From 3ad4ef8e38cfed7e32818e090a66c553e69903b3 Mon Sep 17 00:00:00 2001 From: markquintontulloch Date: Fri, 5 May 2023 21:23:33 +0100 Subject: [PATCH 1/8] Secondary identifiers update --- model/schema/affectedGenomicModel.yaml | 30 ++++++++++++++++++++++++++ model/schema/alleleDTO.yaml | 10 +-------- model/schema/core.yaml | 10 +++++++-- model/schema/gene.yaml | 26 ++++++++++++++++++++++ test/data/agm_test.json | 20 +++++++++++++---- test/data/allele_test.json | 11 +++++++++- test/data/gene_test.json | 9 ++++++++ 7 files changed, 100 insertions(+), 16 deletions(-) diff --git a/model/schema/affectedGenomicModel.yaml b/model/schema/affectedGenomicModel.yaml index e1915fb95..604282754 100644 --- a/model/schema/affectedGenomicModel.yaml +++ b/model/schema/affectedGenomicModel.yaml @@ -43,6 +43,7 @@ classes: slots: - name - subtype + - agm_secondary_ids - components - sequence_targeting_reagents - parental_populations @@ -54,10 +55,22 @@ classes: slots: - name - subtype_name + - agm_secondary_id_dtos - reference_curies - sequence_targeting_reagent_curies - component_dtos + AgmSecondaryIdSlotAnnotation: + is_a: SlotAnnotation + slots: + - single_agm + - secondary_id + slot_usage: + single_allele: + required: true + secondary_id: + required: true + AffectedGenomicModelComponent: is_a: AuditedObject description: >- @@ -86,6 +99,10 @@ slots: range: string required: true + single_agm: + range: AffectedGenomicModel + multivalued: false + subtype: description: >- Subtype of affected genomic model - permissible values: strain / genotype @@ -102,6 +119,19 @@ slots: range: string required: true + agm_secondary_ids: + description: Secondary IDs of a given allele + domain: AffectedGenomicModel + range: AgmSecondaryIdSlotAnnotation + multivalued: true + + agm_secondary_id_dtos: + domain: AffectedGenomicModelDTO + range: SecondaryIdSlotAnnotationDTO + multivalued: true + inlined: true + inlined_as_list: true + components: singular_name: component description: >- diff --git a/model/schema/alleleDTO.yaml b/model/schema/alleleDTO.yaml index 33ea42580..619605ccd 100644 --- a/model/schema/alleleDTO.yaml +++ b/model/schema/alleleDTO.yaml @@ -170,14 +170,6 @@ classes: note_dto: required: true - AlleleSecondaryIdSlotAnnotationDTO: - is_a: SlotAnnotationDTO - slots: - - secondary_id - slot_usage: - secondary_id: - required: true - ## ------------ ## ALLELE DTO ASSOCIATION CLASSES @@ -376,7 +368,7 @@ slots: allele_secondary_id_dtos: domain: AlleleDTO - range: AlleleSecondaryIdSlotAnnotationDTO + range: SecondaryIdSlotAnnotationDTO multivalued: true inlined: true inlined_as_list: true diff --git a/model/schema/core.yaml b/model/schema/core.yaml index fca952ccb..9c7b35e37 100644 --- a/model/schema/core.yaml +++ b/model/schema/core.yaml @@ -120,14 +120,12 @@ classes: RNA transcript translation). slots: - cross_references - - secondary_identifiers - genomic_location_associations GenomicEntityDTO: is_a: BiologicalEntityDTO slots: - cross_reference_dtos - - secondary_identifiers - genomic_location_association_dtos Transcript: @@ -277,6 +275,14 @@ classes: any_of: - equals_string: systematic_name + SecondaryIdSlotAnnotationDTO: + is_a: SlotAnnotationDTO + slots: + - secondary_id + slot_usage: + secondary_id: + required: true + Association: is_a: AuditedObject diff --git a/model/schema/gene.yaml b/model/schema/gene.yaml index b2b9dd699..dd34d8fb3 100644 --- a/model/schema/gene.yaml +++ b/model/schema/gene.yaml @@ -54,6 +54,7 @@ classes: - gene_full_name - gene_systematic_name - gene_synonyms + - gene_secondary_ids - related_notes - gene_type - gene_types_secondary @@ -91,6 +92,7 @@ classes: - gene_full_name_dto - gene_systematic_name_dto - gene_synonym_dtos + - gene_secondary_id_dtos - gene_type_curie GeneSymbolSlotAnnotation: @@ -119,6 +121,17 @@ classes: notes: >- permissible_values: full_name (VocabularyTerm) + GeneSecondaryIdSlotAnnotation: + is_a: SlotAnnotation + slots: + - single_gene + - secondary_id + slot_usage: + single_gene: + required: true + secondary_id: + required: true + GeneSystematicNameSlotAnnotation: is_a: NameSlotAnnotation description: >- @@ -239,6 +252,19 @@ slots: required: false inlined: true + gene_secondary_ids: + description: Secondary IDs of a given gene + domain: Gene + range: GeneSecondaryIdSlotAnnotation + multivalued: true + + gene_secondary_id_dtos: + domain: GeneDTO + range: SecondaryIdSlotAnnotationDTO + multivalued: true + inlined: