Skip to content

Commit

Permalink
Update rules to ensure use of correct ROBOT version
Browse files Browse the repository at this point in the history 
The desired version of ROBOT is set by the ROBOT_VRS variable.
Change the value for that variable in the Makefile to update the
desired version.

If another version is in use, it will be replaced automatically.

Current version: 1.9.4
  • Loading branch information
@allenbaron
allenbaron committed Oct 13, 2023
1 parent d0e4c95 commit 500f4ff
Showing 1 changed file with 65 additions and 48 deletions.
113 changes: 65 additions & 48 deletions Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,9 @@ DM = src/ontology/doid-merged
DNC = src/ontology/doid-non-classified
HD = src/ontology/HumanDO

# Set the ROBOT version to use
ROBOT_VRS = 1.9.4

# to make a release, use `make release`
# to update imports, use `make imports`
# to run QC tests on doid-edit.owl, use `make test`
Expand Down Expand Up @@ -52,15 +55,29 @@ build build/update build/reports build/reports/temp:
# ROBOT
# ----------------------------------------

# run `make refresh_robot` to ensure correct version of ROBOT
# ROBOT is automatically updated
ROBOT := java -jar build/robot.jar

.PHONY: check_robot
check_robot:
@if [[ -f build/robot.jar ]]; then \
VRS=$$($(ROBOT) --version) ; \
if [[ "$$VRS" != *"$(ROBOT_VRS)"* ]]; then \
echo "Updating ROBOT from version $$VRS to $(ROBOT_VRS)..." ; \
rm -rf build/robot.jar && $(MAKE) build/robot.jar ; \
fi ; \
else \
echo "Downloading ROBOT version $(ROBOT_VRS)..." ; \
$(MAKE) build/robot.jar ; \
fi

# run `make refresh_robot` if ROBOT is not working correctly
.PHONY: refresh_robot
refresh_robot:
rm -rf build/robot.jar && $(MAKE) build/robot.jar

build/robot.jar: | build
curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.9.4/robot.jar

ROBOT := java -jar build/robot.jar
@curl -L -o $@ https://github.com/ontodev/robot/releases/download/v$(ROBOT_VRS)/robot.jar

# ----------------------------------------
# FASTOBO
Expand Down Expand Up @@ -89,7 +106,7 @@ test: reason report verify-edit
report: build/reports/report.tsv

.PRECIOUS: build/reports/report.tsv
build/reports/report.tsv: $(EDIT) src/sparql/report/report_profile.txt | build/robot.jar build/reports
build/reports/report.tsv: $(EDIT) src/sparql/report/report_profile.txt | check_robot build/reports
@echo ""
@$(ROBOT) report \
--input $< \
Expand All @@ -102,7 +119,7 @@ build/reports/report.tsv: $(EDIT) src/sparql/report/report_profile.txt | build/r
# Simple reasoning test
reason: build/update/doid-edit-reasoned.owl

build/update/doid-edit-reasoned.owl: $(EDIT) | build/robot.jar build/update
build/update/doid-edit-reasoned.owl: $(EDIT) | check_robot build/update
@$(ROBOT) reason \
--input $< \
--create-new-ontology false \
Expand All @@ -114,7 +131,7 @@ build/update/doid-edit-reasoned.owl: $(EDIT) | build/robot.jar build/update
# Verify doid-edit.owl
EDIT_V_QUERIES := $(wildcard src/sparql/verify/edit-verify-*.rq)

verify-edit: $(EDIT) | build/robot.jar
verify-edit: $(EDIT) | check_robot
@echo "Verifying $< (see build/reports on error)"
@$(ROBOT) verify \
--input $< \
Expand All @@ -125,7 +142,7 @@ verify-edit: $(EDIT) | build/robot.jar
QUARTER_V_QUERIES := $(wildcard src/sparql/verify/quarter-verify-*.rq)

quarterly_test: build/reports/quarterly_test.csv
build/reports/quarterly_test.csv: $(EDIT) | build/robot.jar build/reports/temp
build/reports/quarterly_test.csv: $(EDIT) | check_robot build/reports/temp
@echo "Verifying $<..."
@$(ROBOT) verify \
--input $< \
Expand Down Expand Up @@ -163,11 +180,11 @@ build/reports/quarterly_test.csv: $(EDIT) | build/robot.jar build/reports/temp
build/update/british_english_dictionary.csv: | build/update
curl -Lk -o $@ https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/src/ontology/hpo_british_english_dictionary.csv

