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DO NOT MERGE YET change MIxS import to 6.2 #1386

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9becea7
#1368 generate-import-slots-regardless --mixs-schema-url option
turbomam Nov 17, 2023
2e31c2d
minimal to pass MongoDB contents
turbomam Nov 20, 2023
904855a
builds and local tests pass
turbomam Jul 17, 2024
b29d77c
remove seq_meth annotations
turbomam Jul 17, 2024
b4e7709
more decisve removals
turbomam Jul 17, 2024
fd65049
remove temporary fixes
turbomam Jul 17, 2024
d4b37a9
one line frs instantiation
turbomam Jul 17, 2024
d2bfcf1
talk to @eecavanna about schema length doc tests
turbomam Jul 17, 2024
74cf8e6
add GSC's schema settings
turbomam Jul 17, 2024
9c9f652
today's data in MongoDB passes make-rdf
turbomam Jul 18, 2024
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490 changes: 0 additions & 490 deletions assets/import_mixs_slots_regardless.tsv
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485 changes: 485 additions & 0 deletions assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv
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1 change: 0 additions & 1 deletion assets/other_mixs_yaml_files/mixs_template.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ id: https://w3id.org/nmdc/mixs
subsets:
mixs_environmental_triad:
title: MIxS Environmental Triad
mixs extension: { }

notes:
- removed several MIxS terms/slots that were sharing slot uris; commented out Biosample assignments
Expand Down
79 changes: 74 additions & 5 deletions assets/yq-for-mixs_subset_modified.txt
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Original file line number Diff line number Diff line change
@@ -1,28 +1,46 @@

