diff --git a/Makefile b/Makefile index ed62ec849c..7d26911412 100644 --- a/Makefile +++ b/Makefile @@ -229,7 +229,7 @@ site-clean: clean rm -rf nmdc_schema/*.tsv rm -rf nmdc_schema/*.yaml -squeaky-clean: clean OmicsProcessing-clean accepting-legacy-ids-clean examples-clean mongodb-clean rdf-clean shuttle-clean site-clean # does not include mixs-yaml-clean +squeaky-clean: clean accepting-legacy-ids-clean examples-clean rdf-clean shuttle-clean site-clean # does not include mixs-yaml-clean project/nmdc_schema_merged.yaml: $(RUN) gen-linkml \ diff --git a/assets/import_mixs_slots_regardless.tsv b/assets/import_mixs_slots_regardless.tsv new file mode 100644 index 0000000000..ddcdd44eea --- /dev/null +++ b/assets/import_mixs_slots_regardless.tsv @@ -0,0 +1,490 @@ +source class source file or URL slot section column order destination class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml abs_air_humidity placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml add_recov_method placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml additional_info placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml address placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml adj_room placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml aero_struc placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml agrochem_addition placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml air_PM_concen placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml air_temp placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml air_temp_regm placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml al_sat placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml al_sat_meth placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml alkalinity placeholder_class +soil MIMS 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https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bac_prod placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bac_resp placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bacteria_carb_prod placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml barometric_press placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml basin placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bathroom_count placeholder_class +soil MIMS 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https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml bromide placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml build_docs placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml build_occup_type placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml building_setting placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml built_struc_age placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml built_struc_set placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml built_struc_type placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml calcium placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml carb_dioxide placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml carb_monoxide placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml carb_nitro_ratio placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_area placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_cond placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_finish_mat placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_struc placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_texture placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_thermal_mass placeholder_class +soil MIMS https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml ceil_type placeholder_class +soil MIMS 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OmicsProcessing-to-catted-Biosamples.tsv +rdf-clean shuttle-clean accepting-legacy-ids-clean: rm -rf nmdc_schema/nmdc_schema_accepting_legacy_ids* @@ -25,11 +21,6 @@ mixs-yaml-clean: rm -rf src/schema/mixs.yaml rm -rf local/mixs_regen/mixs_subset_modified.yaml -mongodb-clean: - date - rm -rf local/mongo_as_nmdc_database* - rm -rf local/mongo_as_unvalidated_nmdc_database.yaml - rdf-clean: rm -rf \ OmicsProcessing.rq \ @@ -40,18 +31,9 @@ rdf-clean: local/mongo_as_unvalidated_nmdc_database.yaml shuttle-clean: - rm -rf local/mixs_regen/import_slots_regardless_gen.tsv - rm -rf local/mixs_regen/mixs_slots_associated_with_biosample_omics_processing.tsv - rm -rf local/mixs_regen/mixs_slots_associated_with_biosample_omics_processing_augmented.tsv - rm -rf local/mixs_regen/mixs_slots_used_in_schema.tsv - rm -rf local/mixs_regen/mixs_subset.yaml #rm -rf local/mixs_regen/mixs_subset_modified.yaml # triggers complete regeneration + rm -rf local/mixs_regen/mixs_subset.yaml rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak - rm -rf local/mixs_regen/mixs_subset_repaired.yaml - rm -rf local/mixs_regen/mixs_subset_repaired.yaml.bak - rm -rf local/mixs_regen/slots_associated_with_biosample.tsv - rm -rf local/mixs_regen/slots_associated_with_biosample_omics_processing.tsv - rm -rf local/mixs_regen/slots_associated_with_omics_processing.tsv mkdir -p local/mixs_regen touch local/mixs_regen/.gitkeep @@ -60,28 +42,7 @@ src/schema/mixs.yaml: shuttle-clean local/mixs_regen/mixs_subset_modified_inj_la mv $(word 2,$^) $@ rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak -local/mixs_regen/slots_associated_with_biosample.tsv: - yq '.classes.Biosample.slots.[]' src/schema/nmdc.yaml | sort | cat > $@ - -local/mixs_regen/slots_associated_with_omics_processing.tsv: - yq '.classes.OmicsProcessing.slots.[]' src/schema/nmdc.yaml | sort | cat > $@ - -local/mixs_regen/slots_associated_with_biosample_omics_processing.tsv: \ -local/mixs_regen/slots_associated_with_biosample.tsv \ -local/mixs_regen/slots_associated_with_omics_processing.tsv - cat $^ > $@ - -local/mixs_regen/mixs_slots_associated_with_biosample_omics_processing.tsv: \ -local/mixs_regen/slots_associated_with_biosample_omics_processing.tsv - $(RUN) get-mixs-slots-matching-slot-list \ - --slot_list_file $< \ - --output_file $@ - -local/mixs_regen/import_slots_regardless_gen.tsv: \ -local/mixs_regen/mixs_slots_associated_with_biosample_omics_processing.tsv - $(RUN) generate-import-slots-regardless --input_file $< --output_file $@ - -local/mixs_regen/mixs_subset.yaml: local/mixs_regen/import_slots_regardless_gen.tsv +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 $< \