Crashes when clicking edge

cbizon commented 3 years ago
Using the notebook plugin, I get a message and view it.
Click on Answers Table
Use the arrow to open an answer so that the screen looks like:
Clicking the edge crashes the viewer (it vanishes)
cbizon commented 3 years ago
Seems to happen no matter what the answer is, but if needed I can provide this exact example.
maximusunc commented 3 years ago
@cbizon Could you provide this exact example please? All of the messages that I have open the edge explorer modal fine.
cbizon commented 3 years ago
{'message': {'query_graph': {'nodes': {'a': {'id': None,
     'category': 'biolink:ChemicalSubstance',
     'is_set': False},
    'b': {'id': 'NCBIGene:2710', 'category': 'biolink:Gene', 'is_set': False}},
   'edges': {'ab': {'subject': 'a',
     'object': 'b',
     'predicate': None,
     'relation': None}}},
  'knowledge_graph': {'nodes': {'CHEBI:15422': {'category': ['biolink:NamedThing',
      'biolink:MolecularEntity',
      'biolink:Entity',
      'biolink:ChemicalSubstance',
      'biolink:BiologicalEntity'],
     'name': 'ATP',
     'attributes': [{'type': 'NA',
       'value': ["adenosine 5'-(tetrahydrogen triphosphate)",
        'ATP',
        "Adenosine 5'-triphosphate",
        'Adenosine triphosphate',
        "ADENOSINE-5'-TRIPHOSPHATE",
        'H4atp'],
       'name': 'synonyms',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'ATP',
       'name': 'name',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': ['gtpo:1713',
        'DRUGBANK:DB00171',
        'CHEMBL.COMPOUND:CHEMBL14249',
        'MESH:D000255',
        'CHEBI:15422',
        'INCHIKEY:OOCDCJVAHKFZHI-CQSZACIVSA-N',
        'HMDB:HMDB0000538',
        'KEGG:C00002',
        'PUBCHEM.COMPOUND:5957',
        'UNII:8L70Q75FXE'],
       'name': 'equivalent_identifiers',
       'url': None,
       'source': None}]},
    'CHEBI:17754': {'category': ['biolink:NamedThing',
      'biolink:MolecularEntity',
      'biolink:Entity',
      'biolink:ChemicalSubstance',
      'biolink:BiologicalEntity'],
     'name': 'glycerol',
     'attributes': [{'type': 'NA',
       'value': ['glycerol',
        'Glycerol',
        'GLYCEROL',
        'propane-1,2,3-triol',
        '1,2,3-Propanetriol',
        '1,2,3-Trihydroxypropane',
        'Glycerin',
        'glycerine',
        'Glyceritol',
        'glycerolum',
        'glycyl alcohol',
        'Glyzerin',
        'Gro',
        'Oelsuess',
        'Propanetriol',
        'Trihydroxypropane'],
       'name': 'synonyms',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'glycerol',
       'name': 'name',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': ['DRUGBANK:DB09462',
        'MESH:D003451',
        'KEGG:C00116',
        'gtpo:5195',
        'MESH:D005990',
        'HMDB:HMDB0000131',
        'CHEBI:17754',
        'INCHIKEY:FCMSAPXDFYCBGJ-PWJLMRLQSA-N',
        'PUBCHEM.COMPOUND:753',
        'UNII:PDC6A3C0OX',
        'MESH:C043941',
        'CHEMBL.COMPOUND:CHEMBL692'],
       'name': 'equivalent_identifiers',
       'url': None,
       'source': None}]},
    'CHEBI:16761': {'category': ['biolink:NamedThing',
      'biolink:MolecularEntity',
      'biolink:Entity',
      'biolink:ChemicalSubstance',
      'biolink:BiologicalEntity'],
     'name': 'ADP',
     'attributes': [{'type': 'NA',
       'value': ["adenosine 5'-(trihydrogen diphosphate)",
        'ADP',
        "5'-adenylphosphoric acid",
        "Adenosine 5'-diphosphate",
        "ADENOSINE-5'-DIPHOSPHATE",
        'H3adp'],
       'name': 'synonyms',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'ADP',
       'name': 'name',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': ['KEGG:C00008',
        'CHEMBL.COMPOUND:CHEMBL14830',
        'MESH:D000244',
        'HMDB:HMDB0001341',
        'PUBCHEM.COMPOUND:6022',
        'gtpo:1712',
        'CHEBI:16761',
