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project.Makefile
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project.Makefile
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## Add your own custom Makefile targets here
RUN=poetry run
JENA_DIR=~/apache-jena/bin/
SCHEMA_NAME = $(shell bash ./utils/get-value.sh name)
SOURCE_SCHEMA_PATH = $(shell bash ./utils/get-value.sh source_schema_path)
PLANTUML_JAR = local/plantuml-lgpl-1.2024.3.jar
.PHONY: examples-clean mixs-yaml-clean rdf-clean shuttle-clean
examples-clean:
rm -rf examples/output
mixs-yaml-clean:
rm -rf src/schema/mixs.yaml
rm -rf local/mixs_regen/mixs_subset_modified*yaml
rdf-clean:
rm -rf \
OmicsProcessing.rq \
local/mongo_as_nmdc_database.ttl \
local/mongo_as_nmdc_database_cuire_repaired.ttl \
local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl \
local/mongo_as_nmdc_database_rdf_safe.yaml \
local/mongo_as_nmdc_database_validation.log \
local/mongo_as_unvalidated_nmdc_database.yaml
shuttle-clean:
#rm -rf local/mixs_regen/mixs_subset_modified.yaml # triggers complete regeneration
rm -rf local/mixs_regen/*.yaml
rm -rf [email protected]
mkdir -p local/mixs_regen
touch local/mixs_regen/.gitkeep
src/schema/mixs.yaml: shuttle-clean local/mixs_regen/mixs_subset_modified_inj_env_medium_alt_description.yaml
mv $(word 2,$^) $@
rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak
local/mixs_regen/mixs_subset.yaml: assets/import_mixs_slots_regardless.tsv
$(RUN) do_shuttle \
--recipient_model assets/other_mixs_yaml_files/mixs_template.yaml \
--config_tsv $< \
--yaml_output $@
local/mixs_regen/mixs_subset_modified.yaml: local/mixs_regen/mixs_subset.yaml assets/yq-for-mixs_subset_modified.txt
# switching to TextValue may not add any value. the other range changes do improve the structure of the data.
# ironically changing back to strings for the submission-schema, data harmonizer, submission portal etc.
# may switch source of truth to the MIxS 6.2.2 release candidate
sed 's/quantity value/QuantityValue/' $(word 1, $^) > $@
sed -i.bak 's/range: string/range: TextValue/' $@
sed -i.bak 's/range: text value/range: TextValue/' $@
grep "^'" $(word 2, $^) | while IFS= read -r line ; do echo $$line ; eval yq -i $$line $@ ; done
rm -rf [email protected]
local/mixs_regen/mixs_subset_modified_inj_land_use.yaml: local/mixs_regen/mixs_subset_modified.yaml \
assets/other_mixs_yaml_files/cur_land_use_enum.yaml
# inject re-structured cur_land_use_enum
# using '| cat > ' because yq doesn't seem to like redirecting out to a file
yq eval-all \
'select(fileIndex==0).enums.cur_land_use_enum = select(fileIndex==1).enums.cur_land_use_enum | select(fileIndex==0)' \
$^ | cat > $@
local/mixs_regen/mixs_subset_modified_inj_TargetGeneEnum.yaml: local/mixs_regen/mixs_subset_modified_inj_land_use.yaml \
assets/other_mixs_yaml_files/TargetGeneEnum.yaml
yq eval-all \
'select(fileIndex==0).enums.TargetGeneEnum = select(fileIndex==1).enums.TargetGeneEnum | select(fileIndex==0)' \
$^ | cat > $@
yq -i '.slots.target_gene.range = "TargetGeneEnum"' $@
local/mixs_regen/mixs_subset_modified_inj_env_broad_scale_alt_description.yaml: local/mixs_regen/mixs_subset_modified_inj_TargetGeneEnum.yaml \
assets/other_mixs_yaml_files/nmdc_mixs_env_triad_tooltips.yaml
yq eval-all \