true + inlined_as_list: true + gene_systematic_name: description: >- The one current systematic name for a gene: e.g., YHR084W, R09F10.2. diff --git a/test/data/agm_test.json b/test/data/agm_test.json index 6f913933b..424b33f8a 100644 --- a/test/data/agm_test.json +++ b/test/data/agm_test.json @@ -8,8 +8,14 @@ "updated_by_curie": "ZFIN", "internal": false, "name": "TL + MO1-hars", - "secondary_identifiers": [ - "ZFIN:ZDB-FISH-123456-1" + "agm_secondary_id_dtos": [ + { + "secondary_id": "ZFIN:ZDB-FISH-123456-1", + "evidence_curies": [ + "PMID:00020012" + ], + "internal": false + } ], "reference_curies": [], "sequence_targeting_reagent_curies": [ @@ -35,8 +41,14 @@ "updated_by_curie": "ZFIN", "internal": false, "name": "pax2atb21/tb21", - "secondary_identifiers": [ - "ZFIN:ZDB-FISH-123456-1" + "agm_secondary_id_dtos": [ + { + "secondary_id": "ZFIN:ZDB-FISH-123456-1", + "evidence_curies": [ + "PMID:00020012" + ], + "internal": false + } ], "reference_curies": [], "component_dtos": [ diff --git a/test/data/allele_test.json b/test/data/allele_test.json index 3f9c3c6e4..dc5ac7813 100644 --- a/test/data/allele_test.json +++ b/test/data/allele_test.json @@ -39,7 +39,16 @@ "PMID:01231002" ], "internal": false - } + }, + "allele_secondary_id_dtos": [ + { + "secondary_id": "scnd_id", + "evidence_curies": [ + "PMID:00020012" + ], + "internal": false + } + ] }, { "curie": "ZFIN:ZDB-ALT-130411-947", diff --git a/test/data/gene_test.json b/test/data/gene_test.json index 84b92725e..6fe0811ce 100644 --- a/test/data/gene_test.json +++ b/test/data/gene_test.json @@ -64,6 +64,15 @@ "internal": false } ], + "gene_secondary_id_dtos": [ + { + "secondary_id": "scnd_id", + "evidence_curies": [ + "PMID:00020012" + ], + "internal": false + } + ], "cross_reference_dtos": [ { "referenced_curie": "ZFIN:ZDB-GENE-010226-1", From 392d7613dbf7ed3b9a752d451c64ad5ba19cbd9c Mon Sep 17 00:00:00 2001 From: markquintontulloch Date: Fri, 5 May 2023 21:41:53 +0100 Subject: [PATCH 2/8] Remove remaining secondary IDs from sqtr test --- test/data/sqtr_test.json | 9 --------- 1 file changed, 9 deletions(-) diff --git a/test/data/sqtr_test.json b/test/data/sqtr_test.json index 4558c0d0c..d61e128e2 100644 --- a/test/data/sqtr_test.json +++ b/test/data/sqtr_test.json @@ -7,9 +7,6 @@ "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN", "internal": false, - "secondary_identifiers": [ - "ZFIN:ZDB-MRPHLNO-123456-1" - ], "reference_curies": [ "PMID:19648295" ], @@ -42,9 +39,6 @@ "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN", "internal": false, - "secondary_identifiers": [ - "ZFIN:ZDB-MRPHLNO-123456-1" - ], "reference_curies": [ "PMID:19648295" ] @@ -66,9 +60,6 @@ "created_by_curie": "ZFIN", "updated_by_curie": "ZFIN", "internal": false, - "secondary_identifiers": [ - "ZFIN:ZDB-MRPHLNO-123456-1" - ], "reference_curies": [ "PMID:19648295" ] From 96f471d2b05a4bd942dda10b62abdbc69af27e4f Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 5 May 2023 20:55:56 +0000 Subject: [PATCH 3/8] Automated artifacts regeneration [skip actions] --- .../jsonschema/allianceModel.schema.json | 381 ++++++++++-------- 1 file changed, 208 insertions(+), 173 deletions(-) diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json index d569dd085..7f7354232 100644 --- a/generated/jsonschema/allianceModel.schema.json +++ b/generated/jsonschema/allianceModel.schema.json @@ -687,6 +687,13 @@ "additionalProperties": false, "description": "Includes inbred strains, stocks, disease models and mutant genotypes", "properties": { + "agm_secondary_ids": { + "description": "Secondary IDs of a given allele", + "items": { + "$ref": "#/$defs/AgmSecondaryIdSlotAnnotation" + }, + "type": "array" + }, "components": { "description": "Collection of genomic components that make up a model, i.e. 