect_s3(aws_access_key_id=settings.AWS_ACCESS_KEY_ID,\\n aws_secret_access_key=settings.AWS_SECRET_ACCESS_KEY)\\n b = c.get_bucket(bucket_name)\\n\\n return b\",\n \"def get_object(self, key):\\n try:\\n return self.client.get_object(Bucket=self.bucket, Key=key)['Body'].read().decode('utf-8')\\n except:\\n return None\",\n \"def s3_download(path):\\n with s3_read(path):\\n # Reading the file will cache the file locally.\\n pass\",\n \"def get_s3_client():\\n return boto3.resource('s3')\",\n \"def s3_get(url, temp_file, proxies=None):\\n\\ts3_resource = boto3.resource (\\\"s3\\\", config=Config (proxies=proxies))\\n\\tbucket_name, s3_path = split_s3_path (url)\\n\\ts3_resource.Bucket (bucket_name).download_fileobj (s3_path, temp_file)\",\n \"def get_object(self, bucket_name, key, version_id=None):\\n if version_id:\\n return self._client.get_object(Bucket=bucket_name, Key=key, VersionId=version_id)\\n return self._client.get_object(Bucket=bucket_name, Key=key)\",\n \"def read_object(self, bucket_name, object_name, offset=0, size=0):\\n\\n data, done = h3lib.read_object(self._handle, bucket_name, object_name, offset, size, self._user_id)\\n if data is None:\\n data = b''\\n return H3Bytes(data, done=done)\",\n \"def __retrieve_from_bucket(fname):\\n blob = BUCKET.blob(fname)\\n json_data = json.loads(blob.download_as_string())\\n return json_data\",\n \"def get_blob(self, download_meta):\\n bucket_name, key = self._get_bucket_key(download_meta)\\n response = self.s3.get_object(Bucket=bucket_name,\\n Key=key)\\n return response['Body'].read().decode()\",\n \"def download_file_from_s3_public_bucket(bucket, object, output_file):\\n botocore_config = Config(signature_version=UNSIGNED)\\n s3_client = boto3.client(\\\"s3\\\", config=botocore_config)\\n s3_client.download_file(bucket, object, output_file)\",\n \"def get_file_from_s3(bucket_name, file_name, json_parse=True):\\n s3_client = boto3.client('s3')\\n s3_file = s3_client.get_object(Bucket=bucket_name, Key=file_name)\\n try:\\n file_contents = s3_file['Body'].read()\\n if json_parse:\\n file_contents = json.loads(file_contents)\\n except Exception as exc:\\n LOGGER.error('Encountered error reading s3 file')\\n raise exc\\n return file_contents\",\n \"def read_bucket_objects(bucket_name):\\n s3 = boto3.resource('s3')\\n bucket = s3.Bucket(bucket_name)\\n for obj in bucket.objects.all():\\n response = obj.get()\\n body = response['Body'].read().decode('utf-8')\\n print(body)\",\n \"def read(path, bucket=None, show_progressbar=True,\\n *args, **kwargs):\\n path = s3_path_utils.clean_path(path)\\n bucket = bucket or s3_path_utils.get_default_bucket()\\n bucket = s3_path_utils.clean_bucket(bucket)\\n\\n filetype = s3_path_utils.get_filetype(path)\\n read_fn = get_storage_fn(filetype, 'read')\\n\\n s3 = boto3.client('s3')\\n s3_kwargs = get_s3_client_kwargs(path, bucket,\\n operation='read',\\n show_progressbar=show_progressbar)\\n\\n with NamedTemporaryFile(suffix='.' + filetype) as tmpfile:\\n inform('Downloading from s3://{}/{}...'.format(bucket, path))\\n s3.download_file(bucket, path, tmpfile.name, **s3_kwargs)\\n inform('Reading from tempfile...')\\n obj = read_fn(tmpfile, *args, **kwargs)\\n return obj\",\n \"def get_amazon_adj_cls_from_s3(s3_resource, bucket_name, prefix='') -> dict:\\n amzn_filename = \\\"AMZN.json\\\"\\n complete_path = os.path.join(prefix, amzn_filename)\\n json_object = s3_resource.Object(bucket_name, complete_path)\\n file_content = json_object.get()['Body'].read().decode('utf-8')\\n json_content = json.loads(file_content)\\n return json_content\",\n \"def s3_retrieve(key_path, study_object_id, raw_path=False, number_retries=DEFAULT_S3_RETRIES):\\n if not raw_path:\\n key_path = study_object_id + \\\"/\\\" + key_path\\n encrypted_data = _do_retrieve(S3_BUCKET, key_path, number_retries=number_retries)['Body'].read()\\n return encryption.decrypt_server(encrypted_data, study_object_id)\",\n \"def get_bytes(bucket: str, key: str) -> bytes:\\n logger.debug(f'Reading from s3://{bucket}/{key}')\\n response = client().get_object(Bucket=bucket, Key=key)\\n return response['Body'].read()\",\n \"def s3(self) -> Optional[pulumi.Input[str]]:\\n return pulumi.get(self, \\\"s3\\\")\",\n \"def download_object(object_location: ObjectLocation) -> io.BytesIO:\\n s3 = boto3.client(\\\"s3\\\")\\n stream = io.BytesIO()\\n try:\\n result = s3.download_fileobj(\\n object_location.bucket.name, object_location.key, stream\\n )\\n except botocore.exceptions.ClientError as err:\\n if err.response.get(\\\"Error\\\", {}).get(\\\"Message\\\", \\\"Unknown\\\") == \\\"Not Found\\\":\\n log.debug(f\\\"S3 object {object_location} does not exist.\\\")\\n raise KeyError(f\\\"S3 object {object_location} does not exist.\\\") from err\\n raise\\n\\n stream.seek(0)\\n log.debug(f\\\"Result of download from {object_location}: {result}\\\")\\n return stream\",\n \"def get_boto3(args=None, logger=None, stats=None):\\n return Boto3(**__get_arguments(args, logger, stats))\",\n \"def download(self, bucket_name=None,\\n object_key=None,\\n dest=None):\\n\\n if bucket_name == None or \\\\\\n object_key == None or \\\\\\n dest == None:\\n u_print(\\\" Error - argument is missing\\\")\\n\\n u_print_d('S3.download() - bucket=[{}] key=[{}] dest=[{}]'.format(bucket_name,\\n object_key,\\n dest))\\n return self.s3.Object(bucket_name, object_key).download_file(dest)\",\n \"def read_data_from_s3(self, name, loc):\\n try:\\n filename = loc + name + \\\".json\\\"\\n logger.info('Retrieving the data from the S3 file %s' % filename)\\n return self._retrieve_dict(filename)\\n except Exception as e:\\n logger.error(e)\\n return False\",\n \"def download_object(self, path, dest):\\n bucket, key = self.split_name(path)\\n if os.path.isdir(dest):\\n dest = os.path.join(dest, os.path.basename(key))\\n assert os.path.exists(os.path.dirname(dest)), \\\\\\n \\\"Destination directory does not exist: {}\\\".format(os.path.dirname(dest))\\n try:\\n self.s3_resource.Bucket(bucket).download_file(key, dest)\\n except botocore.exceptions.ClientError as e:\\n if e.response['Error']['Code'] == \\\"404\\\" or e.response['Error']['Code'] == \\\"403\\\" or \\\\\\n e.response['Error']['Code'] == 'NoSuchKey':\\n print(\\\"The object does not exist. {}\\\".format(path))\\n dest = False\\n elif e.response['Error']['Code'] == 'NoSuchBucket':\\n print(\\\"The Bucket not exist. {}\\\".format(bucket))\\n dest = False\\n else:\\n raise e\\n return dest\",\n \"async def read(self, size=-1):\\n # read the object using the bucket and path already determined in\\n # __init__, and using the connection object\\n try:\\n # get the file size first\\n file_size = await self._getsize()\\n if size== -1:\\n range_start = 0\\n range_end = file_size\\n range_size = file_size\\n else:\\n range_start = self._seek_pos\\n range_end = self._seek_pos+size-1\\n if range_end > file_size:\\n range_end = file_size-1\\n range_size = range_end-range_start+1\\n\\n # if multipart download is not supported\\n if not self._multipart_download:\\n # get the full file\\n s3_object = await self._conn_obj.conn.get_object(\\n Bucket = self._bucket,\\n Key = self._path,\\n )\\n body = s3_object['Body']\\n data = await body.read()\\n # if the file is smaller than the MAXIMUM_PART_SIZE\\n elif (range_size < self._part_size):\\n # the requested range is the full file, it is fastest to\\n # not specify the range\\n if (range_start == 0 and range_size == file_size):\\n # get the full file\\n s3_object = await self._conn_obj.conn.get_object(\\n Bucket = self._bucket,\\n Key = self._path,\\n )\\n # a portion of the file is requested\\n else:\\n s3_object = await self._conn_obj.conn.get_object(\\n Bucket = self._bucket,\\n Key = self._path,\\n Range = 'bytes={}-{}'.format(\\n range_start, range_end\\n )\\n )\\n body = s3_object['Body']\\n data = await body.read()\\n # multipart download version\\n else:\\n \\\"\\\"\\\"Use range get to split up a file into the MAXIMUM_PART_SIZE\\n and download each part asynchronously.\\\"\\\"\\\"\\n # calculate the number of necessary parts\\n n_parts = int(range_size / self._part_size + 1)\\n # don't go above the maximum number downloadable\\n if n_parts > self._max_parts:\\n n_parts = self._max_parts\\n # (re)calculate the download size\\n part_size = float(range_size) / n_parts\\n # create the tasks and assign the return data buffer\\n tasks = []\\n data_buf = io.BytesIO()\\n\\n for p in range(0, n_parts):\\n event_loop = asyncio.get_event_loop()\\n task = event_loop.create_task(self._read_partial_file(\\n p, part_size\\n ))\\n tasks.append(task)\\n # wait for all the tasks to finish\\n results = await asyncio.gather(*tasks)\\n # read each chunk of data and write into the global buffer\\n for r in results:\\n data_buf.write(r)\\n r = None # indicate ready for garbage collection\\n data_buf.seek(0)\\n data = data_buf.read()\\n\\n except ClientError as e:\\n raise IOException(\\n \\\"Could not read from object {} {}\\\".format(self._path, e)\\n )\\n except AttributeError as e:\\n self._handle_connection_exception(e)\\n return data\",\n \"def loadS3Blob(self, oid, serial):\\n\\n # Check if it's already in the cache\\n cache_filename = self.fshelper.getBlobFilename(oid, serial)\\n if os.path.exists(cache_filename):\\n return ZEO.ClientStorage._accessed(cache_filename)\\n\\n # If not, download from S3...\\n # First, we'll create the directory for this oid, if it doesn't exist.\\n self.fshelper.createPathForOID(oid)\\n\\n # OK, it's not here and we (or someone) needs to get it. We\\n # want to avoid getting it multiple times. We want to avoid\\n # getting it multiple times even accross separate client\\n # processes on the same machine. We'll use file locking.\\n\\n lock = ZEO.ClientStorage._lock_blob(cache_filename)\\n try:\\n # We got the lock, so it's our job to download it. First,\\n # we'll double check that someone didn't download it while we\\n # were getting the lock:\\n\\n if os.path.exists(cache_filename):\\n return ZEO.ClientStorage._accessed(cache_filename)\\n\\n # Actually download the blob. When this function\\n # returns, it will have been sent. (The receiving will\\n # have been handled by the asyncore thread.)\\n self.downloadBlob(oid, serial)\\n\\n if os.path.exists(cache_filename):\\n return ZEO.ClientStorage._accessed(cache_filename)\\n\\n raise ZODB.POSException.POSKeyError(\\\"No blob file\\\", oid, serial)\\n finally:\\n lock.close()\",\n \"def list_s3_content(bucket, access_id, access_secret, prefix=\\\"\\\"):\\n try:\\n response = s3_client(access_id, access_secret).list_objects(Bucket=bucket, Prefix=prefix)\\n objects = []\\n if response.get(\\\"Contents\\\"):\\n for key in response['Contents']:\\n objects.append(key['Key'])\\n return objects\\n except ClientError as error:\\n LOGGER.error(error)\\n return None\",\n \"def make_s3(sitename):\\n return s3.S3(sitename)\",\n \"def load_archives_from_s3(self):\\n s3_bucket = S3Backend(self.conf).bucket\\n try:\\n k = Key(s3_bucket)\\n k.key = self.backup_key\\n\\n return json.loads(k.get_contents_as_string())\\n except S3ResponseError, exc:\\n log.error(exc)\\n return {}\",\n \"def get_google_adj_cls_from_s3(s3_resource, bucket_name, prefix='') -> dict:\\n googl_filename = \\\"GOOGL.json\\\"\\n complete_path = os.path.join(prefix, googl_filename)\\n json_object = s3_resource.Object(bucket_name, complete_path)\\n file_content = json_object.get()['Body'].read().decode('utf-8')\\n json_content = json.loads(file_content)\\n return json_content\",\n \"def get_file(object_name: str, **kwargs) -> HTTPResponse:\\n data = client.get_object(DATASETS_BUCKET, object_name, **kwargs)\\n return data\",\n \"def access_s3():\\n try:\\n s3helper = S3Helper()\\n bucket = s3helper.get_bucket(get_archive_bucket())\\n LOG.info('Access S3 bucket name: {0}'.format(bucket.name))\\n except Exception:\\n LOG.exception('check_database_connection')\\n return False\\n\\n return True\",\n \"def s3(self) -> Optional['outputs.DataRepositoryAssociationS3']:\\n return pulumi.get(self, \\\"s3\\\")\",\n \"def get_text(bucket, key):\\n s3 = boto3.resource(\\\"s3\\\")\\n\\n ocr_obj = s3.Object(bucket, key)\\n response = ocr_obj.get()\\n data = response[\\\"Body\\\"].read()\\n\\n return data\",\n \"def list_public_s3_objects(self):\\n _response = urllib.urlopen(self.options.s3_bucket_url)\\n _html = _response.read()\\n\\n if LOCAL_DEBUG:\\n print _html\\n\\n try:\\n assert \\\"AccessDenied\\\" not in _html\\n assert \\\"NoSuchBucket\\\" not in _html\\n except:\\n print(\\\"ERROR: AccessDenied or NoSuchBucket for {}\\\".format(self.options.s3_bucket_url))\\n raise\",\n \"def downloadObject(bucket:str, object:str, region:str, path:Path) -> None:\\n client = boto3.client('s3', region_name=region)\\n try:\\n with open(str(path), 'wb') as data:\\n client.download_fileobj(Bucket=bucket, Object=object, Data=data)\\n except Exception as e:\\n raise ObjectDownloadError(e)\",\n \"def download(self, key: str = None, tmp: str = '/tmp/') -> str:\\n path = self._get_object_path(key)\\n return s3.copy(path, dest=tmp, verbose=False)\",\n \"def __get_s3_client(self):\\n if self.AWS_ACCESS_KEY:\\n s3_client = boto3.client(\\n \\\"s3\\\",\\n aws_access_key_id=self.AWS_ACCESS_KEY,\\n aws_secret_access_key=self.AWS_SECRET_ACCESS_KEY,\\n )\\n else:\\n s3_client = boto3.client(\\\"s3\\\")\\n return s3_client\",\n \"def get_s3_objects_from_dict(session, event, object_handler_function):\\n\\n objects = []\\n s3 = session.client(\\\"s3\\\")\\n # Get the object from the event and show its content type\\n for record in event.get(\\\"Records\\\", []):\\n bucket = record[\\\"s3\\\"][\\\"bucket\\\"][\\\"name\\\"]\\n unprocessed_key = record[\\\"s3\\\"][\\\"object\\\"][\\\"key\\\"]\\n # urllib changes structure and encoding is different\\n # between python 2 and 3\\n key = (\\n urllib.parse.unquote_plus(unprocessed_key)\\n # if sys.version_info[0] >= 3\\n # else urllib.unquote_plus(unprocessed_key.encode(\\\"utf-8\\\"))\\n )\\n logging.info(\\\"Bucket: %s. Key: %s\\\", bucket, key)\\n\\n # get S3 object and add it to return list\\n response = s3.get_object(Bucket=bucket, Key=key)\\n objects.append(object_handler_function(response))\\n return objects\",\n \"def _get_resource(\\n session: Optional[boto3.Session] = None, region: Optional[str] = None\\n) -> S3ServiceResource:\\n return (\\n session.resource(\\\"s3\\\") if session else boto3.resource(\\\"s3\\\", region_name=region)\\n )\",\n \"def get_apple_adj_cls_from_s3(s3_resource, bucket_name, prefix='') -> dict:\\n aapl_filename = \\\"AAPL.json\\\"\\n complete_path = os.path.join(prefix, aapl_filename)\\n json_object = s3_resource.Object(bucket_name, complete_path)\\n