build/update/synonyms.csv: $(EDIT) src/sparql/update/doid_synonyms.rq | build/robot.jar build/update
build/update/synonyms.csv: $(EDIT) src/sparql/update/doid_synonyms.rq | check_robot build/update
@echo "Retrieving DO synonyms..."
@$(ROBOT) query -i $< --query $(word 2,$^) $@

build/update/labels.csv: $(EDIT) src/sparql/update/doid_labels.rq | build/robot.jar build/update
build/update/labels.csv: $(EDIT) src/sparql/update/doid_labels.rq | check_robot build/update
@echo "Retrieving DO labels..."
@$(ROBOT) query -i $< --query $(word 2,$^) $@

Expand All @@ -177,10 +194,10 @@ build/be_synonyms.csv: src/util/compute_british_synonyms.py \
@echo "Building synonyms template..."
@python3 $^ $@

build/update/british_synonyms.owl: $(EDIT) build/update/be_synonyms.csv | build/robot.jar
build/update/british_synonyms.owl: $(EDIT) build/update/be_synonyms.csv | check_robot
@$(ROBOT) template --input $< --template $(word 2,$^) --output $@

add_british_synonyms: $(EDIT) build/update/british_synonyms.owl | build/robot.jar
add_british_synonyms: $(EDIT) build/update/british_synonyms.owl | check_robot
@$(ROBOT) merge \
--input $< \
--input $(word 2,$^) \
Expand All @@ -205,7 +222,7 @@ update_slims: $(SUB_ADD) $(SUB_AUTO)
# easier to keep one rule for all slim templates at the moment; may change
# this if multiple slims don't need reasoned file.
build/update/%-template.tsv: build/update/doid-edit-reasoned.owl \
src/sparql/update/subsets/%.rq | build/robot.jar build/update
src/sparql/update/subsets/%.rq | check_robot build/update
@echo "CHECKING $* subset for missing classes..."
@$(ROBOT) query \
--input $< \
Expand All @@ -214,7 +231,7 @@ build/update/%-template.tsv: build/update/doid-edit-reasoned.owl \
sed -E 's|<(.+)>|\1\tdoid:$*|' > build/update/$*-template.tsv
@rm build/update/$*-missing.tsv

$(SUB_ADD): update_%: $(EDIT) build/update/%-template.tsv | build/robot.jar
$(SUB_ADD): update_%: $(EDIT) build/update/%-template.tsv | check_robot
@if [ $$(awk 'END{print NR}' $(word 2,$^)) -gt "0" ]; then \
echo "UPDATING in $<..." ; \
$(ROBOT) template \
Expand All @@ -230,7 +247,7 @@ $(SUB_ADD): update_%: $(EDIT) build/update/%-template.tsv | build/robot.jar
else echo " -> Already up-to-date" ; \
fi

$(SUB_AUTO): update_%: $(EDIT) src/sparql/update/subsets/%.ru | build/robot.jar \
$(SUB_AUTO): update_%: $(EDIT) src/sparql/update/subsets/%.ru | check_robot \
src/sparql/update/doid-edit_prefixes.json build/update
@echo "UPDATING $* subset in $<..."
@NEW_DE=build/update/$*.ofn ; \
Expand Down Expand Up @@ -274,7 +291,7 @@ fix_cmds:
fix_data: $(FIX)

$(FIX): fix_%: $(EDIT) src/sparql/update/fix_%.ru | \
build/robot.jar src/sparql/update/doid-edit_prefixes.json
check_robot src/sparql/update/doid-edit_prefixes.json
@$(ROBOT) \
--add-prefixes $(word 2,$|) \
query \
Expand All @@ -299,15 +316,15 @@ IMPS := chebi cl eco foodon geno hp ncbitaxon ro so symp trans uberon
# define imports updated manually, solely for versioning
MANUAL_IMPS := disdriv omim_susc

imports: | build/robot.jar
imports: | check_robot
@echo "Checking import modules..."
@cd src/ontology/imports && $(MAKE) imports

refresh_imports: | build/robot.jar
refresh_imports: | check_robot
@echo "Refreshing import modules (this may take some time)..."
@cd src/ontology/imports && $(MAKE) refresh_imports

