Skip to content

Commit

Permalink
Add a few more mapping sets to upheno odk config
Browse files Browse the repository at this point in the history
  • Loading branch information
matentzn committed Aug 30, 2024
1 parent eae3bf1 commit c9c7e40
Show file tree
Hide file tree
Showing 2 changed files with 23 additions and 4 deletions.
19 changes: 15 additions & 4 deletions src/ontology/Makefile
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= 0d88b281f5388a191c13c6760ac8d250484320c0d43bac1cc8a5866a73cb5c90
CONFIG_HASH= 90f34a71057877c34dae996fe3fa4b7dd7f81dcbb4ea7c3a4206bed892c0c2ff


# ----------------------------------------
Expand Down Expand Up @@ -65,7 +65,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
MAPPINGDIR= ../mappings
MAPPING_TESTER= sssom validate
SSSOMPY= sssom
MAPPINGS= upheno-oba upheno-species-independent nbo-go
MAPPINGS= upheno-oba upheno-species-independent upheno-cross-species nbo-go uberon
MAPPING_RELEASE_FILES= $(foreach n,$(MAPPINGS), $(MAPPINGDIR)/$(n).sssom.tsv)


Expand Down Expand Up @@ -133,7 +133,7 @@ custom_robot_plugins:


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


# Install all ROBOT plugins to the runtime plugins directory
Expand All @@ -153,6 +153,9 @@ $(ROBOT_PLUGINS_DIRECTORY)/%.jar:

# Specific rules for supplementary plugins defined in configuration

$(ROBOT_PLUGINS_DIRECTORY)/sssom.jar:
curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.9.0/sssom-robot-plugin-0.9.0.jar


# ----------------------------------------
# Release assets
Expand Down Expand Up @@ -199,7 +202,7 @@ all_subsets: $(SUBSET_FILES)
# ----------------------------------------


MAPPINGS = upheno-oba upheno-species-independent nbo-go
MAPPINGS = upheno-oba upheno-species-independent upheno-cross-species nbo-go uberon

MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS))

Expand Down Expand Up @@ -879,10 +882,18 @@ $(MAPPINGDIR)/upheno-oba.sssom.tsv:
$(MAPPINGDIR)/upheno-species-independent.sssom.tsv:
test -f $@

# This mappingset is manually curated, so we only check that the file actually exists.
$(MAPPINGDIR)/upheno-cross-species.sssom.tsv:
test -f $@

# This mappingset is manually curated, so we only check that the file actually exists.
$(MAPPINGDIR)/nbo-go.sssom.tsv:
test -f $@

# This mappingset is manually curated, so we only check that the file actually exists.
$(MAPPINGDIR)/uberon.sssom.tsv:
test -f $@

validate_mappings:
$(MAKE_FAST) $(foreach n,$(MAPPINGS), validate-sssom-$(n))

Expand Down
8 changes: 8 additions & 0 deletions src/ontology/upheno-odk.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -267,14 +267,22 @@ sssom_mappingset_group:
maintenance: manual
- id: upheno-species-independent
maintenance: manual
- id: upheno-cross-species
maintenance: manual
- id: nbo-go
maintenance: manual
- id: uberon
maintenance: manual
primary_release: full
use_mappings: TRUE
export_formats:
- owl
- obo
- json
robot_plugins:
plugins:
- name: sssom
mirror_from: https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.9.0/sssom-robot-plugin-0.9.0.jar
import_group:
use_base_merging: TRUE
base_merge_drop_equivalent_class_axioms: TRUE
Expand Down

0 comments on commit c9c7e40

Please # to comment.