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ElixirTeSS / bioschemas-validator

This is the validation suite targeting metadata conforming to Bioschemas profiles.
MIT License
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Web fails to validate JSON that validates on the CLI #6

Open sneumann opened 1 year ago

sneumann commented 1 year ago

Describe the bug I am trying to validate the file https://msbi.ipb-halle.de/~sneumann/molecule6338.json by entering the URL into Metadata URL of https://bioschemas-validator.herokuapp.com/ but the web application is giving me

File "/validator/web/report.py", line 10, in generate_report_summary
    ##### {fmt.header("Against profile:")}  {result['Profile Name']} {result['Profile Version']}

Same error when pasting the JSON into Raw metadata.

Expected behavior I would like to see the error report similar to what I get from the CLI (branch web: https://github.com/ElixirTeSS/bioschemas-validator/tree/web)

Additional context The dct:conformsTo markup in my JSON comes straight from the bioschemas example in the profile. 

python src/command.py validate  --target_data=/tmp/molecule6338.json && cat output.txt 
Action: validate
/tmp/molecule6338.json is a file
The target metadata is /tmp/molecule6338.json
['dct:conformsTo']
###########Start Validation#############
Validating against profile MolecularEntity 0.5-RELEASE.json
=======================Validator Message:=================================
The data is valid against this profile
============Properties Marginality Report:============
Marginality: Minimum
    The data has all the required property(ies).
    Implemented required property has no error.
Marginality: Recommended
    The data has all the recommended property(ies).
    Implemented recommended property has no error.
Marginality: Optional
    Optional property that are missing: ['disambiguatingDescription', 'isInvolvedInBiologicalProcess', 'sameAs', 'image', 'potentialUse', 'monoisotopicMolecularWeight', 'hasBioChemEntityPart', 'description', 'bioChemSimilarity', 'isPartOfBioChemEntity', 'associatedDisease', 'chemicalRole', 'taxonomicRange', 'hasRepresentation', 'alternateName', 'isLocatedInSubcellularLocation', 'isEncodedByBioChemEntity', 'bioChemInteraction', 'biologicalRole', 'hasMolecularFunction']
    Implemented optional property has no error.

These properties names are in the metadata but not in the Bioschemas profile:['subjectOf']
###########End Validation#############
sneumann commented 1 year ago

Hi, running the latest webapp from branch develop did not fix the issue. The issue is also present with the "official" example https://raw.githubusercontent.com/BioSchemas/specifications/master/MolecularEntity/examples/0.5-RELEASE/metabolights-MTBLC11449.json

It works with the MassBank page pointing the validator at https://msbi.ipb-halle.de/MassBank/RecordDisplay?id=MSBNK-MSSJ-MSJ00024&dsn=MSSJ which does not specify a profile in the first place. Again it does not work when cut&pasting the JSON of that MassBank record (see below) directly into Raw metadata.

Yours, Steffen 

{
"identifier": "MSBNK-MSSJ-MSJ00024",
"url": "https://massbank.eu/MassBank/RecordDisplay?id=MSBNK-MSSJ-MSJ00024",
"name": "Tetrahydroalstonine",
"alternateName": "Tetrahydroalstonine",
"inchikey": "GRTOGORTSDXSFK-DLLGKBFGSA-N",
"description": "This MassBank record with Accession MSBNK-MSSJ-MSJ00024 contains the MS2 mass spectrum of Tetrahydroalstonine.",
"molecularFormula": "C21H24N2O3",
"monoisotopicMolecularWeight": "352.17869",
"inChI": "InChI=1S/C21H24N2O3/c1-12-16-10-23-8-7-14-13-5-3-4-6-18(13)22-20(14)19(23)9-15(16)17(11-26-12)21(24)25-2/h3-6,11-12,15-16,19,22H,7-10H2,1-2H3/t12-,15-,16-,19-/m0/s1",
"smiles": "C[C@H]1[C@@H]2CN3CCC4=C([C@@H]3C[C@@H]2C(=CO1)C(=O)OC)NC5=CC=CC=C45",
"@context": "http://schema.org",
"@type": "MolecularEntity"
}