'allele', each with a zygosity", "items": { @@ -761,12 +768,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "sequence_targeting_reagents": { "items": { "type": "string" @@ -909,6 +910,12 @@ "additionalProperties": false, "description": "Ingest class for AGMs", "properties": { + "agm_secondary_id_dtos": { + "items": { + "$ref": "#/$defs/SecondaryIdSlotAnnotationDTO" + }, + "type": "array" + }, "component_dtos": { "items": { "$ref": "#/$defs/AffectedGenomicModelComponentDTO" @@ -978,12 +985,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "sequence_targeting_reagent_curies": { "items": { "type": "string" @@ -1068,6 +1069,67 @@ "title": "AggregationDatabaseEnum", "type": "string" }, + "AgmSecondaryIdSlotAnnotation": { + "additionalProperties": false, + "description": "", + "properties": { + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "evidence": { + "description": "", + "items": { + "type": "string" + }, + "type": "array" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "secondary_id": { + "type": "string" + }, + "single_agm": { + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "secondary_id", + "internal" + ], + "title": "AgmSecondaryIdSlotAnnotation", + "type": "object" + }, "Allele": { "additionalProperties": false, "description": "One of multiple possible forms of a functional genomic element (most often described as a locus or gene), differing from the reference DNA sequence. The genomic element can be endogenous or constructed.", @@ -1284,12 +1346,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -1804,7 +1860,7 @@ }, "allele_secondary_id_dtos": { "items": { - "$ref": "#/$defs/AlleleSecondaryIdSlotAnnotationDTO" + "$ref": "#/$defs/SecondaryIdSlotAnnotationDTO" }, "type": "array" }, @@ -1897,12 +1953,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -4253,64 +4303,6 @@ "title": "AlleleSecondaryIdSlotAnnotation", "type": "object" }, - "AlleleSecondaryIdSlotAnnotationDTO": { - "additionalProperties": false, - "description": "", - "properties": { - "created_by_curie": { - "description": "Curie of the Person object representing the individual that created the entity", - "type": "string" - }, - "date_created": { - "description": "The date on which an entity was created. This can be applied to nodes or edges.", - "format": "date-time", - "type": "string" - }, - "date_updated": { - "description": "Date on which an entity was last modified.", - "format": "date-time", - "type": "string" - }, - "db_date_created": { - "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", - "format": "date-time", - "type": "string" - }, - "db_date_updated": { - "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", - "format": "date-time", - "type": "string" - }, - "evidence_curies": { - "description": "Curies of InformationContentEntity objects given as evidence", - "items": { - "type": "string" - }, - "type": "array" - }, - "internal": { - "description": "Classifies the entity as private (for internal use) or not (for public use).", - "type": "boolean" - }, - "obsolete": { - "description": "Entity is no longer current.", - "type": "boolean" - }, - "secondary_id": { - "type": "string" - }, - "updated_by_curie": { - "description": "Curie of the Person object representing the individual that updated the entity", - "type": "string" - } - }, - "required": [ - "secondary_id", - "internal" - ], - "title": "AlleleSecondaryIdSlotAnnotationDTO", - "type": "object" - }, "AlleleSymbolSlotAnnotation": { "additionalProperties": false, "description": "The one current symbol for the allele.", @@ -6356,12 +6348,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -6436,12 +6422,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -6783,12 +6763,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -6864,12 +6838,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -7036,12 +7004,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -9598,6 +9560,13 @@ "$ref": "#/$defs/GeneFullNameSlotAnnotation", "description": "The one current full name for a gene: e.g., wingless, paired box 2a." }, + "gene_secondary_ids": { + "description": "Secondary IDs of a given gene", + "items": { + "$ref": "#/$defs/GeneSecondaryIdSlotAnnotation" + }, + "type": "array" + }, "gene_symbol": { "$ref": "#/$defs/GeneSymbolSlotAnnotation", "description": "The one current accepted symbol for a gene: e.g., wg, pax2a." @@ -9652,12 +9621,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -10013,6 +9976,12 @@ "$ref": "#/$defs/FullNameSlotAnnotationDTO", "description": "The one current full name for a gene: e.g., wingless, paired box 2a." }, + "gene_secondary_id_dtos": { + "items": { + "$ref": "#/$defs/SecondaryIdSlotAnnotationDTO" + }, + "type": "array" + }, "gene_symbol_dto": { "$ref": "#/$defs/SymbolSlotAnnotationDTO", "description": "The one current accepted symbol for a gene: e.g., wg, pax2a." @@ -10045,12 +10014,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -10876,6 +10839,68 @@ "title": "GenePhenotypeAnnotation", "type": "object" }, + "GeneSecondaryIdSlotAnnotation": { + "additionalProperties": false, + "description": "", + "properties": { + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "evidence": { + "description": "", + "items": { + "type": "string" + }, + "type": "array" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "secondary_id": { + "type": "string" + }, + "single_gene": { + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "single_gene", + "secondary_id", + "internal" + ], + "title": "GeneSecondaryIdSlotAnnotation", + "type": "object" + }, "GeneSymbolSlotAnnotation": { "additionalProperties": false, "description": "The one current symbol for the gene.", @@ -11610,12 +11635,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -11691,12 +11710,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -11771,12 +11784,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -15160,12 +15167,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -16156,6 +16157,64 @@ "title": "SOTerm", "type": "object" }, + "SecondaryIdSlotAnnotationDTO": { + "additionalProperties": false, + "description": "", + "properties": { + "created_by_curie": { + "description": "Curie of the Person object representing the individual that created the entity", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "evidence_curies": { + "description": "Curies of InformationContentEntity objects given as evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "secondary_id": { + "type": "string" + }, + "updated_by_curie": { + "description": "Curie of the Person object representing the individual that updated the entity", + "type": "string" + } + }, + "required": [ + "secondary_id", + "internal" + ], + "title": "SecondaryIdSlotAnnotationDTO", + "type": "object" + }, "SequenceTargetingReagent": { "additionalProperties": false, "description": "", @@ -16220,12 +16279,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -16307,12 +16360,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon_curie": { "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives", "type": "string" @@ -16918,12 +16965,6 @@ "description": "Entity is no longer current.", "type": "boolean" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "taxon": { "description": "The taxon from which the biological entity derives.", "type": "string" @@ -17191,12 +17232,6 @@ }, "type": "array" }, - "secondary_identifiers": { - "items": { - "type": "string" - }, - "type": "array" - }, "source_general_consequence": { "description": "SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference when no transcript ID is provided. Since a curator would determine variant location and consequences relative to at least one specific genome assembly, transcript and/or polypeptide, no slot for curated general consequence is provided.", "type": "string" From 7c7042483ffeb86c33821eacea96d8fcfd377c12 Mon Sep 17 00:00:00 2001 From: markquintontulloch Date: Wed, 10 May 2023 09:34:38 +0100 Subject: [PATCH 4/8] Fix copy paste errors --- model/schema/affectedGenomicModel.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/schema/affectedGenomicModel.yaml b/model/schema/affectedGenomicModel.yaml index 604282754..e40015244 100644 --- a/model/schema/affectedGenomicModel.yaml +++ b/model/schema/affectedGenomicModel.yaml @@ -66,7 +66,7 @@ classes: - single_agm - secondary_id slot_usage: - single_allele: + single_agm: required: true secondary_id: required: true @@ -120,7 +120,7 @@ slots: required: true agm_secondary_ids: - description: Secondary IDs of a given allele + description: Secondary IDs of a given AGM domain: AffectedGenomicModel range: AgmSecondaryIdSlotAnnotation multivalued: true From 49038f19589bdc9f87da87d00cdca2aeb849330f Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 10 May 2023 08:37:06 +0000 Subject: [PATCH 5/8] Automated artifacts regeneration [skip actions] --- generated/jsonschema/allianceModel.schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json index 7f7354232..fcf088086 100644 --- a/generated/jsonschema/allianceModel.schema.json +++ b/generated/jsonschema/allianceModel.schema.json @@ -688,7 +688,7 @@ "description": "Includes inbred strains, stocks, disease models and mutant genotypes", "properties": { "agm_secondary_ids": { - "description": "Secondary IDs of a given allele", + "description": "Secondary IDs of a given AGM", "items": { "$ref": "#/$defs/AgmSecondaryIdSlotAnnotation" }, @@ -1124,6 +1124,7 @@ } }, "required": [ + "single_agm", "secondary_id", "internal" ], From 