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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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