file_content = json_object.get()['Body'].read().decode('utf-8')\\n json_content = json.loads(file_content)\\n return json_content\",\n \"def s3_etag(url, proxies=None):\\n\\ts3_resource = boto3.resource (\\\"s3\\\", config=Config (proxies=proxies))\\n\\tbucket_name, s3_path = split_s3_path (url)\\n\\ts3_object = s3_resource.Object (bucket_name, s3_path)\\n\\treturn s3_object.e_tag\",\n \"def load_pickle(self, bucket, key):\\n\\n with BytesIO() as obj_buffer:\\n self._s3.Bucket(bucket).download_fileobj(key, obj_buffer)\\n obj_buffer.seek(0)\\n obj = pickle.load(obj_buffer)\\n\\n return obj\",\n \"def read_s3_file(bucket, key):\\r\\n try:\\r\\n s_3 = boto3.client('s3')\\r\\n file = s_3.get_object(Bucket=bucket, Key=key)\\r\\n file_body = file['Body'].read().decode(\\\"utf-8\\\")\\r\\n return file_body\\r\\n\\r\\n except (FileNotFoundError, IndexError, SystemExit, OSError, IOError) as err:\\r\\n print(\\\"Error in reading file\\\", str(err))\\r\\n return \\\"\\\"\",\n \"def openBucket(name):\\n conn = boto.connect_s3() \\n print \\\"Connecting to bucket: {}\\\".format(name)\\n bucket = conn.get_bucket(name, validate=True)\\n return bucket\",\n \"def s3_resource(self):\\n return boto3.resource('s3', \\n aws_access_key_id=os.environ.get(\\\"MINIO_ACCESS_KEY\\\"),\\n aws_secret_access_key=os.environ.get(\\\"MINIO_SECRET_KEY\\\"),\\n endpoint_url=f'http://{os.environ.get(\\\"MINIO_SERVER\\\")}',\\n config=Config(signature_version='s3v4')\\n )\",\n \"def get_s3_client(profile_name):\\n try:\\n session = boto3.session.Session(profile_name=profile_name)\\n except ProfileNotFound as e:\\n print(e, file=sys.stderr)\\n raise FailureException from e\\n return session.resource('s3')\",\n \"def get_objects(self, bucket, s3_client=None):\\n\\n try:\\n all_objects = s3_client.list_objects_v2(Bucket=bucket)\\n except botocore.exceptions.EndpointConnectionError:\\n logging.error(\\\"Couldn't connect to an S3 endpoint. If you're using an S3 compatible provider other than AWS, remember to set --s3-endpoint-url\\\")\\n sys.exit(1)\\n\\n if 'Contents' in all_objects.keys():\\n all_objects = [ k['Key'] for k in [ obj for obj in all_objects['Contents'] ]] # pylint: disable=unnecessary-comprehension\\n else:\\n all_objects = []\\n\\n return all_objects\",\n \"def get_boto_client(self) -> S3Client:\\n if self._boto_client is None:\\n config = Config(signature_version=botocore.UNSIGNED)\\n self._boto_client = self.session.client(\\n \\\"s3\\\",\\n region_name=settings.S3_REGION,\\n endpoint_url=settings.S3_ENDPOINT_URL,\\n config=config,\\n )\\n return self._boto_client\",\n \"def download_keypair ( s3_infra_conn, aws_account_type, region_name, keypair_type ) :\\n keypair_name = get_keypair_name( aws_account_type, region_name, keypair_type )\\n keypair_bucket = get_admin_bucket_name( region_name = region_name )\\n return retrieve_s3_contents( s3_conn = s3_infra_conn,\\n bucket_name = keypair_bucket,\\n key_name = get_keypair_keypath( aws_account_type ) + get_keypair_keyname( keypair_name ),\\n stored_filename = keypair_name )\",\n \"def s3_data_conn ( self ) :\\n if not self.s3_data :\\n self.s3_data = boto.s3.connection.S3Connection( self.access_key, self.access_key_secret )\\n return self.s3_data\",\n \"def head_object(self, bucket_name, object_name):\\n try:\\n return self._client.head_object(Bucket=bucket_name, Key=object_name)\\n except ClientError as client_error:\\n raise AWSClientError(\\n function_name=\\\"head_object\\\",\\n message=_process_s3_bucket_error(client_error, bucket_name),\\n error_code=client_error.response[\\\"Error\\\"][\\\"Code\\\"],\\n )\",\n \"def s3_etag(url):\\n s3_resource = boto3.resource(\\\"s3\\\")\\n bucket_name, s3_path = split_s3_path(url)\\n s3_object = s3_resource.Object(bucket_name, s3_path)\\n return s3_object.e_tag\",\n \"def s3_etag(url):\\n s3_resource = boto3.resource(\\\"s3\\\")\\n bucket_name, s3_path = split_s3_path(url)\\n s3_object = s3_resource.Object(bucket_name, s3_path)\\n return s3_object.e_tag\",\n \"def read_file_from_s3(bucket, key, profile):\\n s3_client = boto3.Session(profile_name=profile).client('s3')\\n resp = s3_client.get_object(Bucket=bucket, Key=key)\\n # Python 3.8/3.9 can't download files over 2GB via HTTP, so file is \\n # streamed in chunks just in case\\n content = ''.join([\\n chunk.decode() for chunk in resp['Body'].iter_chunks()\\n ])\\n \\n return content\",\n \"def readFileFromS3(self, keyname, path):\\n try:\\n k = Key(self.BUCKET)\\n k.key = keyname\\n k.get_contents_to_filename(path)\\n return True\\n except IOError:\\n return False\",\n \"def get_pickle_from_s3(path):\\n return load_pickle_from_s3(*load_bucket_and_path(path))\",\n \"def _get_s3_bucket(bucket_name: str):\\n s3 = getattr(_resources_for_thread, \\\"s3\\\", None)\\n if s3 is None:\\n # When multi-threaded, we can't use the default session. So keep one per thread.\\n session = boto3.session.Session()\\n s3 = session.resource(\\\"s3\\\")\\n _resources_for_thread.s3 = s3\\n return s3.Bucket(bucket_name)\",\n \"def get(self, key):\\n try:\\n return self.resource.Object(self.bucketname, key).get()\\n except botocore.exceptions.ClientError as error:\\n if error.response['Error']['Code'] == 'NoSuchKey':\\n # key does not exists\\n raise KeyError(error.response['Error'])\\n else:\\n # unexpected error\\n raise error\",\n \"def test_get_object(self):\\n err = None\\n try:\\n response = self.bos.put_object_from_string(self.BUCKET,\\n self.KEY,\\n \\\"This is a string.\\\",\\n user_metadata={\\\"private\\\": \\\"private\\\"})\\n except BceServerError as e:\\n err = e\\n finally:\\n self.assertIsNone(err)\\n self.check_headers(response)\\n\\n err = None\\n try:\\n response = self.bos.get_object(self.BUCKET, self.KEY)\\n except BceServerError as e:\\n err = e\\n finally:\\n self.assertIsNone(err)\\n\\n self.check_headers(response)\\n self.assertEqual(response.metadata.etag, '13562b471182311b6eea8d241103e8f0')\\n self.assertDictEqual(response.metadata.user_metadata, {u\\\"private\\\":u\\\"private\\\"})\\n data = BytesIO(response.data.read())\\n response.data.close()\",\n \"def _get_aws_s3_connection(cls, access_key, secret_access_key):\\n return boto.connect_s3(access_key, secret_access_key)\",\n \"def s3client(self):\\n return self._s3client\",\n \"def load_pickle_from_s3(bucket, path):\\n pkl = get_from_s3(bucket, path)\\n try:\\n return pickle.loads(pkl, encoding='utf-8') # python3\\n except TypeError:\\n return pickle.loads(pkl) # python2\",\n \"def getBucket(self, name=None, create=True):\\n try:\\n return self.CONNECTION.get_bucket(name)\\n except boto.exception.S3ResponseError:\\n if create:\\n bucket = self.CONNECTION.create_bucket(name)\\n print 'created new bucket %s' % name\\n return bucket\\n return None\",\n \"def s3_client(s3_url):\\n with moto.mock_s3():\\n with clients.S3Client(s3_url) as client:\\n yield client\",\n \"def s3_object_exists(s3_path: Path) -> bool:\\n\\n s3_args, unknown = get_s3_args().parse_known_args()\\n s3_client = get_s3_client(s3_args)\\n log = get_logger(\\\"s3_object_exists\\\")\\n\\n try:\\n s3_client.get_object(Bucket=s3_args.s3_bucket, Key=str(s3_path))\\n return True\\n except s3_client.exceptions.NoSuchKey:\\n return False\",\n \"def get_blob(self, blob_name):\\n return self.bucket.get_blob(blob_name)\",\n \"def s3_client(self):\\n return boto3.client('s3', \\n aws_access_key_id=os.environ.get(\\\"MINIO_ACCESS_KEY\\\"),\\n aws_secret_access_key=os.environ.get(\\\"MINIO_SECRET_KEY\\\"),\\n endpoint_url=f'http://{os.environ.get(\\\"MINIO_SERVER\\\")}',\\n config=Config(signature_version='s3v4')\\n )\",\n \"async def getStorJSONObj(app, key, bucket=None):\\n\\n client = _getStorageClient(app)\\n if not bucket:\\n bucket = app['bucket_name']\\n if key[0] == '/':\\n key = key[1:] # no leading slash\\n log.info(f\\\"getStorJSONObj({bucket})/{key}\\\")\\n\\n data = await client.get_object(key, bucket=bucket)\\n\\n try:\\n json_dict = json.loads(data.decode('utf8'))\\n except UnicodeDecodeError:\\n log.error(f\\\"Error loading JSON at key: {key}\\\")\\n raise HTTPInternalServerError()\\n\\n log.debug(f\\\"storage key {key} returned: {json_dict}\\\")\\n return json_dict\",\n \"def stream_object(self, bucket, key) -> StreamingBody:\\n return self.resource.Object(bucket, key).get()['Body']\",\n \"def read_badpractice(path, bucket=None, filetype=None, show_progressbar=True,\\n *args, **kwargs):\\n logging.warning('You are using rivet\\\\'s read function that allows for '\\n 'files stored with inadvisible S3 paths. It is highly '\\n 'recommended that you use the standard \\\\'read\\\\' '\\n 'function to ensure that good naming practices are '\\n 'followed.')\\n\\n bucket = bucket or s3_path_utils.get_default_bucket()\\n\\n if filetype is None:\\n filetype = s3_path_utils.get_filetype(path)\\n\\n read_fn = get_storage_fn(filetype, 'read')\\n\\n s3 = boto3.client('s3')\\n s3_kwargs = get_s3_client_kwargs(path, bucket,\\n operation='read',\\n show_progressbar=show_progressbar)\\n\\n with NamedTemporaryFile(suffix='.' + filetype) as tmpfile:\\n inform('Downloading from s3://{}/{}...'.format(bucket, path))\\n s3.download_file(bucket, path, tmpfile.name, **s3_kwargs)\\n inform('Reading object from tempfile...')\\n obj = read_fn(tmpfile, *args, **kwargs)\\n return obj\",\n \"def authorizedClientCall(self):\\n\\t\\tclient \\t\\t= boto3.client(\\\"s3\\\")\\n\\t\\treturn(client)\"\n]","isConversational":false},"negative_scores":{"kind":"list like","value":["0.8539686","0.8165444","0.7961786","0.7722801","0.7547169","0.74239224","0.74183124","0.73820263","0.731202","0.71821254","0.7147931","0.7108089","0.71075475","0.70903015","0.7077998","0.7044556","0.7038838","0.701147","0.7006739","0.698413","0.698143","0.6966881","0.6917425","0.6892031","0.6886335","0.688423","0.6877141","0.6840009","0.6840009","0.6811229","0.67487395","0.67350346","0.6734062","0.6722922","0.6718564","0.67177916","0.6714727","0.6641474","0.66102135","0.65987456","0.65881974","0.65790516","0.6574842","0.65710694","0.6515344","0.65138495","0.6504164","0.64707136","0.6470175","0.6426663","0.64112955","0.6410018","0.6402607","0.63941073","0.6371136","0.636446","0.6359029","0.63355374","0.6330731","0.63259286","0.6324197","0.63123786","0.63057226","0.63049185","0.6303739","0.62831527","0.62767184","0.62740064","0.6252592","0.62508696","0.62377733","0.62358636","0.62270176","0.6225757","0.6221521","0.6216483","0.62020326","0.6195875","0.61948436","0.6190733","0.6188265","0.6188265","0.61790013","0.61750966","0.6165552","0.6165384","0.6138831","0.6135612","0.6131199","0.6130088","0.61244583","0.6119651","0.6117121","0.611509","0.61097574","0.6091579","0.60733765","0.6047018","0.6044488","0.603384"],"string":"[\n \"0.8539686\",\n \"0.8165444\",\n \"0.7961786\",\n \"0.7722801\",\n \"0.7547169\",\n \"0.74239224\",\n \"0.74183124\",\n \"0.73820263\",\n \"0.731202\",\n \"0.71821254\",\n \"0.7147931\",\n \"0.7108089\",\n \"0.71075475\",\n \"0.70903015\",\n \"0.7077998\",\n \"0.7044556\",\n \"0.7038838\",\n \"0.701147\",\n \"0.7006739\",\n \"0.698413\",\n \"0.698143\",\n \"0.6966881\",\n \"0.6917425\",\n \"0.6892031\",\n \"0.6886335\",\n \"0.688423\",\n \"0.6877141\",\n \"0.6840009\",\n \"0.6840009\",\n \"0.6811229\",\n \"0.67487395\",\n \"0.67350346\",\n \"0.6734062\",\n \"0.6722922\",\n \"0.6718564\",\n \"0.67177916\",\n \"0.6714727\",\n \"0.6641474\",\n \"0.66102135\",\n \"0.65987456\",\n \"0.65881974\",\n \"0.65790516\",\n \"0.6574842\",\n \"0.65710694\",\n \"0.6515344\",\n \"0.65138495\",\n \"0.6504164\",\n \"0.64707136\",\n \"0.6470175\",\n \"0.6426663\",\n \"0.64112955\",\n \"0.6410018\",\n \"0.6402607\",\n \"0.63941073\",\n \"0.6371136\",\n \"0.636446\",\n \"0.6359029\",\n \"0.63355374\",\n \"0.6330731\",\n \"0.63259286\",\n \"0.6324197\",\n \"0.63123786\",\n \"0.63057226\",\n \"0.63049185\",\n \"0.6303739\",\n \"0.62831527\",\n \"0.62767184\",\n \"0.62740064\",\n \"0.6252592\",\n \"0.62508696\",\n \"0.62377733\",\n \"0.62358636\",\n \"0.62270176\",\n \"0.6225757\",\n \"0.6221521\",\n \"0.6216483\",\n \"0.62020326\",\n \"0.6195875\",\n \"0.61948436\",\n \"0.6190733\",\n \"0.6188265\",\n \"0.6188265\",\n \"0.61790013\",\n \"0.61750966\",\n \"0.6165552\",\n \"0.6165384\",\n \"0.6138831\",\n \"0.6135612\",\n \"0.6131199\",\n \"0.6130088\",\n \"0.61244583\",\n \"0.6119651\",\n \"0.6117121\",\n \"0.611509\",\n \"0.61097574\",\n \"0.6091579\",\n \"0.60733765\",\n \"0.6047018\",\n \"0.6044488\",\n \"0.603384\"\n]","isConversational":false},"document_score":{"kind":"string","value":"0.7761224"},"document_rank":{"kind":"string","value":"3"}}}],"truncated":false,"partial":true},"paginationData":{"pageIndex":806,"numItemsPerPage":100,"numTotalItems":95772,"offset":80600,"length":100}},"jwt":"eyJhbGciOiJFZERTQSIsImtpZCI6IjVHZDBvd0g5MTM2eDZjc1FvbE1zcktNWUZoRVFoUm5PVVVybEpjOUhaUEEifQ.eyJyZWFkIjp0cnVlLCJwZXJtaXNzaW9ucyI6eyJyZXBvLmNvbnRlbnQucmVhZCI6dHJ1ZX0sImlhdCI6MTc4NjIxNjEwNCwianRpIjoiOWI1YWI4NWEtZDkwNi00NjNjLTgzMmYtZmMzOWY0NmY2Yzc3Iiwic3ViIjoiL2RhdGFzZXRzL25vbWljLWFpL2Nvcm5zdGFjay1weXRob24tdjEiLCJleHAiOjE3ODYyMTk3MDQsImlzcyI6Imh0dHBzOi8vaHVnZ2luZ2ZhY2UuY28ifQ.tSzg-QL2JhRIigucNQEFDm8-TxiiFYsje-EzOgRh_qmYxKL6IuKGtVihl-XNSVbD0XMzFGceOEuypZzSEwzoAA","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 |
|---|---|---|---|---|---|---|
Logbinning of a distribution. | def logbin_distribution(data, nbins = 30):
# define the support of the distribution
lower_bound = min(data)
upper_bound = max(data)
# define bin edges
log = np.log10
lower_bound = log(lower_bound) if lower_bound > 0 else -1
upper_bound = log(upper_bound)
bins = np.logspace(lower_bound, u... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def bincalc(nbin=0.1,bmin=5,bmax=2000):\n\n logbmin=np.log10(bmin)\n logbmax=np.log10(bmax)\n\n logbins=np.arange(logbmin,logbmax,nbin)\n\n bins=10**logbins\n\n #bins=np.linspace(bmin,bmax,60)\n return (bins)",
"def logbin(data, scale = 1.3, zeros = False):\n if scale < 1:\n raise Val... | [
"0.66757274",
"0.6646079",
"0.62253493",
"0.6120671",
"0.6099856",
"0.60060704",
"0.5891733",
"0.5800523",
"0.5758203",
"0.5757172",
"0.5721329",
"0.57009387",
"0.5697628",
"0.56797785",
"0.5635742",
"0.5630419",
"0.5628087",
"0.56177866",
"0.5596117",
"0.55869347",
"0.558515... | 0.73683405 | 0 |
Get CCDF from a degree sequence. | def get_ccdf(degseq):
uniques, counts = np.unique(degseq, return_counts=True)
cumprob = np.cumsum(counts).astype(np.double) / (degseq.size)
return uniques[::-1], (1. - cumprob)[::-1] | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_cdf(self, points=None):\n if points is not None:\n return self.parent.cdf(points)\n else:\n raise ValueError( 'Please digit an input for getCDF method')",
"def getCDF(self):\n return self.cdfSample",
