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How to use get_valueOf_ method in autotest
Best Python code snippet using autotest_python
clinvar_xml_parser.py
Source:clinvar_xml_parser.py 
...120 if (variation_type == 'copy number loss') or (variation_type == 'copy number gain'):121 for AttributeSet in measure_obj.AttributeSet:122 if 'HGVS, genomic, top level' in AttributeSet.Attribute.Type:123 if AttributeSet.Attribute.integerValue == 37:124 hgvs_genome = AttributeSet.Attribute.get_valueOf_()125 if 'genomic' in AttributeSet.Attribute.Type:126 HGVS['genomic'].append(AttributeSet.Attribute.get_valueOf_())127 elif 'non-coding' in AttributeSet.Attribute.Type:128 HGVS['non-coding'].append(AttributeSet.Attribute.get_valueOf_())129 elif 'coding' in AttributeSet.Attribute.Type:130 HGVS['coding'].append(AttributeSet.Attribute.get_valueOf_())131 elif 'protein' in AttributeSet.Attribute.Type:132 HGVS['protein'].append(AttributeSet.Attribute.get_valueOf_())133 else:134 for AttributeSet in measure_obj.AttributeSet:135 if 'genomic' in AttributeSet.Attribute.Type:136 HGVS['genomic'].append(AttributeSet.Attribute.get_valueOf_())137 elif 'non-coding' in AttributeSet.Attribute.Type:138 HGVS['non-coding'].append(AttributeSet.Attribute.get_valueOf_())139 elif 'coding' in AttributeSet.Attribute.Type:140 HGVS['coding'].append(AttributeSet.Attribute.get_valueOf_())141 elif 'protein' in AttributeSet.Attribute.Type:142 HGVS['protein'].append(AttributeSet.Attribute.get_valueOf_())143 if not hgvs_coding and AttributeSet.Attribute.Type == 'HGVS, coding, RefSeq':144 hgvs_coding = AttributeSet.Attribute.get_valueOf_()145 if not hgvs_genome and AttributeSet.Attribute.Type == 'HGVS, genomic, top level, previous':146 hgvs_genome = AttributeSet.Attribute.get_valueOf_()147 if chrom and chromStart and chromEnd:148 # if its SNP, make sure chrom, chromStart, chromEnd, ref, alt are all provided149 if variation_type == 'single nucleotide variant':150 if ref and alt:151 hgvs_id = "chr%s:g.%s%s>%s" % (chrom, chromStart, ref, alt)152 else:153 print('hgvs not found chr {}, chromStart {}, chromEnd {}, ref {}, alt {}, allele id {}'.154 format(chrom, chromStart, chromEnd, ref, alt, allele_id))155 # items whose type belong to 'Indel, Insertion, \156 # Duplication' might not hava explicit alt information, \157 # so we will parse from hgvs_genome158 elif variation_type == 'Indel':159 # RCV000156073, NC_000010.10:g.112581638_112581639delinsG160 if hgvs_genome:161 indel_position = hgvs_genome.find('del')162 indel_alt = hgvs_genome[indel_position+3:]163 hgvs_id = "chr%s:g.%s_%sdel%s" % (chrom, chromStart, chromEnd, indel_alt)164 elif variation_type == 'Deletion':165 if chromStart == chromEnd:166 # RCV000048406, chr17:g.41243547del167 hgvs_id = "chr%s:g.%sdel" % (chrom, chromStart)168 else:169 hgvs_id = "chr%s:g.%s_%sdel" % (chrom, chromStart, chromEnd)170 elif variation_type == 'Insertion':171 if hgvs_genome:172 ins_position = hgvs_genome.find('ins')173 if 'ins' in hgvs_genome:174 ins_ref = hgvs_genome[ins_position+3:]175 if chromStart == chromEnd:176 hgvs_id = "chr%s:g.%sins%s" % (chrom, chromStart, ins_ref)177 else:178 hgvs_id = "chr%s:g.%s_%sins%s" % (chrom, chromStart, chromEnd, ins_ref)179 elif variation_type == 'Duplication':180 if hgvs_genome:181 dup_position = hgvs_genome.find('dup')182 if 'dup' in hgvs_genome:183 dup_ref = hgvs_genome[dup_position+3:]184 if chromStart == chromEnd:185 hgvs_id = "chr%s:g.%sdup%s" % (chrom, chromStart, dup_ref)186 else:187 hgvs_id = "chr%s:g.%s_%sdup%s" % (chrom, chromStart, chromEnd, dup_ref)188 elif variation_type == 'copy number loss' or variation_type == 'copy number gain':189 if hgvs_genome and chrom:190 hgvs_id = "chr" + chrom + ":" + hgvs_genome.split('.')