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VirtualFlyBrain / vfb-pipeline-polishing

Final cypher steps after complete pipeline load
MIT License
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scRNAseq queries missing #1

Open Robbie1977 opened 1 year ago

Robbie1977 commented 1 year ago

For 'Single cell transcriptomics data for $NAME'

We need Class, Anatomy and hasScRNAseq labels. The latter is missing. This should be added in the dumps stage so this needs to be investigated further but would likely be caused by the removal of scRNAseq_DataSet labels at this stage.

So to fix in the short term this will be added to the polishing step after the fix for the scRNAseq_DataSet labels:

MATCH (primary)<-[:composed_primarily_of]-(c:Cluster)-[:has_source]->(ds:scRNAseq_DataSet) WHERE not primary:hasScRNAseq SET primary:hasScRNAseq

Once the scRNAseq_DataSet label revert is done in the ontology this could be removed.

Robbie1977 commented 1 year ago

'Genes expressed in $NAME' seems to be working as looks for just Individual and Cluster which are present and queries show in all my tests. @dosumis do you have the example you tested earlier that failed?

Robbie1977 commented 1 year ago

Ref Dataset schema for scRNAseq #124

Robbie1977 commented 1 year ago

Ref https://github.com/VirtualFlyBrain/VFB2/issues/345

Robbie1977 commented 1 year ago

Ref https://github.com/VirtualFlyBrain/VFB_json_schema/issues/112