"def cdf(self,x):\n if self.method == 'spline':\n co... | [
"0.66865236",
"0.66738886",
"0.6528202",
"0.6394472",
"0.6394472",
"0.6280722",
"0.612189",
"0.6061525",
"0.6054699",
"0.6042136",
"0.6035633",
"0.6016287",
"0.59556776",
"0.59411925",
"0.593399",
"0.59306073",
"0.5848178",
"0.5825168",
"0.5806766",
"0.5793067",
"0.5657572",
... | 0.6885644 | 0 |
Get `eps_stop` from AMSE upper bound. Upper bound for order statistic to consider for doublebootstrap AMSE minimizer. Entries that are smaller or equal to the border value are ignored during AMSE minimization. | def get_eps_stop(data, amse_border=1, sort=True):
if sort:
data = np.sort(data)[::-1]
return 1 - len(data[np.where(data <= amse_border)]) / len(data) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def find_eps(self, target_ess, upper, min_bisection_its=50, max_ess_error=0.01):\n # Return upper bound if it can't achieve target ESS\n w = self.get_alternate_weights(upper)\n ess = effective_sample_size(w)\n if ess < target_ess:\n return upper\n\n # Return lower boun... | [
"0.54890054",
"0.5254461",
"0.5224461",
"0.5161098",
"0.50961953",
"0.50945413",
"0.4922195",
"0.4905253",
"0.49029648",
"0.4899326",
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"0.48665237",
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"0.47960132",
"0.47947425",
"0.47858372",
"0.47762918",
"0.47524136",
"0.47450542",
"0... | 0.71831954 | 0 |
Factory function for transforming any iterable to a WindowedIterable. Can be used as a function in pipey pipeline. | def windowify(window_size):
def windowed(iterable):
return WindowedIterable(iterable, window_size)
return windowed | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def dewindowify(iterable):\n for _, current, _ in iterable:\n yield current",
"def window(iterable, stride=3):\n for i in range(len(iterable) - stride + 1):\n yield iterable[i: i + stride]",
"def iwindow(seq, n):\n it = iter(seq)\n result = tuple(islice(it, n))\n\n if len(result) =... | [
"0.65870017",
"0.6276887",
"0.6252061",
"0.5979201",
"0.59202135",
"0.5901803",
"0.5901803",
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"0.5884487",
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"0.58312255",
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"0.5824383",
"0.5805883",
"0.5774541",
"0.57557213",
"0.5744897",
"0.5730951",
"0.57180876",
"0.5696275",
"0.5636358... | 0.79773754 | 0 |
Yields elements from a WindowedIterable without the cached windows. Can be used as a function in pipey pipeline. | def dewindowify(iterable):
for _, current, _ in iterable:
yield current | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def unique_window(iterable, window, key = None):\n seen = collections.deque(maxlen = window)\n seen_add = seen.append\n if key is None:\n for element in iterable:\n if element not in seen:\n yield element\n seen_add(element)\n else:\n for element in it... | [
"0.64814496",
"0.64370525",
"0.63999337",
"0.6393452",
"0.6304972",
"0.6201049",
"0.61454827",
"0.61207074",
"0.59631115",
"0.59161437",
"0.588799",
"0.5862907",
"0.5833489",
"0.5828903",
"0.5827851",
"0.5813124",
"0.5795005",
"0.5790015",
"0.57886785",
"0.5785899",
"0.576882... | 0.73613864 | 0 |
Used to verify your account. $verify SpiesWithin na | async def verify(self,ctx,ign='',region=''):
if ign =='' or region =='':
await self.bot.say("Please type in a ign and region.")
return
if not ctx.message.channel.is_private: #Makes sure channel is private
await self.bot.say('Sorry. But this process must be done i... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def verify():",
"async def check(self,ctx):\r\n try:\r\n check = verify.check(ctx.message.author.id)\r\n except Exception as e:\r\n await self.bot.say('Error: ' +str(e)+'\\n\\nIf your match hasn\\'t registered yet, wait 5-10 minutes or check http://discord.me/EZLBot for update... | [
"0.62231475",
"0.5896493",
"0.5764052",
"0.5706635",
"0.5706635",
"0.569275",
"0.5588584",
"0.55374587",
"0.54390234",
"0.5343147",
"0.5337591",
"0.5284817",
"0.52805984",
"0.5266697",
"0.5257193",
"0.525256",
"0.52475417",
"0.5245184",
"0.51888824",
"0.5128513",
"0.510791",
... | 0.5602167 | 6 |
Check for your latest match to verify $check | async def check(self,ctx):
try:
check = verify.check(ctx.message.author.id)
except Exception as e:
await self.bot.say('Error: ' +str(e)+'\n\nIf your match hasn\'t registered yet, wait 5-10 minutes or check http://discord.me/EZLBot for updates. Else, signup again with {}verify... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def check():",
"def match(self) -> bool:",
"def verify():",
"def check(self) -> None:",
"def test_version_check_update_available(self):\n output = self.run_command(\"selfupdate --check bennr01:selfupdate_test_future\", exitcode=0)\n self.assertIn(\"Target: bennr01:selfupdate_test_future\", ou... | [
"0.6599547",
"0.61560607",
"0.60273844",
"0.60122466",
"0.59057695",
"0.5849235",
"0.58330333",
"0.58012295",
"0.5780078",
"0.5763232",
"0.5735489",
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"0.5669704",
"0.56647074",
"0.56647074",
"0.56647074",
"0.56647074",
"0.56266236",
"0.5582165",
"0.55417573",
"0.... | 0.64390785 | 1 |
Forward pass of the convolutional neural network. Should not be called manually but by calling a model instance directly. | def forward(self, x):
#print('output of fetures.children() : %s'%str([i for i in self.features.children()]))
#print("shape of input is %s" % str(x.size()))
for layer_no, layer in enumerate(self.features.children()):
if layer_no is 23:
y = layer(x)
if laye... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def forward(self, x):\n x = self.conv1(x)\n if self.use_bn:\n x = self.batchnorm(x)\n if self.use_dropout:\n x = self.dropout(x)\n x = self.activation(x)\n x = self.conv2(x)\n if self.use_bn:\n x = self.batchnorm(x)\n if self.use_dro... | [
"0.74265546",
"0.72891587",
"0.72310466",
"0.71984327",
"0.71327746",
"0.70876646",
"0.7082048",
"0.7066212",
"0.7045469",
"0.7042458",
"0.7019415",
"0.6999947",
"0.6985048",
"0.6975621",
"0.69695985",
"0.6968059",
"0.69360054",
"0.69360054",
"0.6899931",
"0.68841743",
"0.687... | 0.0 | -1 |
Check if model parameters are allocated on the GPU. | def is_cuda(self):
return next(self.parameters()).is_cuda | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def is_cuda(model):\n\treturn next(model.parameters()).is_cuda",
"def is_gpu_available():\n ret = get_gpu_count() > 0\n if _HAS_PADDLE:\n import paddle\n if ret is True and not paddle.is_compiled_with_cuda():\n logger.warning(\"Found non-empty CUDA_VISIBLE_DEVICES. \\\n ... | [
"0.7035844",
"0.67039204",
"0.6659393",
"0.65733784",
"0.6548726",
"0.6418005",
"0.6284684",
"0.61922556",
"0.6084889",
"0.60580724",
"0.60226715",
"0.60047615",
"0.59713936",
"0.5916576",
"0.5914285",
"0.5895965",
"0.588647",
"0.58627695",
"0.584468",
"0.58226997",
"0.579909... | 0.64029634 | 9 |
Save model with its parameters to the given path. Conventionally the path should end with ".model". | def save(self, path):
print('Saving model... %s' % path)
torch.save(self, path) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def save_model(self, model_path: str):",
"def save(path_to_model):\n pass",
"def save_model(self, path):\n pass",
"def save_model(model, model_filepath):",
"def save_model(self, path):\n self._model.save(path)",
"def save(\n self,\n modelSavePath\n ):\n ... | [
"0.9188017",
"0.8917799",
"0.8776302",
"0.87582433",
"0.8621109",
"0.85514325",
"0.82969207",
"0.8235511",
"0.81234485",
"0.8070782",
"0.8021807",
"0.8004452",
"0.79982024",
"0.7997642",
"0.79857653",
"0.79795116",
"0.7919307",
"0.7912375",
"0.7908963",
"0.79005027",
"0.78822... | 0.7686676 | 60 |
Rolls a dice in NdN format. | async def roll(dice: str):
try:
rolls, limit = map(int, dice.split('d'))
except Exception:
await rose.say('Format has to be in NdN!')
return
result = ', '.join(str(random.randint(1, limit)) for r in range(rolls))
await rose.say(result) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def roll(self, dice: str):\n try:\n rolls, limit = map(int, dice.split('d'))\n except Exception:\n await self.bot.say('Format has to be in NdN!')\n return\n\n result = ', '.join(str(random.randint(1, limit)) for r in range(rolls))\n await self.bot.... | [
"0.755448",
"0.74622107",
"0.7365103",
"0.73002577",
"0.7191522",
"0.7023106",
"0.6970918",
"0.6968365",
"0.69634557",
"0.69537085",
"0.6942039",
"0.6915231",
"0.6908482",
"0.688081",
"0.68375415",
"0.6817635",
"0.68015164",
"0.67889714",
"0.6771499",
"0.67671233",
"0.6754963... | 0.71320593 | 5 |
[Get categorical & numerical columns] | def num_cat_variables(self, data):
is_cat = np.array([dt.kind == "O" for dt in data.dtypes])
cat_cols = data.columns.values[is_cat]
num_cols = data.columns.values[~is_cat]
return cat_cols, num_cols | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def categorical(df):\r\n categorical_var=df.select_dtypes(include ='object').columns.tolist()\r\n\r\n return categorical_var",
"def identify_nominal_columns(dataset):\n return identify_columns_by_type(dataset, include=['object', 'category'])",
"def num_and_cat_columns(df):\n \n \n cols = df.c... | [
"0.79687566",
"0.7539611",
"0.7244404",
"0.71197504",
"0.7072402",
"0.70692486",
"0.70692486",
"0.706313",
"0.6996327",
"0.69746363",
"0.68318164",
"0.68226284",
"0.6712321",
"0.6663871",
"0.65088147",
"0.64935565",
"0.6454352",
"0.6430965",
"0.6424896",
"0.63983136",
"0.6371... | 0.6754961 | 12 |
[Initiate the prediction function] | def make_predictions(self):
if is_classification(self.model):
if self.ct == None:
prediction = self.model.predict(self.input_data.to_numpy())
probabilities = self.model.predict_proba(self.input_data.to_numpy())
return prediction, probabilities
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self) :\n self.prediction_ = None",
"def __init__(self) :\n self.prediction_ = None",
"def __init__(self) :\n self.prediction_ = None",
"def run_prediction(self):\r\n self.get_prediction_indices()\r\n self.walk_forward_prediction()",
"def predict_proba(self):... | [
"0.7213135",
"0.7213135",
"0.7213135",
"0.71546817",
"0.7110174",
"0.7085127",
"0.70659715",
"0.7040501",
"0.7040501",
"0.70266724",
"0.70256954",
"0.70132285",
"0.69427246",
"0.6924442",
"0.6908858",
"0.6908858",
"0.6908858",
"0.68776196",
"0.6865355",
"0.6865355",
"0.679594... | 0.0 | -1 |
[Create prediction columns and add them to the self.predicted_columns dictionary] | def create_prediction_columns(self):
if is_classification(self.model) == True:
prediction, probabilities = self.make_predictions()
self.predicted_columns['Model Decision'] = prediction
self.predicted_columns['True Values'] = self.target_data
for i in range(len(np.... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def predict(self, data, only_lp=True):\n df = self.model.transpose(data)\n if only_lp:\n df = df.select(self.label_index_name, self.prediction_name, self.probability)\n return df",
"def predict(data, model, final_columns, category_features, averages):\n new_data = extend_dummy_... | [
"0.66258246",
"0.66254413",
"0.66087073",
"0.6596617",
"0.6541436",
"0.653981",
"0.6455183",
"0.633809",
"0.6312074",
"0.62493366",
"0.6248378",
"0.6227264",
"0.61748564",
"0.6172468",
"0.61246616",
"0.6104596",
"0.6046965",
"0.6040922",
"0.60071677",
"0.59578884",
"0.594849"... | 0.85224473 | 0 |
[Calculates the metrics for classification problems] | def classification_metrics(self, target_data, predicted):
from sklearn import preprocessing
from sklearn import metrics
y_true_copy, predictions = pd.DataFrame(self.target_data), predicted
#y_true_copy.unique()
np.unique(y_true_copy)
encode = {}
for i in range(l... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def evaluate_classifications(self):\n test_labels = open('./digitdata/testlabels', 'r')\n self.init_confusion_matrix()\n i = 0\n class_stats = {0:[0,0], 1:[0,0], 2:[0,0], 3:[0,0], 4:[0,0], 5:[0,0], 6:[0,0], 7:[0,0], 8:[0,0], 9:[0,0]}\n total_correct = 0\n num_labels = 1000... | [
"0.76563865",
"0.73574686",
"0.7215205",
"0.7158094",
"0.7139988",
"0.7071734",
"0.70559233",
"0.7028776",
"0.7013852",
"0.69567895",
"0.6920448",
"0.69164896",
"0.6915393",
"0.68986934",
"0.6862297",
"0.68464446",
"0.6821253",
"0.6814688",
"0.68041426",
"0.6802625",
"0.67856... | 0.6284864 | 91 |
[Calculates the metrics for regression problems] | def regression_metrics(self, target_data, predicted):
from sklearn import metrics
if len(target_data) != 0:
#Mean Absolute Error
mae = round(metrics.mean_absolute_error(target_data, predicted),2)
#Mean Squared Error
mse = round(metrics.mean_squared_error(... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def nnRegression(data):",
"def metrics_regression(y_real, y_pred):\n mae=mean_absolute_error(y_real, y_pred)\n mape= mean_absolute_percentage_error(y_real, y_pred)\n mse=mean_squared_error(y_real, y_pred)\n evs= explained_variance_score(y_real, y_pred)\n maximo_error= max_error(y_real, y_pred)\n ... | [
"0.7045143",
"0.69846684",
"0.6826172",
"0.6746359",
"0.6659643",
"0.65737325",
"0.65525055",
"0.654626",
"0.65024227",
"0.64893055",
"0.64601713",
"0.645842",
"0.6457579",
"0.6452948",
"0.6445572",
"0.6427412",
"0.6411009",
"0.63788265",
"0.6367059",
"0.63479114",
"0.6253903... | 0.65989304 | 5 |
Return name of the columns created by FeatureOperations applied on ``column`` | def derived_columns_from_col(self, column: str) -> List[str]:
derived_columns = []
operations = self.operations_from_original_column(column)
for operation in operations:
if operation.derived_columns is not None:
derived_columns.extend(operation.derived_columns)
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def update_column_title(col):\n col_type = self.features_bucket_mapping_.get(col).type\n return [f\"Feature '{col}'\"], [col_type]",
"def column_name(self) -> pulumi.Input[str]:\n return pulumi.get(self, \"column_name\")",
"def column_name(self) -> pulumi.Input[str]:\n return pulumi... | [
"0.6876426",
"0.68675435",
"0.68675435",
"0.68417263",
"0.669856",
"0.6658086",
"0.6653428",
"0.66112936",
"0.66074544",
"0.65204847",
"0.6458184",
"0.64255005",
"0.639284",
"0.63239753",
"0.62822115",
"0.62794644",
"0.62625235",
"0.625934",
"0.6234871",
"0.6232935",
"0.62093... | 0.62644273 | 16 |
Return the FeatureOperations that generated ``derived_column`` | def operations_from_derived_column(
self, derived_column: str
) -> List["FeatureOperation"]:
return list(
filter(
lambda op: op.derived_columns is not None
and derived_column in op.derived_columns,
self[derived_column],
)