'select(fileIndex==0).slots.env_broad_scale.annotations.tooltip = select(fileIndex==1).slots.env_broad_scale.annotations.tooltip | select(fileIndex==0)' \
$^ | cat > $@
local/mixs_regen/mixs_subset_modified_inj_env_local_scale_alt_description.yaml: local/mixs_regen/mixs_subset_modified_inj_env_broad_scale_alt_description.yaml \
assets/other_mixs_yaml_files/nmdc_mixs_env_triad_tooltips.yaml
yq eval-all \
'select(fileIndex==0).slots.env_local_scale.annotations.tooltip = select(fileIndex==1).slots.env_local_scale.annotations.tooltip | select(fileIndex==0)' \
$^ | cat > $@
local/mixs_regen/mixs_subset_modified_inj_env_medium_alt_description.yaml: local/mixs_regen/mixs_subset_modified_inj_env_local_scale_alt_description.yaml \
assets/other_mixs_yaml_files/nmdc_mixs_env_triad_tooltips.yaml
yq eval-all \
'select(fileIndex==0).slots.env_medium.annotations.tooltip = select(fileIndex==1).slots.env_medium.annotations.tooltip | select(fileIndex==0)' \
$^ | cat > $@
examples/output: nmdc_schema/nmdc_materialized_patterns.yaml
mkdir -p $@
$(RUN) linkml-run-examples \
--schema $< \
--input-directory src/data/valid \
--counter-example-input-directory src/data/invalid \
--output-directory $@ > $@/README.md
local/usage_template.tsv: nmdc_schema/nmdc_materialized_patterns.yaml # replaces local/usage_template.tsv target
mkdir -p $(@D) # create parent directory
$(RUN) linkml2schemasheets-template \
--source-path $< \
--output-path $@ \
--debug-report-path [email protected] \
--log-file [email protected] \
--report-style exhaustive
examples/output/Biosample-exhaustive-pretty-sorted.yaml: src/data/valid/Database-interleaved.yaml
$(RUN) pretty-sort-yaml \
-i $< \
-o $@
# this setup is required if you want to retreive any content or statistics from PyMongo
# pure-export doesn't require a PyMongo connection when run in the --skip-collection-check mode
# 1. . ~/sshproxy.sh -u {YOUR_NERSC_USERNAME}
# 2. ssh -i ~/.ssh/nersc -L27777:mongo-loadbalancer.nmdc.production.svc.spin.nersc.org:27017 -o ServerAliveInterval=60 {YOUR_NERSC_USERNAME}@dtn01.nersc.gov
pure-export-and-validate: local/mongo_as_nmdc_database_validation.log
make-rdf: rdf-clean \
local/mongo_as_nmdc_database_validation.log \
local/mongo_as_nmdc_database_cuire_repaired.ttl \
local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl # could omit rdf-clean. then this could build incrementally on top of pure-export-and-validate
# statistics of large collections as of 2024-05-17
#ns size count avgObjSize storageSize totalIndexSize totalSize scaleFactor
#nmdc.functional_annotation_agg 2194573252 16167688 135 567922688 1772920832 2340843520 1
#nmdc.data_object_set 81218633 179620 452 24301568 29847552 54149120 1
#nmdc.biosample_set 10184792 8158 1248 2887680 1753088 4640768 1
# --selected-collections calibration_set
# --selected-collections configuration_set
#[ERROR] [local/mongo_as_nmdc_database_rdf_safe.yaml/0] 'mass' is not one of ['mass_charge_ratio', 'retention_time', 'retention_index'] in /calibration_set/2/calibration_target