        'INCHIKEY:HMHDTAYXNLPCEI-UHFFFAOYSA-N',
        'MESH:C020332',
        'UNII:61D2G4IYVH'],
       'name': 'equivalent_identifiers',
       'url': None,
       'source': None}]},
    'CHEBI:15978': {'category': ['biolink:NamedThing',
      'biolink:MolecularEntity',
      'biolink:Entity',
      'biolink:ChemicalSubstance',
      'biolink:BiologicalEntity'],
     'name': 'sn-glycerol 3-phosphate',
     'attributes': [{'type': 'NA',
       'value': ['(2R)-2,3-dihydroxypropyl dihydrogen phosphate',
        'sn-glycerol 3-(dihydrogen phosphate)',
        'sn-Glycerol 3-phosphate',
        '(R)-glycerol 1-phosphate',
        'D-(glycerol 1-phosphate)',
        'D-Glycerol 1-phosphate',
        'Glycerol-3-phosphate',
        'Glycerophosphoric acid',
        'L-(glycerol 3-phosphate)',
        'phosphoric acid mono-((R)-2,3-dihydroxy-propyl) ester',
        'Phosphorsaeure-mono-((R)-2,3-dihydroxy-propylester)',
        'SN-GLYCEROL-3-PHOSPHATE',
        'sn-Gro-1-P'],
       'name': 'synonyms',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'sn-glycerol 3-phosphate',
       'name': 'name',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': ['CHEMBL.COMPOUND:CHEMBL1232920',
        'INCHIKEY:YINNFAZGMMIJFN-UHFFFAOYSA-N',
        'UNII:370V52HE4B',
        'HMDB:HMDB0000126',
        'PUBCHEM.COMPOUND:439162',
        'KEGG:C00093',
        'CHEBI:15978',
        'DRUGBANK:DB02515'],
       'name': 'equivalent_identifiers',
       'url': None,
       'source': None}]},
    'NCBIGene:2710': {'category': ['biolink:NamedThing',
      'biolink:MolecularEntity',
      'biolink:BiologicalEntity',
      'biolink:GenomicEntity',
      'biolink:GeneOrGeneProduct',
      'biolink:Gene',
      'biolink:MacromolecularMachine'],
     'name': 'GK',
     'attributes': [{'type': 'NA',
       'value': [],
       'name': 'synonyms',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'GK',
       'name': 'name',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': ['NCBIGene:2710',
        'HGNC:4289',
        'UniProtKB:P32189',
        'NCBIGene:2710',
        'ENSEMBL:ENSG00000198814'],
       'name': 'equivalent_identifiers',
       'url': None,
       'source': None}]}},
   'edges': {'774fe02786513ea94ec35a344755c528': {'subject': 'NCBIGene:2710',
     'object': 'CHEBI:17754',
     'predicate': 'biolink:increases_degradation_of',
     'relation': None,
     'attributes': [{'type': 'NA',
       'value': 'increases degradation of',
       'name': 'relation_label',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 1604318245.068261,
       'name': 'ctime',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg.chemical_get_enzyme',
       'name': 'provided_by',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CHEBI:17754',
       'name': 'target_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'NCBIGene:2710',
       'name': 'source_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg',
       'name': 'source_database',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CTD:increases_degradation_of',
       'name': 'relation',
       'url': None,
       'source': None},
      {'type': 'EDAM:data_0971',
       'value': [],
       'name': 'publications',
       'url': None,
       'source': None}]},
    'd7d01150b89f887cc3a863a35c873bb5': {'subject': 'NCBIGene:2710',
     'object': 'CHEBI:15978',
     'predicate': 'biolink:increases_synthesis_of',
     'relation': None,
     'attributes': [{'type': 'NA',
       'value': 'increases synthesis of',
       'name': 'relation_label',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 1604317276.2124817,
       'name': 'ctime',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg.chemical_get_enzyme',
       'name': 'provided_by',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CHEBI:15978',
       'name': 'target_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'NCBIGene:2710',