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def original_columns_from_derived_column(self, derived_column: str) -> List[str]:\n operations = self.operations_from_derived_column(derived_column)\n\n if len(operations) > 1:\n raise RuntimeError(\n \"Multiple FeatureOperation found that generated column \"\n ... | [
"0.7034697",
"0.6264205",
"0.58456624",
"0.55798423",
"0.5506693",
"0.53352195",
"0.5264634",
"0.5252218",
"0.5208565",
"0.5165842",
"0.51332474",
"0.513137",
"0.51287925",
"0.512307",
"0.5089447",
"0.5088569",
"0.5083715",
"0.50238687",
"0.5020082",
"0.49969816",
"0.4994706"... | 0.7685979 | 0 |
Return the FeatureOperations applied on ``original_column`` | def operations_from_original_column(
self, original_column: str
) -> List["FeatureOperation"]:
return list(
filter(
lambda op: original_column in op.columns,
self[original_column],
)
) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def original_columns_from_derived_column(self, derived_column: str) -> List[str]:\n operations = self.operations_from_derived_column(derived_column)\n\n if len(operations) > 1:\n raise RuntimeError(\n \"Multiple FeatureOperation found that generated column \"\n ... | [
"0.61692166",
"0.61273307",
"0.58502436",
"0.55084825",
"0.54451436",
"0.54365456",
"0.53751487",
"0.52888155",
"0.5206171",
"0.5201663",
"0.508027",
"0.50541335",
"0.50530684",
"0.50475353",
"0.5007608",
"0.4991465",
"0.49836087",
"0.49430266",
"0.49388215",
"0.49367413",
"0... | 0.7905143 | 0 |
Return the name of the columns from which ``derived_column`` is generated. | def original_columns_from_derived_column(self, derived_column: str) -> List[str]:
operations = self.operations_from_derived_column(derived_column)
if len(operations) > 1:
raise RuntimeError(
"Multiple FeatureOperation found that generated column "
f"{derived_... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def derived_columns_from_col(self, column: str) -> List[str]:\n derived_columns = []\n operations = self.operations_from_original_column(column)\n\n for operation in operations:\n if operation.derived_columns is not None:\n derived_columns.extend(operation.derived_col... | [
"0.68002284",
"0.6473398",
"0.6276224",
"0.62645346",
"0.624039",
"0.62050974",
"0.61963874",
"0.6118237",
"0.61114836",
"0.60975206",
"0.6070955",
"0.60598886",
"0.60405964",
"0.60157603",
"0.60076255",
"0.5958728",
"0.5958728",
"0.5935321",
"0.5919565",
"0.59103626",
"0.590... | 0.7360953 | 0 |
Return True if ``other`` is a OperationsList containing the same operations. | def __eq__(self, other: Any) -> bool:
if not isinstance(other, OperationsList):
return False
if not self._operations_list == other._operations_list:
return False
return True | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __eq__(self, other: SymbolicObject) -> bool:\n\n if isinstance(other, ListObject):\n return self._subobjects == other._subobjects\n else:\n return False",
"def __eq__(self, other):\n if not isinstance(other, CashFlowList):\n return False\n\n return... | [
"0.7605562",
"0.7011663",
"0.68128866",
"0.67968446",
"0.6753017",
"0.6692754",
"0.6628194",
"0.6615114",
"0.6595707",
"0.6594383",
"0.6566219",
"0.6549629",
"0.65435344",
"0.6532957",
"0.6516649",
"0.6473852",
"0.6468497",
"0.646396",
"0.645403",
"0.64523",
"0.64292806",
"... | 0.8506768 | 0 |
Helper function used in src.api.routes.main_urls.py for routing URLs to the appropriate view functions | def re_path(route, view, **kwargs):
return view, route, kwargs | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def urlpath( request, *args, **kwargs ):",
"def pathfor( request, *args, **kwargs ):",
"def __create_routes__(self):\n self.app.add_url_rule('/', 'main_page', self.main_page)\n self.app.add_url_rule('/day', 'day', self.get_current_iteration, methods=['GET'])\n self.app.add_url_rule('/trade... | [
"0.72670937",
"0.6907818",
"0.66150296",
"0.65024936",
"0.64763063",
"0.63228345",
"0.63206047",
"0.6313643",
"0.6229998",
"0.6178121",
"0.61501104",
"0.61366874",
"0.6130338",
"0.6113",
"0.6111944",
"0.6090943",
"0.60885",
"0.60818",
"0.606321",
"0.60524136",
"0.60514635",
... | 0.5981405 | 25 |
Helper function to add a song to db | def add_song(name, duration):
song = Song(
name=name,
duration=duration,
)
db.session.add(song)
db.session.commit()
return song | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def add_song(_name_of_the_song, _duration_in_number_of_seconds):\r\n # creating an instance of our Song constructor\r\n new_song = Song(name_of_the_song=_name_of_the_song,\r\n duration_in_number_of_seconds=_duration_in_number_of_seconds)\r\n db.session.add(new_song) # a... | [
"0.7740324",
"0.76434267",
"0.75772154",
"0.7524001",
"0.7350646",
"0.7221055",
"0.71301234",
"0.7102691",
"0.70967597",
"0.7082078",
"0.7064771",
"0.6968714",
"0.6960384",
"0.69075376",
"0.68390363",
"0.6826875",
"0.6817456",
"0.68168634",
"0.67879635",
"0.67730844",
"0.6766... | 0.74220836 | 4 |
Helper function to add an audiobook to database | def add_audiobook(name, duration, author, narrator):
audiobook = AudioBook(
name=name,
duration=duration,
author=author,
narrator=narrator
)
db.session.add(audiobook)
db.session.commit()
return audiobook | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def add_audiobook(_title_of_the_audiobook, _author_of_the_title, _narrator,\r\n _duration_in_number_of_seconds):\r\n # creating an instance of our Audiobook constructor\r\n new_audiobook = Audiobook(title_of_the_audiobook=_title_of_the_audiobook,\r\n ... | [
"0.77613556",
"0.70807827",
"0.65985125",
"0.6316089",
"0.6239264",
"0.62226313",
"0.6193941",
"0.6126204",
"0.611152",
"0.6100338",
"0.60866594",
"0.6031406",
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"0.5952915",
"0.59519464",
"0.5949488",
"0.59182364",
"0.58955574",
"0.58570... | 0.7655839 | 1 |
Shortcut for ``bot.send_chat_action(update.message.chat.id, args, kwargs)`` | def send_action(self, *args, **kwargs):
return self.bot.send_chat_action(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def send_action(action):\n def decorator(func):\n @wraps(func)\n def command_func(self, update, context, *args, **kwargs):\n context.bot.send_chat_action(chat_id=update.effective_message.chat_id, action=action)\n return func(self, update, context, *args, **kwargs)\n re... | [
"0.7509384",
"0.7375992",
"0.6927227",
"0.6501493",
"0.6169821",
"0.6134623",
"0.6082273",
"0.60704964",
"0.60244894",
"0.6001735",
"0.596165",
"0.5954815",
"0.59119594",
"0.5823286",
"0.5799726",
"0.5714884",
"0.57128656",
"0.5614297",
"0.55790704",
"0.55705637",
"0.55119675... | 0.7766484 | 0 |
Shortcut for ``bot.leave_chat(update.message.chat.id, args, kwargs)`` | def leave(self, *args, **kwargs):
return self.bot.leave_chat(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def leave_chat(self, chat_id: typing.Union[base.Integer, base.String]) -> base.Boolean:\n payload = generate_payload(**locals())\n result = await self.request(api.Methods.LEAVE_CHAT, payload)\n\n return result",
"def leave(bot, event, conversation_id=None, *args):\n\n arglist = list... | [
"0.6716415",
"0.6618045",
"0.6549425",
"0.6191924",
"0.6101038",
"0.6079317",
"0.6001494",
"0.5859587",
"0.5734056",
"0.57170254",
"0.5706082",
"0.5672748",
"0.5663437",
"0.5622406",
"0.5606106",
"0.55953854",
"0.5537519",
"0.55289155",
"0.54851896",
"0.5475721",
"0.54088616"... | 0.8217309 | 0 |
Shortcut for ``bot.get_chat_administrators(update.message.chat.id, args, kwargs)`` | def get_administrators(self, *args, **kwargs):
return self.bot.get_chat_administrators(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_admin_ids(bot, chat_id):\r\n return [admin.user.id for admin in bot.get_chat_administrators(chat_id)]",
"def get_admin_ids(bot, chat_id):\n return [admin.user.id for admin in bot.get_chat_administrators(chat_id)]",
"def get_admin_ids(bot, chat_id):\n return [admin.user.id for admin in bot.get_... | [
"0.72916365",
"0.7257801",
"0.7257801",
"0.7257801",
"0.71312785",
"0.63350284",
"0.6305754",
"0.6275993",
"0.6170726",
"0.6099674",
"0.58945954",
"0.58601385",
"0.58280176",
"0.58112365",
"0.577033",
"0.5728004",
"0.5673534",
"0.5667694",
"0.5667427",
"0.5659937",
"0.5639199... | 0.8342136 | 0 |
Shortcut for ``bot.get_chat_members_count(update.message.chat.id, args, kwargs)`` | def get_members_count(self, *args, **kwargs):
return self.bot.get_chat_members_count(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def get_chat_members_count(self, chat_id: typing.Union[base.Integer, base.String]) -> base.Integer:\n payload = generate_payload(**locals())\n result = await self.request(api.Methods.GET_CHAT_MEMBERS_COUNT, payload)\n\n return result",
"async def membercount(ctx, *args):\n if ctx.me... | [
"0.7653538",
"0.7079209",
"0.67141974",
"0.64766777",
"0.6410987",
"0.63265955",
"0.63157445",
"0.6290398",
"0.6003215",
"0.5918783",
"0.5874979",
"0.5852854",
"0.5671665",
"0.56622785",
"0.5651697",
"0.5633376",
"0.55913067",
"0.5557523",
"0.5552522",
"0.5539572",
"0.5515641... | 0.8773616 | 0 |
Shortcut for ``bot.get_chat_member(update.message.chat.id, args, kwargs)`` | def get_member(self, *args, **kwargs):
return self.bot.get_chat_member(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def get_chat_member(self, chat_id: typing.Union[base.Integer, base.String],\n user_id: base.Integer) -> types.ChatMember:\n payload = generate_payload(**locals())\n result = await self.request(api.Methods.GET_CHAT_MEMBER, payload)\n\n return types.ChatMember(... | [
"0.6845233",
"0.59359425",
"0.59342927",
"0.59342927",
"0.5720699",
"0.5720276",
"0.56279147",
"0.56157714",
"0.55889475",
"0.5583294",
"0.5564403",
"0.55140746",
"0.54459745",
"0.5426997",
"0.5400163",
"0.53775513",
"0.53349453",
"0.53254014",
"0.53250545",
"0.529635",
"0.52... | 0.8052762 | 0 |
Shortcut for ``bot.kick_chat_member(update.message.chat.id, args, kwargs)`` | def kick_member(self, *args, **kwargs):
return self.bot.kick_chat_member(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def kick(ctx, member: discord.Member, *, reason=None):\n await member.kick(reason=reason)\n await ctx.send(f\"User {member} has been kicked\")",
"async def kick(self, member: discord.Member, *, reason=None): # asterix=all parameters after member and reason will just be added to reason\n await... | [
"0.67335683",
"0.6692941",
"0.6343571",
"0.6296833",
"0.6268952",
"0.6116799",
"0.60498536",
"0.603678",
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"0.59897",
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"0.57337326",
"0.5710275",
"0.5696058",
"0.5683905",
"0.56561285",
"0.56306046",
... | 0.83216196 | 0 |
Shortcut for ``bot.unban_chat_member(update.message.chat.id, args, kwargs)`` | def unban_member(self, *args, **kwargs):
return self.bot.unban_chat_member(self.id, *args, **kwargs) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def unban_chat_member(self, chat_id: typing.Union[base.Integer, base.String],\n user_id: base.Integer) -> base.Boolean:\n payload = generate_payload(**locals())\n result = await self.request(api.Methods.UNBAN_CHAT_MEMBER, payload)\n\n return result",
"asy... | [
"0.73356986",
"0.70719296",
"0.70260084",
"0.6497744",
"0.64395726",
"0.6274795",
"0.6266587",
"0.6266034",
"0.6130883",
"0.6102467",
"0.5987942",
"0.5970644",
"0.5834732",
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"0.57180315",
"0.57048714",
"0.5699499",
"0.56516176",
"0.5640035",
"0.5636267",
"0.562204... | 0.86313546 | 0 |
Gets all the meshes inside all the piper skinned nodes in the scene. | def getMeshes():
nodes = pipernode.get('piperSkinnedMesh')
return {mesh.getParent() for skin in nodes for mesh in skin.getChildren(ad=True, type='mesh') if mesh.getParent()} | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_meshes(self):\n for meta_mesh in self.gltf.meshes:\n # Returns a list of meshes\n meshes = meta_mesh.load(self.materials)\n self.meshes.append(meshes)\n\n for mesh in meshes:\n self.scene.meshes.append(mesh)",
"def get_meshes(scene):\r\n ... | [
"0.6114167",
"0.60293436",
"0.5757967",
"0.5612728",
"0.5534438",
"0.54922056",
"0.54847145",
"0.54710627",
"0.54542154",
"0.5363654",
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"0.5282078",
"0.5273619",
"0.5245254",
"0.52361906",
"0.5214873",
"0.521100... | 0.8215878 | 0 |
Locks or unlocks all the transforms under piper skinned nodes that have mesh shapes. | def setLockOnMeshes(lock):
meshes = getMeshes()
for mesh in meshes:
try:
mesh.overrideEnabled.set(1)
mesh.overrideDisplayType.set(lock)
except RuntimeError as error:
pm.warning('Can\'t set lock on mesh! ' + str(error)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def lockMeshes():\n setLockOnMeshes(2)",
"def unlockMeshes():\n setLockOnMeshes(0)",
"def setupForRigPose(self):\n\n # unlock joint movers\n cmds.select(\"JointMover\", hi=True)\n jmNodes = cmds.ls(sl=True)\n for node in jmNodes:\n cmds.lockNode(node, lock=False)\n\... | [
"0.6720721",
"0.63663757",
"0.55522466",
"0.5495686",
"0.5413373",
"0.5364269",
"0.5231629",
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"0.48477027",
"0.48028678",
"0.4737559",
"0.4709482",
"0.47019863",
"0.46750396",
"0.4672... | 0.601429 | 2 |
Locks all the transforms under piper skinned nodes that have mesh shapes. | def lockMeshes():
setLockOnMeshes(2) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def unlockMeshes():\n setLockOnMeshes(0)",
"def setLockOnMeshes(lock):\n meshes = getMeshes()\n for mesh in meshes:\n try:\n mesh.overrideEnabled.set(1)\n mesh.overrideDisplayType.set(lock)\n except RuntimeError as error:\n pm.warning('Can\\'t set lock on m... | [
"0.5996941",
"0.5933928",
"0.56343156",
"0.5437628",
"0.5400132",
"0.5262749",
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"0.49469054",
"0.49222684",
"0.48831803",
"0.4858286",
"0.48506966",
"0.48... | 0.6672777 | 0 |
Unlocks all the transforms under piper skinned nodes that have mesh shapes. | def unlockMeshes():
setLockOnMeshes(0) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def lockMeshes():\n setLockOnMeshes(2)",
"def cleanUpRigPose(self):\n\n # show the proxy geo\n cmds.select(self.name + \"_mover_grp\", hi=True)\n allNodes = cmds.ls(sl=True)\n for node in allNodes:\n if node.find(\"_proxy_geo\") != -1:\n if cmds.nodeType(n... | [
"0.5675033",
"0.5524052",
"0.5401451",
"0.53727466",
"0.53193283",
"0.5234211",
"0.51849127",
"0.5175909",
"0.51477677",
"0.5075064",
"0.50477535",
"0.5032112",
"0.5016843",
"0.49993888",
"0.49989218",
"0.4995508",
"0.49578157",
"0.4956141",
"0.49486592",
"0.49314776",
"0.492... | 0.6947981 | 0 |
Prepares the scene for a rig. | def prepare():
# getRelativeArt checks if scene is saved
skeleton_path = paths.getRelativeArt()
# if scene is modified, ask user if they would like to save, not save, or cancel operation
if not uiwindow.save():
pm.error('Scene not saved.')
