From 69ee3915520faa03e4432a0f1f8ba052058dcd93 Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Thu, 18 Jan 2024 14:50:52 -0800 Subject: [PATCH] Remove hardcoded enums and update ranges with new enum names --- schemasheets/tsv_in/enums.tsv | 53 ------------------- .../tsv_in/modifications_long.tsv | 25 ++++----- 2 files changed, 10 insertions(+), 68 deletions(-) diff --git a/schemasheets/tsv_in/enums.tsv b/schemasheets/tsv_in/enums.tsv index b02256da..edb8f6cb 100644 --- a/schemasheets/tsv_in/enums.tsv +++ b/schemasheets/tsv_in/enums.tsv @@ -27,34 +27,6 @@ DnaSampleFormatEnum RNAStable placeholder PV descr DnaSampleFormatEnum TE placeholder PV descr DnaSampleFormatEnum Water placeholder PV descr DnaSampleFormatEnum placeholder enum descr -EcosystemCategoryEnum Terrestrial placeholder PV descr https://github.com/microbiomedata/sheets_and_friends/issues/22 -EcosystemCategoryEnum placeholder enum descr -EcosystemEnum Environmental placeholder PV descr -EcosystemEnum placeholder enum descr -EcosystemSubtypeEnum Biocrust placeholder PV descr -EcosystemSubtypeEnum Biofilm placeholder PV descr -EcosystemSubtypeEnum Bulk soil placeholder PV descr -EcosystemSubtypeEnum Clay placeholder PV descr -EcosystemSubtypeEnum Floodplain placeholder PV descr -EcosystemSubtypeEnum Fossil placeholder PV descr -EcosystemSubtypeEnum Glacier placeholder PV descr -EcosystemSubtypeEnum Loam placeholder PV descr -EcosystemSubtypeEnum Mineral horizon placeholder PV descr -EcosystemSubtypeEnum Nature reserve placeholder PV descr -EcosystemSubtypeEnum Organic layer placeholder PV descr -EcosystemSubtypeEnum Paddy field/soil placeholder PV descr -EcosystemSubtypeEnum Pasture placeholder PV descr -EcosystemSubtypeEnum Peat placeholder PV descr -EcosystemSubtypeEnum Ranch placeholder PV descr -EcosystemSubtypeEnum Sand placeholder PV descr -EcosystemSubtypeEnum Silt placeholder PV descr -EcosystemSubtypeEnum Soil crust placeholder PV descr -EcosystemSubtypeEnum Unclassified placeholder PV descr -EcosystemSubtypeEnum Watershed placeholder PV descr -EcosystemSubtypeEnum Wetlands placeholder PV descr -EcosystemSubtypeEnum placeholder enum descr -EcosystemTypeEnum Soil placeholder PV descr -EcosystemTypeEnum placeholder enum descr EnvPackageEnum soil placeholder PV descr I don't think this is a MIxS term anymore, so it make sense to define it here EnvPackageEnum placeholder enum descr GrowthFacilEnum experimental_garden placeholder PV descr growth_facility https://genomicsstandardsconsortium.github.io/mixs/growth_facil/ string range according to MIxS @@ -89,31 +61,6 @@ RnaSampleFormatEnum placeholder enum descr SampleTypeEnum soil placeholder PV descr SampleTypeEnum water_extract_soil placeholder PV descr SampleTypeEnum placeholder enum descr -SpecificEcosystemEnum Agricultural placeholder PV descr -SpecificEcosystemEnum Agricultural land placeholder PV descr -SpecificEcosystemEnum Agricultural soil placeholder PV descr -SpecificEcosystemEnum Alpine placeholder PV descr -SpecificEcosystemEnum Bog placeholder PV descr -SpecificEcosystemEnum Boreal forest placeholder PV descr -SpecificEcosystemEnum Contaminated placeholder PV descr -SpecificEcosystemEnum Desert placeholder PV descr -SpecificEcosystemEnum Farm placeholder PV descr -SpecificEcosystemEnum Forest soil placeholder PV descr -SpecificEcosystemEnum Forest Soil placeholder PV descr -SpecificEcosystemEnum Grasslands placeholder PV descr -SpecificEcosystemEnum Meadow placeholder PV descr -SpecificEcosystemEnum Mine placeholder PV descr -SpecificEcosystemEnum Mine drainage placeholder PV descr -SpecificEcosystemEnum Oil-contaminated placeholder PV descr -SpecificEcosystemEnum Orchard soil placeholder PV descr -SpecificEcosystemEnum Permafrost placeholder PV descr -SpecificEcosystemEnum Riparian soil placeholder PV descr -SpecificEcosystemEnum River placeholder PV descr -SpecificEcosystemEnum Shrubland placeholder PV descr -SpecificEcosystemEnum Tropical rainforest placeholder PV descr -SpecificEcosystemEnum Unclassified placeholder PV descr -SpecificEcosystemEnum Uranium contaminated placeholder PV descr -SpecificEcosystemEnum placeholder enum descr StoreCondEnum fresh placeholder PV descr storage_condt