Workflow 5

[stevencox]

Verify workflow 5 works with biological_process_or_activity reverse associated with phenotypic_feature.

/beta2

[frostyfan109]

The new query is

SELECT population_of_individual_organisms->chemical_substance->gene->biological_process_or_activity<-phenotypic_feature FROM "/schema" WHERE icees.table = 'patient' AND icees.year = 2010 AND icees.cohort_features.AgeStudyStart = '0-2' AND icees.feature.EstResidentialDensity < 1 AND icees.maximum_p_value = 1 AND drug_exposure !=~ '^(SCTID.*|rxcui.*|CAS.*|SMILES.*|umlscui.*)$'

but for some reason the response that we receive from the tranql/query endpoint contains invalid json, which results in an error when we try to parse it.

Update: The culprit of the invalidity is the many NaN literals it contains. paste.txt is the entire response (400k lines)

[stevencox]

Ah. Thanks. I'll contact the ICEES folks about this. Perhaps, in the mean time, can we delete these in the response object before parsing? e.g., replace NaN in response.text then json.loads().

[frostyfan109]

For now, I'm adding JSON5 as a dependency, which supports an extended syntax. The query above now runs successfully. We can also use JSON5 with the find tool which is convenient.

[stevencox]

From Hao:

ok, it's fixed now it'll return null instead of NaN which is valid jsons