# perform a bone health check before referencing t... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def create_scene(self, ):\n self.scene = create_scene(\n self.opt.splats_img_size, self.opt.splats_img_size, self.opt.fovy,\n self.opt.focal_length, self.opt.n_splats)",
"def set_up_scenes():\n cmd.zoom('Cathepsin', 10) # Zoom out to get a view on the whole complex\n cmd.scene... | [
"0.6489929",
"0.61271745",
"0.6016473",
"0.60112846",
"0.58737195",
"0.58737195",
"0.5808305",
"0.58061624",
"0.58061624",
"0.58061624",
"0.57967305",
"0.5735352",
"0.5718494",
"0.5693235",
"0.5693235",
"0.5693235",
"0.5693235",
"0.5693235",
"0.5693235",
"0.5693235",
"0.56932... | 0.6952782 | 0 |
Returns all available categories. | def get_all_categories():
return jsonify({
"success": True,
"categories": _read_all_categories()
}) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def getAllCategories(self):\n return self.categories",
"def get_categories(self):\n _url = urljoin(self.base_url, self.API_CATEGORIES)\n return requests.get(_url)",
"def _get_all_categories() -> dict:\n categories = database.fetchall(\"Categories\", \"id\", \"name_ua\")\n ret... | [
"0.84352666",
"0.8040093",
"0.795076",
"0.7868622",
"0.78226036",
"0.781811",
"0.78094435",
"0.7806805",
"0.7805045",
"0.77995926",
"0.7742181",
"0.7735259",
"0.7709532",
"0.7694586",
"0.769186",
"0.7655308",
"0.76461715",
"0.7583643",
"0.7582509",
"0.7538103",
"0.7518969",
... | 0.7982361 | 2 |
DELETE question using a question ID. | def delete_question(question_id):
try:
question = Question.query.get(question_id)
if question is None:
abort(404)
question.delete()
db.session.commit()
return jsonify({
"success": True,
"deleted_question_... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def delete_question(request, question_id):\n raise NotImplementedError",
"def delete_question(self, question_id):\n\n question = self.sql.fetch_details_by_criteria(\n \"question_id\", question_id, \"questions\")\n\n if not question:\n\n return self.makeresp(\"This question ... | [
"0.87092954",
"0.8384955",
"0.8353129",
"0.81277585",
"0.810169",
"0.8093647",
"0.79760695",
"0.79537916",
"0.7660801",
"0.7504361",
"0.74473095",
"0.73947793",
"0.7327632",
"0.71958506",
"0.7178379",
"0.7133595",
"0.7054951",
"0.6951195",
"0.68221045",
"0.67974144",
"0.65992... | 0.801446 | 6 |
Creates a new question | def create_question():
if request.content_type != "application/json":
abort(415)
question_text = request.json['question']
answer = request.json['answer']
difficulty = request.json['difficulty']
category = request.json['category']
question_object = Question(qu... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def create_question():\n body = request.get_json()\n\n question_text = body.get('question', None)\n answer = body.get('answer', None)\n category = body.get('category', 1)\n difficulty = body.get('difficulty', 1)\n\n try:\n question = Question(question=question_t... | [
"0.79055667",
"0.7813074",
"0.76496226",
"0.75417274",
"0.7536455",
"0.7524911",
"0.7431518",
"0.7412654",
"0.7412654",
"0.73918843",
"0.73026544",
"0.7290407",
"0.7285686",
"0.7280948",
"0.7277673",
"0.7270049",
"0.7219192",
"0.7162589",
"0.70821846",
"0.70660996",
"0.705721... | 0.80899006 | 0 |
Returns case insensitive matches for a search term | def search_questions():
if request.content_type != "application/json":
abort(415)
search_term: str = request.json.get('searchTerm')
if search_term is None:
abort(400)
if search("^\\s*$", search_term) is not None:
abort(422)
questions = Question... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def make_query(term):\n def search(text):\n s=term.lower()\n if s in text.lower():\n return True\n return False\n return search",
"def search(self, term):",
"def search(self, word):",
"def searchable(query):\n if query is None:\n return ''\n return strip_acc... | [
"0.7639096",
"0.7310269",
"0.7139636",
"0.6653358",
"0.65988",
"0.6546445",
"0.64347154",
"0.6413569",
"0.640629",
"0.6398818",
"0.63864064",
"0.6377819",
"0.63540596",
"0.6295629",
"0.62894785",
"0.62558854",
"0.6229605",
"0.6159774",
"0.61374915",
"0.6110191",
"0.6094641",
... | 0.0 | -1 |
Get all questions filtered by a category | def get_questions_by_category(category_id: int):
category = Category.query.get(category_id)
if category is None:
abort(400)
questions_by_category = Question.query.filter(
Question.category == str(category_id)).all()
return jsonify({
"success": True,
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def retrieve_questions_by_category(category_id):\n try:\n selection = Question.query.filter(\n Question.category == category_id).order_by(Question.id).all()\n\n if len(selection) == 0:\n abort(404)\n\n questions = []\n\n for question ... | [
"0.7045061",
"0.70348823",
"0.7026578",
"0.68939084",
"0.6882774",
"0.6860482",
"0.6797814",
"0.6765122",
"0.6690764",
"0.6680299",
"0.6671632",
"0.6665664",
"0.6628369",
"0.6480059",
"0.64080924",
"0.6332876",
"0.6249306",
"0.62117636",
"0.61584663",
"0.61449456",
"0.6097295... | 0.7141734 | 0 |
This endpoint should take category and previous question parameters and return a random questions within the given category, if provided, and that is not one of the previous questions. | def get_quiz_question():
if request.content_type != "application/json":
abort(415)
previous_questions: list[int] = request.json['previous_questions']
category: str = request.json['quiz_category']
filtered_category: list[Category] = Category.query.filter(
Category... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_questions_toplay():\n data = request.get_json()\n category = data.get('category', 'None')\n previous_questions = data.get('previous_questions', None)\n questions = Question.query.filter(Question.category == category).all()\n all_questions = Question.query.all()\n c... | [
"0.74568665",
"0.6912038",
"0.6561906",
"0.6539811",
"0.65362525",
"0.6439181",
"0.64383984",
"0.63652915",
"0.63634086",
"0.6346514",
"0.62832403",
"0.6261533",
"0.61639524",
"0.6094321",
"0.6050536",
"0.6016344",
"0.5915583",
"0.5853105",
"0.58042264",
"0.57684845",
"0.5714... | 0.7499 | 0 |
Return True if closed and False otherwise. | def _is_closed(self) -> bool:
return self._status == Status.CLOSED | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def is_closed(self) -> bool:",
"def is_close(self) -> bool:\n return not self.open",
"def is_closed(self): # -> bool | Any:\n ...",
"def closed(self):\n\n return not self.open",
"def is_closed(self) -> bool | None:\n if self._is_open is None:\n return None\n r... | [
"0.86177653",
"0.81572",
"0.80928993",
"0.80755955",
"0.79734445",
"0.7967501",
"0.79415077",
"0.79415077",
"0.7935826",
"0.7887935",
"0.78787166",
"0.7871184",
"0.7847067",
"0.7829436",
"0.7829436",
"0.78189903",
"0.78124225",
"0.77931994",
"0.7779017",
"0.77337986",
"0.7634... | 0.799 | 4 |
Validate status transition and set next status. The caller of the transition method will have to aquire conditional variable. | def _transition(self, next_status: Status) -> None:
if next_status == Status.CLOSED:
self._status = next_status
elif (
self._status == Status.AWAITING_SERVER_MESSAGE
and next_status == Status.SERVER_MESSAGE_AVAILABLE
and self._server_message is not None
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def next_status(self):\n if self.status == self.DRAFT:\n self._advance_to_registration()\n elif self.status == self.REGISTRATION:\n self._advance_to_pending()\n elif self.status == self.PENDING:\n self._advance_to_running()",
"def _set_status(self, status, in... | [
"0.6936471",
"0.6545385",
"0.61415124",
"0.6049134",
"0.59733415",
"0.5904015",
"0.58512765",
"0.580843",
"0.5763939",
"0.57431453",
"0.5728972",
"0.5710814",
"0.57087004",
"0.5695417",
"0.5690907",
"0.564556",
"0.5603299",
"0.55643886",
"0.55600923",
"0.5519623",
"0.55151504... | 0.8059536 | 0 |
Set bridge status to closed. | def close(self) -> None:
with self._cv:
self._transition(Status.CLOSED) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def close(self, state):\n pass",
"def is_closed(self, is_closed):\n\n self._is_closed = is_closed",
"def close(self):\n self.state = STATE_STOPPED",
"def close(self) -> None:\n self._connected = False",
"def handle_close(self):\n self.active = False\n self.close()"... | [
"0.6226209",
"0.61714906",
"0.6165825",
"0.60678107",
"0.6056273",
"0.60554194",
"0.6015147",
"0.6015147",
"0.6001937",
"0.5994272",
"0.5922576",
"0.5888235",
"0.5880483",
"0.5880483",
"0.5865483",
"0.58528066",
"0.5836694",
"0.58268356",
"0.5815143",
"0.58124125",
"0.5787924... | 0.61619353 | 3 |
Set server massage and wait for client message. | def request(self, server_message: ServerMessage) -> ClientMessage:
# Set server message and transition to SERVER_MESSAGE_AVAILABLE
with self._cv:
self._raise_if_closed()
if self._status != Status.AWAITING_SERVER_MESSAGE:
raise Exception("This should not happen")
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def set_client_message(self, client_message: ClientMessage) -> None:\n with self._cv:\n self._raise_if_closed()\n\n if self._status != Status.AWAITING_CLIENT_MESSAGE:\n raise Exception(\"This should not happen\")\n\n self._client_message = client_message # Wr... | [
"0.6532621",
"0.60829353",
"0.60618067",
"0.60367125",
"0.6031149",
"0.60242295",
"0.600211",
"0.5916708",
"0.5914085",
"0.5873393",
"0.58694917",
"0.5843696",
"0.5749328",
"0.57308495",
"0.570649",
"0.57043403",
"0.56998175",
"0.56871885",
"0.56841075",
"0.5670463",
"0.56438... | 0.56337774 | 23 |
Return iterator over server messages. | def server_message_iterator(self) -> Iterator[ServerMessage]:
while not self._is_closed():
with self._cv:
self._cv.wait_for(
lambda: self._status
in [Status.CLOSED, Status.SERVER_MESSAGE_AVAILABLE]
)
self._raise... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __iter__(self):\n while True:\n m = self.recv(timeout=1.0)\n if m is not None:\n yield m\n logger.debug(\"done iterating over bus messages\")",
"def __iter__(self):\n return iter([self.format_message(record) for record in self._messages])",
"def sen... | [
"0.70293",
"0.681426",
"0.6685467",
"0.65742815",
"0.63746",
"0.6322583",
"0.6322583",
"0.6319159",
"0.6243213",
"0.6237469",
"0.6149023",
"0.6103872",
"0.60832894",
"0.6079954",
"0.597399",
"0.5964599",
"0.59449357",
"0.5915447",
"0.59143317",
"0.59071326",
"0.5888881",
"0... | 0.80226314 | 0 |
Set client message for consumption. | def set_client_message(self, client_message: ClientMessage) -> None:
with self._cv:
self._raise_if_closed()
if self._status != Status.AWAITING_CLIENT_MESSAGE:
raise Exception("This should not happen")
self._client_message = client_message # Write
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def client(self,message):\n self.message = message\n self.run()",
"def _set_message(self, value):\n self.__message = value",
"def setMessage(self, message):\n self._message = message",
"def message(self, message):\n self._message = message",
"def message(self, message):\n... | [
"0.7064386",
"0.6990123",
"0.67184645",
"0.65573794",
"0.65573794",
"0.65327984",
"0.6515193",
"0.6515193",
"0.6515193",
"0.6515193",
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"0.6515193",
"0.6515193",
"0.6515193",
"0.6393413",
"0.6339335",
"0.63246405",
"0.6275719",
"0.62454003",
"0.6086344",
"0.6082703... | 0.7599568 | 0 |
gets the distance between two cities from the database and updates the number of hits if found. | def get_distance_between_cities(self, source, destination):
query = {"$or": [{SOURCE: source, DESTINATION: destination}, {SOURCE: destination, DESTINATION: source}]}
doc1 = self._cities_distance.find_one_and_update(query, {"$inc": {HITS: 1}})
distance = -1
if doc1:
distance =... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def distanceBetweenTwoCities(cityA, cityB):\r\n\r\n return ( ( (cityA[0] - cityB[0]) ** 2 ) + ( (cityA[1] - cityB[1]) ** 2) ) ** 0.5",
"def evaluate_distance(self, city):\n\t\treturn self.distance[city.value]",
"def calculate_distance(loc1, loc2):\n matrix = googlemaps.distance_matrix.distance_matrix(cli... | [
"0.65696883",
"0.63588417",
"0.63102216",
"0.6298032",
"0.6286711",
"0.6248496",
"0.61212575",
"0.60218096",
"0.6021427",
"0.5920487",
"0.5870352",
"0.5845951",
"0.5799753",
"0.57648885",
"0.5758182",
"0.57455",
"0.57340556",
"0.57309353",
"0.572869",
"0.5690227",
"0.56465304... | 0.75209475 | 0 |
adds two citie and their distance to the database. | def add_cities_to_db(self, source, destination, distance, is_post_insert=False):
if not is_post_insert:
self._cities_distance.insert_one(
{SOURCE: source, DESTINATION: destination, DISTANCE: distance, HITS: 1})
else:
self._cities_distance.insert_one(
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def distance(self, other):\n ...",
"def distance(self, keyOne, keyTwo):",
"def distance(self, a, b):\n raise NotImplementedError()",
"def costInsertion(el1,el2):\r\n return 2",
"def distance(self, c1, c2):\r\n x = (c2.x - c1.x) ** 2\r\n y = (c2.y - c1.y) ** 2\r\n d = i... | [
"0.6052168",
"0.59256554",
"0.58947444",
"0.56122863",
"0.5598152",
"0.5561179",
"0.55405825",
"0.5526655",
"0.54927796",
"0.547482",
"0.54159796",
"0.5413959",
"0.5394808",
"0.5382403",
"0.5351781",
"0.5341194",
"0.5296761",
"0.52946454",
"0.5241165",
"0.5225384",
"0.5225066... | 0.6522734 | 0 |
a method that checks if the connection to the database is ok. | def check_connection_to_db(self):
try:
self._client.admin.command('ismaster')
return True
except Exception:
return False | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _check_connection(self):\n if \"_connection\" not in self.__dict__:\n message = \"use connect method before doing operation on this database\"\n raise Exception(message)",
"def check_db_connection(self):\n self.logger.debug('Checking database connection.')\n if self... | [
"0.7988681",
"0.7964591",
"0.7871532",
"0.7792396",
"0.77690375",
"0.7682444",
"0.7531027",
"0.7450076",
"0.74004126",
"0.7381222",
"0.73133624",
"0.7306993",
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"0.71915644",
"0.7104789",
"0.7095957",
"0.70758843",
"0.7065347",
"0.706142",
"0.6992617",... | 0.7153132 | 15 |
resets the data bases. | def reset_db(self):
