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Update foreign SSSOM sets from the ontology. #3415

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merged 3 commits into from
Nov 11, 2024
Merged

Update foreign SSSOM sets from the ontology. #3415

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954c073
Fix bogus xml:base attribute in XML catalog.
gouttegd Nov 10, 2024
b66528b
Check foreign mapping sets against the ontology.
gouttegd Nov 10, 2024
310955a
Use ODK 1.5.3 in GitHub Actions workflows.
gouttegd Nov 10, 2024
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8 changes: 4 additions & 4 deletions .github/workflows/diff.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ jobs:
needs: [branch_status]
if: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
container: obolibrary/odkfull:v1.5.3
steps:
- uses: khan/[email protected]
id: check
Expand Down Expand Up @@ -94,7 +94,7 @@ jobs:
needs: [branch_status]
if: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
container: obolibrary/odkfull:v1.5.3
steps:
- uses: khan/[email protected]
id: check
Expand Down Expand Up @@ -122,7 +122,7 @@ jobs:
needs: [branch_status]
if: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
container: obolibrary/odkfull:v1.5.3
steps:
- uses: khan/[email protected]
id: check
Expand All @@ -147,7 +147,7 @@ jobs:
diff_classification:
needs: [classify_branch, classify_main]
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
container: obolibrary/odkfull:v1.5.3
steps:
- uses: khan/[email protected]
id: check
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/qc.yml
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Expand Up @@ -23,7 +23,7 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5.2
container: obolibrary/odkfull:v1.5.3
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/catalog-v001.xml
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@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public">
<uri name="http://purl.obolibrary.org/obo/ceph.owl" uri="imports/local-ceph.owl"/>
<uri name="http://purl.obolibrary.org/obo/cl.owl" uri="imports/local-cl.owl"/>
<uri name="http://purl.obolibrary.org/obo/cteno.owl" uri="imports/local-cteno.owl"/>
Expand Down
6 changes: 4 additions & 2 deletions src/ontology/uberon.Makefile
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Expand Up @@ -1257,7 +1257,8 @@ ifeq ($(strip $(IMP)),true)
$(MAPPINGDIR)/fbbt.sssom.tsv: .FORCE
wget "http://purl.obolibrary.org/obo/fbbt/fbbt.sssom.tsv" -O - | \
sssom-cli --prefix-map-from-input \
--rule 'object==UBERON:* -> include()' \
--include 'object==UBERON:*' \
--update-from-ontology=$(SRC):object,label,existence \
--output $@

# CL mapping set. We simply fetch it as it is from CL. It already
Expand All @@ -1276,7 +1277,8 @@ $(MAPPINGDIR)/biomappings.sssom.tsv: $(TMPDIR)/biomappings.sssom.tsv \
sssom-cli --input $< --prefix 'UBERON=http://purl.obolibrary.org/obo/UBERON_' \
--rule '!(subject==UBERON:* || object==UBERON:*) -> stop()' \
--rule 'object==UBERON:* -> invert()' \
--include-all | \
--include-all \
--update-from-ontology=$(SRC):subject,label,existence | \
sssom-cli --mangle-iris obo --output $@

$(TMPDIR)/biomappings.sssom.tsv:
Expand Down
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