From 9becea7c11548ecf01f2a83c0c2972c133344902 Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Fri, 17 Nov 2023 15:16:21 -0500 Subject: [PATCH 1/2] #1368 generate-import-slots-regardless --mixs-schema-url option --- .../generate_import_slots_regardless.py | 32 +++++++++++-------- project.Makefile | 6 +++- 2 files changed, 23 insertions(+), 15 deletions(-) diff --git a/nmdc_schema/generate_import_slots_regardless.py b/nmdc_schema/generate_import_slots_regardless.py index 1a1faf5f19..fc64e1ec46 100644 --- a/nmdc_schema/generate_import_slots_regardless.py +++ b/nmdc_schema/generate_import_slots_regardless.py @@ -3,18 +3,19 @@ class ImportSlotsRegardless: - mixs_slots_used_in_schema_tsv = "../assets/mixs_slots_used_in_schema.tsv" - mixs_slots_used_in_schema = list() - - static_value_dict = { - "source class": "soil MIMS", - # "source file or URL": "https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/main/model/schema/mixs.yaml", - "source file or URL": "https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml", - "slot": "", - "section": "", - "column order": "", - "destination class": "placeholder_class" - } + + def __init__(self, mixs_schema_url, slots_tsv): + self.static_value_dict = { + "source class": "soil MIMS", + "source file or URL": mixs_schema_url, + "slot": "", + "section": "", + "column order": "", + "destination class": "placeholder_class" + } + + self.mixs_slots_used_in_schema_tsv = slots_tsv + self.mixs_slots_used_in_schema = list() def populate_mixs_slots_used_in_schema(self, input_file): with open(input_file, 'r') as file: @@ -44,8 +45,11 @@ def write_import_slots_regardless_rows(self, output_file, input_file): @click.command() @click.option("--input_file", required=True, help="input file path from get-mixs-slots-used-in-schema") @click.option("--output_file", required=True, help="output file path for sheets_and_friends") -def main(output_file, input_file): - import_slots = ImportSlotsRegardless() +@click.option("--slots-tsv", default="assets/mixs_slots_used_in_schema.tsv") +@click.option("--mixs-schema-url", + default="https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml") +def main(output_file, input_file, slots_tsv, mixs_schema_url): + import_slots = ImportSlotsRegardless(mixs_schema_url=mixs_schema_url, slots_tsv=slots_tsv) import_slots.write_import_slots_regardless_rows(output_file, input_file) click.echo("Import slots regardless file generated successfully.") diff --git a/project.Makefile b/project.Makefile index 9d7d1712b2..d73298966c 100644 --- a/project.Makefile +++ b/project.Makefile @@ -79,7 +79,11 @@ local/mixs_regen/slots_associated_with_biosample_omics_processing.tsv 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 $@ + $(RUN) generate-import-slots-regardless \ + --input_file $< \ + --mixs-schema-url "https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml" \ + --output_file $@ \ + --slots-tsv assets/mixs_slots_used_in_schema.tsv local/mixs_regen/mixs_subset.yaml: local/mixs_regen/import_slots_regardless_gen.tsv $(RUN) do_shuttle \ From 2e31c2dbb8ce21b3825b86a032b844178e7d347d Mon Sep 17 00:00:00 2001 From: Mark Andrew Miller Date: Sun, 19 Nov 2023 23:03:31 -0500 Subject: [PATCH 2/2] minimal to pass MongoDB contents --- Makefile | 2 +- assets/old_python/get_class_usages.py | 2 +- .../mixs_slots_import_sheet.tsv | 484 +++++++++ .../generate_import_slots_regardless.py | 58 -- nmdc_schema/get_mixs_slots.py | 47 - .../get_mixs_slots_matching_slot_list.py | 50 - nmdc_schema/get_mixs_slots_used_in_schema.py | 40 - nmdc_schema/get_slots_from_class.py | 50 - nmdc_schema/get_slots_from_view.py | 16 - nmdc_schema/test_more_tolerant_schema.py | 2 +- poetry.lock | 984 ++++++++---------- project.Makefile | 284 ++--- pyproject.toml | 7 +- .../{valid => }/Biosample-exhasutive.yaml | 16 +- ...xhaustive-issue-796-bye-yq-for-7-4-10.yaml | 6 +- .../Database-biosample-exhasutive.yaml | 16 +- src/schema/core.yaml | 8 +- src/schema/mixs_legacy.yaml | 23 + src/schema/nmdc.yaml | 39 +- tests/test_getters.py | 35 - 20 files changed, 1059 insertions(+), 1110 deletions(-) create mode 100644 assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv delete mode 100644 nmdc_schema/generate_import_slots_regardless.py delete mode 100644 nmdc_schema/get_mixs_slots.py delete mode 100644 nmdc_schema/get_mixs_slots_matching_slot_list.py delete mode 100644 nmdc_schema/get_mixs_slots_used_in_schema.py delete mode 100644 nmdc_schema/get_slots_from_class.py delete mode 100644 nmdc_schema/get_slots_from_view.py rename src/data/{valid => }/Biosample-exhasutive.yaml (99%) rename src/data/{valid => }/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml (99%) rename src/data/{valid => }/Database-biosample-exhasutive.yaml (99%) create mode 100644 src/schema/mixs_legacy.yaml delete mode 100644 tests/test_getters.py diff --git a/Makefile b/Makefile index b286908d4a..837cf3d6bb 100644 --- a/Makefile +++ b/Makefile @@ -227,7 +227,7 @@ 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 OmicsProcessing-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/old_python/get_class_usages.py b/assets/old_python/get_class_usages.py index f3df50b56a..3c5b19cca6 100644 --- a/assets/old_python/get_class_usages.py +++ b/assets/old_python/get_class_usages.py @@ -8,7 +8,7 @@ import logging -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter +# from nmdc_schema.get_mixs_slots import MIxSSlotsGetter logging.basicConfig(level=logging.WARNING) logger = logging.getLogger(__name__) diff --git a/assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv b/assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv new file mode 100644 index 0000000000..0210d6e4f8 --- /dev/null +++ b/assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv @@ -0,0 +1,484 @@ +source class source file or URL column order section slot destination class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml abs_air_humidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml add_recov_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml additional_info placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml address placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml adj_room placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml aero_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml agrochem_addition placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml air_PM_concen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml air_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml air_temp_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml al_sat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml al_sat_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alkalinity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alkalinity_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alkyl_diethers placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml alt placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml aminopept_act placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ammonium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml amount_light placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ances_data placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml annual_precpt placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml annual_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml antibiotic_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml api placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml arch_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml aromatics_pc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml asphaltenes_pc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml atmospheric_data placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml avg_dew_point placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml avg_occup placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml avg_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bac_prod placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bac_resp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bacteria_carb_prod placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml barometric_press placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml basin placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bathroom_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bedroom_count placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml benzene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biochem_oxygen_dem placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biocide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biocide_admin_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biol_stat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biomass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biotic_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml biotic_relationship placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bishomohopanol placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml blood_press_diast placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml blood_press_syst placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml bromide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml build_docs placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml build_occup_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml building_setting placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml built_struc_age placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml built_struc_set placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml built_struc_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml calcium placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml carb_dioxide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml carb_monoxide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml carb_nitro_ratio placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_area placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_finish_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_struc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_texture placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_thermal_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ceil_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_administration placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_mutagen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_oxygen_dem placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_treat_method placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chem_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chimera_check placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chloride placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml chlorophyll placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml climate_environment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml collection_date placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml conduc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cool_syst_id placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml crop_rotation placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cult_root_med placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cur_land_use placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cur_vegetation placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml cur_vegetation_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml date_last_rain placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml density placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml depos_env placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml depth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml dew_point placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diether_lipids placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_carb_dioxide placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_hydrogen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_inorg_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_inorg_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_inorg_phosp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_iron placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_org_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_org_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_oxygen placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml diss_oxygen_fluid placeholder_class +MimsSoil 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https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml suspend_solids placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tan placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml target_gene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml target_subfragment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml temp_out placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tertiary_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tidal_stage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tillage placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tiss_cult_growth_med placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml toluene placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_depth_water_col placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_diss_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_inorg_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_iron placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_nitro placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_nitro_cont_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_nitro_content placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_org_c_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_org_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_part_carb placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_phosp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_phosphate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tot_sulfur placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml train_line placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml train_stat_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml train_stop_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml turbidity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tvdss_of_hcr_press placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml tvdss_of_hcr_temp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml typ_occup_density placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ventilation_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml ventilation_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml vfa placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml vfa_fw placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml vis_media placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml viscosity placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml volatile_org_comp placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_area placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_const_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_finish_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_height placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_surf_treatment placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_texture placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_thermal_mass placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wall_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wastewater_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_cont_soil_meth placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_content placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_current placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_cut placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_feat_size placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_feat_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_prod_rate placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml water_temp_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml watering_regm placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml weekday placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml win placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wind_direction placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml wind_speed placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_cond placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_cover placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_horiz_pos placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_loc placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_mat placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_open_freq placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_size placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_status placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_type placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_vert_pos placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml window_water_mold placeholder_class +MimsSoil https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml xylene placeholder_class diff --git a/nmdc_schema/generate_import_slots_regardless.py b/nmdc_schema/generate_import_slots_regardless.py deleted file mode 100644 index fc64e1ec46..0000000000 --- a/nmdc_schema/generate_import_slots_regardless.py +++ /dev/null @@ -1,58 +0,0 @@ -import csv -import click - - -class ImportSlotsRegardless: - - def __init__(self, mixs_schema_url, slots_tsv): - self.static_value_dict = { - "source class": "soil MIMS", - "source file or URL": mixs_schema_url, - "slot": "", - "section": "", - "column order": "", - "destination class": "placeholder_class" - } - - self.mixs_slots_used_in_schema_tsv = slots_tsv - self.mixs_slots_used_in_schema = list() - - def populate_mixs_slots_used_in_schema(self, input_file): - with open(input_file, 'r') as file: - self.mixs_slots_used_in_schema = [line.strip().split('\t')[0] for line in file] - - def make_import_slots_regardless_rows(self, input_file): - self.populate_mixs_slots_used_in_schema(input_file) - import_slots_regardless_rows = list() - - for slot in self.mixs_slots_used_in_schema: - final_dict = self.static_value_dict.copy() - final_dict["slot"] = slot - import_slots_regardless_rows.append(final_dict) - - return import_slots_regardless_rows - - def write_import_slots_regardless_rows(self, output_file, input_file): - fieldnames = list(self.static_value_dict.keys()) - slots_regardless_rows = self.make_import_slots_regardless_rows(input_file) - with open(output_file, 'w', newline='') as output_file: - writer = csv.DictWriter(output_file, fieldnames=fieldnames, delimiter='\t') - writer.writeheader() - for row in slots_regardless_rows: - writer.writerow(row) - - -@click.command() -@click.option("--input_file", required=True, help="input file path from get-mixs-slots-used-in-schema") -@click.option("--output_file", required=True, help="output file path for sheets_and_friends") -@click.option("--slots-tsv", default="assets/mixs_slots_used_in_schema.tsv") -@click.option("--mixs-schema-url", - default="https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml") -def main(output_file, input_file, slots_tsv, mixs_schema_url): - import_slots = ImportSlotsRegardless(mixs_schema_url=mixs_schema_url, slots_tsv=slots_tsv) - import_slots.write_import_slots_regardless_rows(output_file, input_file) - click.echo("Import slots regardless file generated successfully.") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_mixs_slots.py b/nmdc_schema/get_mixs_slots.py deleted file mode 100644 index 87669c2f2b..0000000000 --- a/nmdc_schema/get_mixs_slots.py +++ /dev/null @@ -1,47 +0,0 @@ -import csv -import pprint -import urllib.request - -import csv -import io -import urllib.request -from typing import List - - -class MIxSSlotsGetter: - # switch to retrieving from GSC' mixs.yaml - def any_mixs_sheet_getter(self, url): - response = urllib.request.urlopen(url) - tsv_file = io.StringIO(response.read().decode('utf-8')) - - rows = [] - - # Parse the file using DictReader - reader = csv.DictReader(tsv_file, delimiter='\t') - for row in reader: - rows.append(row) - - return rows - - def extract_vals_from_rows(self, rows, var_name): - slots = [] - for row in rows: - if var_name in row and row[var_name] != '': - slots.append(row[var_name]) - slots.sort() - return slots - - def get_unique_slot_names(self, - var_name: str = "Structured comment name", - url_list: List[str] = ( - "https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?gid=178015749&format=tsv", - "https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?gid=750683809&format=tsv" - )): - slot_names = set() - for url in url_list: - parsed = self.any_mixs_sheet_getter(url) - per_page_slots = self.extract_vals_from_rows(parsed, var_name) - slot_names.update(per_page_slots) - slot_names = list(slot_names) - slot_names.sort() - return slot_names diff --git a/nmdc_schema/get_mixs_slots_matching_slot_list.py b/nmdc_schema/get_mixs_slots_matching_slot_list.py deleted file mode 100644 index 09c977aec3..0000000000 --- a/nmdc_schema/get_mixs_slots_matching_slot_list.py +++ /dev/null @@ -1,50 +0,0 @@ -from typing import List - -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter -from nmdc_schema.get_slots_from_view import SchemaSlotsGetter - -import click - - -class IntersectionMixsSlotsGetter: - mixs_term_getter: MIxSSlotsGetter = MIxSSlotsGetter() - mixs_slotnames: List[str] = mixs_term_getter.get_unique_slot_names() - slot_list = [] - - def get_intersection_mixs_slots(self, slot_list_file) -> List[str]: - print(f"slot_list_file: {slot_list_file}") - with open(slot_list_file, 'r') as file: - self.slot_list = [line.strip().split('\t')[0] for line in file] - - used_mixs_slots = list(set(self.mixs_slotnames) & set(self.slot_list)) - used_mixs_slots.sort() - return used_mixs_slots - - -@click.command() -@click.option('--slot_list_file', - '-s', - type=click.Path(exists=True), - required=True, - help='Provide a single-column TSV file listing desired slots.') -@click.option('--output_file', - '-o', - type=click.File('w'), - required=True, - help='Your output will be written as a single-column TSV file.') -def main(slot_list_file, output_file): - print(f"slot_list_file: {slot_list_file}") - print(f"output_file: {output_file}") - - intersection_mixs_slot_getter = IntersectionMixsSlotsGetter() - intersection_mixs_slots = intersection_mixs_slot_getter.get_intersection_mixs_slots(slot_list_file) - - with output_file: - for slot in intersection_mixs_slots: - output_file.write(f"{slot}\n") - - click.echo(f"The result has been written to {output_file.name}") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_mixs_slots_used_in_schema.py b/nmdc_schema/get_mixs_slots_used_in_schema.py deleted file mode 100644 index f0d578b202..0000000000 --- a/nmdc_schema/get_mixs_slots_used_in_schema.py +++ /dev/null @@ -1,40 +0,0 @@ -from typing import List - -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter -from nmdc_schema.get_slots_from_view import SchemaSlotsGetter - -import click - - -class UsedMixsSlotsGetter: - mixs_term_getter: MIxSSlotsGetter = MIxSSlotsGetter() - mixs_slotnames: List[str] = mixs_term_getter.get_unique_slot_names() - - schema_slots_getter: SchemaSlotsGetter = SchemaSlotsGetter() - schema_slots: List[str] = schema_slots_getter.get_schema_slots() - - def get_used_mixs_slots(self) -> List[str]: - used_mixs_slots = list(set(self.mixs_slotnames) & set(self.schema_slots)) - used_mixs_slots.sort() - return used_mixs_slots - - -@click.command() -@click.option('--output_file', - '-o', - type=click.File('w'), - required=True, - help='Your output will be written as a single-column TSV file.') -def main(output_file): - used_mixs_slot_getter = UsedMixsSlotsGetter() - used_mixs_slots = used_mixs_slot_getter.get_used_mixs_slots() - - with output_file: - for slot in used_mixs_slots: - output_file.write(f"{slot}\n") - - click.echo(f"The result has been written to {output_file.name}") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_slots_from_class.py b/nmdc_schema/get_slots_from_class.py deleted file mode 100644 index e9f8190f5c..0000000000 --- a/nmdc_schema/get_slots_from_class.py +++ /dev/null @@ -1,50 +0,0 @@ -import pprint -from typing import List - -import click - -from nmdc_schema.get_nmdc_view import ViewGetter - - -class ClassSlotsGetter: - @staticmethod - def get_class_slots(class_name) -> List[str]: - # assumes user wants slots from induced class - # if the user adds a MIxS slot to class Biosample, will the view be created? - # might need a pure YAML solution - # or user could just add slot name to ??? - # most importantly, this get the view from nmdc_schema,nmdc_schema_merged.yaml - # which won't include the user's changes!!! - view_getter = ViewGetter() - nmdc_view = view_getter.get_view() - nmdc_class = nmdc_view.induced_class(class_name) - class_slots = nmdc_class.attributes - - class_slot_names = [v.name for k, v in class_slots.items()] - class_slot_names.sort() - return class_slot_names - - -@click.command() -@click.option('--output_file', - '-o', - type=click.File('w'), - required=True, - help='Your output will be written as a single-column TSV file.') -@click.option('--class_name', - '-c', - required=True, - help='For what class do you want to retrieve slots?.') -def main(output_file, class_name): - class_slot_getter = ClassSlotsGetter() - class_used_slots = class_slot_getter.get_class_slots(class_name) - - with output_file: - for slot in class_used_slots: - output_file.write(f"{slot}\n") - - click.echo(f"The result has been written to {output_file}") - - -if __name__ == '__main__': - main() diff --git a/nmdc_schema/get_slots_from_view.py b/nmdc_schema/get_slots_from_view.py deleted file mode 100644 index e808aad7a4..0000000000 --- a/nmdc_schema/get_slots_from_view.py +++ /dev/null @@ -1,16 +0,0 @@ -import pprint -from typing import List - -from nmdc_schema.get_nmdc_view import ViewGetter - - -class SchemaSlotsGetter: - def get_schema_slots(self) -> List[str]: - view_getter = ViewGetter() - nmdc_view = view_getter.get_view() - - schema_slots = nmdc_view.all_slots() - schema_slot_names = [v.name for k, v in schema_slots.items()] - schema_slot_names.sort() - return schema_slot_names - diff --git a/nmdc_schema/test_more_tolerant_schema.py b/nmdc_schema/test_more_tolerant_schema.py index a5ec31eac0..3630ed4c30 100644 --- a/nmdc_schema/test_more_tolerant_schema.py +++ b/nmdc_schema/test_more_tolerant_schema.py @@ -12,6 +12,6 @@ def do_test(): term=OntologyClass(id='ENVO:00010483', name='freshwater environment')), env_local_scale=ControlledIdentifiedTermValue( term=OntologyClass(id='ENVO:00010483', name='freshwater environment')), - ) + ), print(yaml_dumper.dumps(bs)) diff --git a/poetry.lock b/poetry.lock index 8651de3360..e2c6513b5e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -135,13 +135,13 @@ chardet = ">=3.0.2" [[package]] name = "bioregistry" -version = "0.10.69" +version = "0.10.80" description = "Integrated registry of biological databases and nomenclatures" optional = false python-versions = ">=3.8" files = [ - {file = "bioregistry-0.10.69-py3-none-any.whl", hash = "sha256:205a3afafe382b63ee172bc32aac0e3c09df26efb2437879eea2703aa11697de"}, - {file = "bioregistry-0.10.69.tar.gz", hash = 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examples-clean linkml-validate-mongodb mixs-yaml-clean mixs-deepdiff \ -mongodb-clean rdf-clean shuttle-clean squeaky-clean +dump-validate-report-convert-mongodb examples-clean linkml-validate-mongodb mixs-yaml-clean \ +rdf-clean shuttle-clean squeaky-clean OmicsProcessing-clean: rm -rf OmicsProcessing.tsv @@ -25,33 +24,14 @@ 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 \ - local/mongo_as_nmdc_database.ttl \ - local/mongo_as_nmdc_database_cuire_repaired.ttl \ - local/mongo_as_nmdc_database_rdf_safe.yaml \ - local/mongo_as_nmdc_database_validation.log \ - local/mongo_as_unvalidated_nmdc_database.yaml + local/mongo_as_* 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_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 @@ -60,199 +40,74 @@ 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 $< \ - --mixs-schema-url "https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml" \ - --output_file $@ \ - --slots-tsv assets/mixs_slots_used_in_schema.tsv - -local/mixs_regen/mixs_subset.yaml: local/mixs_regen/import_slots_regardless_gen.tsv +local/mixs_regen/mixs_subset.yaml: assets/other_mixs_yaml_files/mixs_slots_import_sheet.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 - # 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/' $< > $@ - sed -i.bak 's/range: string/range: TextValue/' $@ - sed -i.bak 's/range: text value/range: TextValue/' $@ - - yq -i '.slots.agrochem_addition.range |= "TextValue"' $@ - yq -i '.slots.air_temp_regm.range |= "TextValue"' $@ - yq -i '.slots.antibiotic_regm.range |= "TextValue"' $@ - yq -i '.slots.aromatics_pc.range |= "TextValue"' $@ - yq -i '.slots.asphaltenes_pc.range |= "TextValue"' $@ - yq -i '.slots.atmospheric_data.range |= "TextValue"' $@ - yq -i '.slots.avg_occup.range |= "TextValue"' $@ - yq -i '.slots.bathroom_count.range |= "TextValue"' $@ - yq -i '.slots.bedroom_count.range |= "TextValue"' $@ - yq -i '.slots.biocide_admin_method.range |= "TextValue"' $@ + cp $< $@ + yq -i '.enums.SOIL_HORIZON_ENUM.permissible_values.["M horizon"] = {}' $@ + yq -i '.id |= "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml"' $@ yq -i '.slots.biomass.range |= "TextValue"' $@ + yq -i '.slots.calcium.range |= "QuantityValue"' $@ + yq -i '.slots.carb_nitro_ratio.range |= "QuantityValue"' $@ yq -i '.slots.chem_administration.range |= "ControlledTermValue"' $@ - yq -i '.slots.chem_mutagen.range |= "TextValue"' $@ - yq -i '.slots.chem_treat_method.range |= "string"' $@ yq -i '.slots.collection_date.range |= "TimestampValue"' $@ - yq -i '.slots.cool_syst_id.range |= "TextValue"' $@ - yq -i '.slots.date_last_rain.range |= "TimestampValue"' $@ - yq -i '.slots.diether_lipids.range |= "TextValue"' $@ - yq -i '.slots.elevator.range |= "TextValue"' $@ - yq -i '.slots.emulsions.range |= "TextValue"' $@ + yq -i '.slots.cur_vegetation.range |= "ControlledTermValue"' $@ + yq -i '.slots.depth.range |= "QuantityValue"' $@ yq -i '.slots.env_broad_scale.range |= "ControlledIdentifiedTermValue"' $@ yq -i '.slots.env_local_scale.range |= "ControlledIdentifiedTermValue"' $@ yq -i '.slots.env_medium.range |= "ControlledIdentifiedTermValue"' $@ - yq -i '.slots.escalator.range |= "TextValue"' $@ - yq -i '.slots.exp_pipe.range |= "QuantityValue"' $@ + yq -i '.slots.experimental_factor.multivalued |= "false"' $@ yq -i '.slots.experimental_factor.range |= "ControlledTermValue"' $@ - yq -i '.slots.ext_door.range |= "TextValue"' $@ - yq -i '.slots.extreme_event.range |= "TimestampValue"' $@ - yq -i '.slots.fertilizer_regm.range |= "TextValue"' $@ - yq -i '.slots.fire.range |= "TimestampValue"' $@ - yq -i '.slots.flooding.range |= "TimestampValue"' $@ - yq -i '.slots.floor_count.range |= "TextValue"' $@ - yq -i '.slots.freq_clean.range |= "QuantityValue"' $@ - yq -i '.slots.freq_cook.range |= "QuantityValue"' $@ - yq -i '.slots.fungicide_regm.range |= "TextValue"' $@ - yq -i '.slots.gaseous_environment.range |= "TextValue"' $@ - yq -i '.slots.gaseous_substances.range |= "TextValue"' $@ - yq -i '.slots.gravity.range |= "TextValue"' $@ + yq -i '.slots.experimental_factor.range |= "ControlledTermValue"' $@ + yq -i '.slots.geo_loc_name.range |= "TextValue"' $@ + yq -i '.slots.gravidity.range |= "TextValue"' $@ yq -i '.slots.growth_facil.range |= "ControlledTermValue"' $@ - yq -i '.slots.growth_hormone_regm.range |= "TextValue"' $@ - yq -i '.slots.hall_count.range |= "TextValue"' $@ - yq -i '.slots.hall_count.range |= "TextValue"' $@ - yq -i '.slots.hcr_pressure.range |= "TextValue"' $@ - yq -i '.slots.hcr_temp.range |= "TextValue"' $@ - yq -i '.slots.heat_sys_deliv_meth.range |= "string"' $@ - yq -i '.slots.heat_system_id.range |= "TextValue"' $@ - yq -i '.slots.heavy_metals.range |= "TextValue"' $@ - yq -i '.slots.herbicide_regm.range |= "TextValue"' $@ + yq -i '.slots.host_age.range |= "QuantityValue"' $@ + yq -i '.slots.host_body_habitat.range |= "TextValue"' $@ yq -i '.slots.host_body_product.range |= "ControlledTermValue"' $@ yq -i '.slots.host_body_site.range |= "ControlledTermValue"' $@ - yq -i '.slots.host_family_relation.range |= "string"' $@ - yq -i '.slots.host_phenotype.range |= "ControlledTermValue"' $@ - yq -i '.slots.host_subspecf_genlin.range |= "string"' $@ - yq -i '.slots.host_symbiont.range |= "string"' $@ - yq -i '.slots.humidity_regm.range |= "TextValue"' $@ - yq -i '.slots.inorg_particles.range |= "TextValue"' $@ - yq -i '.slots.iw_bt_date_well.range |= "TimestampValue"' $@ - yq -i '.slots.last_clean.range |= "TimestampValue"' $@ + yq -i '.slots.host_common_name.range |= "TextValue"' $@ + yq -i '.slots.host_diet.multivalued |= "true"' $@ + yq -i '.slots.host_diet.range |= "TextValue"' $@ + yq -i '.slots.host_genotype.range |= "TextValue"' $@ + yq -i '.slots.host_life_stage.range |= "TextValue"' $@ + yq -i '.slots.host_taxid.range |= "ControlledTermValue"' $@ yq -i '.slots.lat_lon.range |= "GeolocationValue"' $@ - yq -i '.slots.light_regm.range |= "TextValue"' $@ - yq -i '.slots.max_occup.range |= "QuantityValue"' $@ - yq -i '.slots.micro_biomass_meth.range |= "string"' $@ - yq -i '.slots.mineral_nutr_regm.range |= "TextValue"' $@ - yq -i '.slots.misc_param.range |= "TextValue"' $@ - yq -i '.slots.n_alkanes.range |= "TextValue"' $@ - yq -i '.slots.non_min_nutr_regm.range |= "string"' $@ - yq -i '.slots.number_pets.range |= "QuantityValue"' $@ - yq -i '.slots.number_plants.range |= "QuantityValue"' $@ - yq -i '.slots.number_resident.range |= "QuantityValue"' $@ - yq -i '.slots.occup_density_samp.range |= "QuantityValue"' $@ - yq -i '.slots.occup_samp.range |= "QuantityValue"' $@ - yq -i '.slots.org_count_qpcr_info.range |= "string"' $@ - yq -i '.slots.org_particles.range |= "TextValue"' $@ - yq -i '.slots.organism_count.range |= "QuantityValue"' $@ - yq -i '.slots.particle_class.range |= "TextValue"' $@ - yq -i '.slots.permeability.range |= "TextValue"' $@ - yq -i '.slots.pesticide_regm.range |= "TextValue"' $@ - yq -i '.slots.phaeopigments.range |= "TextValue"' $@ - yq -i '.slots.phosplipid_fatt_acid.range |= "TextValue"' $@ - yq -i '.slots.plant_growth_med.range |= "ControlledTermValue"' $@ - yq -i '.slots.plant_struc.range |= "ControlledTermValue"' $@ - yq -i '.slots.pollutants.range |= "TextValue"' $@ - yq -i '.slots.porosity.range |= "TextValue"' $@ - yq -i '.slots.pres_animal_insect.range |= "string"' $@ - yq -i '.slots.prev_land_use_meth.range |= "string"' $@ - yq -i '.slots.prod_start_date.range |= "TimestampValue"' $@ - yq -i '.slots.radiation_regm.range |= "TextValue"' $@ - yq -i '.slots.rainfall_regm.range |= "TextValue"' $@ - yq -i '.slots.resins_pc.range |= "TextValue"' $@ - yq -i '.slots.room_architec_elem.range |= "string"' $@ - yq -i '.slots.room_count.range |= "TextValue"' $@ - yq -i '.slots.room_dim.range |= "TextValue"' $@ - yq -i '.slots.room_door_dist.range |= "TextValue"' $@ - yq -i '.slots.room_net_area.range |= "TextValue"' $@ - yq -i '.slots.room_occup.range |= "QuantityValue"' $@ - yq -i '.slots.room_vol.range |= "TextValue"' $@ - yq -i '.slots.root_med_carbon.range |= "TextValue"' $@ - yq -i '.slots.root_med_macronutr.range |= "TextValue"' $@ - yq -i '.slots.root_med_micronutr.range |= "TextValue"' $@ - yq -i '.slots.root_med_ph.range |= "QuantityValue"' $@ - yq -i '.slots.root_med_regl.range |= "TextValue"' $@ - yq -i '.slots.root_med_suppl.range |= "TextValue"' $@ - yq -i '.slots.salt_regm.range |= "TextValue"' $@ - yq -i '.slots.samp_collec_device.range |= "string"' $@ - yq -i '.slots.samp_collec_method.range |= "string"' $@ - yq -i '.slots.samp_loc_corr_rate.range |= "TextValue"' $@ - yq -i '.slots.samp_mat_process.range |= "ControlledTermValue"' $@ - yq -i '.slots.samp_md.range |= "QuantityValue"' $@ - yq -i '.slots.samp_name.range |= "string"' $@ - yq -i '.slots.samp_preserv.range |= "TextValue"' $@ - yq -i '.slots.samp_room_id.range |= "TextValue"' $@ - yq -i '.slots.samp_time_out.range |= "TextValue"' $@ - yq -i '.slots.samp_transport_cond.range |= "TextValue"' $@ - yq -i '.slots.samp_tvdss.range |= "TextValue"' $@ - yq -i '.slots.saturates_pc.range |= "TextValue"' $@ - yq -i '.slots.shad_dev_water_mold.range |= "string"' $@ + yq -i '.slots.magnesium.range |= "QuantityValue"' $@ + yq -i '.slots.micro_biomass_meth.pattern |= ".*"' $@ # todo too liberal + yq -i '.slots.micro_biomass_meth.structured_pattern.syntax |= ".*"' $@ # todo too liberal + yq -i '.slots.nitrate.range |= "QuantityValue"' $@ + yq -i '.slots.nitro.range |= "QuantityValue"' $@ + yq -i '.slots.org_carb.range |= "QuantityValue"' $@ + yq -i '.slots.perturbation.multivalued |= "true"' $@ + yq -i '.slots.perturbation.range |= "TextValue"' $@ + yq -i '.slots.potassium.range |= "QuantityValue"' $@ + yq -i '.slots.salinity.range |= "QuantityValue"' $@ + yq -i '.slots.samp_size.range |= "QuantityValue"' $@ + yq -i '.slots.samp_store_temp.range |= "QuantityValue"' $@ + yq -i '.slots.samp_taxon_id.range |= "ControlledIdentifiedTermValue"' $@ yq -i '.slots.sieving.range |= "TextValue"' $@ - yq -i '.slots.size_frac.range |= "TextValue"' $@ - yq -i '.slots.soil_texture_meth.range |= "string"' $@ - yq -i '.slots.soluble_inorg_mat.range |= "TextValue"' $@ - yq -i '.slots.soluble_org_mat.range |= "TextValue"' $@ - yq -i '.slots.suspend_solids.range |= "TextValue"' $@ - yq -i '.slots.tot_nitro_cont_meth.range |= "string"' $@ - yq -i '.slots.viscosity.range |= "TextValue"' $@ - yq -i '.slots.volatile_org_comp.range |= "TextValue"' $@ - yq -i '.slots.water_cont_soil_meth.range |= "string"' $@ - yq -i '.slots.water_temp_regm.range |= "TextValue"' $@ - yq -i '.slots.watering_regm.range |= "TextValue"' $@ - yq -i '.slots.window_open_freq.range |= "TextValue"' $@ - yq -i '.slots.window_size.range |= "TextValue"' $@ - - yq -i 'del(.classes)' $@ + yq -i '.slots.source_mat_id.multivalued |= "false"' $@ + yq -i '.slots.source_mat_id.range |= "TextValue"' $@ + yq -i '.slots.store_cond.range |= "TextValue"' $@ + yq -i '.slots.temp.range |= "QuantityValue"' $@ + yq -i '.slots.tot_nitro.range |= "QuantityValue"' $@ + yq -i '.slots.tot_nitro.range |= "QuantityValue"' $@ + yq -i '.slots.tot_nitro_content.range |= "QuantityValue"' $@ + yq -i '.slots.tot_org_carb.range |= "QuantityValue"' $@ + yq -i '.slots.tot_phosp.range |= "QuantityValue"' $@ + yq -i '.slots.water_content.pattern |= ".*"' $@ # todo too liberal + yq -i '.slots.water_content.structured_pattern.syntax |= ".*"' $@ # todo too liberal + yq -i 'del(.classes)' $@ yq -i 'del(.enums.[].name)' $@ yq -i 'del(.enums.[].permissible_values.[].text)' $@ yq -i 'del(.slots.[].name)' $@ - yq -i 'del(.slots.add_recov_method.pattern)' $@ + yq -i 'del(.slots.[].required)' $@ yq -i 'del(.subsets.[].name)' $@ - - yq -i '.id |= "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml"' $@ - -# # update host_taxid and samp_taxon_id. may want to flatten to a string or URIORCURIE eventually - yq -i 'del(.slots.host_taxid.examples)' $@ - yq -i 'del(.slots.host_taxid.string_serialization)' $@ - yq -i 'del(.slots.samp_taxon_id.examples)' $@ - yq -i 'del(.slots.samp_taxon_id.string_serialization)' $@ - - yq -i '.slots.host_taxid.comments |= ["Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value"]' $@ - yq -i '.slots.host_taxid.range = "ControlledIdentifiedTermValue"' $@ - yq -i '.slots.samp_taxon_id.comments |= ["coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value"]' $@ - yq -i '.slots.samp_taxon_id.range = "ControlledIdentifiedTermValue"' $@ - - - # add "M horizon" to soil_horizon_enum - yq -i '.enums.soil_horizon_enum.permissible_values.