self._cities_distance.drop() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def reset():\n teardown_db()\n build()",
"def reset_database(self):\n\n self.db.reset_database()",
"def reset(self, reset_from):\n self._grants.clear()\n self._groups.clear()\n self._reset_cached()\n self._id += 1\n for name, backend in self._backends.items():\n ... | [
"0.70161057",
"0.6995996",
"0.69501084",
"0.6918107",
"0.69116414",
"0.69109124",
"0.67918694",
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"0.64869547",
"0.6480793",
"0.6437938",
"0.64327985",
"0.64327985",
"0.64327985",
"0.6428... | 0.0 | -1 |
The send() method is disabled in DummyConnection | async def send(self, message): | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def send(self):\n raise NotImplementedError()",
"def send(self):\n return False",
"def send(self, msg):\n pass",
"def send(self, msg):\n pass",
"def send(self, msg):\n pass",
"def send(self, message):\n pass",
"def test_save_send(self):\r\n # Don't reall... | [
"0.75775987",
"0.7284872",
"0.71137285",
"0.71137285",
"0.71137285",
"0.7007816",
"0.6987256",
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"0.6949789",
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"0.6863206",
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"0.6704559",
"0.6691615",
"0.6684624",
"0.6666767",
"0.66444695",
"0.6639989",
"0.659800... | 0.6332149 | 44 |
Captures the response to a message | def respond(self, response):
self.response = response | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def on_message(self, event):\n self.response = event.message\n self.connection.container.yield_() # Wake up the wait() loop to handle the message.",
"def message_recording(client):\n client.register_and_login('foo', 'default')\n client.add_message('test message 1')\n client.add_message('<t... | [
"0.6729939",
"0.6371365",
"0.6274233",
"0.6257684",
"0.6242246",
"0.624042",
"0.6186375",
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"0.6071888",
"0.6071641",
"0.6012938",
"0.6002373",
"0.5995019",
"0.59876066",
"0.5974825",
... | 0.5608025 | 58 |
Captures the HTML response to a message | async def respondHTML(self, html):
self.HTMLResponse = html | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def message_body_html(self):\n ...",
"def _html(self, message):\n content = f\"<html><body><h1>{message}</h1></body></html>\"\n return content.encode(\"utf8\") # NOTE: must return a bytes object!",
"def _html(self, message):\n content = f\"<html><body><h1>{message}</h1></body></htm... | [
"0.6637344",
"0.6620112",
"0.65681136",
"0.64055985",
"0.62257975",
"0.62002647",
"0.604187",
"0.6003477",
"0.5985468",
"0.59392756",
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"0.5726305",
"0.5707939",
"0.5704044",
"0.5688189",
"0.5646242",
"0.5642735... | 0.68577594 | 0 |
Called at decoration time, with the bare function being decorated | def __call__(self, func):
LOG.debug("@function %s", func)
func.handler = True
func.function = True
# Circuits properties
func.names = self.names
func.priority = self.kwargs.get("priority", 0)
func.channel = self.kwargs.get("channel", ",".join(["functions.{}".for... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def decorated(origFunc, newFunc, decoration='None'):\n\n pass",
"def get_decorated_function(self):",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decor... | [
"0.7754051",
"0.7553801",
"0.7309605",
"0.7309605",
"0.7309605",
"0.7270114",
"0.7269324",
"0.70715153",
"0.7051411",
"0.69272476",
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"0.657433",
"0.65073574",
"0.6471143",
"0.6452122",
"0.64488125",
"0.6425963",
"0.64155096"... | 0.0 | -1 |
Called at decoration time, with the bare method being decorated | def __call__(self, ia):
ia.handler = True
ia.inbound_handler = True
# Circuits properties
ia.names = self.names
ia.priority = self.kwargs.get("priority", 0)
ia.channel = "{0}.{1}".format(constants.INBOUND_MSG_DEST_PREFIX, self.names[0])
ia.override = self.kwargs.... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def get_decorated_function(self):",
"def setDecorated(self, decorated):",
"def deco... | [
"0.728691",
"0.728691",
"0.728691",
"0.7025943",
"0.69668305",
"0.666403",
"0.64638346",
"0.6426368",
"0.6348816",
"0.63256234",
"0.6299635",
"0.62492776",
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"0.61859363",
"0.61783594",
"0.61721826",
"0.61710614",
"0.6159806",
"0.6103955",
"0.6100871",
"0.60811365... | 0.0 | -1 |
The code to call when a method with the decorator `()` is invoked. Returns result_list when method with the decorator `()` is finished processing. A method that has this handler should yield a str when done | def _invoke_inbound_app(evt, **kwds):
result_list = []
LOG.debug("Running _invoke_inbound_app in Thread: %s", threading.currentThread().name)
# Invoke the actual Function
ia_results = ia(itself, evt.message, evt.message.get("action", "Unknown"))
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def execute(self):\n results = []\n\n for callNumber in xrange(len(self.callback)):\n results.append( (self.callback.pop(0))(*self.args.pop(0)) )\n\n return results",
"def test_returns_list(self):\n metrics = ('input', 'output')\n\n @callback_return(*metrics)\n ... | [
"0.5730961",
"0.571719",
"0.5681547",
"0.56003",
"0.5579488",
"0.55392265",
"0.5468535",
"0.54375017",
"0.54157335",
"0.5337627",
"0.5329474",
"0.52912915",
"0.52912664",
"0.5280508",
"0.5269396",
"0.52686286",
"0.52246803",
"0.5219803",
"0.5192265",
"0.5190813",
"0.5187031",... | 0.0 | -1 |
Called at decoration time, with the bare function being decorated | def __call__(self, fn):
fn.handler = True
fn.function = True
# Circuits properties
fn.names = self.names
fn.priority = self.kwargs.get("priority", 0)
fn.channel = "functions.{0}".format(self.names[0])
fn.override = self.kwargs.get("override", False)
fn.ev... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def decorated(origFunc, newFunc, decoration='None'):\n\n pass",
"def get_decorated_function(self):",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decor... | [
"0.7754051",
"0.7553801",
"0.7309605",
"0.7309605",
"0.7309605",
"0.7270114",
"0.7269324",
"0.70715153",
"0.7051411",
"0.69272476",
"0.6877044",
"0.6687945",
"0.6658759",
"0.66349643",
"0.657433",
"0.65073574",
"0.6471143",
"0.6452122",
"0.64488125",
"0.6425963",
"0.64155096"... | 0.0 | -1 |
The code to call when a function with the decorator `(api_name)` is invoked. Returns result_list when function with the decorator `(api_name)` is finished processing. A method that has this handler should yield a StatusMessage or a FunctionResult When a StatusMessage is yield'ed a StatusMessageEvent is fired with the t... | def _invoke_app_function(evt, **kwds):
LOG.debug("Running _invoke_app_function in Thread: %s", threading.currentThread().name)
result_list = []
# Validate the fn_inputs in the Message
fn_inputs = validate_fields([], kwds)
LOG.info("[%s] V... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __call__(self, fn):\n fn.handler = True\n fn.function = True\n\n # Circuits properties\n fn.names = self.names\n fn.priority = self.kwargs.get(\"priority\", 0)\n fn.channel = \"functions.{0}\".format(self.names[0])\n fn.override = self.kwargs.get(\"override\", F... | [
"0.59578174",
"0.5911615",
"0.57482475",
"0.5733824",
"0.549491",
"0.5357246",
"0.5351939",
"0.5299015",
"0.5251983",
"0.5232291",
"0.5200426",
"0.5197246",
"0.51885444",
"0.5169449",
"0.51555896",
"0.5143685",
"0.5096061",
"0.50952315",
"0.50873774",
"0.5064264",
"0.5055664"... | 0.5020217 | 23 |
Called at decoration time | def __call__(self, func):
# Set or extend the function's "custom_fields" attribute
func.required_fields = getattr(func, "required_fields", {})
func.required_fields[self.fieldname] = self.input_type
# The decorated function is unchanged
return func | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __call__( self ):\n pass",
"def __call__(self):\n pass",
"def __c... | [
"0.67608446",
"0.67608446",
"0.67608446",
"0.6426024",
"0.6418647",
"0.6418647",
"0.6292791",
"0.629227",
"0.6245761",
"0.6233334",
"0.62161237",
"0.6214014",
"0.61665714",
"0.61352736",
"0.60767996",
"0.6046218",
"0.59930605",
"0.59683245",
"0.59683245",
"0.59683245",
"0.596... | 0.0 | -1 |
Called at decoration time | def __call__(self, func):
# Set or extend the function's "action_fields" attribute
func.required_action_fields = getattr(func,
"required_action_fields", {})
func.required_action_fields[self.fieldname] = self.input_type
# The decorated functio... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __call__( self ):\n pass",
"def __call__(self):\n pass",
"def __c... | [
"0.67608446",
"0.67608446",
"0.67608446",
"0.6426024",
"0.6418647",
"0.6418647",
"0.6292791",
"0.629227",
"0.6245761",
"0.6233334",
"0.62161237",
"0.6214014",
"0.61665714",
"0.61352736",
"0.60767996",
"0.6046218",
"0.59930605",
"0.59683245",
"0.59683245",
"0.59683245",
"0.596... | 0.0 | -1 |
Called at decoration time, with function | def __call__(self, func):
LOG.debug("@defer %s", func)
@wraps(func)
def decorated(itself, event, *args, **kwargs):
"""the decorated function"""
LOG.debug("decorated")
if event.defer(itself, delay=self.delay):
# OK, let's handle it later
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_decorated_function(self):",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def decorated(origFunc, newFunc, decoration='Non... | [
"0.7237454",
"0.69157207",
"0.69157207",
"0.69157207",
"0.67605",
"0.6554005",
"0.65471756",
"0.65029734",
"0.64229554",
"0.63622516",
"0.6257818",
"0.62327325",
"0.62327325",
"0.62327325",
"0.62327325",
"0.62327325",
"0.6222223",
"0.6181449",
"0.6173241",
"0.61729336",
"0.61... | 0.5763306 | 59 |
Callback to return the debouncekey for an event. Multiple events with this key will be debounced together. | def debounce_get_incident_key(event):
key = "{} for {}".format(event.name, event.message["incident"]["id"])
return key | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def debounce(self):\n return self._debounce",
"def __call__(self, func):\n LOG.debug(\"@debounce %s\", func)\n\n @wraps(func)\n def decorated(itself, event, *args, **kwargs):\n \"\"\"the decorated function\"\"\"\n LOG.debug(\"decorated\")\n # De-bounce... | [
"0.69050074",
"0.6123342",
"0.5904678",
"0.52922404",
"0.5247472",
"0.5242694",
"0.5129239",
"0.51142675",
"0.5103602",
"0.50961006",
"0.50425494",
"0.5007442",
"0.49957982",
"0.4994945",
"0.49930578",
"0.49906588",
"0.49828362",
"0.49241093",
"0.49202102",
"0.4884297",
"0.48... | 0.57593954 | 3 |
Called at decoration time, with function | def __call__(self, func):
LOG.debug("@debounce %s", func)
@wraps(func)
def decorated(itself, event, *args, **kwargs):
"""the decorated function"""
LOG.debug("decorated")
# De-bounce messages for this event and the same key:
# (key is the incident-... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_decorated_function(self):",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def __init__(self, decorated):\n self.decorated = decorated",
"def decorated(origFunc, newFunc, decoration='Non... | [
"0.72377807",
"0.69162107",
"0.69162107",
"0.69162107",
"0.6759313",
"0.65535724",
"0.654546",
"0.6501962",
"0.6421653",
"0.6363204",
"0.6257508",
"0.6234376",
"0.6234376",
"0.6234376",
"0.6234376",
"0.6234376",
"0.6224008",
"0.6180461",
"0.617621",
"0.6172303",
"0.61428994",... | 0.0 | -1 |
Max limit is number of the combinations. | def generate_operations(self):
combinations = self.COMBINATIONS.items()[:self.limit]
for (term1, term2), type in combinations:
yield (term1, term2, type) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_max_combination(total_cuts):\n max_pieces = 0\n for i in range(total_cuts):\n result = i * (total_cuts - i)\n if result > max_pieces:\n max_pieces = result\n print(max_pieces)",
"def brute(limit):\n c_lengths = {s: collatz_length(s) for s in range(1, limit+1)}\n re... | [
"0.6800466",
"0.6524601",
"0.6210363",
"0.6164436",
"0.6090136",
"0.6063205",
"0.5984609",
"0.59758997",
"0.5967854",
"0.59423184",
"0.5904825",
"0.58632207",
"0.5821482",
"0.5780177",
"0.5776541",
"0.5754548",
"0.5750066",
"0.57412267",
"0.5734265",
"0.5721653",
"0.5720588",... | 0.0 | -1 |
Check for Walabot connectivity. loop until detect a Walabot. | def verifyWalabotIsConnected():
while True:
try:
wlbt.ConnectAny()
except wlbt.WalabotError as err:
input("- Connect Walabot and press 'Enter'.")
else:
print('- Connection to Walabot established.')
return | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def check_connection():\n if connected():\n ws.emit(Message('mycroft.internet.connected'))\n # check for pairing, if not automatically start pairing\n if not is_paired():\n # begin the process\n payload = {\n 'utterances': [\"pair my device\"],\n ... | [
"0.67418945",
"0.67034936",
"0.6321306",
"0.6317192",
"0.6138319",
"0.6137619",
"0.6137448",
"0.6100447",
"0.6077443",
"0.6034586",
"0.5992254",
"0.5982001",
"0.5950899",
"0.5919076",
"0.5894772",
"0.58944863",
"0.5866478",
"0.5837735",
"0.5822696",
"0.5799287",
"0.57872075",... | 0.8310073 | 0 |
Configure Walabot's profile, arena (r, theta, phi), threshold and the image filter. | def setWalabotSettings():
wlbt.SetProfile(wlbt.PROF_SENSOR)
wlbt.SetArenaR(R_MIN, R_MAX, R_RES)
wlbt.SetArenaTheta(THETA_MIN, THETA_MAX, THETA_RES)
wlbt.SetArenaPhi(PHI_MIN, PHI_MAX, PHI_RES)
#wlbt.SetThreshold(THRESHOLD)
wlbt.SetDynamicImageFilter(wlbt.FILTER_TYPE_DERIVATIVE) #Also test with FI... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def pibooth_setup_camera(cfg):",
"def __init__(self):\n\n # self.threshold = 3.\n self.gamma_min = 3\n self.gamma_max = 12\n self.n_samples = 40\n # self.do_plots = False\n # self.do_albedo = True\n # self.verbose = True\n\n self.nbands = 7\n sel... | [
"0.55619794",
"0.5276887",
"0.5156513",
"0.51370335",
"0.512774",
"0.51219815",
"0.5073326",
"0.5047057",
"0.50075054",
"0.49671337",
"0.4966661",
"0.49465856",
"0.4934728",
"0.49258626",
"0.49199712",
"0.49144244",
"0.48763582",
"0.48478684",
"0.48258424",
"0.4820601",
"0.48... | 0.75236595 | 0 |
Start the Walabot and calibrate it. | def startAndCalibrateWalabot():
wlbt.StartCalibration()
print('- Calibrating...')
