Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Uncouple bridge generation from mappings refresh. #3439

Merged
merged 1 commit into from
Nov 28, 2024
Merged

Uncouple bridge generation from mappings refresh. #3439

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 10 additions & 10 deletions src/ontology/uberon.Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1249,8 +1249,8 @@ EXTERNAL_SSSOM_PROVIDERS = fbbt cl biomappings
# All the sets coming from the above ontologies.
EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv)

# We only refresh external resources under IMP=true
ifeq ($(strip $(IMP)),true)
# We only refresh external resources under MIR=true
ifeq ($(strip $(MIR)),true)

# FBbt mapping set. We filter it to only keep UBERON-related mappings
# (CL-related mappings are already bundled with the CL set).
Expand Down Expand Up @@ -1296,7 +1296,7 @@ endif
ifeq ($(BRI),true)

# Those bridges are generated separately (see below).
CUSTOM_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
EXTERN_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
$(BRIDGEDIR)/uberon-bridge-to-dmba.owl

# 1. Prepare the ruleset file.
Expand All @@ -1312,7 +1312,7 @@ $(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/sssomt.m4 $(BRIDGEDIR)/bridges.rules.m4
$(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl \
$(MAPPINGDIR)/uberon.sssom.tsv $(MAPPINGDIR)/cl.sssom.tsv \
$(TMPDIR)/bridges.rules $(BRIDGEDIR)/bridges.dispatch \
$(CUSTOM_BRIDGES) | all_robot_plugins
$(EXTERN_BRIDGES) | all_robot_plugins
$(ROBOT) merge -i $(SRC) -i $(IMPORTDIR)/local-cl.owl \
sssom:inject --sssom $(MAPPINGDIR)/uberon.sssom.tsv \
--sssom $(MAPPINGDIR)/cl.sssom.tsv \
Expand Down Expand Up @@ -1342,8 +1342,8 @@ UBERON_BRIDGE_MBA = "https://raw.githubusercontent.com/brain-bican/mouse_brain_a
UBERON_BRIDGE_DMBA = "https://raw.githubusercontent.com/brain-bican/developing_mouse_brain_atlas_ontology/main/src/ontology/new-bridges/new-uberon-bridge-to-dmba.owl"

# Only refresh those bridges when we explicitly allow refreshing
# external resources (IMP=true).
ifeq ($(strip $(IMP)),true)
# external resources (MIR=true).
ifeq ($(strip $(MIR)),true)
$(BRIDGEDIR)/uberon-bridge-to-mba.owl: $(SRC)
$(ROBOT) annotate -I $(UBERON_BRIDGE_MBA) --ontology-iri $(ONTBASE)/$@ -o $@

Expand Down Expand Up @@ -1408,7 +1408,7 @@ DEPLOY_GH=true

.PHONY: uberon
uberon:
$(MAKE) prepare_release IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo
$(MAKE) prepare_release MIR=false IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo
$(MAKE) release-diff
if [ $(DEPLOY_GH) = true ]; then $(MAKE) deploy_release GHVERSION="v$(TODAY)"; fi

Expand Down Expand Up @@ -1489,15 +1489,15 @@ clean: clean_uberon

.PHONY: refresh-mappings
refresh-mappings:
$(MAKE) MIR=true IMP=true $(EXTERNAL_SSSOM_SETS)
$(MAKE) MIR=true $(EXTERNAL_SSSOM_SETS)

.PHONY: refresh-bridges
refresh-bridges:
$(MAKE) MIR=true IMP=true BRI=true tmp/bridges
$(MAKE) MIR=true BRI=true tmp/bridges

.PHONY: refresh-external-resources
refresh-external-resources:
$(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports tmp/bridges
$(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports $(EXTERNAL_SSSOM_SETS) $(EXTERN_BRIDGES)


# ----------------------------------------
Expand Down