see samp_store_dur, samp_store_loc, samp_store_temp and store_cond (which takes a string range according to mixs-source). StoreCondEnum frozen placeholder PV descr StoreCondEnum lyophilized placeholder PV descr diff --git a/sheets_and_friends/tsv_in/modifications_long.tsv b/sheets_and_friends/tsv_in/modifications_long.tsv index 579cc7e3..a2f79c3f 100644 --- a/sheets_and_friends/tsv_in/modifications_long.tsv +++ b/sheets_and_friends/tsv_in/modifications_long.tsv @@ -55,21 +55,17 @@ JgiMgInterface dna_seq_project_name replace_attribute required true JgiMgInterface dna_seq_project_pi replace_attribute required true JgiMgInterface dna_volume replace_attribute required true JgiMtInterface dnase_rna replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem add_attribute notes range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. -SoilInterface ecosystem replace_attribute range EcosystemEnum -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem replace_attribute range string +SoilInterface ecosystem replace_attribute range EcosystemForSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem replace_attribute range EcosystemEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_category add_attribute notes string or EcosystemCategoryEnum range? -SoilInterface ecosystem_category replace_attribute range EcosystemCategoryEnum -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_category replace_attribute range string +SoilInterface ecosystem_category replace_attribute range EcosystemCategoryForSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_category replace_attribute range EcosystemCategoryEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_category replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_subtype add_attribute notes string or EcosystemSubtypeEnum range? -SoilInterface ecosystem_subtype replace_attribute range EcosystemSubtypeEnum -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_subtype replace_attribute range string +SoilInterface ecosystem_subtype replace_attribute range EcosystemSubtypeForSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_subtype replace_attribute range EcosystemSubtypeEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_subtype replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_type add_attribute notes string or EcosystemTypeEnum range? -SoilInterface ecosystem_type replace_attribute range EcosystemTypeEnum -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_type replace_attribute range string +SoilInterface ecosystem_type replace_attribute range EcosystemTypeForSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_type replace_attribute range EcosystemTypeEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_type replace_attribute recommended true AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev overwrite_examples examples 225| 0|1250 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev replace_attribute range float @@ -199,9 +195,8 @@ DhMultiviewCommonColumnsMixin source_mat_id overwrite_examples examples IGSN:A DhMultiviewCommonColumnsMixin source_mat_id add_attribute notes The source material IS the Globally Unique ID DhMultiviewCommonColumnsMixin source_mat_id replace_attribute string_serialization {text}:{text} DhMultiviewCommonColumnsMixin source_mat_id add_attribute todos Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID. -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface specific_ecosystem add_attribute notes string or SpecificEcosystemEnum range? -SoilInterface specific_ecosystem replace_attribute range SpecificEcosystemEnum -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface specific_ecosystem replace_attribute range string +SoilInterface specific_ecosystem replace_attribute range SpecificEcosystemForSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface specific_ecosystem replace_attribute range SpecificEcosystemEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface specific_ecosystem replace_attribute recommended true SoilInterface store_cond replace_attribute description Explain how the soil sample is stored (fresh/frozen/other). SoilInterface store_cond replace_attribute range StoreCondEnum