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Hot fix - reinstate the old cob-base #279

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merged 2 commits into from
Aug 22, 2024
Merged

Hot fix - reinstate the old cob-base #279

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6b47792
Hot fix - reinstate the old cob-base
matentzn Aug 21, 2024
9963fad
Make RO module custom
matentzn Aug 21, 2024
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2 changes: 1 addition & 1 deletion docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -16,7 +16,7 @@ These are the current imports in COB

| Import | URL | Type |
| ------ | --- | ---- |
| ro | http://purl.obolibrary.org/obo/ro.owl | slme |
| ro | http://purl.obolibrary.org/obo/ro.owl | custom |
| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |

## Components
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10 changes: 3 additions & 7 deletions src/ontology/Makefile
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Expand Up @@ -19,7 +19,7 @@
# 6. [Run everything (COB products and release pipeline)](all)

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= ee0faa650404ebb7b2d591feab04561dbd60f347a990a5e1c925bb6cb0ef0904
CONFIG_HASH= 5daef41d99e802417bd9ad0f378f72168e2d30f0488f5b2423330cbc561ec834


# ----------------------------------------
Expand Down Expand Up @@ -377,12 +377,8 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt

## Module for ontology: ro

$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/ro_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in cob.Makefile!" && false
## Module for ontology: omo

$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt
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2 changes: 1 addition & 1 deletion src/ontology/cob-odk.yaml
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Expand Up @@ -23,7 +23,7 @@ import_group:
- IAO:0000111
products:
- id: ro
module_type: slme
module_type: custom
slme_individuals: exclude
- id: omo
module_type: mirror
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15 changes: 15 additions & 0 deletions src/ontology/cob.Makefile
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Expand Up @@ -61,6 +61,13 @@ cob-native.owl: $(SRC)
#cob-base.owl: cob.owl $(COB_TO_EXTERNAL)
# $(ROBOT) merge $(patsubst %, -i %, $^) -o $@

$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
$(SHARED_ROBOT_COMMANDS) \
annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output [email protected] && mv [email protected] $@

cob-base-reasoned.owl: cob-base.owl
$(ROBOT) remove --input $< --select imports --trim false \
reason -r HERMIT \
Expand Down Expand Up @@ -103,6 +110,14 @@ $(COB_ANNOTATIONS): $(TMPDIR)/cob-annotations.ttl
--annotation owl:versionInfo $(TODAY) \
--output $@

# This is the custom import: removing all COB related axioms from RO, but otherwise pulling in logical dependencies.

$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/ro_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \
remove --base-iri http://purl.obolibrary.org/obo/COB_ --axioms internal --preserve-structure false --trim false \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

########################################
# -- TESTING --
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