$(IMPS): | build/robot.jar
$(IMPS): | check_robot
@echo "Generating $@ import module..."
@cd src/ontology/imports && $(MAKE) $@

Expand Down Expand Up @@ -364,7 +381,7 @@ endef
.PHONY: primary
primary: $(DO).owl $(DO).obo $(DO).json

$(DO).owl: $(EDIT) build/reports/report.tsv | build/robot.jar
$(DO).owl: $(EDIT) build/reports/report.tsv | check_robot
@$(ROBOT) reason \
--input $< \
--create-new-ontology false \
Expand All @@ -377,11 +394,11 @@ $(DO).owl: $(EDIT) build/reports/report.tsv | build/robot.jar
--output $@
@echo "Created $@"

$(DO).obo: $(DO).owl | build/robot.jar
$(DO).obo: $(DO).owl | check_robot
$(call build_obo,$@,$<,"$(RELEASE_PREFIX)$(notdir $@)","")
@echo "Created $@"

$(DO).json: $(DO).owl | build/robot.jar
$(DO).json: $(DO).owl | check_robot
@$(ROBOT) convert --input $< --output $@
@echo "Created $@"

Expand All @@ -392,7 +409,7 @@ $(DO).json: $(DO).owl | build/robot.jar
.PHONY: base
base: $(DB).owl $(DB).obo $(DB).json

$(DB).owl: $(EDIT) | build/robot.jar
$(DB).owl: $(EDIT) | check_robot
@$(ROBOT) remove \
--input $< \
--select imports \
Expand All @@ -404,11 +421,11 @@ $(DB).owl: $(EDIT) | build/robot.jar
--output $@
@echo "Created $@"

$(DB).obo: $(DB).owl | build/robot.jar
$(DB).obo: $(DB).owl | check_robot
$(call build_obo,$@,$<,"$(RELEASE_PREFIX)$(notdir $@)","$(OBO)doid/$(notdir $(basename $@))")
@echo "Created $@"

$(DB).json: $(DB).owl | build/robot.jar
$(DB).json: $(DB).owl | check_robot
@$(ROBOT) convert --input $< --output $@
@echo "Created $@"

Expand All @@ -419,7 +436,7 @@ $(DB).json: $(DB).owl | build/robot.jar
.PHONY: merged
merged: $(DM).owl $(DM).obo $(DM).json

$(DM).owl: $(DO).owl | build/robot.jar
$(DM).owl: $(DO).owl | check_robot
@$(ROBOT) merge \
--input $< \
--collapse-import-closure true \
Expand All @@ -429,11 +446,11 @@ $(DM).owl: $(DO).owl | build/robot.jar
--output $@
@echo "Created $@"

$(DM).obo: $(DM).owl | build/robot.jar
$(DM).obo: $(DM).owl | check_robot
$(call build_obo,$@,$<,"$(RELEASE_PREFIX)$(notdir $@)","$(OBO)doid/$(notdir $(basename $@))")
@echo "Created $@"

$(DM).json: $(DM).owl | build/robot.jar
$(DM).json: $(DM).owl | check_robot
@$(ROBOT) convert --input $< --output $@
@echo "Created $@"

Expand All @@ -444,7 +461,7 @@ $(DM).json: $(DM).owl | build/robot.jar
.PHONY: human
human: $(DNC).owl $(DNC).obo $(DNC).json

$(DNC).owl: $(EDIT) | build/robot.jar
$(DNC).owl: $(EDIT) | check_robot
@$(ROBOT) remove \
--input $< \
--select imports \
Expand All @@ -460,12 +477,12 @@ $(DNC).owl: $(EDIT) | build/robot.jar
@cp $@ $(HD).owl
@echo "Created $@"

$(DNC).obo: $(DNC).owl | build/robot.jar
$(DNC).obo: $(DNC).owl | check_robot
$(call build_obo,$@,$<,"$(RELEASE_PREFIX)$(notdir $@)","$(OBO)doid/$(notdir $(basename $@))")
@cp $@ $(HD).obo
@echo "Created $@"

