Dataset schema for scRNAseq

[dosumis]

Neo label on scRNAseq datasets is now just DataSet (set here) - was scRNAseq DataSet.

This affects the current scRNAseq query here:

       MATCH=Template("MATCH ($pvar$labels)<-[:composed_primarily_of]-(c:Cluster:Individual)"
                       "-[:has_source]->(ds:scRNAseq_DataSet:Individual)"
                       "OPTIONAL MATCH (ds)-[:has_reference]->(p:pub)")

(https://github.com/VirtualFlyBrain/VFB_json_schema/blob/master/src/vfb_query_builder/query_roller.py#LL295C2-L297C76)

With it set to scRNAseq_DataSet - the generic dataset_license query is broken for scRNAseq datasets:

        MATCH=Template("OPTIONAL MATCH "
                       "($pvar$labels)-[:$prel]-(ds:DataSet)"
                       "-[:has_license|license]->(l:License)"),

(https://github.com/VirtualFlyBrain/VFB_json_schema/blob/master/src/vfb_query_builder/query_roller.py#L483)

There are various queries that use the :DataSet label that are designed for image data. These are fine where they match patterns specific to image data - no scRNAseq data will be returned. However, there are some cases that are more generic:

e.g.

    def all_datasets_wrapper(self):
        return Clause(MATCH=Template("MATCH (ds:DataSet)"),
                      WITH="ds",
                      vars=[],
                      node_vars=['ds'],
                      RETURN="%s as dataset" % (roll_min_node_info('ds')))

TBD:

Option1: all_datasets query returns scRNAseq datasets - this should just work if we use the all_datasets query - but will look a bit odd as the technique column will not show scRNAseq and template and image columns will be blank.

Option2: We add a new query for scRNAseq datasets. This needs some way to distinguish them.

[dosumis]

Decision: Option 1 for now.

• we just need to fix this https://github.com/VirtualFlyBrain/VFB_json_schema/blob/master/src/vfb_query_builder/query_roller.py#LL295C2-L297C76) turn this to datasets.

Make a new ticket to implement option 2 - this can potentially work using the scRNAseq flag set here https://github.com/VirtualFlyBrain/vfb-pipeline-dumps/blob/vfb_pipeline/sparql/construct_scRNAseq.sparql (although this may be broken in pdb-alpha currently - not clear why.

[dosumis]

@Robbie1977 @Clare72 - assume this can be closed. Please re-open if needed.