# https://nmdc-group.slack.com/archives/CFVF3G3H7/p1729101060720919?thread_ts=1729100685.966959&cid=CFVF3G3H7
# Katherine Heal
# https://github.com/microbiomedata/issues/issues/750#issuecomment-2369147228 for Calibration records to be uploaded
# https://github.com/microbiomedata/issues/issues/748#issuecomment-2369150887 and https://github.com/microbiomedata/issues/issues/749#issuecomment-2369163551
# for Configuration records
local/mongo_as_unvalidated_nmdc_database.yaml:
date
time $(RUN) pure-export \
--max-docs-per-coll 200000 \
--output-yaml $@ \
--schema-source src/schema/nmdc.yaml \
--selected-collections biosample_set \
--selected-collections chemical_entity_set \
--selected-collections collecting_biosamples_from_site_set \
--selected-collections data_generation_set \
--selected-collections data_object_set \
--selected-collections field_research_site_set \
--selected-collections functional_annotation_set \
--selected-collections genome_feature_set \
--selected-collections instrument_set \
--selected-collections material_processing_set \
--selected-collections processed_sample_set \
--selected-collections protocol_execution_set \
--selected-collections storage_process_set \
--selected-collections study_set \
--selected-collections workflow_execution_set \
dump-from-api \
--client-base-url "https://api.microbiomedata.org" \
--endpoint-prefix nmdcschema \
--page-size 200000
## ALTERNATIVELY:
#local/mongo_as_unvalidated_nmdc_database.yaml:
# date
# time $(RUN) pure-export \
# --max-docs-per-coll 200000 \
# --output-yaml $@ \
# --schema-source src/schema/nmdc.yaml \
# --selected-collections biosample_set \
# --selected-collections study_set \
# dump-from-database \
# --admin-db "admin" \
# --auth-mechanism "DEFAULT" \
# --env-file local/.env \
# --mongo-db-name nmdc \
# --mongo-host localhost \
# --mongo-port 27777 \
# --direct-connection
local/mongo_as_nmdc_database_rdf_safe.yaml: nmdc_schema/nmdc_materialized_patterns.yaml local/mongo_as_unvalidated_nmdc_database.yaml
date # 449.56 seconds on 2023-08-30 without functional_annotation_agg or metaproteomics_analysis_activity_set
time $(RUN) migration-recursion \
--input-path $(word 2,$^) \
--schema-path $(word 1,$^) \
--output-path $@
.PRECIOUS: local/mongo_as_nmdc_database_validation.log
local/mongo_as_nmdc_database_validation.log: nmdc_schema/nmdc_materialized_patterns.yaml local/mongo_as_nmdc_database_rdf_safe.yaml
date # 5m57.559s without functional_annotation_agg or metaproteomics_analysis_activity_set
time $(RUN) linkml-validate --schema $^ > $@
local/mongo_as_nmdc_database.ttl: nmdc_schema/nmdc_materialized_patterns.yaml local/mongo_as_nmdc_database_rdf_safe.yaml
date # 681.99 seconds on 2023-08-30 without functional_annotation_agg or metaproteomics_analysis_activity_set
time $(RUN) linkml-convert --output $@ --schema $^
mv $@ [email protected]
cat assets/my_emsl_prefix.ttl [email protected] > $@
rm -rf [email protected]
- export _JAVA_OPTIONS=-Djava.io.tmpdir=local ; $(JENA_DIR)/riot --validate $@ # < 1 minute
date
# todo: still getting anyurl typed string statement objects in RDF. I added a workaround in anyuri-strings-to-iris
local/mongo_as_nmdc_database_cuire_repaired.ttl: local/mongo_as_nmdc_database.ttl
date
time $(RUN) anyuri-strings-to-iris \
--input-ttl $< \
--jsonld-context-jsons project/jsonld/nmdc.context.jsonld \
--emsl-uuid-replacement emsl_uuid_like \
--output-ttl $@
- export _JAVA_OPTIONS=-Djava.io.tmpdir=local && $(JENA_DIR)/riot --validate $@ # < 1 minute