$(DNC).json: $(DNC).owl | build/robot.jar
$(DNC).json: $(DNC).owl | check_robot
@$(ROBOT) convert --input $< --output $@
@cp $@ $(HD).json
@echo "Created $@"
Expand All @@ -486,7 +503,7 @@ JSON_SUBS = $(foreach N,$(SUBS),$(addsuffix .json, $(N)))
.PHONY: subsets
subsets: $(OWL_SUBS) $(OBO_SUBS) $(JSON_SUBS)

$(OWL_SUBS): $(DNC).owl | build/robot.jar
$(OWL_SUBS): $(DNC).owl | check_robot
@$(ROBOT) filter \
--input $< \
--select "oboInOwl:inSubset=<$(OBO)doid#$(basename $(notdir $@))> annotations" \
Expand All @@ -496,11 +513,11 @@ $(OWL_SUBS): $(DNC).owl | build/robot.jar
--output $@
@echo "Created $@"

src/ontology/subsets/%.obo: src/ontology/subsets/%.owl | build/robot.jar
src/ontology/subsets/%.obo: src/ontology/subsets/%.owl | check_robot
$(call build_obo,$@,$<,"$(RELEASE_PREFIX)subsets/$(notdir $@)","$(OBO)doid/subsets/$(notdir $(basename $@))")
@echo "Created $@"

src/ontology/subsets/%.json: src/ontology/subsets/%.owl | build/robot.jar
src/ontology/subsets/%.json: src/ontology/subsets/%.owl | check_robot
@$(ROBOT) annotate \
--input $< \
--version-iri "$(RELEASE_PREFIX)subsets/$(notdir $@)" \
Expand All @@ -524,20 +541,20 @@ release_reports: $(REL_REPORTS) DOreports/DO-subClassOf-anonymous.tsv \
DOreports:
mkdir $@

DOreports/%.tsv: $(EDIT) src/sparql/DOreports/%.rq | DOreports build/robot.jar
DOreports/%.tsv: $(EDIT) src/sparql/DOreports/%.rq | DOreports check_robot
@$(ROBOT) query --input $< --query $(word 2,$^) $@
@sed '1 s/?//g' $@ > $@.tmp && mv $@.tmp $@
@echo "Created $@"

DOreports/DO-subClassOf-anonymous.tsv: $(EDIT) | DOreports build/robot.jar
DOreports/DO-subClassOf-anonymous.tsv: $(EDIT) | DOreports check_robot
@robot export \
--input $< \
--header "ID|LABEL|SubClass Of [ANON]" \
--export $@
@awk -F"\t" '$$3!=""' $@ > $@.tmp && mv $@.tmp $@
@echo "Created $@"

DOreports/DO-equivalentClass.tsv: $(EDIT) | DOreports build/robot.jar
DOreports/DO-equivalentClass.tsv: $(EDIT) | DOreports check_robot
@robot export \
--input $< \
--header "ID|LABEL|Equivalent Class" \
Expand All @@ -556,14 +573,14 @@ VERSION_IMPS = $(foreach I,$(IMPS) $(MANUAL_IMPS),$(addprefix version_, $(I)))
.PHONY: version_imports version_ext $(VERSION_IMPS)
version_imports: $(VERSION_IMPS) version_ext

version_ext: src/ontology/ext.owl | build/robot.jar
version_ext: src/ontology/ext.owl | check_robot
@$(ROBOT) annotate \
--input $< \
--version-iri "$(RELEASE_PREFIX)ext.owl" \
--output $<
@echo "Updated versionIRI of $<"

$(VERSION_IMPS): version_%: src/ontology/imports/%_import.owl | build/robot.jar
$(VERSION_IMPS): version_%: src/ontology/imports/%_import.owl | check_robot
@$(ROBOT) annotate \
--input $< \
--version-iri "$(RELEASE_PREFIX)imports/$(notdir $<)" \
Expand Down Expand Up @@ -609,7 +626,7 @@ $(OBO_V): validate-%: src/ontology/%.obo | $(FASTOBO)

