From 31a2d7ed5db4388ca60db4de33e66bb36a222de1 Mon Sep 17 00:00:00 2001 From: Kyle Ferriter Date: Thu, 7 Nov 2024 09:46:12 -0700 Subject: [PATCH] Delete all json/rst files compiled by tests. Aren't used. --- tests/data/gnomAD/json/GnomadCAF | 116 ------------------ tests/data/vrs/def/Adjacency.rst | 93 -------------- tests/data/vrs/def/Allele.rst | 90 -------------- tests/data/vrs/def/CopyNumber.rst | 80 ------------ tests/data/vrs/def/CopyNumberChange.rst | 90 -------------- tests/data/vrs/def/CopyNumberCount.rst | 90 -------------- tests/data/vrs/def/Expression.rst | 38 ------ .../data/vrs/def/Ga4ghIdentifiableObject.rst | 67 ---------- tests/data/vrs/def/Haplotype.rst | 88 ------------- tests/data/vrs/def/LengthExpression.rst | 72 ----------- .../vrs/def/LiteralSequenceExpression.rst | 72 ----------- tests/data/vrs/def/Location.rst | 3 - tests/data/vrs/def/MolecularVariation.rst | 3 - tests/data/vrs/def/Range.rst | 8 -- .../vrs/def/ReferenceLengthExpression.rst | 82 ------------- tests/data/vrs/def/Residue.rst | 8 -- tests/data/vrs/def/SequenceExpression.rst | 62 ---------- tests/data/vrs/def/SequenceLocation.rst | 87 ------------- tests/data/vrs/def/SequenceReference.rst | 77 ------------ tests/data/vrs/def/SequenceString.rst | 8 -- tests/data/vrs/def/SystemicVariation.rst | 3 - tests/data/vrs/def/ValueObject.rst | 3 - tests/data/vrs/def/Variation.rst | 75 ----------- tests/data/vrs/json/Adjacency | 91 -------------- tests/data/vrs/json/Allele | 85 ------------- tests/data/vrs/json/CopyNumberChange | 85 ------------- tests/data/vrs/json/CopyNumberCount | 82 ------------- tests/data/vrs/json/Expression | 36 ------ tests/data/vrs/json/Haplotype | 78 ------------ tests/data/vrs/json/LengthExpression | 55 --------- tests/data/vrs/json/LiteralSequenceExpression | 50 -------- tests/data/vrs/json/Location | 11 -- tests/data/vrs/json/MolecularVariation | 18 --- tests/data/vrs/json/Range | 21 ---- tests/data/vrs/json/ReferenceLengthExpression | 67 ---------- tests/data/vrs/json/Residue | 9 -- tests/data/vrs/json/SequenceExpression | 18 --- tests/data/vrs/json/SequenceLocation | 84 ------------- tests/data/vrs/json/SequenceReference | 53 -------- tests/data/vrs/json/SequenceString | 9 -- tests/data/vrs/json/SystemicVariation | 18 --- tests/data/vrs/json/Variation | 27 ---- 42 files changed, 2212 deletions(-) delete mode 100644 tests/data/gnomAD/json/GnomadCAF delete mode 100644 tests/data/vrs/def/Adjacency.rst delete mode 100644 tests/data/vrs/def/Allele.rst delete mode 100644 tests/data/vrs/def/CopyNumber.rst delete mode 100644 tests/data/vrs/def/CopyNumberChange.rst delete mode 100644 tests/data/vrs/def/CopyNumberCount.rst delete mode 100644 tests/data/vrs/def/Expression.rst delete mode 100644 tests/data/vrs/def/Ga4ghIdentifiableObject.rst delete mode 100644 tests/data/vrs/def/Haplotype.rst delete mode 100644 tests/data/vrs/def/LengthExpression.rst delete mode 100644 tests/data/vrs/def/LiteralSequenceExpression.rst delete mode 100644 tests/data/vrs/def/Location.rst delete mode 100644 tests/data/vrs/def/MolecularVariation.rst delete mode 100644 tests/data/vrs/def/Range.rst delete mode 100644 tests/data/vrs/def/ReferenceLengthExpression.rst delete mode 100644 tests/data/vrs/def/Residue.rst delete mode 100644 tests/data/vrs/def/SequenceExpression.rst delete mode 100644 tests/data/vrs/def/SequenceLocation.rst delete mode 100644 tests/data/vrs/def/SequenceReference.rst delete mode 100644 tests/data/vrs/def/SequenceString.rst delete mode 100644 tests/data/vrs/def/SystemicVariation.rst delete mode 100644 tests/data/vrs/def/ValueObject.rst delete mode 100644 tests/data/vrs/def/Variation.rst delete mode 100644 tests/data/vrs/json/Adjacency delete mode 100644 tests/data/vrs/json/Allele delete mode 100644 tests/data/vrs/json/CopyNumberChange delete mode 100644 tests/data/vrs/json/CopyNumberCount delete mode 100644 tests/data/vrs/json/Expression delete mode 100644 tests/data/vrs/json/Haplotype delete mode 100644 tests/data/vrs/json/LengthExpression delete mode 100644 tests/data/vrs/json/LiteralSequenceExpression delete mode 100644 tests/data/vrs/json/Location delete