date
.PHONY: migration-doctests migrator
# Runs all doctests defined within the migrator modules, adapters, and CLI scripts.
#
# To run in non-verbose mode:
# ```
# $ make migration-doctests DOCTEST_OPT=''
# ```
DOCTEST_OPT ?= -v
migration-doctests: nmdc_schema/nmdc_materialized_patterns.yaml
$(RUN) python -m doctest $(DOCTEST_OPT) nmdc_schema/migrators/*.py
$(RUN) python -m doctest $(DOCTEST_OPT) nmdc_schema/migrators/partials/**/*.py
$(RUN) python -m doctest $(DOCTEST_OPT) nmdc_schema/migrators/adapters/*.py
$(RUN) python -m doctest $(DOCTEST_OPT) nmdc_schema/migrators/cli/*.py
# Generates a migrator skeleton for the specified schema versions.
# Note: `create-migrator` is a Poetry script registered in `pyproject.toml`.
migrator:
$(RUN) create-migrator
.PHONY: filtered-status
filtered-status:
git status | grep -v 'project/' | grep -v 'nmdc_schema/.*yaml' | grep -v 'nmdc_schema/.*json' | \
grep -v 'nmdc.py' | grep -v 'examples/output/' # | grep -v 'nmdc_materialized_patterns.py' |
local/biosample-slot-range-type-report.tsv: src/schema/nmdc.yaml
$(RUN) slot-range-type-reporter \
--schema $< \
--output $@ \
--schema-class Biosample
## we can get a report of biosamples per study with the following
## may help predict how long it will take to run study-id-from-filename on a particular study
## will become unnecessary once aggregation queries are available in the napa nmdc-runtime API
local/biosamples-per-study.txt:
$(RUN) report-biosamples-per-study \
--api-server api \
--max-page-size 10000 > $@
## getting a report of GOLD study identifiers, which might have been used a Study ids in legacy (pre-Napa) data
local/gold-study-ids.json:
curl -X 'GET' \
--output $@ \
'https://api.microbiomedata.org/nmdcschema/study_set?max_page_size=999&projection=id%2Cgold_study_identifiers' \
-H 'accept: application/json'
local/nmdc-no-use-native-uris.owl.ttl: src/schema/nmdc.yaml
$(RUN) gen-owl --no-use-native-uris $< > $@
local/nmdc_materialized.ttl: src/schema/nmdc.yaml
$(RUN) schema-view-relation-graph \
--schema $< \
--output $@
local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl: local/mongo_as_nmdc_database_cuire_repaired.ttl
$(RUN) date-created-blank-node > local/date_created_blank_node.ttl
cat $^ local/date_created_blank_node.ttl > $@
rm local/date_created_blank_node.ttl
###
diagrams-clean:
rm -rf assets/mermaid-erd* \
assets/plantuml*
# requires java and the plantuml jar https://plantuml.com/download
# https://github.com/plantuml/plantuml/releases/download/v1.2024.3/plantuml-lgpl-1.2024.3.jar
# requires npm and https://www.npmjs.com/package/@mermaid-js/mermaid-cli
# requires inkscape
diagrams-all: diagrams-clean assets/plantuml.png assets/plantuml.pdf assets/mermaid-erd.pdf assets/mermaid-erd.png
# --classes ChemicalConversionProcess \
# --classes ChemicalEntity \
# --classes ChromatographicSeparationProcess \
# --classes DissolvingProcess \
# --classes Extraction \
# --classes FluidHandling \
# --classes MassSpectrometry \
# --classes MaterialProcessing \
# --classes MetaboliteQuantification \
# --classes PlannedProcess \
# --classes PortionOfSubstance \
# --classes Solution \
# --classes SubstanceEntity
assets/plantuml.puml: src/schema/nmdc.yaml
$(RUN) gen-plantuml \
--classes ChemicalConversionProcess \
--classes ChemicalEntity \
--classes ChromatographicSeparationProcess \
--classes DissolvingProcess \
--classes Extraction \
--classes MobilePhaseSegment \
--classes PortionOfSubstance \
$< > $@
assets/plantuml.svg: assets/plantuml.puml # https://plantuml.com/download