# Verify doid.obo
V_QUERIES := $(wildcard src/sparql/verify/verify-*.rq)
verify-do: $(DO).obo | build/robot.jar build/reports/report.tsv
verify-do: $(DO).obo | check_robot build/reports/report.tsv
@echo "Verifying $< (see build/reports on error)"
@$(ROBOT) verify \
--input $< \
Expand All @@ -621,7 +638,7 @@ DNC_V_QUERIES := src/sparql/verify/dnc-verify-connectivity.rq
# We are not reduced to single inheritence in DNC
# Once this is cleaned up, we can change to all DNC verifications
#DNC_V_QUERIES := $(wildcard src/sparql/dnc-verify-*.rq)
verify-dnc: $(DNC).obo | build/robot.jar build/reports/report.tsv
verify-dnc: $(DNC).obo | check_robot build/reports/report.tsv
@echo "Verifying $< (see build/reports on error)"
@$(ROBOT) verify \
--input $< \
Expand All @@ -641,13 +658,13 @@ post: build/reports/report-diff.txt \

# Get the last build of DO from IRI
# .PHONY: build/doid-last.owl
build/doid-last.owl: | build/robot.jar
build/doid-last.owl: | check_robot
@$(ROBOT) merge \
--input-iri http://purl.obolibrary.org/obo/doid/doid-merged.owl \
--collapse-import-closure true \
--output $@

build/reports/doid-diff.html: build/doid-last.owl $(DM).owl | build/robot.jar build/reports
build/reports/doid-diff.html: build/doid-last.owl $(DM).owl | check_robot build/reports
@$(ROBOT) diff --left $< --right $(word 2, $^) --format html --output $@
@echo "Generated DOID diff report at $@"

Expand All @@ -657,7 +674,7 @@ QUERIES := $(wildcard src/sparql/build/*-report.rq)
# target names for previous release reports
LAST_REPORTS := $(foreach Q,$(QUERIES), build/reports/$(basename $(notdir $(Q)))-last.tsv)
last-reports: $(LAST_REPORTS)
build/reports/%-last.tsv: src/sparql/build/%.rq build/doid-last.owl | build/robot.jar build/reports
build/reports/%-last.tsv: src/sparql/build/%.rq build/doid-last.owl | check_robot build/reports
@echo "Counting: $(notdir $(basename $@))"
@$(ROBOT) query \
--input $(word 2,$^) \
Expand All @@ -666,7 +683,7 @@ build/reports/%-last.tsv: src/sparql/build/%.rq build/doid-last.owl | build/robo
# target names for current release reports
NEW_REPORTS := $(foreach Q,$(QUERIES), build/reports/$(basename $(notdir $(Q)))-new.tsv)
new-reports: $(NEW_REPORTS)
build/reports/%-new.tsv: src/sparql/build/%.rq $(DM).owl | build/robot.jar build/reports
build/reports/%-new.tsv: src/sparql/build/%.rq $(DM).owl | check_robot build/reports
@echo "Counting: $(notdir $(basename $@))"
@$(ROBOT) query \
--input $(word 2,$^) \
Expand All @@ -683,7 +700,7 @@ branch_reports = $(foreach O, doid-non-classified doid, build/reports/temp/branc

.INTERMEDIATE: $(branch_reports)
$(branch_reports): build/reports/temp/branch-count-%.tsv: src/ontology/%.owl \
src/sparql/build/branch-count.rq | build/robot.jar build/reports/temp
src/sparql/build/branch-count.rq | check_robot build/reports/temp
@echo "Counting all branches in $<..."
@$(ROBOT) query \
--input $< \
Expand All @@ -697,7 +714,7 @@ build/reports/branch-count.tsv: $(branch_reports)


# the following targets are used to build a smaller diff with only removed axioms to review
build/robot.diff: build/doid-last.owl $(DM).owl | build/robot.jar
build/robot.diff: build/doid-last.owl $(DM).owl | check_robot
@echo "Comparing axioms in previous release to current release"
@$(ROBOT) diff \
--left $< \
Expand All @@ -708,7 +725,7 @@ build/robot.diff: build/doid-last.owl $(DM).owl | build/robot.jar
build/reports/missing-axioms.txt: src/util/parse-diff.py build/robot.diff | build/reports
@python3 $^ $@

build/hp-do-terms.tsv: $(DM).owl src/sparql/build/hp-and-do-terms.rq | build/robot.jar
build/hp-do-terms.tsv: $(DM).owl src/sparql/build/hp-and-do-terms.rq | check_robot
@echo "Finding overlap between HP and DO terms..."
@$(ROBOT) query --input $< --query $(word 2,$^) $@

Expand Down

0 comments on commit 500f4ff

Please sign in to comment.