while wlbt.GetStatus()[0] == wlbt.STATUS_CALIBRATING:
wlbt.Trigger()
wlbt.Start()
print('- Calibration ended.\n- Ready!') | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def setWalabotSettings():\n wlbt.SetProfile(wlbt.PROF_SENSOR)\n wlbt.SetArenaR(R_MIN, R_MAX, R_RES)\n wlbt.SetArenaTheta(THETA_MIN, THETA_MAX, THETA_RES)\n wlbt.SetArenaPhi(PHI_MIN, PHI_MAX, PHI_RES)\n #wlbt.SetThreshold(THRESHOLD)\n wlbt.SetDynamicImageFilter(wlbt.FILTER_TYPE_DERIVATIVE) #Also t... | [
"0.61959416",
"0.6061523",
"0.60181415",
"0.60077643",
"0.58197683",
"0.5722696",
"0.5720339",
"0.56705564",
"0.56593007",
"0.5618712",
"0.56180704",
"0.56057066",
"0.56027627",
"0.5589759",
"0.5566517",
"0.55604434",
"0.5554661",
"0.5530717",
"0.5525474",
"0.5512045",
"0.550... | 0.84001803 | 0 |
Stops Walabot and disconnect the device. | def stopAndDisconnectWalabot():
wlbt.Stop()
wlbt.Disconnect()
print ('Termination successful') | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def stop(self) -> None:\n self.mqttc.disconnect()",
"def stop(self):\n self.conn.stop()",
"def stop(self):\n self.bus.log('Stopping down OLA Plugin.')\n self.bus.unsubscribe(\n self.channel_names['channel_request'],\n self.handle_channel\n )\n sel... | [
"0.73858374",
"0.69355065",
"0.6850796",
"0.6815512",
"0.68138057",
"0.68138057",
"0.6790304",
"0.67658573",
"0.676303",
"0.6745841",
"0.67418426",
"0.67080593",
"0.6698249",
"0.66884",
"0.6684982",
"0.6664148",
"0.66465163",
"0.663873",
"0.66383976",
"0.66383976",
"0.6627888... | 0.832489 | 0 |
Detect and record whether or not there is a target and whether or not it is breathing. | def catExists():
currentTime = datetime.now().strftime('%H:%M:%S')
while True:
#wlbt.Trigger()
target = wlbt.GetSensorTargets()
if target:
breathing = isBreathing()
if breathing == 1:
#print("the cat is alive!")
catStatus = 2
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def check_ball_on_target():\n\n pass",
"async def is_target_reached(self) -> bool: # type: ignore\n ...",
"def is_gentarget(self, target):\r\n raise NotImplementedError",
"def has_target(self):\n return self.target is not None",
"def need_target(self):\n\t\t# if we search for color tar... | [
"0.73965406",
"0.69133866",
"0.659677",
"0.65672535",
"0.65581936",
"0.6413436",
"0.6356345",
"0.62851787",
"0.62369335",
"0.61396855",
"0.6083162",
"0.60699123",
"0.6033767",
"0.6033767",
"0.60063726",
"0.59937567",
"0.5978707",
"0.5915004",
"0.590908",
"0.58708715",
"0.5870... | 0.0 | -1 |
Assign lipids to respective leaflets | def identify_leaflets(u, time_ts):
z = u.select_atoms("all").center_of_geometry()[2]
COM_z= np.array([0,0,z]) #defines the global midplane position along z
x, y, z = u.trajectory.ts.triclinic_dimensions[0][0], u.trajectory.ts.triclinic_dimensions[1][1], u.trajectory.ts.triclinic_dimensions[2][2]
box = ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def replace_lipid(membrane,cholesterol,nreplace) :\n\n if nreplace % 2 != 0 :\n raise ValueError(\"Number of replacements must be divisible by 2\")\n \n lipids_wat = [\"W\"]\n lipids_wat.extend(lipids)\n \n # Store away residues\n lipid_res = [r for r in membrane.residues if r.resname.upper().strip() in ... | [
"0.57010627",
"0.56445384",
"0.56101805",
"0.5581516",
"0.55390495",
"0.5480422",
"0.5306147",
"0.5279905",
"0.52695376",
"0.5215408",
"0.5198409",
"0.51911825",
"0.5180127",
"0.515217",
"0.5136848",
"0.5120094",
"0.51109314",
"0.5096809",
"0.50735694",
"0.5068601",
"0.505996... | 0.53537464 | 6 |
Returns the unit vector of the vector. | def unit_vector(vector):
return vector / np.linalg.norm(vector) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def unit_vector(vector):\n #print 'unit_vector'\n #print vector\n #print type(vector)\n #npvector = np.array(vector)\n return vector / np.linalg.norm(vector)",
"def _get_unit_vector(self, v):\n return v / np.linalg.norm(v)",
"def get_unit_vector(self, vector):\n return vector / la.... | [
"0.8355314",
"0.8344175",
"0.83402044",
"0.83041203",
"0.8288785",
"0.82710177",
"0.8263843",
"0.8237869",
"0.8219826",
"0.8203201",
"0.8180198",
"0.8180198",
"0.8180198",
"0.8157419",
"0.80363405",
"0.8024346",
"0.7914348",
"0.7900733",
"0.78349787",
"0.7770651",
"0.77661633... | 0.8116172 | 22 |
Returns the angle in radians between vectors 'v1' and 'v2' The sign of the angle is dependent on the order of v1 and v2 | def compute_angle(v1, v2):
cosang = np.dot(v1, v2)
sinang = la.norm(np.cross(v1, v2))
angle = np.arctan2(sinang, cosang)
return angle | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def angleBetweenVectors(v1, v2):\n v2Size = vectorLength(v2)\n if not v2Size:\n theta = 0.0\n else:\n theta = math.acos(dotProduct(v1, v2) / v2Size)\n return theta",
"def angle(self, v1, v2):\r\n cosang = np.dot(v1, v2)\r\n sinang = np.linalg.norm(np.cross(v1, v2))\r\n return n... | [
"0.89745975",
"0.89499927",
"0.89068824",
"0.8855927",
"0.8761891",
"0.87150687",
"0.86889726",
"0.8623233",
"0.8622836",
"0.8610433",
"0.86037433",
"0.8565726",
"0.85333735",
"0.83600396",
"0.83338356",
"0.8310569",
"0.8287398",
"0.82812274",
"0.8280104",
"0.82704085",
"0.82... | 0.8954668 | 1 |
computes ID reward, +1 if player scores a point, 1 otherwise | def rewardID(score1, score2):
reward = score1 - score2
return reward, -reward | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def reward(self, player, winning_state):\n if winning_state == \"Tie\":\n return 1\n elif winning_state == \"Resume\":\n return -1\n else:\n if player == \"agent\":\n return 10\n else:\n return -10",
"def r_point(self)... | [
"0.6437977",
"0.64029753",
"0.6254412",
"0.61305016",
"0.6119045",
"0.6057819",
"0.60051566",
"0.59680796",
"0.595627",
"0.59547967",
"0.58996826",
"0.5880871",
"0.5861454",
"0.58425546",
"0.5823367",
"0.58139914",
"0.5804704",
"0.57948387",
"0.5769876",
"0.57661957",
"0.5737... | 0.7202625 | 0 |
computes SE reward, depending on whether the agent is 'catching up' or 'getting ahead' | def rewardSE(score1, score2, cum_score1, cum_score2):
score_diff = score1 - score2
diff = cum_score1 - cum_score2
return unitRewardSE(score_diff, diff), unitRewardSE(-score_diff, diff) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_reward(self):\n if self.status():\n return self.current_step/self.ep_length # the reward is proportional to the duration \n else:\n return 0",
"def get_reward(self, is_terminal_state, result, reward, is_agent_move):\n if is_terminal_state:\n reward += 0 if result == \"... | [
"0.69249827",
"0.68843967",
"0.68833375",
"0.68820304",
"0.68806565",
"0.6787305",
"0.6781655",
"0.67804056",
"0.67503536",
"0.6675589",
"0.66218454",
"0.6619695",
"0.66102624",
"0.6590536",
"0.6574249",
"0.65695703",
"0.65641147",
"0.65584797",
"0.6543265",
"0.6542407",
"0.6... | 0.0 | -1 |
Load the pcb metal dataset | def load_pcb(self, dataset_dir, subset, file_list=None, image_ext="jpg", object_class=None):
self.image_dir = os.path.join(dataset_dir, "images")
self.annotations_dir = os.path.join(dataset_dir, "annotations")
# add classes.
if object_class is None:
obj = glob.glob... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_data_pkl(self):\n pkl_name = '{}/data/mini-imagenet-cache-{}.pkl'.format(self.root_dir, self.split)\n print('Loading pkl dataset: {} '.format(pkl_name))\n\n try:\n with open(pkl_name, \"rb\") as f:\n data = pkl.load(f, encoding='bytes')\n image_d... | [
"0.6541246",
"0.6287889",
"0.6214803",
"0.6182117",
"0.6064615",
"0.60214704",
"0.5922483",
"0.5921194",
"0.5889621",
"0.58767706",
"0.5812144",
"0.5799",
"0.5793534",
"0.5788472",
"0.5771795",
"0.5732959",
"0.5713654",
"0.5689809",
"0.5689483",
"0.5679353",
"0.5677678",
"0... | 0.0 | -1 |
Generate instance masks for an image. | def load_mask(self, image_id):
image_info = self.image_info[image_id]
if image_info["source"] != "pcb":
return super(self.__class__, self).load_mask(image_id)
# convert polygons to a bitmap mask of shape
# [height, width, instance_count]
info = self.image_info[image... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def load_mask(self, image_id):\n # If not a vesicle dataset image, delegate to parent class.\n image_info = self.image_info[image_id]\n if image_info[\"source\"] != \"vesicle\":\n return super(self.__class__, self).load_mask(image_id)\n\n # Convert polygons to a bitmap mask o... | [
"0.6926018",
"0.6916978",
"0.6871326",
"0.6845947",
"0.67575824",
"0.67555743",
"0.67047006",
"0.6701396",
"0.6675392",
"0.6627721",
"0.6609718",
"0.6604988",
"0.6547317",
"0.65468746",
"0.6392952",
"0.63381743",
"0.63316107",
"0.6330832",
"0.6304875",
"0.62868094",
"0.628625... | 0.69285274 | 0 |
Return the path of the image | def image_reference(self, image_id):
info = self.image_info[image_id]
if info["source"] == "pcb":
return info["path"]
else:
super(self.__class__, self).image_reference(image_id) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def imagePath(self):\n return self.path",
"def get_pathname(self):\n return self.image_data.path",
"def imagePath(self):\n if self.use_dic:\n if self.imlist:\n paths = []\n for img in self.allimgs:\n paths.append(join(self.home, '... | [
"0.85880727",
"0.8271568",
"0.8216832",
"0.7946613",
"0.7911829",
"0.7874524",
"0.7848652",
"0.77885175",
"0.7750109",
"0.76651067",
"0.75987107",
"0.7574366",
"0.7495351",
"0.74785393",
"0.74669605",
"0.7447827",
"0.7440666",
"0.7435005",
"0.7424479",
"0.74243397",
"0.740057... | 0.0 | -1 |
Simple wget get line | def fetch(file):
print "Fetching {0}...".format(file.split("/")[-1])
subprocess.call("wget {0} > /dev/null 2>&1".format(file), shell=True) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def wget(URL):\n URL = URL.replace(\"http://\",\"\")\n ip_address = URL.split(\"/\")[0]\n script = \"/\"+\"/\".join(URL.split(\"/\")[1:])\n if not ip_address in connections:\n from httplib import HTTPConnection\n connection = HTTPConnection(ip_address)\n connections[ip_address] = c... | [
"0.73125535",
"0.71006334",
"0.69523764",
"0.648822",
"0.6264116",
"0.6225872",
"0.60921",
"0.6089753",
"0.6039321",
"0.60207665",
"0.60082555",
"0.59652096",
"0.59531015",
"0.5945191",
"0.5940594",
"0.5929515",
"0.59092826",
"0.58861315",
"0.5877554",
"0.5873468",
"0.5867955... | 0.67773914 | 3 |
Makes a GET request to the {url}. Searches for an html element(s) by its xpath. | def find_html_element_by_xpath(url, xpath, proxies=None):
try:
response = requests.get(url, proxies=proxies).text
except requests.RequestException as e:
logging.error("Request error: {}".format(e))
# TODO: exception handling
return None
tree = ht... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_tag(url, xpathExpression, params=None):\n headers = {'User-Agent': 'curl/7.35.0'}\n page = requests.get(url, params=params, headers=headers)\n page.raise_for_status()\n tree = html.fromstring(page.content)\n return tree.xpath(xpathExpression)",
"def do_get(self, url):\n self.driver.... | [
"0.64967495",
"0.6384309",
"0.6333756",
"0.6136398",
"0.61055344",
"0.59896374",
"0.5950545",
"0.5900976",
"0.58881927",
"0.5864435",
"0.5814219",
"0.57650304",
"0.5764316",
"0.57599485",
"0.5714126",
"0.5696378",
"0.5645251",
"0.5619285",
"0.5600905",
"0.5598952",
"0.5590954... | 0.5867571 | 9 |
Coefficients are taken from the official codes of DUFVSR This conversion is also the same as that in BasicSR | def rgb_to_ycbcr(img):
T = np.array([
[0.256788235294118, -0.148223529411765, 0.439215686274510],
[0.504129411764706, -0.290992156862745, -0.367788235294118],
[0.097905882352941, 0.439215686274510, -0.071427450980392],
], dtype=np.float64)
O = np.array([16, 128, 128], dtype=np.fl... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def d_coefficients(x1,x2,x3,CCoefficients):\n\tDCoefficients = np.array([\t(CCoefficients[1]-CCoefficients[0])/(3*(x2-x1)), \\\n\t\t\t\t\t\t\t\t(CCoefficients[2]-CCoefficients[1])/(3*(x3-x2))\t], \\\n\t\t\t\t\t\t\t\tfloat)\n\treturn(DCoefficients)",
"def b_coefficients(x1,x2,x3,y1,y2,y3,CCoefficients,DCoeffici... | [
"0.6410733",
"0.63527215",
"0.6306684",
"0.6229015",
"0.6164668",
"0.6134661",
"0.60982096",
"0.6057532",
"0.60417587",
"0.60015625",
"0.5875096",
"0.5800425",
"0.5776809",
"0.57378215",
"0.5697484",
"0.56964654",
"0.56898993",
"0.5680222",
"0.56543076",
"0.5653175",
"0.56488... | 0.0 | -1 |
Convert np.float32 array to np.uint8 | def float32_to_uint8(inputs):
return np.uint8(np.clip(np.round(inputs * 255), 0, 255)) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def cast_float_to_uint8(array_float):\n if not numpy.issubdtype(array_float.dtype, numpy.float):\n raise TypeError('`array_float.dtype` is not smaller than `numpy.float` in type hierarchy.')\n \n # If the above check did not exist and `array_float`\n # contained integers, the clipping below woul... | [
"0.7408117",
"0.73111886",
"0.7305541",
"0.7285258",
"0.7285258",
"0.7240387",
"0.7012514",
"0.69310755",
"0.68306875",
"0.68195",
"0.64354885",
"0.6360376",
"0.6294902",
"0.6274729",
"0.6251667",
"0.6224117",
"0.6179129",
"0.6171993",
"0.60785764",
"0.60785764",
"0.60175484"... | 0.80445904 | 0 |
Convert data to torch tensor with type float32 Assume data has type np.uint8/np.float32 or torch.uint8/torch.float32, and uint8 data ranges in [0, 255] and float32 data ranges in [0, 1] | def canonicalize(data):
if isinstance(data, np.ndarray):
if data.dtype == np.uint8:
data = data.astype(np.float32) / 255.0
data = torch.from_numpy(np.ascontiguousarray(data))
elif isinstance(data, torch.Tensor):
if data.dtype == torch.uint8:
data = data.float() ... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def data_convert2float32 (self, data):\r\n data = data.astype(np.float32)\r\n\r\n return data",
"def list_to_tensor(data):\n return torch.as_tensor(data, dtype=torch.float32, device=global_device())",
"def __to_tensor__(data: Union[int, float, np.ndarray, List]) -> torch.tensor:\n\n if ... | [
"0.7918191",
"0.75068885",
"0.73765385",
"0.6987699",
"0.6949261",
"0.6949261",
"0.6949261",
"0.67039037",
"0.6699868",
"0.66764146",
"0.6664306",
"0.6650705",
"0.6586295",
"0.6581201",
"0.65121454",
"0.64635706",
"0.64152795",
"0.6371685",
"0.63533086",
"0.63247216",
"0.6193... | 0.75479096 | 1 |
Save each frame of a sequence to .png image in seq_dir | def save_sequence(seq_dir, seq_data, frm_idx_lst=None, to_bgr=False):
if to_bgr:
seq_data = seq_data[..., ::-1] # rgb2bgr
# use default frm_idx_lst is not specified
tot_frm = len(seq_data)
if frm_idx_lst is None:
frm_idx_lst = ['{:04d}.png'.format(i) for i in range(tot_frm)]
# sa... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def saveFrames(filepath, frames):\n\n for i, frame in enumerate(frames):\n image = Image.fromarray(frame)\n image.save(filepath + str(i).zfill(8) + '.png')",
"def _save_frame_as_png(\n self : \"animation\",\n frame : \"np.ndarray\",\n filename : \"str\"\n ... | [
"0.7453527",
"0.70677906",
"0.70371145",
"0.68463975",
"0.6716898",
"0.66529393",
"0.656279",
"0.6541152",
"0.64740807",
"0.64529353",
"0.63749933",
"0.6366781",
"0.6315768",
"0.62766594",
"0.62292975",
"0.62225884",
"0.6212714",
"0.6183725",
"0.6175805",
"0.61635643",
"0.610... | 0.7877584 | 0 |
Test Codon Adaptation Index (CAI) using default E. coli data. | def test_codon_usage_ecoli(self):
CAI = CodonAdaptationIndex()
self.assertEqual("%0.5f" % CAI.cai_for_gene("ATGCGTATCGATCGCGATACGATTAGGCGGATG"),
"0.09978") | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_codon_usage_custom(self):\n # We need a FASTA file of CDS sequences to count the codon usage...\n dna_fasta_filename = \"fasta.tmp\"\n dna_genbank_filename = \"GenBank/NC_005816.gb\"\n record = SeqIO.read(dna_genbank_filename, \"genbank\")\n records = []\n for fea... | [
"0.6492251",
"0.63939977",
"0.5973257",
"0.58685595",
"0.58200365",
"0.5816378",
"0.5812816",
"0.5785232",
"0.5783167",
"0.5756506",
"0.5725458",
"0.57007027",
"0.5692516",
"0.56283003",
"0.5610308",
"0.5608039",
"0.55863476",
"0.55578107",
"0.55529904",
"0.5548385",
"0.55437... | 0.73449653 | 0 |
Test Codon Adaptation Index (CAI) using FASTA file for background. | def test_codon_usage_custom(self):
