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Update hra_subset component pipeline #2975

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Update hra_subset component pipeline #2975

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ccdb536
update hra_subset component pipeline
anitacaron Jul 18, 2023
f364e29
Merge branch 'master' into update-pipeline-hra-subset
anitacaron Sep 27, 2023
46ead89
Merge branch 'master' into update-pipeline-hra-subset
anitacaron Mar 22, 2024
cb6f019
config hra components in odk yaml
anitacaron Mar 22, 2024
6210c0d
update components
anitacaron Mar 22, 2024
a2217b8
Merge branch 'master' into update-pipeline-hra-subset
anitacaron May 17, 2024
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4 changes: 2 additions & 2 deletions docs/odk-workflows/RepositoryFileStructure.md
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,6 @@ These are the components in UBERON
| disjoint_union_over.owl | None |
| mappings.owl | None |
| in-subset.owl | None |
| hra_subset.owl | None |
| hra_subset.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/UB_ASCTB_subset.owl |
| vasculature_class.owl | None |
| hra_depiction_3d_images.owl | None |
| hra_depiction_3d_images.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/hra_uberon_3d_images.owl |
35 changes: 34 additions & 1 deletion src/ontology/Makefile
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Expand Up @@ -10,7 +10,7 @@
# More information: https://github.com/INCATools/ontology-development-kit/

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= d9dd1f14c02c9157faa08c0c33d811609f31616c2917255ed4dca5559cb438ec
CONFIG_HASH= 5b43938035885714e882948608e09a43483b1e19dbe9e3bf1559f6869da6ea6a


# ----------------------------------------
Expand Down Expand Up @@ -475,7 +475,40 @@ $(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)



.PHONY: component-download-hra_subset.owl
component-download-hra_subset.owl: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/UB_ASCTB_subset.owl \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/[email protected]; fi

$(COMPONENTSDIR)/hra_subset.owl: component-download-hra_subset.owl
if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-hra_subset.owl.owl $(TMPDIR)/component-download-hra_subset.owl.tmp.owl ; then echo "Component identical."; \
else echo "Component is different, updating." &&\
cp $(TMPDIR)/component-download-hra_subset.owl.owl $(TMPDIR)/component-download-hra_subset.owl.tmp.owl &&\
$(ROBOT) annotate -i $(TMPDIR)/component-download-hra_subset.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi

.PRECIOUS: $(COMPONENTSDIR)/hra_subset.owl


$(COMPONENTSDIR)/vasculature_class.owl: $(TEMPLATEDIR)/vasculature_class.tsv
if [ $(COMP) = true ] ; then $(ROBOT) template --input imports/merged_import.owl \
$(patsubst %, --template %, $^) \
$(ANNOTATE_CONVERT_FILE); fi

.PRECIOUS: $(COMPONENTSDIR)/vasculature_class.owl


.PHONY: component-download-hra_depiction_3d_images.owl
component-download-hra_depiction_3d_images.owl: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/hra_uberon_3d_images.owl \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/[email protected]; fi

$(COMPONENTSDIR)/hra_depiction_3d_images.owl: component-download-hra_depiction_3d_images.owl
if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-hra_depiction_3d_images.owl.owl $(TMPDIR)/component-download-hra_depiction_3d_images.owl.tmp.owl ; then echo "Component identical."; \
else echo "Component is different, updating." &&\
cp $(TMPDIR)/component-download-hra_depiction_3d_images.owl.owl $(TMPDIR)/component-download-hra_depiction_3d_images.owl.tmp.owl &&\
$(ROBOT) annotate -i $(TMPDIR)/component-download-hra_depiction_3d_images.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi

.PRECIOUS: $(COMPONENTSDIR)/hra_depiction_3d_images.owl
# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
Expand Down
1,206 changes: 609 additions & 597 deletions src/ontology/components/hra_depiction_3d_images.owl
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