mode 100644 tests/data/vrs/json/MolecularVariation delete mode 100644 tests/data/vrs/json/Range delete mode 100644 tests/data/vrs/json/ReferenceLengthExpression delete mode 100644 tests/data/vrs/json/Residue delete mode 100644 tests/data/vrs/json/SequenceExpression delete mode 100644 tests/data/vrs/json/SequenceLocation delete mode 100644 tests/data/vrs/json/SequenceReference delete mode 100644 tests/data/vrs/json/SequenceString delete mode 100644 tests/data/vrs/json/SystemicVariation delete mode 100644 tests/data/vrs/json/Variation diff --git a/tests/data/gnomAD/json/GnomadCAF b/tests/data/gnomAD/json/GnomadCAF deleted file mode 100644 index 313a0d4..0000000 --- a/tests/data/gnomAD/json/GnomadCAF +++ /dev/null @@ -1,116 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/gk-pilot/main/gnomAD/json/GnomadCAF", - "title": "GnomadCAF", - "type": "object", - "$defs": { - "GnomadCafProperties": { - "description": "Additional properties specific to the gnomAD CAF model.", - "protectedClassOf": "GnomadCAF", - "type": "object", - "maturity": "draft", - "properties": { - "ancillaryResults": { - "type": "object", - "properties": { - "grpMaxFAF95": { - "$ref": "#/$defs/GrpMaxFAF95" - }, - "jointGrpMaxFAF95": { - "description": "The Group Max Filtering Allele Frequency (95% confidence interval) calculated jointly from genome and exome data.", - "$ref": "#/$defs/GrpMaxFAF95" - }, - "homozygotes": { - "type": "integer" - }, - "hemizygotes": { - "type": "integer" - } - }, - "additionalProperties": false - }, - "qualityMeasures": { - "type": "object", - "properties": { - "meanDepth": { - "description": "The mean depth of coverage.", - "type": "number" - }, - "fractionCoverage20x": { - "description": "The fraction of individuals with at least 20x coverage.", - "type": "number" - }, - "qcFilters": { - "type": "array", - "items": { - "type": "string" - } - }, - "monoallelic": { - "description": "All samples are homozygous alternate for the variant.", - "type": "boolean" - }, - "lowComplexityRegion": { - "description": "This flag indicates the variant is found in a low complexity region. These regions were identified with the symmetric DUST algorithm at a score threshold of 30.", - "type": "boolean" - }, - "lowConfidenceLossOfFunctionError": { - "description": "Low confidence in predicted Loss of Function (pLoF), where variant is determined by LOFTEE to be unlikely loss of function for a transcript.", - "type": "boolean" - }, - "lossOfFunctionWarning": { - "description": "A warning provided by LOFTEE to use caution when interpreting the transcript or variant.", - "type": "boolean" - }, - "noncodingTranscriptError": { - "description": "Marked in a putative loss of function category by VEP (essential splice, stop-gained, or frameshift) but appears on a non-protein-coding transcript.", - "type": "boolean" - }, - "heterozygousSkewedAlleleCount": { - "description": "The count of individuals called as heterozygous for this variant with a skewed allele balance, indicating some of these individuals may be miscalled homozygous alternative allele.", - "type": "integer" - } - }, - "additionalProperties": false - } - }, - "required": [] - }, - "GrpMaxFAF95": { - "description": "The group maximum filtering allele frequency at 95% CI", - "protectedClassOf": "GnomadCAF", - "type": "object", - "maturity": "draft", - "properties": { - "frequency": { - "type": "number" - }, - "confidenceInterval": { - "type": "number", - "const": 0.95, - "default": 0.95 - }, - "groupId": { - "type": "string", - "description": "The genetic ancestry group from which the max frequency was calculated." - } - }, - "required": [ - "confidenceInterval", - "frequency", - "groupId" - ], - "additionalProperties": false - } - }, - "maturity": "draft", - "description": "The GA4GH Cohort Allele Frequency model, with additional schema properties specific to the gnomAD resource. ", - "allOf": [ - { - "$ref": "/ga4gh/schema/va-spec/1.x/profiles/caf/json/CohortAlleleFrequency" - }, - { - "$ref": "#/$defs/GnomadCafProperties" - } - ] -} \ No newline at end of file diff --git a/tests/data/vrs/def/Adjacency.rst