8bd99586d1318b548a9340bbcfc1f9d2826ba7ef Mon Sep 17 00:00:00 2001 From: markquintontulloch Date: Mon, 15 May 2023 11:15:48 +0100 Subject: [PATCH 6/8] Create SecondaryIdSlotAnnotation parent class --- model/schema/allele.yaml | 5 +---- model/schema/core.yaml | 8 ++++++++ model/schema/gene.yaml | 5 +---- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/model/schema/allele.yaml b/model/schema/allele.yaml index 3c2b5295c..3c6a93e67 100644 --- a/model/schema/allele.yaml +++ b/model/schema/allele.yaml @@ -289,15 +289,12 @@ classes: required: true AlleleSecondaryIdSlotAnnotation: - is_a: SlotAnnotation + is_a: SecondaryIdSlotAnnotation slots: - single_allele - - secondary_id slot_usage: single_allele: required: true - secondary_id: - required: true AlleleSymbolSlotAnnotation: description: >- diff --git a/model/schema/core.yaml b/model/schema/core.yaml index 9c7b35e37..6599751e3 100644 --- a/model/schema/core.yaml +++ b/model/schema/core.yaml @@ -275,6 +275,14 @@ classes: any_of: - equals_string: systematic_name + SecondaryIdSlotAnnotation: + is_a: SlotAnnotation + slots: + - secondary_id + slot_usage: + secondary_id: + required: true + SecondaryIdSlotAnnotationDTO: is_a: SlotAnnotationDTO slots: diff --git a/model/schema/gene.yaml b/model/schema/gene.yaml index dd34d8fb3..df40b3995 100644 --- a/model/schema/gene.yaml +++ b/model/schema/gene.yaml @@ -122,15 +122,12 @@ classes: permissible_values: full_name (VocabularyTerm) GeneSecondaryIdSlotAnnotation: - is_a: SlotAnnotation + is_a: SecondaryIdSlotAnnotation slots: - single_gene - - secondary_id slot_usage: single_gene: required: true - secondary_id: - required: true GeneSystematicNameSlotAnnotation: is_a: NameSlotAnnotation From b6a411ae3b12276a42960bdcf195b1c1b5599b55 Mon Sep 17 00:00:00 2001 From: markquintontulloch Date: Mon, 15 May 2023 11:18:36 +0100 Subject: [PATCH 7/8] Fix indentation --- model/schema/core.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/schema/core.yaml b/model/schema/core.yaml index 6599751e3..777516d2d 100644 --- a/model/schema/core.yaml +++ b/model/schema/core.yaml @@ -275,7 +275,7 @@ classes: any_of: - equals_string: systematic_name - SecondaryIdSlotAnnotation: + SecondaryIdSlotAnnotation: is_a: SlotAnnotation slots: - secondary_id From 499ad6bf740f69b1e1bdfbf6987ebb2e1188e5b4 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 15 May 2023 10:19:55 +0000 Subject: [PATCH 8/8] Automated artifacts regeneration [skip actions] --- .../jsonschema/allianceModel.schema.json | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json index fcf088086..d5c040af2 100644 --- a/generated/jsonschema/allianceModel.schema.json +++ b/generated/jsonschema/allianceModel.schema.json @@ -16158,6 +16158,64 @@ "title": "SOTerm", "type": "object" }, + "SecondaryIdSlotAnnotation": { + "additionalProperties": false, + "description": "", + "properties": { + "created_by": { + "description": "The individual that created the entity.", + "type": "string" + }, + "date_created": { + "description": "The date on which an entity was created. This can be applied to nodes or edges.", + "format": "date-time", + "type": "string" + }, + "date_updated": { + "description": "Date on which an entity was last modified.", + "format": "date-time", + "type": "string" + }, + "db_date_created": { + "description": "The date on which an entity was created in the Alliance database. This is disinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).", + "format": "date-time", + "type": "string" + }, + "db_date_updated": { + "description": "Date on which an entity was last modified in the Alliance database. This is disinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.", + "format": "date-time", + "type": "string" + }, + "evidence": { + "description": "", + "items": { + "type": "string" + }, + "type": "array" + }, + "internal": { + "description": "Classifies the entity as private (for internal use) or not (for public use).", + "type": "boolean" + }, + "obsolete": { + "description": "Entity is no longer current.", + "type": "boolean" + }, + "secondary_id": { + "type": "string" + }, + "updated_by": { + "description": "The individual that last modified the entity.", + "type": "string" + } + }, + "required": [ + "secondary_id", + "internal" + ], + "title": "SecondaryIdSlotAnnotation", + "type": "object" + }, "SecondaryIdSlotAnnotationDTO": { "additionalProperties": false, "description": "",