[2]191 elif hgvs_coding:192 hgvs_id = hgvs_coding193 coding_hgvs_only = True194 else:195 return196 else:197 return198 for key in HGVS:199 HGVS[key].sort()200 rsid = None201 cosmic = None202 dbvar = None203 uniprot = None204 omim = None205 # loop through XRef to find rsid as well as other ids206 if measure_obj.XRef:207 for XRef in measure_obj.XRef:208 if XRef.Type == 'rs':209 rsid = 'rs' + str(XRef.ID)210 elif XRef.DB == 'COSMIC':211 cosmic = XRef.ID212 elif XRef.DB == 'OMIM':213 omim = XRef.ID214 elif XRef.DB == 'UniProtKB/Swiss-Prot':215 uniprot = XRef.ID216 elif XRef.DB == 'dbVar':217 dbvar = XRef.ID218 # make sure the hgvs_id is not none219 if hgvs_id:220 one_snp_json = {221 "_id": hgvs_id,222 "clinvar": {223 "allele_id": allele_id,224 "chrom": chrom,225 "omim": omim,226 "cosmic": cosmic,227 "uniprot": uniprot,228 "dbvar": dbvar,229 "hg19": {230 "start": chromStart_19,231 "end": chromEnd_19232 },233 "hg38": {234 "start": chromStart_38,235 "end": chromEnd_38236 },237 "type": variation_type,238 "gene": {239 "id": gene_id,240 "symbol": symbol241 },242 "rcv": {243 "preferred_name": name,244 },245 "rsid": rsid,246 "cytogenic": cytogenic,247 "hgvs": HGVS,248 "coding_hgvs_only": coding_hgvs_only,249 "ref": ref,250 "alt": alt251 }252 }253 return one_snp_json254def _map_public_set_to_json(public_set_obj, hg19: bool):255 """256 Convert a `clinvarlib.PublicSetType` object into a json document.257 Each `clinvarlib.PublicSetType` object is mapped to a `<ClinVarSet>` block in the XML.258 E.g., `public_set_obj.ReferenceClinVarAssertion.MeasureSet` is the parsed value from a block structure below:259 <ClinVarSet ...>260 <ReferenceClinVarAssertion ...>261 <MeasureSet ...>262 ...263 </MeasureSet>264 </ReferenceClinVarAssertion>265 </ClinVarSet>266 """267 try:268 clinical_significance = public_set_obj.ReferenceClinVarAssertion.ClinicalSignificance.Description269 except:270 clinical_significance = None271 rcv_accession = public_set_obj.ReferenceClinVarAssertion.ClinVarAccession.Acc272 try:273 review_status = public_set_obj.ReferenceClinVarAssertion.ClinicalSignificance.ReviewStatus274 except:275 review_status = None276 try:277 last_evaluated = public_set_obj.ReferenceClinVarAssertion.ClinicalSignificance.DateLastEvaluated278 except:279 last_evaluated = None280 281 number_submitters = len(public_set_obj.ClinVarAssertion)282 # some items in clinvar_xml doesn't have origin information283 try:284 origin = public_set_obj.ReferenceClinVarAssertion.ObservedIn[0].Sample.Origin285 except:286 origin = None287 conditions = []288 for _trait in public_set_obj.ReferenceClinVarAssertion.TraitSet.Trait:289 synonyms = []290 conditions_name = ''291 for name in _trait.Name:292 if name.ElementValue.Type == 'Alternate':293 synonyms.append(name.ElementValue.get_valueOf_())294 if name.ElementValue.Type == 'Preferred':295 conditions_name += name.ElementValue.get_valueOf_()296 identifiers = {}297 for item in _trait.XRef:298 if item.DB == 'Human Phenotype Ontology':299 key = 'Human_Phenotype_Ontology'300 else:301 key = item.DB302 identifiers[key.lower()] = item.ID303 for symbol in _trait.Symbol:304 if symbol.ElementValue.Type == 'Preferred':305 conditions_name += ' (' + symbol.ElementValue.get_valueOf_() + ')'306 age_of_onset = ''307 for _set in _trait.AttributeSet:308 if _set.Attribute.Type == 'age of onset':309 age_of_onset = _set.Attribute.get_valueOf_()310 conditions.append({"name": conditions_name, "synonyms": synonyms, "identifiers": identifiers,311 "age_of_onset": age_of_onset})312 try:313 genotypeset = public_set_obj.ReferenceClinVarAssertion.GenotypeSet314 except:315 genotypeset = None316 if genotypeset:317 obj_list = []318 id_list = []319 for _set in public_set_obj.ReferenceClinVarAssertion.GenotypeSet.MeasureSet:320 variant_id = _set.ID321 for _measure in _set.Measure:322 json_obj = _map_measure_to_json(_measure, hg19=hg19)323 if json_obj:...
