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Match what VFB's loaders and indexers expect of scRNAseq files - #100
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Checked against VFB production and VFBquery (the old FlyBase/SCEA files did the same): - Dataset licence: VFB's License node vfb:VFBlicense_CC_BY_4_0, not the licence URL (term info reads the logo and link from that node). - Dataset node labels scRNAseq_DataSet and hasScRNAseq (neo_label is now multivalued): the pipeline set them only on FBlc datasets, and VFBquery's scRNAseq queries and the hasScRNAseq labels on cell types and genes depend on them. - hide_in_terminfo typed xsd:boolean: the term-info indexer compares it with true, so a string would list every gene in a cluster's term info. - expression/FBgn_list.txt (scripts/write_fbgn_list.py, checked in CI) for VFB's scRNAseq gene ontology. - scripts/emit_expression_owl.py re-emits the expression OWL from the committed expression.tsv; all 17 re-emitted (only the boolean changed) and all metadata rebuilt (only licence and labels changed). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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This makes our OWL behave like the old FlyBase/SCEA files in VFB's pipeline, indexer and VFBquery. I checked against VFB production and the VFBquery / indexer / pipeline code.
Changes
vfb:VFBlicense_CC_BY_4_0instead of the CC URL. Term info reads the licence logo and link from that node; with the URL, the licence would be missing. An unknown config licence now fails the build.DataSet,scRNAseq_DataSetandhasScRNAseq(neo_labelis now multivalued). The pipeline (vfb-pipeline-polishing) sets the two scRNAseq labels only onFBlcdatasets. VFBquery's scRNAseq queries depend on them, and so do thehasScRNAseqlabels the pipeline then adds to cell types and genes.hide_in_terminfo: now typedxsd:boolean. The term-info indexer compares it withtrue, so a plain string would list every expressed gene in a cluster's term info.expression/FBgn_list.txt: every gene in the expression output (15,516). It's written byscripts/write_fbgn_list.py, and CI checks it's current. It's for VirtualFlyBrain/vfb-scRNAseq-gene-annotations, which builds VFB's Gene classes and their function labels.scripts/emit_expression_owl.py: re-emits the expression OWL from the committedexpression.tsv, with no matrices needed.Rebuilt outputs
Docs: DESIGN (What VFB's loaders and indexers expect, CI, release layout) and the expression README.
Checks: pytest (101),
validate_project_files.py,check_mapping_tsv.py,write_fbgn_list.py --check: all pass.Related PRs
expression/FBgn_list.txtfrom main. It opens after this one merges.File collection (which pipeline picks up these files under which names) is still to do.
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