java -jar $(PLANTUML_JAR) $< -tsvg
assets/plantuml.png: assets/plantuml.puml # https://plantuml.com/download
# docker run \
# -v plantuml_diagrams:/plantuml/in \
# -v plantuml_images:/plantuml/out \
# plantuml/plantuml render /plantuml/in/chemistry.puml -f png -o /plantuml/out/chemistry.png
java -jar $(PLANTUML_JAR) $< -tpng
assets/plantuml.pdf: assets/plantuml.svg
inkscape --export-filename=$@ $<
assets/mermaid-erd.mmd: src/schema/nmdc.yaml
$(RUN) gen-erdiagram \
--format mermaid \
--classes ChemicalConversionProcess \
--classes ChemicalEntity \
--classes ChromatographicSeparationProcess \
--classes DissolvingProcess \
--classes Extraction \
--classes MobilePhaseSegment \
--classes PortionOfSubstance \
$< > [email protected]
sed 's/language code/language_code/g' [email protected] > $@
rm -rf [email protected]
assets/mermaid-erd.svg: assets/mermaid-erd.mmd
mmdc -i $< -o $@
assets/mermaid-erd.pdf: assets/mermaid-erd.mmd
mmdc -i $< -o $@
assets/mermaid-erd.png: assets/mermaid-erd.mmd
mmdc -i $< -o $@
#assets/mermaid-erd.pdf: assets/mermaid-erd.svg # illegible
# inkscape --export-filename=$@ $<
assets/check_examples_class_coverage.txt:
$(RUN) check-examples-class-coverage \
--source_directory src/data/valid \
--schema_file src/schema/nmdc.yaml > $@
assets/schema_pattern_linting.txt:
$(RUN) schema-pattern-linting \
--schema-file src/schema/nmdc.yaml > $@
assets/enum_pv_result.tsv: src/schema/nmdc.yaml assets/enum_pv_template.tsv
$(RUN) linkml2sheets \
--output $@ \
--schema $< $(word 2,$^)
local/Database-interleaved-class-count.tsv: src/data/valid/Database-interleaved.yaml
cat $< | grep ' type: ' | sed 's/.*type: //' | sort | uniq -c | awk '{ OFS="\t"; $$1=$$1; print $$0 }' > $@
local/class_instantiation_counts.tsv: local/usage_template.tsv local/Database-interleaved-class-count.tsv
$(RUN) class-instantiation-counts \
--schemasheets-input $(word 1,$^) \
--counts-input $(word 2,$^) \
--output $@
.PHONY: generate-json-collections
generate-json-collections: src/data/valid/Database-interleaved.yaml
$(RUN) database-to-json-list-files \
--yaml-input $< \
--output-dir assets/jsons-for-mongodb
.PHONY: populate-mongodb-form-json-collections
populate-mongodb-form-json-collections: generate-json-collections
src/scripts/json-dir-to-mongodb.sh # requires that the script's permissions have been set like: chmod +x src/scripts/json-dir-to-mongodb.sh
# ---- NMDC NCBI mapping process ---- #
assets/ncbi_mappings/ncbi_attribute_mappings.tsv:
$(RUN) nmdc-ncbi-mapping create-unmapped-ncbi-mapping-file \
--tsv-output $@
assets/ncbi_mappings/ncbi_attribute_mappings_filled.tsv: assets/ncbi_mappings/ncbi_attribute_mappings.tsv
$(RUN) nmdc-ncbi-mapping exact-term-matching \
--tsv-input $< \
--tsv-output $@
$(RUN) nmdc-ncbi-mapping ignore-import-schema-slots $@
src/data/valid/Database-interleaved-new.yaml: src/schema/nmdc.yaml
$(RUN) interleave-yaml \
--directory-path src/data/valid \
--output-file $@ \
--schema-file $<
assets/mentions-of-ids-analysis.txt: src/schema/nmdc.yaml
$(RUN) analyze-mentions-of-ids \
--schema-file $< 1> $@ 2> [email protected]
assets/usages-report.txt: src/schema/nmdc.yaml
$(RUN) report-usages \
--schema-file $< > $@
assets/element-scrutiny.tsv: nmdc_schema/nmdc_materialized_patterns.yaml
$(RUN) scrutinize-elements \
--schema-file $< \
--output-file assets/element-scrutiny.tsv
# EXPERIMENTAL
assets/partial-imports-graph.pdf: src/schema/nmdc.yaml
$(RUN) python src/scripts/experimental/partial_imports_graph.py # needs networkx and plotly