wxCSV.py
Source:wxCSV.py
...23def processForecast(inXML, N):24 rootObj = ForeSupermod.parseString(inXML, True)25 print "----------------------------------------------"26 print "Forecast Length (hrs): " + str(len(rootObj.data[0].parameters[0].temperature[0].value))27 print "Date: " + rootObj.head.product.creation_date.get_valueOf_()28 pyObsTime = datetime.datetime.strptime(rootObj.head.product.creation_date.get_valueOf_()[:-6], 29 "%Y-%m-%dT%H:%M:%S")30 print "Location: " + rootObj.data[0].location[0].city.get_valueOf_()31 print "Multiple Prediction Test"32 for ii in range(0,len(rootObj.data[0].parameters[0].temperature[0].value)):33 forecast = Forecast()34 forecast.forecasttime = pyObsTime35 forecast.location = rootObj.data[0].location[0].city.get_valueOf_()36 print "Time: " + rootObj.data[0].time_layout[0].start_valid_time[ii].get_valueOf_(),37 starttime = datetime.datetime.strptime(rootObj.data[0].time_layout[0].start_valid_time[ii].get_valueOf_()[:-6], 38 "%Y-%m-%dT%H:%M:%S")39 forecast.starttime = starttime40 print "to " + str(rootObj.data[0].time_layout[0].end_valid_time[ii])41 endtime = datetime.datetime.strptime(str(rootObj.data[0].time_layout[0].end_valid_time[ii])[:-6], 42 "%Y-%m-%d %H:%M:%S")43 forecast.stoptime = endtime44 for t in rootObj.data[0].parameters[0].temperature:45 print "Temp type " + t.get_type(),46 if(t.value[ii].get_valueOf_() == ''):47 v = None48 else:49 v = t.value[ii].get_valueOf_()50 if(t.get_type() == 'dew point'):51 forecast.dewpoint = v52 if(t.get_type() == 'wind chill'):53 forecast.windchill = v54 if(t.get_type() == 'hourly'):55 forecast.temperature = v56 print v57 print "precipitation probability: " + rootObj.data[0].parameters[0].probability_of_precipitation[0].value[ii].get_valueOf_()58 if(rootObj.data[0].parameters[0].probability_of_precipitation[0].value[ii].get_valueOf_() == ''):59 forecast.precipprob = None60 else:61 forecast.precipprob = rootObj.data[0].parameters[0].probability_of_precipitation[0].value[ii].get_valueOf_()62 for w in rootObj.data[0].parameters[0].wind_speed:63 print "wind " + w.get_type() + ': ' + w.value[ii].get_valueOf_()64 if(w.get_type() == 'sustained'):65 forecast.windspeed = w.value[ii].get_valueOf_()66 if(w.value[ii].get_valueOf_() == ''):67 forecast.windspeed = None68 print "no wind speed value"69 else:70 forecast.windspeed = w.value[ii].get_valueOf_()71 if(w.get_type() == 'gust'):72 if(w.value[ii].get_valueOf_() == ''):73 forecast.windgust = None74 print "no wind gust value"75 else:76 forecast.windgust = w.value[ii].get_valueOf_()77 for d in rootObj.data[0].parameters[0].direction:78 print "direction of " + d.get_type() + ": " + d.value[ii].get_valueOf_()79 if(d.get_type() == 'wind'):80 if(d.value[ii].get_valueOf_() == ''):81 forecast.winddir = None82 print "no wind dir value"83 else:84 forecast.winddir = d.value[ii].get_valueOf_()85 forecast.save()86def processCurrent(inXML):87 rootObj = CurSupermod.parseString(inXML, True)88 curObs = Currentobs() # current observation sql object89 print "Current Observation"90 print "Station ID: " + rootObj.station_id91 curObs.station = rootObj.station_id92 print "Observation Time: " + rootObj.observation_time_rfc82293 #pyObsTime = datetime.datetime.strptime(rootObj.observation_time_rfc822, "Last Updated on %b %d %Y, %I:%M %p %Z")94 pyObsTime = datetime.datetime.strptime(rootObj.observation_time_rfc822[:-6], "%a, %d %b %Y %H:%M:%S")95 curObs.obstime = pyObsTime96 print "Current Temp: " + str(rootObj.temp_f) + " F"97 curObs.temperature = rootObj.temp_f98 print "Rel Humidity: " + str(rootObj.relative_humidity) + "%"...
script.py
Source:script.py
...18 for event in instance.AuditTrailEntry:19 e = xes.Event()20 activity = event.get_WorkflowModelElement()21 e.add_attribute(xes.Attribute(type="string", key="concept:name", value=activity))22 event_type = event.get_EventType().get_valueOf_()23 e.add_attribute(xes.Attribute(type="string", key="lifecycle:transition", value=event_type))24 timestamp = event.Timestamp.get_valueOf_()25 e.add_attribute(xes.Attribute(type="date", key="time:timestamp", value=timestamp))26 attributes = {}27 for attribute in event.Data.Attribute:28 attributes[attribute.get_name()]=attribute.get_valueOf_()29 for key,value in attributes.items():30 e.add_attribute(xes.Attribute(type="string", key=key, value=value))31 trace.add_event(e)32 output.add_trace(trace)33base_filename = ".".join(os.path.basename(filename).split('.')[0:-1])34#output_filename = filename.replace(".mxml",".xes")35output_filename = base_filename+".xes"36with open(output_filename, "w") as f:...
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