       'name': 'source_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg',
       'name': 'source_database',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CTD:increases_synthesis_of',
       'name': 'relation',
       'url': None,
       'source': None},
      {'type': 'EDAM:data_0971',
       'value': [],
       'name': 'publications',
       'url': None,
       'source': None}]},
    '236eaaf7d5787a08b6972b58b11532bb': {'subject': 'NCBIGene:2710',
     'object': 'CHEBI:15422',
     'predicate': 'biolink:increases_degradation_of',
     'relation': None,
     'attributes': [{'type': 'NA',
       'value': 'increases degradation of',
       'name': 'relation_label',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 1604291125.6539216,
       'name': 'ctime',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg.chemical_get_enzyme',
       'name': 'provided_by',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CHEBI:15422',
       'name': 'target_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'NCBIGene:2710',
       'name': 'source_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg',
       'name': 'source_database',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CTD:increases_degradation_of',
       'name': 'relation',
       'url': None,
       'source': None},
      {'type': 'EDAM:data_0971',
       'value': [],
       'name': 'publications',
       'url': None,
       'source': None}]},
    '0b24bc573b87d26962ef3ca2735a0aab': {'subject': 'NCBIGene:2710',
     'object': 'CHEBI:16761',
     'predicate': 'biolink:increases_synthesis_of',
     'relation': None,
     'attributes': [{'type': 'NA',
       'value': 'increases synthesis of',
       'name': 'relation_label',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 1604300467.0079234,
       'name': 'ctime',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg.chemical_get_enzyme',
       'name': 'provided_by',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CHEBI:16761',
       'name': 'target_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'NCBIGene:2710',
       'name': 'source_id',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'kegg',
       'name': 'source_database',
       'url': None,
       'source': None},
      {'type': 'NA',
       'value': 'CTD:increases_synthesis_of',
       'name': 'relation',
       'url': None,
       'source': None},
      {'type': 'EDAM:data_0971',
       'value': [],
       'name': 'publications',
       'url': None,
       'source': None}]}}},
  'results': [{'node_bindings': {'a': [{'id': 'CHEBI:17754'}],
     'b': [{'id': 'NCBIGene:2710'}]},
    'edge_bindings': {'ab': [{'id': '774fe02786513ea94ec35a344755c528'}]}},
   {'node_bindings': {'a': [{'id': 'CHEBI:15978'}],
     'b': [{'id': 'NCBIGene:2710'}]},
    'edge_bindings': {'ab': [{'id': 'd7d01150b89f887cc3a863a35c873bb5'}]}},
   {'node_bindings': {'a': [{'id': 'CHEBI:16761'}],
     'b': [{'id': 'NCBIGene:2710'}]},
    'edge_bindings': {'ab': [{'id': '0b24bc573b87d26962ef3ca2735a0aab'}]}},
   {'node_bindings': {'a': [{'id': 'CHEBI:15422'}],
     'b': [{'id': 'NCBIGene:2710'}]},
    'edge_bindings': {'ab': [{'id': '236eaaf7d5787a08b6972b58b11532bb'}]}}]},
 'knowledge_graph': {'nodes': [], 'edges': []},
 'results': []}
maximusunc commented 3 years ago
Issue fixed in v.0.2.1. The issue was caused by the UI not handling null values in edge properties when displaying the edge explorer modal.
A few notes on the example message you posted:
There are extra top-level knowledge_graph and results in this message. The UI doesn't care about them, but it's unusual that they're in there.
'None' and 'False' properties aren't valid JSON. They should be 'null' and 'false' respectively. I'm assuming you fixed them locally or else the notebook would have thrown an error when trying to read the file.
ranking-agent / gamma-viewer

Crashes when clicking edge #14