["M horizon"] = {}' $@ rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak @@ -263,11 +118,6 @@ local/mixs_regen/mixs_subset_modified_inj_land_use.yaml: assets/other_mixs_yaml_ 'select(fileIndex==1).enums.cur_land_use_enum = select(fileIndex==0).enums.cur_land_use_enum | select(fileIndex==1)' \ $^ | cat > $@ -mixs-deepdiff: src/schema/mixs.yaml - mv src/schema/mixs.yaml.bak src/schema/mixs.bak.yaml - $(RUN) deep diff src/schema/mixs.bak.yaml $^ - mv src/schema/mixs.bak.yaml src/schema/mixs.yaml.bak - project/nmdc_schema_generated.yaml: $(SOURCE_SCHEMA_PATH) # the need for this may be eliminated by adding mandatory pattern materialization to gen-json-schema $(RUN) gen-linkml \ @@ -295,7 +145,7 @@ local/usage_template.tsv: src/schema/nmdc.yaml --columns-to-insert slot \ --source-schema-path $< -examples/output/Biosample-exhasutive_report.yaml: src/data/valid/Biosample-exhasutive.yaml +examples/output/Biosample-exhasutive_report.yaml: src/data/Biosample-exhasutive.yaml poetry run exhaustion-check \ --class-name Biosample \ --instance-yaml-file $< \ @@ -310,7 +160,7 @@ examples/output/Pooling-minimal-report.yaml: src/data/valid/Pooling-minimal.yaml --output-yaml-file $@ \ --schema-path src/schema/nmdc.yaml -examples/output/Biosample-exhasutive-pretty-sorted.yaml: src/data/valid/Biosample-exhasutive.yaml +examples/output/Biosample-exhasutive-pretty-sorted.yaml: src/data/Biosample-exhasutive.yaml poetry run pretty-sort-yaml \ -i $< \ -o $@ @@ -465,11 +315,7 @@ local/mongo_as_unvalidated_nmdc_database.yaml: --selected-collections read_based_taxonomy_analysis_activity_set \ --selected-collections read_qc_analysis_activity_set \ --selected-collections study_set \ - --skip-collection-check \ - - -# --migrator-name Migrator_from_8_0_to_8_1 \ -# --migrator-name Migrator_from_8_1_to_9_0 + --skip-collection-check local/mongo_as_nmdc_database_rdf_safe.yaml: nmdc_schema/nmdc_schema_accepting_legacy_ids.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 @@ -481,12 +327,16 @@ local/mongo_as_nmdc_database_rdf_safe.yaml: nmdc_schema/nmdc_schema_accepting_le .PRECIOUS: local/mongo_as_nmdc_database_validation.log -local/mongo_as_nmdc_database_validation.log: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml local/mongo_as_nmdc_database_rdf_safe.yaml +# make local/mongo_as_nmdc_database_rdf_safe.yaml ; linkml-validate \ +# --schema nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml \ +# local/mongo_as_nmdc_database_rdf_safe.yaml > local/mongo_as_nmdc_database_validation.log + +local/mongo_as_nmdc_database_validation.log: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml mongo_as_nmdc_database_rdf_safe.yaml # nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml or nmdc_schema/nmdc_materialized_patterns.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_schema_accepting_legacy_ids.yaml local/mongo_as_nmdc_database_rdf_safe.yaml +local/mongo_as_nmdc_database.ttl: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml 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 $^ export _JAVA_OPTIONS=-Djava.io.tmpdir=local @@ -528,24 +378,6 @@ OmicsProcessing.tsv: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml --target-class-name $(firstword $(subst ., ,$(lastword $(subst /, ,$@)))) \ --target-p-o-constraint "dcterms:isPartOf nmdc:sty-11-34xj1150" -#tdb-steps: -## # clean up tdbcontent -## $(JENA_PATH)/tdb2.tdbloader \ -## --loc=tdbcontent \ -## --graph=https://w3id.org/nmdc/nmdc project/owl/nmdc.owl.ttl -## $(JENA_PATH)/tdb2.tdbloader \ -## --loc=tdbcontent \ -## --graph=mongodb://mongo-loadbalancer.nmdc.production.svc.spin.nersc.gov:27017 local/research_study_injected_for_Gs0114663_cuire_repaired.ttl -## $(JENA_PATH)/tdb2.tdbquery \ -## --loc=tdbcontent \ -## --query=assets/sparql/tdb-test.rq -## $(JENA_PATH)/tdb2.tdbquery \ -## --loc=tdbcontent \ -## --query=assets/sparql/tdb-graph-list.rq -## $(JENA_PATH)/tdb2.tdbquery \ -## --loc=tdbcontent \ -## --query=assets/sparql/Gs0114663-construct.rq - validate-filtered-request-all: validate-filtered-request-clean assets/filtered-api-requests/filtered-request-validation-log.txt .PHONY: validate-filtered-request-all validate-filtered-request-clean diff --git a/pyproject.toml b/pyproject.toml index ec5292cb6a..4392cf9fd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,8 +43,8 @@ packages = [ ] [tool.poetry.dependencies] -linkml = ">=1.5.0, <1.6.2" -linkml-runtime = ">=1.5.0, <1.6.3" +linkml = "^1.6.3" +linkml-runtime = "^1.6.2" python = "^3.9" click-log = "^0.4.0" ruamel-yaml = "^0.18.5" @@ -107,9 +107,6 @@ build-datafile-from-api-requests = "nmdc_schema.build_datafile_from_api_requests class-sparql = "nmdc_schema.class_sparql:main" fetch-nmdc-schema = "nmdc_schema.nmdc_data:get_nmdc_jsonschema" generate-import-slots-regardless = "nmdc_schema.generate_import_slots_regardless:main" -get-mixs-slots-matching-slot-list = "nmdc_schema.get_mixs_slots_matching_slot_list:main" -get-mixs-slots-used-in-schema = "nmdc_schema.get_mixs_slots_used_in_schema:main" # see nmdc_schema/generate_import_slots_regardless.py -get-slots-from-class = "nmdc_schema.get_slots_from_class:main" # see tests/test_getters.py migration-recursion = 'nmdc_schema.migration_recursion:main' nmdc-data = "nmdc_schema.nmdc_data:cli" nmdc-version = "nmdc_schema.nmdc_version:cli" diff --git a/src/data/valid/Biosample-exhasutive.yaml b/src/data/Biosample-exhasutive.yaml similarity index 99% rename from src/data/valid/Biosample-exhasutive.yaml rename to src/data/Biosample-exhasutive.yaml index 1b2474390a..a5b41a676e 100644 --- a/src/data/valid/Biosample-exhasutive.yaml +++ b/src/data/Biosample-exhasutive.yaml @@ -274,8 +274,8 @@ redox_potential: has_raw_value: 300 millivolt salinity: has_raw_value: 25 practical salinity unit -salinity_meth: - has_raw_value: PMID:22895776 +#salinity_meth: +# has_raw_value: PMID:22895776 samp_mat_process: has_raw_value: filtering of seawater samp_store_dur: @@ -377,7 +377,7 @@ phosphate: #samp_collec_method: # has_raw_value: swabbing -samp_collec_method: swabbing +#samp_collec_method: swabbing samp_size: has_raw_value: 5 liters source_mat_id: @@ -563,8 +563,8 @@ host_diet: - has_raw_value: xxx host_dry_mass: has_raw_value: xxx -host_family_relation: - - xxx +#host_family_relation: +# - xxx host_genotype: has_raw_value: xxx host_growth_cond: @@ -841,7 +841,7 @@ root_med_suppl: salt_regm: - has_raw_value: xxx samp_capt_status: other -samp_collec_device: xxx +#samp_collec_device: xxx samp_collect_point: well samp_dis_stage: dissemination @@ -914,8 +914,8 @@ sludge_retent_time: has_raw_value: xxx soil_horizon: O horizon -soil_text_measure: - has_raw_value: xxx +#soil_text_measure: +# has_raw_value: xxx soil_texture_meth: xxx solar_irradiance: diff --git a/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml b/src/data/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml similarity index 99% rename from src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml rename to src/data/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml index 9b205e3778..50ed0cc7a5 100644 --- a/src/data/valid/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml +++ b/src/data/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml @@ -195,8 +195,8 @@ redox_potential: has_raw_value: 300 millivolt salinity: has_raw_value: 25 practical salinity unit -salinity_meth: - has_raw_value: PMID:22895776 +#salinity_meth: +# has_raw_value: PMID:22895776 samp_mat_process: has_raw_value: filtering of seawater samp_store_dur: @@ -304,7 +304,7 @@ light_regm: phosphate: has_raw_value: 0.7 micromole per liter -samp_collec_method: swabbing +#samp_collec_method: swabbing samp_size: has_raw_value: 5 liters source_mat_id: diff --git a/src/data/valid/Database-biosample-exhasutive.yaml b/src/data/Database-biosample-exhasutive.yaml similarity index 99% rename from src/data/valid/Database-biosample-exhasutive.yaml rename to src/data/Database-biosample-exhasutive.yaml index e3b318c298..04a85d77a9 100644 --- a/src/data/valid/Database-biosample-exhasutive.yaml +++ b/src/data/Database-biosample-exhasutive.yaml @@ -275,8 +275,8 @@ biosample_set: has_raw_value: 300 millivolt salinity: has_raw_value: 25 practical salinity unit - salinity_meth: - has_raw_value: PMID:22895776 +# salinity_meth: +# has_raw_value: PMID:22895776 samp_mat_process: has_raw_value: filtering of seawater samp_store_dur: @@ -377,7 +377,7 @@ biosample_set: has_raw_value: 0.7 micromole per liter #samp_collec_method: # has_raw_value: swabbing - samp_collec_method: swabbing +# samp_collec_method: swabbing samp_size: has_raw_value: 5 liters source_mat_id: @@ -563,8 +563,8 @@ biosample_set: - has_raw_value: xxx host_dry_mass: has_raw_value: xxx - host_family_relation: - - xxx +# host_family_relation: +# - xxx host_genotype: has_raw_value: xxx host_growth_cond: @@ -841,7 +841,7 @@ biosample_set: salt_regm: - has_raw_value: xxx samp_capt_status: other - samp_collec_device: xxx +# samp_collec_device: xxx samp_collect_point: well samp_dis_stage: dissemination @@ -914,8 +914,8 @@ biosample_set: has_raw_value: xxx soil_horizon: O horizon - soil_text_measure: - has_raw_value: xxx +# soil_text_measure: +# has_raw_value: xxx soil_texture_meth: xxx solar_irradiance: diff --git a/src/schema/core.yaml b/src/schema/core.yaml index b33eebdcd9..7adebe4b89 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -28,10 +28,10 @@ default_range: string subsets: - environment: { } - investigation: { } - nucleic acid sequence source: { } - sequencing: { } +# environment: { } +# investigation: { } +# nucleic acid sequence source: { } +# sequencing: { } types: diff --git a/src/schema/mixs_legacy.yaml b/src/schema/mixs_legacy.yaml new file mode 100644 index 0000000000..a2faaa763b --- /dev/null +++ b/src/schema/mixs_legacy.yaml @@ -0,0 +1,23 @@ +name: mixs_legacy +title: MIxS legacy terms for NMDC +id: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs_legacy.yaml +prefixes: + MIXS: + prefix_prefix: MIXS + prefix_reference: https://w3id.org/mixs/ + linkml: + prefix_prefix: linkml + prefix_reference: https://w3id.org/linkml/ + xsd: + prefix_prefix: xsd + prefix_reference: http://www.w3.org/2001/XMLSchema# + shex: + prefix_prefix: shex + prefix_reference: http://www.w3.org/ns/shex# + schema: + prefix_prefix: schema + prefix_reference: http://schema.org/ +default_prefix: MIXS +slots: + samp_collec_method: { } # todo too liberal + samp_collec_device: { } # todo too liberal diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 2b9a992838..6a544aa5e0 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -25,6 +25,7 @@ imports: - external_identifiers - linkml:types - mixs + - mixs_legacy - portal/emsl - portal/jgi_metagenomics - portal/jgi_metatranscriptomics @@ -544,7 +545,7 @@ classes: - collection_date - conduc - cool_syst_id - - core field + # - core field - crop_rotation - cult_root_med - cur_land_use @@ -593,7 +594,7 @@ classes: - env_local_scale - env_medium - env_package - - environment field + # - environment field - escalator - ethylbenzene - exp_duct @@ -636,9 +637,9 @@ classes: - growth_hormone_regm - hall_count - handidness - - has numeric value - - has raw value - - has unit + # - has numeric value + # - has raw value + # - has unit - hc_produced - hcr - hcr_fw_salinity @@ -663,7 +664,7 @@ classes: - host_common_name - host_diet - host_dry_mass - - host_family_relation + # - host_family_relation - host_genotype - host_growth_cond - host_height @@ -688,7 +689,7 @@ classes: - inorg_particles - inside_lux - int_wall_cond - - investigation field + # - investigation field - iw_bt_date_well - iwf - last_clean @@ -725,7 +726,7 @@ classes: - non_min_nutr_regm - nucl_acid_amp - nucl_acid_ext - - nucleic acid sequence source field + # - nucleic acid sequence source field - number_pets - number_plants - number_resident @@ -813,11 +814,11 @@ classes: - root_med_solid - root_med_suppl - salinity - - salinity_meth + # - salinity_meth - salt_regm - samp_capt_status - - samp_collec_device - - samp_collec_method + - samp_collec_device # todo legacy + - samp_collec_method # todo legacy - samp_collect_point - samp_dis_stage - samp_floor @@ -851,7 +852,7 @@ classes: - sediment_type - seq_meth - seq_quality_check - - sequencing field + # - sequencing field - sewage_type - shad_dev_water_mold - shading_device_cond @@ -868,7 +869,7 @@ classes: - sludge_retent_time - sodium - soil_horizon - - soil_text_measure + # - soil_text_measure - soil_texture_meth - soil_type - soil_type_meth @@ -1008,7 +1009,7 @@ classes: - light_regm # - micro_biomass_meth - phosphate - - samp_collec_method + # - samp_collec_method - samp_size # - soil_text_measure # - soil_texture_meth @@ -1101,8 +1102,8 @@ classes: examples: value: 100 - oxy_stat_samp: - range: oxy_stat_samp_enum + # oxy_stat_samp: + # range: oxy_stat_samp_enum id: required: true @@ -1324,9 +1325,9 @@ classes: - value: 5 mg N/ L todos: - check description. How are they different? - salinity_meth: - examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 + # salinity_meth: + # examples: + # - value: https://doi.org/10.1007/978-1-61779-986-0_28 sieving: comments: - Describe how samples were composited or sieved. diff --git a/tests/test_getters.py b/tests/test_getters.py deleted file mode 100644 index f93c032f26..0000000000 --- a/tests/test_getters.py +++ /dev/null @@ -1,35 +0,0 @@ -import logging - -import unittest - -from nmdc_schema.get_mixs_slots import MIxSSlotsGetter -from nmdc_schema.get_nmdc_view import ViewGetter -from nmdc_schema.get_slots_from_class import ClassSlotsGetter -from nmdc_schema.get_slots_from_view import SchemaSlotsGetter - - -class Getters(unittest.TestCase): - def test_view_getter(self): - view_getter = ViewGetter() - nmdc_view = view_getter.get_view() - self.assertEqual(nmdc_view.schema.name, "NMDC") - - def test_schema_slots_getter(self): - schema_slots_getter = SchemaSlotsGetter() - schema_slots = schema_slots_getter.get_schema_slots() - self.assertIsNotNone(schema_slots) - - def test_get_slots_from_class(self): - class_name = "Study" - class_slot_getter = ClassSlotsGetter() - class_slots = class_slot_getter.get_class_slots(class_name) - self.assertIsNotNone(class_slots) - - def test_get_mixs_slots(self): - mg = MIxSSlotsGetter() - mixs_slots = mg.get_unique_slot_names() - self.assertIsNotNone(mixs_slots) - - -if __name__ == "__main__": - unittest.main()