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loader crashe with "Cannot handle negative start index nor negative length" #4

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motey opened this issue Apr 6, 2021 · 0 comments
Open

loader crashe with "Cannot handle negative start index nor negative length" #4

motey opened this issue Apr 6, 2021 · 0 comments
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@KirstenLangendorf
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Type: Bug Something isn't working

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@motey
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motey commented Apr 6, 2021 

motherlode_1  | 2021-04-06 17:28:34,287 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.284940554Z Run query 
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,287 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.284961218Z '
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,288 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.284973266Z call apoc.load.json('https://clinicaltrials.gov/api/query/study_fields?expr=COVID+AND+AREA%5BStudyType%5DInterventional&fields=NCTId&fmt=json&max_rnk=1000') yield value
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,288 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.284984251Z with value.StudyFieldsResponse.NStudiesFound as NStudies, RANGE(0,(value.StudyFieldsResponse.NStudiesFound/1000)) as nloop
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,289 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.284994124Z UNWIND nloop as i
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,290 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285002594Z with range(1+1000*i,1000+1000*i,999) as RANGES
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,290 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285010985Z with RANGES, RANGES[1] as urange, RANGES[0] as lrange
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,290 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285019532Z call apoc.load.json('https://clinicaltrials.gov/api/query/study_fields?expr=COVID+AND+AREA%5BStudyType%5DInterventional&fields=NCTId,Gender,GenderBased,GenderDescription,MinimumAge,MaximumAge,HealthyVolunteers,StudyPopulation,SamplingMethod,EligibilityCriteria&min_rnk='+lrange+'&max_rnk='+urange+'&fmt=json') yield value
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,291 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285030036Z with value.StudyFieldsResponse.StudyFields as coll unwind coll as study_metadata
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,291 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285038689Z UNWIND study_metadata.NCTId as Id
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,291 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285046995Z match(ct:ClinicalTrial{NCTId:Id})
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,292 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285055775Z UNWIND study_metadata.EligibilityCriteria as EligibilityCriteria
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,292 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285064462Z with ct, EligibilityCriteria,
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,293 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285072760Z   CASE WHEN apoc.text.indexOf(toUpper(EligibilityCriteria),'INCLUSION CRITERIA')> -1 THEN split(replace(replace(trim(substring(EligibilityCriteria,19,size(split(EligibilityCriteria,"Exclusion")[0])-19)),'\n','#'),'##','#'),'#') ELSE ["none"] END AS Inclusion,
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,293 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285082624Z   CASE WHEN apoc.text.indexOf(toUpper(EligibilityCriteria),'EXCLUSION CRITERIA')> -1 THEN split(replace(replace(trim(substring(EligibilityCriteria,size(split(EligibilityCriteria,"Exclusion")[0])+19,size(EligibilityCriteria))),'\n','#'),'##','#'),'#')  ELSE ["none"] END AS Exclusion
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,293 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285092953Z with ct, Inclusion, Exclusion, RANGE(0,size(Inclusion)-1) as nincl
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,294 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285146161Z FOREACH(i in nincl |
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,294 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285156104Z MERGE(incl:InclusionCriteria{criteria:Inclusion[i]}) MERGE(ct)-[:HAS_INCLUSION_CRITERIA]->(incl))
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,294 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285164284Z with ct, Inclusion, Exclusion, RANGE(0,size(Exclusion)-1) as nexcl
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,295 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285171973Z FOREACH(i in nexcl |
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,295 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285179359Z MERGE(excl:ExclusionCriteria{criteria:Exclusion[i]}) MERGE(ct)-[:HAS_EXCLUSION_CRITERIA]->(excl))
motherlode_1  | 
motherlode_1  | 2021-04-06 17:28:34,295 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:28:34.285187252Z '
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,242 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239208226Z Traceback (most recent call last):
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,243 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239364902Z   File "./main.py", line 100, in <module>
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,243 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239407745Z     tx.run(q)
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,244 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239432332Z   File "/usr/local/lib/python3.6/site-packages/py2neo/database/work.py", line 125, in run
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,244 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239465677Z     hydrant=hydrant)
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,244 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239487940Z   File "/usr/local/lib/python3.6/site-packages/py2neo/client/__init__.py", line 956, in run_in_tx
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,245 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239514811Z     cx.sync(result)
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,245 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239532618Z   File "/usr/local/lib/python3.6/site-packages/py2neo/client/bolt.py", line 516, in sync
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,246 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239550064Z     self._audit(result)
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,246 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239565412Z   File "/usr/local/lib/python3.6/site-packages/py2neo/client/bolt.py", line 626, in _audit
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,246 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239583569Z     task.audit()
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,247 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239599787Z   File "/usr/local/lib/python3.6/site-packages/py2neo/client/bolt.py", line 883, in audit
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,247 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239618485Z     item.audit()
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,247 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239634140Z   File "/usr/local/lib/python3.6/site-packages/py2neo/client/bolt.py", line 1062, in audit
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,247 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239652211Z     raise self._failure
motherlode_1  | 
motherlode_1  | 2021-04-06 17:31:29,248 CLINICAL_TRIALS_GOV INFO: 2021-04-06T17:31:29.239669701Z py2neo.database.work.DatabaseError: [Statement.ExecutionFailed] Cannot handle negative start index nor negative length
motherlode_1  |
@motey motey added the Type: Bug Something isn't working label Apr 6, 2021
KirstenLangendorf added a commit that referenced this issue Apr 7, 2021
@KirstenLangendorf
Solving issue on In/Exclusion Criteria
d0fbf8e 
Solving Issue: 
#4
KirstenLangendorf added a commit that referenced this issue Apr 7, 2021
@KirstenLangendorf
Solving issue on In/Exclusion Criteria
506d203 
Solving Issue: 
#4
KirstenLangendorf added a commit that referenced this issue Apr 7, 2021
@KirstenLangendorf
Solving issue on In/Exclusion Criteria
773ba49 
Solving Issue: 
#4
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