'.slots.abs_air_humidity.range |= "QuantityValue"'
'.slots.agrochem_addition.range |= "TextValue"'
'.slots.air_temp_regm.range |= "TextValue"'
'.slots.ammonium.range |= "QuantityValue"'
'.slots.antibiotic_regm.range |= "TextValue"'
'.slots.aromatics_pc.range |= "TextValue"'
'.slots.asphaltenes_pc.range |= "TextValue"'
'.slots.atmospheric_data.range |= "TextValue"'
'.slots.avg_occup.range |= "TextValue"'
'.slots.avg_temp.range |= "QuantityValue"'
'.slots.bathroom_count.range |= "TextValue"'
'.slots.bedroom_count.range |= "TextValue"'
'.slots.biocide_admin_method.range |= "TextValue"'
'.slots.biomass.range |= "TextValue"'
'.slots.calcium.range |= "QuantityValue"'
'.slots.carb_nitro_ratio.range |= "QuantityValue"'
'.slots.chem_administration.range |= "ControlledTermValue"'
'.slots.chem_mutagen.range |= "TextValue"'
'.slots.chem_treat_method.range |= "string"'
'.slots.chloride.range |= "QuantityValue"'
'.slots.chlorophyll.range |= "QuantityValue"'
'.slots.collection_date.range |= "TimestampValue"'
'.slots.conduc.range |= "QuantityValue"'
'.slots.cool_syst_id.range |= "TextValue"'
'.slots.cur_vegetation.range |= "QuantityValue"'
'.slots.cur_vegetation.range |= "TextValue"'
'.slots.date_last_rain.range |= "TimestampValue"'
'.slots.depth.range |= "QuantityValue"'
'.slots.diether_lipids.range |= "TextValue"'
'.slots.diss_inorg_carb.range |= "QuantityValue"'
'.slots.diss_inorg_nitro.range |= "QuantityValue"'
'.slots.diss_iron.range |= "QuantityValue"'
'.slots.diss_org_carb.range |= "QuantityValue"'
'.slots.diss_oxygen.range |= "QuantityValue"'
'.slots.elevator.range |= "TextValue"'
'.slots.emulsions.range |= "TextValue"'
'.slots.env_broad_scale.range |= "ControlledIdentifiedTermValue"'
'.slots.env_local_scale.range |= "ControlledIdentifiedTermValue"'
'.slots.env_medium.range |= "ControlledIdentifiedTermValue"'
'.slots.env_medium.range |= "ControlledIdentifiedTermValue"'
'.slots.escalator.range |= "TextValue"'
'.slots.exp_pipe.range |= "QuantityValue"'
'.slots.experimental_factor.multivalued |= false'
'.slots.experimental_factor.range |= "ControlledTermValue"'
'.slots.ext_door.range |= "TextValue"'
'.slots.extreme_event.range |= "TimestampValue"'
Expand All @@ -35,6 +53,7 @@
'.slots.fungicide_regm.range |= "TextValue"'
'.slots.gaseous_environment.range |= "TextValue"'
'.slots.gaseous_substances.range |= "TextValue"'
'.slots.gravidity.range |= "TextValue"'
'.slots.gravity.range |= "TextValue"'
'.slots.growth_facil.range |= "ControlledTermValue"'
'.slots.growth_hormone_regm.range |= "TextValue"'
Expand All @@ -46,41 +65,52 @@
'.slots.heat_system_id.range |= "TextValue"'
'.slots.heavy_metals.range |= "TextValue"'
'.slots.herbicide_regm.range |= "TextValue"'
'.slots.host_age.range |= "QuantityValue"'
'.slots.host_body_product.range |= "ControlledTermValue"'
'.slots.host_body_site.range |= "ControlledTermValue"'
'.slots.host_family_relation.range |= "string"'
'.slots.host_dry_mass.range |= "QuantityValue"'
'.slots.host_height.range |= "QuantityValue"'
'.slots.host_life_stage.range |= "TextValue"'
'.slots.host_phenotype.range |= "ControlledTermValue"'
'.slots.host_subspecf_genlin.range |= "string"'
'.slots.host_symbiont.range |= "string"'
'.slots.humidity.range |= "QuantityValue"'
'.slots.humidity_regm.range |= "TextValue"'
'.slots.inorg_particles.range |= "TextValue"'
'.slots.iw_bt_date_well.range |= "TimestampValue"'
'.slots.last_clean.range |= "TimestampValue"'
'.slots.lat_lon.range |= "GeolocationValue"'
'.slots.light_regm.range |= "TextValue"'
'.slots.magnesium.range |= "QuantityValue"'
'.slots.max_occup.range |= "QuantityValue"'
'.slots.micro_biomass_meth.range |= "string"'
'.slots.mineral_nutr_regm.range |= "TextValue"'
'.slots.misc_param.range |= "TextValue"'
'.slots.n_alkanes.range |= "TextValue"'
'.slots.nitrate.range |= "QuantityValue"'
'.slots.nitro.range |= "QuantityValue"'
'.slots.non_min_nutr_regm.range |= "string"'
'.slots.number_pets.range |= "QuantityValue"'
'.slots.number_plants.range |= "QuantityValue"'
'.slots.number_resident.range |= "QuantityValue"'
'.slots.occup_density_samp.range |= "QuantityValue"'
'.slots.occup_samp.range |= "QuantityValue"'
'.slots.org_carb.range |= "QuantityValue"'
'.slots.org_count_qpcr_info.range |= "string"'
'.slots.org_particles.range |= "TextValue"'
'.slots.organism_count.range |= "QuantityValue"'
'.slots.particle_class.range |= "TextValue"'
'.slots.permeability.range |= "TextValue"'
'.slots.perturbation.range |= "TextValue"'
'.slots.pesticide_regm.range |= "TextValue"'
'.slots.phaeopigments.range |= "TextValue"'
'.slots.phosplipid_fatt_acid.range |= "TextValue"'
'.slots.photon_flux.range |= "QuantityValue"'
'.slots.plant_growth_med.range |= "ControlledTermValue"'
'.slots.plant_struc.range |= "ControlledTermValue"'
'.slots.pollutants.range |= "TextValue"'
'.slots.porosity.range |= "TextValue"'
'.slots.potassium.range |= "QuantityValue"'
'.slots.pres_animal_insect.range |= "string"'
'.slots.prev_land_use_meth.range |= "string"'
'.slots.prod_start_date.range |= "TimestampValue"'
Expand All @@ -101,31 +131,46 @@
'.slots.root_med_regl.range |= "TextValue"'
'.slots.root_med_suppl.range |= "TextValue"'
'.slots.salt_regm.range |= "TextValue"'
'.slots.samp_collec_device.range |= "string"'
'.slots.samp_collec_method.range |= "string"'
'.slots.samp_loc_corr_rate.range |= "TextValue"'
'.slots.samp_mat_process.range |= "ControlledTermValue"'
'.slots.samp_md.range |= "QuantityValue"'
'.slots.samp_name.range |= "string"'
'.slots.samp_preserv.range |= "TextValue"'
'.slots.samp_room_id.range |= "TextValue"'
'.slots.samp_size.range |= "QuantityValue"'
'.slots.samp_store_temp.range |= "QuantityValue"'
'.slots.samp_time_out.range |= "TextValue"'
'.slots.samp_transport_cond.range |= "TextValue"'
'.slots.samp_tvdss.range |= "TextValue"'
'.slots.saturates_pc.range |= "TextValue"'
'.slots.shad_dev_water_mold.range |= "string"'
'.slots.sieving.range |= "TextValue"'
'.slots.size_frac.range |= "TextValue"'
'.slots.sodium.range |= "QuantityValue"'
'.slots.soil_texture_meth.range |= "string"'
'.slots.solar_irradiance.multivalued |= false'
'.slots.solar_irradiance.range |= "QuantityValue"'
'.slots.soluble_inorg_mat.range |= "TextValue"'
'.slots.soluble_org_mat.range |= "TextValue"'
'.slots.soluble_react_phosp.range |= "QuantityValue"'
'.slots.source_mat_id.multivalued |= false'
'.slots.source_mat_id.range |= "TextValue"'
'.slots.store_cond.range |= "TextValue"'
'.slots.sulfate.range |= "QuantityValue"'
'.slots.suspend_solids.range |= "TextValue"'
'.slots.temp.range |= "QuantityValue"'
'.slots.tot_carb.range |= "QuantityValue"'
'.slots.tot_nitro.range |= "QuantityValue"'
'.slots.tot_nitro_cont_meth.range |= "string"'
'.slots.tot_nitro_content.range |= "QuantityValue"'
'.slots.tot_org_carb.range |= "QuantityValue"'
'.slots.tot_phosp.range |= "QuantityValue"'
'.slots.viscosity.range |= "TextValue"'
'.slots.volatile_org_comp.range |= "TextValue"'
'.slots.water_cont_soil_meth.range |= "string"'
'.slots.water_temp_regm.range |= "TextValue"'
'.slots.watering_regm.range |= "TextValue"'
'.slots.wind_speed.range |= "QuantityValue"'
'.slots.window_open_freq.range |= "TextValue"'
'.slots.window_size.range |= "TextValue"'