# We need a FASTA file of CDS sequences to count the codon usage...
dna_fasta_filename = "fasta.tmp"
dna_genbank_filename = "GenBank/NC_005816.gb"
record = SeqIO.read(dna_genbank_filename, "genbank")
records = []
for feature in record.fe... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_fasta_one_sequence(self):\n record = list(SeqIO.parse(\"Registry/seqs.fasta\", \"fasta\"))[0]\n input_file = \"seq.fasta\"\n with open(input_file, \"w\") as handle:\n SeqIO.write(record, handle, \"fasta\")\n\n cline = XXmotifCommandline(outdir=self.out_dir, seqfile=i... | [
"0.6029809",
"0.6004039",
"0.5884848",
"0.58040977",
"0.57673204",
"0.5664929",
"0.5589991",
"0.5577867",
"0.5553025",
"0.5465446",
"0.5464523",
"0.54561615",
"0.54151857",
"0.5407253",
"0.5386596",
"0.5384784",
"0.5371423",
"0.5339712",
"0.52890664",
"0.527738",
"0.5269766",... | 0.59767234 | 2 |
Test getting Elgato Light state in temperature mode. | async def test_state_temperature(aresponses):
aresponses.add(
"example.com:9123",
"/elgato/lights",
"GET",
aresponses.Response(
status=200,
headers={"Content-Type": "application/json"},
text=load_fixture("state-temperature.json"),
),
)
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def test_light_state(\n hass: HomeAssistant, aioclient_mock: AiohttpClientMocker\n) -> None:\n await init_integration(hass, aioclient_mock)\n\n entity_registry = er.async_get(hass)\n\n state = hass.states.get(\"light.modernformsfan_light\")\n assert state\n assert state.attributes.get(ATTR_... | [
"0.6878956",
"0.6712697",
"0.6622997",
"0.661685",
"0.65766895",
"0.6493358",
"0.64604175",
"0.64513606",
"0.63721883",
"0.63063693",
"0.62966764",
"0.6294307",
"0.62630814",
"0.6253732",
"0.6194373",
"0.6189593",
"0.61587435",
"0.6146471",
"0.6141874",
"0.6124011",
"0.612033... | 0.727813 | 0 |
Test getting Elgato Light state in color mode. | async def test_state_color(aresponses):
aresponses.add(
"example.com:9123",
"/elgato/lights",
"GET",
aresponses.Response(
status=200,
headers={"Content-Type": "application/json"},
text=load_fixture("state-color.json"),
),
)
async wi... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_color(self):\n self._calibration_test(\"color_full\")",
"def test_change_color_of_the_device__true():",
"def check_light(light: pykulersky.Light):\n light.connect()\n light.get_color()",
"def test_change_color_of_the_device__false():",
"async def test_light_state(\n hass: HomeAssis... | [
"0.7008754",
"0.699675",
"0.68415654",
"0.6793344",
"0.6721419",
"0.66686684",
"0.66600657",
"0.65265566",
"0.6461606",
"0.6447308",
"0.6429285",
"0.6395175",
"0.6358749",
"0.6337252",
"0.6333656",
"0.63308775",
"0.62578654",
"0.6250418",
"0.6241562",
"0.62268525",
"0.6144565... | 0.6693482 | 5 |
Test changing Elgato Light State in temperature mode. | async def test_change_state_temperature(aresponses):
async def response_handler(request):
"""Response handler for this test."""
data = await request.json()
assert data == {
"numberOfLights": 1,
"lights": [{"on": 1, "brightness": 100, "temperature": 200}],
}
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def test_thermostat_heatit_z_trm2fx(\n hass: HomeAssistant, client, climate_heatit_z_trm2fx, integration\n) -> None:\n node = climate_heatit_z_trm2fx\n state = hass.states.get(CLIMATE_FLOOR_THERMOSTAT_ENTITY)\n\n assert state\n assert state.state == HVACMode.HEAT\n assert state.attributes[A... | [
"0.69498336",
"0.6923428",
"0.681475",
"0.6802302",
"0.6794112",
"0.67801625",
"0.6736621",
"0.65671206",
"0.65611637",
"0.65540653",
"0.6538566",
"0.652884",
"0.6527561",
"0.6511185",
"0.64904994",
"0.6450532",
"0.64299566",
"0.639926",
"0.6396049",
"0.63834566",
"0.6369441"... | 0.0 | -1 |
Response handler for this test. | async def response_handler(request):
data = await request.json()
assert data == {
"numberOfLights": 1,
"lights": [{"on": 1, "brightness": 100, "temperature": 200}],
}
return aresponses.Response(
status=200,
headers={"Content-Type": "applica... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def _response_handler(self):",
"def response_handling(self) -> global___Snippet.SimpleResponseHandling:",
"def response_handling(self) -> global___Snippet.SimpleResponseHandling:",
"def responseHandler(self, factory):\n pass",
"def main_response(self, data):",
"def main_response(self, data):... | [
"0.79522353",
"0.76998967",
"0.76998967",
"0.7572021",
"0.75436866",
"0.75436866",
"0.74242777",
"0.72418624",
"0.71199226",
"0.71199226",
"0.7052633",
"0.70363975",
"0.6936624",
"0.693356",
"0.69223917",
"0.69198334",
"0.6851695",
"0.683862",
"0.683862",
"0.6835354",
"0.6757... | 0.0 | -1 |
Test changing Elgato Light State in color mode. | async def test_change_state_color(aresponses):
async def response_handler(request):
"""Response handler for this test."""
data = await request.json()
assert data == {
"numberOfLights": 1,
"lights": [{"on": 1, "brightness": 100, "hue": 10.1, "saturation": 20.2}],
... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def test_change_color_of_the_device__true():",
"def test_change_color_of_the_device__false():",
"async def test_color_light(\n hass: HomeAssistant, bulb: MagicMock, transition: float | None\n) -> None:\n already_migrated_config_entry = MockConfigEntry(\n domain=DOMAIN, data={}, unique_id=MAC_ADDRE... | [
"0.7458252",
"0.72283345",
"0.7105034",
"0.6960823",
"0.6951184",
"0.68336487",
"0.6811411",
"0.6783545",
"0.67750144",
"0.6621819",
"0.66058975",
"0.6532489",
"0.6530398",
"0.65095425",
"0.6417558",
"0.6401113",
"0.6388816",
"0.63654095",
"0.63467056",
"0.63447046",
"0.63100... | 0.0 | -1 |
Response handler for this test. | async def response_handler(request):
data = await request.json()
assert data == {
"numberOfLights": 1,
"lights": [{"on": 1, "brightness": 100, "hue": 10.1, "saturation": 20.2}],
}
return aresponses.Response(
status=200,
headers={"Content-Ty... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"async def _response_handler(self):",
"def response_handling(self) -> global___Snippet.SimpleResponseHandling:",
"def response_handling(self) -> global___Snippet.SimpleResponseHandling:",
"def responseHandler(self, factory):\n pass",
"def main_response(self, data):",
"def main_response(self, data):... | [
"0.79537404",
"0.7702842",
"0.7702842",
"0.75738364",
"0.7545603",
"0.7545603",
"0.7425096",
"0.724262",
"0.71217763",
"0.71217763",
"0.7053156",
"0.70377403",
"0.69370884",
"0.69352",
"0.69240254",
"0.6920867",
"0.6853209",
"0.684176",
"0.684176",
"0.6834451",
"0.675802",
... | 0.0 | -1 |
Test changing Elgato Light State with invalid values. | async def test_change_state_errors(state, message):
elgato = Elgato("example.com")
with pytest.raises(ElgatoError, match=message):
await elgato.light(**state) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def the_changed_brightness_should_be_reflected_in_the_state_10():\n assert web_app.get_state()\n assert web_app.check_value_in_state(\"brightness\",\"10\")",
"def the_changed_brightness_should_be_reflected_in_the_state_5():\n assert web_app.get_state()\n assert web_app.check_value_in_state(\"brightne... | [
"0.6809742",
"0.66639435",
"0.66344774",
"0.66061795",
"0.6496359",
"0.6360549",
"0.6340057",
"0.6306056",
"0.6299002",
"0.62746155",
"0.6260993",
"0.6253095",
"0.62426645",
"0.62362736",
"0.62243295",
"0.6211078",
"0.6190869",
"0.6169105",
"0.6162311",
"0.61528707",
"0.61483... | 0.72896004 | 0 |
Test all AWS SGE related features. Grouped all tests in a single function so that cluster can be reused for all of them. | def test_sge(region, pcluster_config_reader, clusters_factory):
scaledown_idletime = 3
max_queue_size = 5
max_slots = 4
maintain_initial_size = "false"
cluster_config = pcluster_config_reader(
scaledown_idletime=scaledown_idletime,
max_queue_size=max_queue_size,
maintain_init... | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def run_feature_extraction_tests():\n test_feature_extraction()\n test_distributed_feature_extraction()\n test_multimodel_feature_extraction()\n test_distributed_multimodel_feature_extraction()",
"def test_KGE_methods(model_name):\n testing_function(model_name)",
"def test_all(test_fn):\n suc... | [
"0.68769574",
"0.6050843",
"0.59764224",
"0.59701645",
"0.5910464",
"0.58170825",
"0.5778389",
"0.5770995",
"0.570061",
"0.5699018",
"0.56946063",
"0.56882393",
"0.5659208",
"0.5657952",
"0.56547195",
"0.5646147",
"0.5645969",
"0.56331563",
"0.56217706",
"0.5608319",
"0.56032... | 0.52178943 | 54 |
Initialize Legifrance client with client_id and client_secret. | def __init__(self, client_id: str, client_secret: str):
self._client_id: str = client_id
self._client_secret: str = client_secret
self._client: OAuth2Session = _get_legifrance_client(client_id, client_secret)
self._last_compute_time = time.time() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def __init__(self,\n client_id,\n client_secret):\n self.__client_id = client_id\n self.__client_secret = client_secret",
"def __init__(self, client_id, client_secret):\n self.client_id = client_id\n self.client_secret = client_secret\n self.toke... | [
"0.7384509",
"0.7032771",
"0.69361496",
"0.6745765",
"0.6422078",
"0.63998556",
"0.6372419",
"0.63556576",
"0.6346859",
"0.62635595",
"0.6213391",
"0.62095",
"0.6143803",
"0.6129101",
"0.60696596",
"0.605228",
"0.6049244",
"0.6039157",
"0.60341024",
"0.6029901",
"0.60164165",... | 0.7158159 | 1 |
Fetches the consolidated version of a law/decree/arrete by text identifier for a specific date. If no date is provided, today's date is used. | def consult_law_decree(self, text_id: str, date: Optional[datetime] = None) -> Dict[str, Any]:
self._update_client_if_necessary()
return _consult_law_decree(text_id, date, self._client) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def by_date(self, date_=None):\n\n if date_ is None:\n try:\n date_ = date.fromtimestamp(\n mktime(strptime(self.date, '%Y-%m-%d'))\n )\n return self.by_date(date_)\n except (TypeError, ValueError):\n try:\n... | [
"0.5327379",
"0.5118535",
"0.50998086",
"0.50386214",
"0.501414",
"0.5004253",
"0.49816415",
"0.49502483",
"0.49380118",
"0.49352133",
"0.49011025",
"0.47921678",
"0.47635776",
"0.47317624",
"0.4716115",
"0.47025126",
"0.46872622",
"0.46852967",
"0.46658716",
"0.4610747",
"0.... | 0.56007445 | 0 |
Fetches the JORF version of a law/decree/arrete by text identifier. | def consult_jorf(self, text_id: str) -> Dict[str, Any]:
self._update_client_if_necessary()
return _consult_jorf(text_id, self._client) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def get_element_from_id(self, identifier):\n classification, org, rel, com = classify_id(identifier)\n if classification == id_classification.org:\n return self.get_org_question(org)\n elif classification == id_classification.rel:\n return self.get_rel_question(org, rel)\... | [
"0.49641275",
"0.46501428",
"0.4630191",
"0.45927075",
"0.4589712",
"0.4521436",
"0.44825307",
"0.44575438",
"0.44496873",
"0.44368324",
"0.43593493",
"0.43212026",
"0.43087837",
"0.42987674",
"0.42854863",
"0.42817187",
"0.42626467",
"0.4260149",
"0.4252432",
"0.4248289",
"0... | 0.5531085 | 0 |
Fetches article by id | def consult_article(self, article_id: str) -> Dict[str, Any]:
self._update_client_if_necessary()
return _article_by_id(article_id, self._client) | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def article_by_id(self, id):\n return self.es.get(index=self.index, doc_type=self.doc_type, id=id)",
"def get_article_by_id(article_id):\n return Article.query.get(article_id)",
"def get_article(db:Session, article_id:int):\n return db.query(ArticleModel).filter(ArticleModel.id==article_id).fi... | [
"0.78759176",
"0.7567833",
"0.71963876",
"0.71949047",
"0.70986164",
"0.69430614",
"0.6830546",
"0.6741828",
"0.6676814",
"0.6666822",
"0.6655588",
"0.6580953",
"0.6569796",
"0.65317386",
"0.65252817",
"0.65047145",
"0.64999455",
"0.64910865",
"0.6478443",
"0.64600855",
"0.64... | 0.6894055 | 6 |
Gets an object from S3. | def get(self, key):
return s3.Object(self.bucket.name, key).get()['Body'].read() | {
"objective": {
"self": [],
"paired": [],
"triplet": [
[
"query",
"document",
"negatives"
]
]
}
} | [
"def _get_s3_object(self, s3_path):\n bucket_name, key = S3Util.get_bucket_and_key(s3_path)\n return self.s3_resource.Object(bucket_name, key)",
"def get_s3_object(self, key):\n try:\n bucket_name = app.config['S3_BUCKET_NAME']\n s3_client = app.config['S3']\n ... | [
"0.8539686",
"0.8165444",
"0.7961786",
"0.7722801",
"0.7547169",
"0.74239224",
"0.74183124",
"0.73820263",
"0.731202",
"0.71821254",
"0.7147931",
"0.7108089",
"0.71075475",
"0.70903015",
"0.7077998",
"0.7044556",
"0.7038838",
"0.701147",
"0.7006739",
"0.698413",
"0.698143",
... | 0.7761224 | 3 |
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