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update sssom loading into solr for new filenames with headers
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kevinschaper committed Jul 4, 2024
1 parent 1988507 commit 09c22a6
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions scripts/load_solr.sh
Original file line number Diff line number Diff line change
Expand Up @@ -60,10 +60,12 @@ scripts/add_update_processor.sh
# todo: this should probably happen after associations, but putting it first for testing
echo "Loading SSSOM mappings"
grep -v "^#" data/monarch/mondo.sssom.tsv > headless.mondo.sssom.tsv
grep -v "^#" data/monarch/gene_mappings.sssom.tsv > headless.gene_mappings.sssom.tsv
grep -v "^#" data/monarch/mesh_chebi_biomappings.sssom.tsv > headless.mesh_chebi_biomappings.sssom.tsv
# todo: copy the mappings to output/mappings as part of an earlier step
poetry run lsolr bulkload -C sssom -s model.yaml headless.mondo.sssom.tsv
poetry run lsolr bulkload -C sssom -s model.yaml data/monarch/gene_mappings.tsv
poetry run lsolr bulkload -C sssom -s model.yaml data/monarch/chebi-mesh.biomappings.sssom.tsv
poetry run lsolr bulkload -C sssom -s model.yaml headless.gene_mappings.sssom.tsv
poetry run lsolr bulkload -C sssom -s model.yaml headless.mesh_chebi_biomappings.sssom.tsv

echo "Loading entities"
poetry run lsolr bulkload -C entity -s model.yaml output/monarch-kg-denormalized-nodes.tsv
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