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Merge pull request #1696 from microbiomedata/1695-move-yq-commands-fr…
…om-localmixs_regenmixs_subset_modifiedyaml-target-into-a-separate-file move lists of yq commands from project.Makefile target into a separate files
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| '.slots.agrochem_addition.range |= "TextValue"' | ||
| '.slots.air_temp_regm.range |= "TextValue"' | ||
| '.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.bathroom_count.range |= "TextValue"' | ||
| '.slots.bedroom_count.range |= "TextValue"' | ||
| '.slots.biocide_admin_method.range |= "TextValue"' | ||
| '.slots.biomass.range |= "TextValue"' | ||
| '.slots.chem_administration.range |= "ControlledTermValue"' | ||
| '.slots.chem_mutagen.range |= "TextValue"' | ||
| '.slots.chem_treat_method.range |= "string"' | ||
| '.slots.collection_date.range |= "TimestampValue"' | ||
| '.slots.cool_syst_id.range |= "TextValue"' | ||
| '.slots.date_last_rain.range |= "TimestampValue"' | ||
| '.slots.diether_lipids.range |= "TextValue"' | ||
| '.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.escalator.range |= "TextValue"' | ||
| '.slots.exp_pipe.range |= "QuantityValue"' | ||
| '.slots.experimental_factor.range |= "ControlledTermValue"' | ||
| '.slots.ext_door.range |= "TextValue"' | ||
| '.slots.extreme_event.range |= "TimestampValue"' | ||
| '.slots.fertilizer_regm.range |= "TextValue"' | ||
| '.slots.fire.range |= "TimestampValue"' | ||
| '.slots.flooding.range |= "TimestampValue"' | ||
| '.slots.floor_count.range |= "TextValue"' | ||
| '.slots.freq_clean.range |= "QuantityValue"' | ||
| '.slots.freq_cook.range |= "QuantityValue"' | ||
| '.slots.fungicide_regm.range |= "TextValue"' | ||
| '.slots.gaseous_environment.range |= "TextValue"' | ||
| '.slots.gaseous_substances.range |= "TextValue"' | ||
| '.slots.gravity.range |= "TextValue"' | ||
| '.slots.growth_facil.range |= "ControlledTermValue"' | ||
| '.slots.growth_hormone_regm.range |= "TextValue"' | ||
| '.slots.hall_count.range |= "TextValue"' | ||
| '.slots.hall_count.range |= "TextValue"' | ||
| '.slots.hcr_pressure.range |= "TextValue"' | ||
| '.slots.hcr_temp.range |= "TextValue"' | ||
| '.slots.heat_sys_deliv_meth.range |= "string"' | ||
| '.slots.heat_system_id.range |= "TextValue"' | ||
| '.slots.heavy_metals.range |= "TextValue"' | ||
| '.slots.herbicide_regm.range |= "TextValue"' | ||
| '.slots.host_body_product.range |= "ControlledTermValue"' | ||
| '.slots.host_body_site.range |= "ControlledTermValue"' | ||
| '.slots.host_family_relation.range |= "string"' | ||
| '.slots.host_phenotype.range |= "ControlledTermValue"' | ||
| '.slots.host_subspecf_genlin.range |= "string"' | ||
| '.slots.host_symbiont.range |= "string"' | ||
| '.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.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.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_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.pesticide_regm.range |= "TextValue"' | ||
| '.slots.phaeopigments.range |= "TextValue"' | ||
| '.slots.phosplipid_fatt_acid.range |= "TextValue"' | ||
| '.slots.plant_growth_med.range |= "ControlledTermValue"' | ||
| '.slots.plant_struc.range |= "ControlledTermValue"' | ||
| '.slots.pollutants.range |= "TextValue"' | ||
| '.slots.porosity.range |= "TextValue"' | ||
| '.slots.pres_animal_insect.range |= "string"' | ||
| '.slots.prev_land_use_meth.range |= "string"' | ||
| '.slots.prod_start_date.range |= "TimestampValue"' | ||
| '.slots.radiation_regm.range |= "TextValue"' | ||
| '.slots.rainfall_regm.range |= "TextValue"' | ||
| '.slots.resins_pc.range |= "TextValue"' | ||
| '.slots.room_architec_elem.range |= "string"' | ||
| '.slots.room_count.range |= "TextValue"' | ||
| '.slots.room_dim.range |= "TextValue"' | ||
| '.slots.room_door_dist.range |= "TextValue"' | ||
| '.slots.room_net_area.range |= "TextValue"' | ||
| '.slots.room_occup.range |= "QuantityValue"' | ||
| '.slots.room_vol.range |= "TextValue"' | ||
| '.slots.root_med_carbon.range |= "TextValue"' | ||
| '.slots.root_med_macronutr.range |= "TextValue"' | ||
| '.slots.root_med_micronutr.range |= "TextValue"' | ||
| '.slots.root_med_ph.range |= "QuantityValue"' | ||
| '.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_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.soil_texture_meth.range |= "string"' | ||
| '.slots.soluble_inorg_mat.range |= "TextValue"' | ||
| '.slots.soluble_org_mat.range |= "TextValue"' | ||
| '.slots.suspend_solids.range |= "TextValue"' | ||
| '.slots.tot_nitro_cont_meth.range |= "string"' | ||
| '.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.window_open_freq.range |= "TextValue"' | ||
| '.slots.window_size.range |= "TextValue"' | ||
|
|
||
| 'del(.classes)' | ||
| 'del(.enums.[].name)' | ||
| 'del(.enums.[].permissible_values.[].text)' | ||
| 'del(.slots.[].name)' | ||
| 'del(.slots.add_recov_method.pattern)' | ||
| 'del(.subsets.[].name)' | ||
|
|
||
| '.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 | ||
| 'del(.slots.host_taxid.examples)' | ||
| 'del(.slots.host_taxid.string_serialization)' | ||
| 'del(.slots.samp_taxon_id.examples)' | ||
| 'del(.slots.samp_taxon_id.string_serialization)' | ||
|
|
||
| '.slots.host_taxid.comments |= ["Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value"]' | ||
| '.slots.host_taxid.range = "ControlledIdentifiedTermValue"' | ||
| '.slots.samp_taxon_id.comments |= ["coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value"]' | ||
| '.slots.samp_taxon_id.range = "ControlledIdentifiedTermValue"' | ||
|
|
||
|
|
||
| # add "M horizon" to soil_horizon_enum | ||
| '.enums.soil_horizon_enum.permissible_values.["M horizon"] = {}' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| # probably should have made a list of classes and then looped over a parameterized version of this | ||
| # could also assert that the range is string | ||
| '(.classes[] | select(.name == "Biosample") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "Biosample") | .slot_usage.part_of.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "Biosample") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "DataObject") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "DataObject") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.part_of.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_input.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_output.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' | ||
| '(.classes[] | select(.name == "Study") | .slot_usage.id.pattern) = ".*"' | ||
| '(.classes[] | select(.name == "Study") | .slot_usage.id.structured_pattern.syntax) = ".*"' |
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