Expand Down Expand Up @@ -155,7 +200,7 @@
'del(.slots.["has unit"])'

# add "M horizon" to soil_horizon_enum
'.enums.soil_horizon_enum.permissible_values.["M horizon"] = {}'
'.enums.SOIL_HORIZON_ENUM.permissible_values.["M horizon"] = {}'

# as of 2024-01-30:
# ValueError: Conflicting URIs (https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml, https://w3id.org/linkml/types) for item: date
Expand All @@ -167,3 +212,27 @@ make: *** [Makefile:102: gen-project] Error 1
'.slots.fire.range |= "string"'
'.slots.flooding.range |= "string"'
'.slots.water_content.range |= "string"'

'del(.slots[].required)'
'del(.slots[].in_subset)'
'del(.subsets)'

'.slots.samp_collec_method = .slots.samp_collect_method'
'.slots.samp_collec_method.notes += "cloned from MIxS 6.2 samp_collect_method"'
'del(.slots.samp_collect_method)'
'.slots.samp_collec_method.range |= "string"'
'del(.slots.samp_collec_method.pattern)'
'del(.slots.samp_collec_method.structured_pattern)'

'.slots.samp_collec_device = .slots.samp_collect_device'
'.slots.samp_collec_device.notes += "cloned from MIxS 6.2 samp_collect_device"'
'del(.slots.samp_collect_device)'
'.slots.samp_collec_device.range |= "string"'
'del(.slots.samp_collec_device.pattern)'
'del(.slots.samp_collec_device.structured_pattern)'

'del(.slots.micro_biomass_meth.pattern)'
'del(.slots.micro_biomass_meth.structured_pattern)'

'del(.slots.water_content.pattern)'
'del(.slots.water_content.structured_pattern)'
54 changes: 0 additions & 54 deletions nmdc_schema/generate_import_slots_regardless.py
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47 changes: 0 additions & 47 deletions nmdc_schema/get_mixs_slots.py
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50 changes: 0 additions & 50 deletions nmdc_schema/get_mixs_slots_matching_slot_list.py
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40 changes: 0 additions & 40 deletions nmdc_schema/get_mixs_slots_used_in_schema.py
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