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Automatically generate text definitions from logical definitions #2349

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merged 8 commits into from
May 1, 2024
Merged

Automatically generate text definitions from logical definitions #2349

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1226b77
Automtically generate missing text definitions.
gouttegd Apr 22, 2024
a2a5fed
Commit re-generated Makefile.
gouttegd Apr 22, 2024
8726bab
Do not insert term IDs within auto-generated definitions.
gouttegd Apr 23, 2024
6d06fd4
Merge branch 'master' into automatic-text-definitions
AvolaAmg Apr 24, 2024
d82c252
Merge branch 'master' into automatic-text-definitions
gouttegd Apr 25, 2024
bfb5a59
Annotate generated definitions.
gouttegd Apr 25, 2024
0556548
Merge branch 'master' into automatic-text-definitions
gouttegd Apr 27, 2024
8d61be3
Merge branch 'master' into automatic-text-definitions
gouttegd Apr 30, 2024
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7 changes: 5 additions & 2 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
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= c05ee03cdbebf8765f9f8f3ed1deb9ecde656b5e92390f6f64bfce43560a3c56
CONFIG_HASH= 3ef44073feb4dd21f093356b564a51bd94638e4a757ed43c0c9ff69e9599cac2


# ----------------------------------------
Expand Down Expand Up @@ -132,7 +132,7 @@ custom_robot_plugins:


.PHONY: extra_robot_plugins
extra_robot_plugins:
extra_robot_plugins: $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar


# Install all ROBOT plugins to the runtime plugins directory
Expand All @@ -152,6 +152,9 @@ $(ROBOT_PLUGINS_DIRECTORY)/%.jar:

# Specific rules for supplementary plugins defined in configuration

$(ROBOT_PLUGINS_DIRECTORY)/flybase.jar:
curl -L -o $@ https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar


# ----------------------------------------
# Release assets
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4 changes: 4 additions & 0 deletions src/ontology/cl-odk.yaml
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Expand Up @@ -26,6 +26,10 @@ release_artefacts:
- custom-cl-plus
documentation:
documentation_system: mkdocs
robot_plugins:
plugins:
- name: flybase
mirror_from: https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar
subset_group:
products:
- id: BDS_subset
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8 changes: 8 additions & 0 deletions src/ontology/cl.Makefile
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Expand Up @@ -74,6 +74,14 @@ tmp/cl_signature.txt: tmp/$(ONT)-stripped.owl tmp/cl_terms.txt
# Note that right now, TypeDefs that are CL native (like has_age) are included in the release!


# Preprocessing: automatically generate text definitions from logical definitions
$(EDIT_PREPROCESSED): $(SRC) all_robot_plugins
$(ROBOT) flybase:rewrite-def -i $< --dot-definitions --null-definitions \
--no-ids --filter-prefix CL_ \
--add-annotation "oboInOwl:hasDbXref FBC:Autogenerated" \
-o $@


# ----------------------------------------
# SSSOM MAPPINGS
# ----------------------------------------
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