ContentService not loading Molecule objects from graph db

PlantReactome / testing-issues

Tracker for issues discovered during pre-release testing.

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ContentService not loading Molecule objects from graph db #1

Closed preecej closed 5 years ago

preecej commented 6 years ago

Throws err when Molecules tab is selected, or at any time when Molecule data is needed:

The received object containing the Molecules for Circadian rhythm is empty or faulty and could not be parsed. ERROR: [Model Factory] -> Was impossible to instantiate {"identifier":"Q10MG9", "schemaClass":null, "displayName":"UniProt:Q10MG9 PHYB", "geneName":["PHYB","PHYB1","Os03g0309200","LOC_Os03g19590"], "dbId":8933798, "url":"http://www.uniprot.org/entry/Q10MG9"}

preecej commented 6 years ago

temp fix: property mapping update in graph.db (already done; works)
medium-term fix: update to the latest versions of the graph-importer & graph-core projects

preecej commented 6 years ago

attribute schemaClass has been replaced by simpleLabel.

temp fix: run this query on any freshly-imported graph.db, for backward compat:

MATCH (c:DatabaseObject) WHERE c.schemaClass IS NULL SET c.schemaClass = c.simpleLabel REMOVE c.simpleLabel

permanent fix: update graph-importer, graph-core, also perhaps reactome-base