diff --git a/README.md b/README.md index 97d44d3c..630ee4a0 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ initiatives, and diagnostic testing laboratories. VRS is licensed under the [Apache License 2.0](LICENSE). -> **NOTE:** VRS is under active development. See [VR +> **NOTE:** VRS is under active development. See [VR > Project Roadmap](https://github.com/orgs/ga4gh/projects/5). @@ -67,12 +67,12 @@ To watch for changes and update automatically: The VR specification documentation is written in reStructuredText and located in `docs/source/`. Commits to this repo are built -automatically at `vrs.ga4gh.org`. +automatically at `vrs.ga4gh.org`. To build documentation locally, type: make -C docs clean watch & - + Then, open `docs/build/html/index.html`. The above make command should build docs when source changes. (Some types of changes require recleaning and building.) @@ -95,7 +95,7 @@ The smoketests require python 3.8+. This is the recommended setup: $ python3 -m venv venv $ source venv/bin/activate $ pip install -U setuptools pip -$ pip install -r requirements.txt -$ pytest +$ pip install -r .requirements.txt +$ python3 -m pytest ``` diff --git a/schema/vrs-source.yaml b/schema/vrs-source.yaml index e2899ba0..2f8e5c6b 100644 --- a/schema/vrs-source.yaml +++ b/schema/vrs-source.yaml @@ -89,6 +89,7 @@ definitions: type: type: string const: "Allele" + default: "Allele" description: >- MUST be "Allele" location: @@ -116,6 +117,7 @@ definitions: type: type: string const: "Haplotype" + default: "Haplotype" description: >- MUST be "Haplotype" members: @@ -143,6 +145,7 @@ definitions: type: type: string const: "Text" + default: "Text" description: MUST be "Text" definition: type: string @@ -160,6 +163,7 @@ definitions: type: type: string const: "VariationSet" + default: "VariationSet" description: MUST be "VariationSet" members: type: array @@ -189,6 +193,7 @@ definitions: type: type: string const: "AbsoluteCopyNumber" + default: "AbsoluteCopyNumber" description: >- MUST be "AbsoluteCopyNumber" subject: @@ -254,6 +259,7 @@ definitions: type: type: string const: "RelativeCopyNumber" + default: "RelativeCopyNumber" description: >- MUST be "RelativeCopyNumber" subject: @@ -302,6 +308,7 @@ definitions: type: type: string const: "ChromosomeLocation" + default: "ChromosomeLocation" description: MUST be "ChromosomeLocation" species_id: $ref: "#/definitions/CURIE" @@ -330,6 +337,7 @@ definitions: type: type: string const: "SequenceLocation" + default: "SequenceLocation" description: MUST be "SequenceLocation" sequence_id: $ref: "#/definitions/CURIE" @@ -364,6 +372,7 @@ definitions: type: type: string const: "SequenceInterval" + default: "SequenceInterval" description: MUST be "SequenceInterval" start: oneOf: @@ -463,6 +472,7 @@ definitions: type: type: string const: "CytobandInterval" + default: "CytobandInterval" description: MUST be "CytobandInterval" start: $ref: "#/definitions/HumanCytoband" @@ -510,6 +520,7 @@ definitions: type: type: string const: "LiteralSequenceExpression" + default: "LiteralSequenceExpression" description: MUST be "LiteralSequenceExpression" sequence: $ref: "#/definitions/Sequence" @@ -530,6 +541,7 @@ definitions: type: type: string const: "DerivedSequenceExpression" + default: "DerivedSequenceExpression" description: MUST be "DerivedSequenceExpression" location: $ref: "#/definitions/SequenceLocation" @@ -551,6 +563,7 @@ definitions: type: type: string const: "RepeatedSequenceExpression" + default: "RepeatedSequenceExpression" description: MUST be "RepeatedSequenceExpression" seq_expr: oneOf: @@ -613,6 +626,7 @@ definitions: type: type: string const: "ComposedSequenceExpression" + default: "ComposedSequenceExpression" description: MUST be "ComposedSequenceExpression" components: type: array @@ -662,6 +676,7 @@ definitions: type: type: string const: "Gene" + default: "Gene" description: MUST be "Gene" gene_id: $ref: "#/definitions/CURIE" @@ -681,6 +696,7 @@ definitions: type: type: string const: "Number" + default: "Number" description: MUST be "Number" value: type: integer @@ -696,6 +712,7 @@ definitions: type: type: string const: "DefiniteRange" + default: "DefiniteRange" description: MUST be "DefiniteRange" min: type: number @@ -717,6 +734,7 @@ definitions: type: type: string const: "IndefiniteRange" + default: "IndefiniteRange" description: MUST be "IndefiniteRange" value: type: number @@ -793,6 +811,7 @@ definitions: type: type: string const: "SequenceState" + default: "SequenceState" description: MUST be "SequenceState" sequence: $ref: "#/definitions/Sequence" @@ -815,6 +834,7 @@ definitions: type: type: string const: "SimpleInterval" + default: "SimpleInterval" description: MUST be "SimpleInterval" start: type: integer diff --git a/schema/vrs.json b/schema/vrs.json index 1b2c3923..653092d0 100644 --- a/schema/vrs.json +++ b/schema/vrs.json @@ -74,6 +74,7 @@ "type": { "type": "string", "const": "Allele", + "default": "Allele", "description": "MUST be \"Allele\"" }, "location": { @@ -122,6 +123,7 @@ "type": { "type": "string", "const": "Haplotype", + "default": "Haplotype", "description": "MUST be \"Haplotype\"" }, "members": { @@ -158,6 +160,7 @@ "type": { "type": "string", "const": "Text", + "default": "Text", "description": "MUST be \"Text\"" }, "definition": { @@ -182,6 +185,7 @@ "type": { "type": "string", "const": "VariationSet", + "default": "VariationSet", "description": "MUST be \"VariationSet\"" }, "members": { @@ -218,6 +222,7 @@ "type": { "type": "string", "const": "AbsoluteCopyNumber", + "default": "AbsoluteCopyNumber", "description": "MUST be \"AbsoluteCopyNumber\"" }, "subject": { @@ -336,6 +341,7 @@ "type": { "type": "string", "const": "RelativeCopyNumber", + "default": "RelativeCopyNumber", "description": "MUST be \"RelativeCopyNumber\"" }, "subject": { @@ -399,6 +405,7 @@ "type": { "type": "string", "const": "ChromosomeLocation", + "default": "ChromosomeLocation", "description": "MUST be \"ChromosomeLocation\"" }, "species_id": { @@ -434,6 +441,7 @@ "type": { "type": "string", "const": "SequenceLocation", + "default": "SequenceLocation", "description": "MUST be \"SequenceLocation\"" }, "sequence_id": { @@ -466,6 +474,7 @@ "type": { "type": "string", "const": "SequenceInterval", + "default": "SequenceInterval", "description": "MUST be \"SequenceInterval\"" }, "start": { @@ -639,6 +648,7 @@ "type": { "type": "string", "const": "CytobandInterval", + "default": "CytobandInterval", "description": "MUST be \"CytobandInterval\"" }, "start": { @@ -689,6 +699,7 @@ "type": { "type": "string", "const": "LiteralSequenceExpression", + "default": "LiteralSequenceExpression", "description": "MUST be \"LiteralSequenceExpression\"" }, "sequence": { @@ -709,6 +720,7 @@ "type": { "type": "string", "const": "DerivedSequenceExpression", + "default": "DerivedSequenceExpression", "description": "MUST be \"DerivedSequenceExpression\"" }, "location": { @@ -734,6 +746,7 @@ "type": { "type": "string", "const": "RepeatedSequenceExpression", + "default": "RepeatedSequenceExpression", "description": "MUST be \"RepeatedSequenceExpression\"" }, "seq_expr": { @@ -841,6 +854,7 @@ "type": { "type": "string", "const": "ComposedSequenceExpression", + "default": "ComposedSequenceExpression", "description": "MUST be \"ComposedSequenceExpression\"" }, "components": { @@ -897,6 +911,7 @@ "type": { "type": "string", "const": "Gene", + "default": "Gene", "description": "MUST be \"Gene\"" }, "gene_id": { @@ -917,6 +932,7 @@ "type": { "type": "string", "const": "Number", + "default": "Number", "description": "MUST be \"Number\"" }, "value": { @@ -937,6 +953,7 @@ "type": { "type": "string", "const": "DefiniteRange", + "default": "DefiniteRange", "description": "MUST be \"DefiniteRange\"" }, "min": { @@ -962,6 +979,7 @@ "type": { "type": "string", "const": "IndefiniteRange", + "default": "IndefiniteRange", "description": "MUST be \"IndefiniteRange\"" }, "value": { @@ -1018,6 +1036,7 @@ "type": { "type": "string", "const": "SequenceState", + "default": "SequenceState", "description": "MUST be \"SequenceState\"" }, "sequence": { @@ -1043,6 +1062,7 @@ "type": { "type": "string", "const": "SimpleInterval", + "default": "SimpleInterval", "description": "MUST be \"SimpleInterval\"" }, "start": { diff --git a/schema/vrs.yaml b/schema/vrs.yaml index 543d03db..424aa9f6 100644 --- a/schema/vrs.yaml +++ b/schema/vrs.yaml @@ -45,6 +45,7 @@ definitions: type: type: string const: Allele + default: Allele description: MUST be "Allele" location: oneOf: @@ -72,6 +73,7 @@ definitions: type: type: string const: Haplotype + default: Haplotype description: MUST be "Haplotype" members: type: array @@ -95,6 +97,7 @@ definitions: type: type: string const: Text + default: Text description: MUST be "Text" definition: type: string @@ -112,6 +115,7 @@ definitions: type: type: string const: VariationSet + default: VariationSet description: MUST be "VariationSet" members: type: array @@ -137,6 +141,7 @@ definitions: type: type: string const: AbsoluteCopyNumber + default: AbsoluteCopyNumber description: MUST be "AbsoluteCopyNumber" subject: oneOf: @@ -200,6 +205,7 @@ definitions: type: type: string const: RelativeCopyNumber + default: RelativeCopyNumber description: MUST be "RelativeCopyNumber" subject: oneOf: @@ -240,6 +246,7 @@ definitions: type: type: string const: ChromosomeLocation + default: ChromosomeLocation description: MUST be "ChromosomeLocation" species_id: $ref: '#/definitions/CURIE' @@ -267,6 +274,7 @@ definitions: type: type: string const: SequenceLocation + default: SequenceLocation description: MUST be "SequenceLocation" sequence_id: $ref: '#/definitions/CURIE' @@ -290,6 +298,7 @@ definitions: type: type: string const: SequenceInterval + default: SequenceInterval description: MUST be "SequenceInterval" start: oneOf: @@ -386,6 +395,7 @@ definitions: type: type: string const: CytobandInterval + default: CytobandInterval description: MUST be "CytobandInterval" start: $ref: '#/definitions/HumanCytoband' @@ -420,6 +430,7 @@ definitions: type: type: string const: LiteralSequenceExpression + default: LiteralSequenceExpression description: MUST be "LiteralSequenceExpression" sequence: $ref: '#/definitions/Sequence' @@ -439,6 +450,7 @@ definitions: type: type: string const: DerivedSequenceExpression + default: DerivedSequenceExpression description: MUST be "DerivedSequenceExpression" location: $ref: '#/definitions/SequenceLocation' @@ -459,6 +471,7 @@ definitions: type: type: string const: RepeatedSequenceExpression + default: RepeatedSequenceExpression description: MUST be "RepeatedSequenceExpression" seq_expr: oneOf: @@ -518,6 +531,7 @@ definitions: type: type: string const: ComposedSequenceExpression + default: ComposedSequenceExpression description: MUST be "ComposedSequenceExpression" components: type: array @@ -555,6 +569,7 @@ definitions: type: type: string const: Gene + default: Gene description: MUST be "Gene" gene_id: $ref: '#/definitions/CURIE' @@ -570,6 +585,7 @@ definitions: type: type: string const: Number + default: Number description: MUST be "Number" value: type: integer @@ -585,6 +601,7 @@ definitions: type: type: string const: DefiniteRange + default: DefiniteRange description: MUST be "DefiniteRange" min: type: number @@ -607,6 +624,7 @@ definitions: type: type: string const: IndefiniteRange + default: IndefiniteRange description: MUST be "IndefiniteRange" value: type: number @@ -663,6 +681,7 @@ definitions: type: type: string const: SequenceState + default: SequenceState description: MUST be "SequenceState" sequence: $ref: '#/definitions/Sequence' @@ -684,6 +703,7 @@ definitions: type: type: string const: SimpleInterval + default: SimpleInterval description: MUST be "SimpleInterval" start: type: integer