b/tests/data/vrs/def/Adjacency.rst deleted file mode 100644 index b8416bc..0000000 --- a/tests/data/vrs/def/Adjacency.rst +++ /dev/null @@ -1,93 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -The `Adjacency` class can represent either the termination of a sequence or the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - AJ - - ['adjoinedSequences', 'linker', 'type'] - - -**Information Model** - -Some Adjacency attributes are inherited from :ref:`Variation`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - MUST be "Adjacency". - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - - * - adjoinedSequences - - - .. raw:: html - - OL - - :ref:`IRI` | :ref:`Location` - - 1..2 - - The terminal sequence or pair of adjoined sequences that defines in the adjacency. - * - linker - - - - :ref:`SequenceExpression` - - 0..1 - - The sequence found between adjoined sequences. diff --git a/tests/data/vrs/def/Allele.rst b/tests/data/vrs/def/Allele.rst deleted file mode 100644 index 28944f2..0000000 --- a/tests/data/vrs/def/Allele.rst +++ /dev/null @@ -1,90 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -The state of a molecule at a :ref:`Location`. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - VA - - ['location', 'state', 'type'] - - -**Information Model** - -Some Allele attributes are inherited from :ref:`Variation`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - MUST be "Allele" - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - - * - location - - - - :ref:`IRI` | :ref:`Location` - - 1..1 - - The location of the Allele - * - state - - - - :ref:`SequenceExpression` - - 1..1 - - An expression of the sequence state diff --git a/tests/data/vrs/def/CopyNumber.rst b/tests/data/vrs/def/CopyNumber.rst deleted file mode 100644 index 9af40ee..0000000 --- a/tests/data/vrs/def/CopyNumber.rst +++ /dev/null @@ -1,80 +0,0 @@ -**Computational Definition** - -A measure of the copies of a :ref:`Location` within a system (e.g. genome, cell, etc.) - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['location', 'type'] - - -**Information Model** - -Some CopyNumber attributes are inherited from :ref:`Variation`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - - * - location - - - - :ref:`IRI` | :ref:`Location` - - 1..1 - - A location for which the number of systemic copies is described. diff --git a/tests/data/vrs/def/CopyNumberChange.rst b/tests/data/vrs/def/CopyNumberChange.rst deleted file mode 100644 index 41b4833..0000000 --- a/tests/data/vrs/def/CopyNumberChange.rst +++ /dev/null @@ -1,90 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a system (e.g. genome, cell, etc.) relative to a baseline ploidy. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - CX - - ['copyChange', 'location', 'type'] - - -**Information Model** - -Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - MUST be "CopyNumberChange" - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - - * - location - - - - :ref:`IRI` | :ref:`Location` - - 1..1 - - A location for which the number of systemic copies is described. - * - copyChange - - - - string - - 1..1 - - MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss), "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy), "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain). diff --git a/tests/data/vrs/def/CopyNumberCount.rst b/tests/data/vrs/def/CopyNumberCount.rst deleted file mode 100644 index 54b709d..0000000 --- a/tests/data/vrs/def/CopyNumberCount.rst +++ /dev/null @@ -1,90 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`, within a system (e.g. genome, cell, etc.). - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - CN - - ['copies', 'location', 'type'] - - -**Information Model** - -Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - MUST be "CopyNumberCount" - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - - * - location - - - - :ref:`IRI` | :ref:`Location` - - 1..1 - - A location for which the number of systemic copies is described. - * - copies - - - - integer | :ref:`Range` - - 1..1 - - The integral number of copies of the subject in a system diff --git a/tests/data/vrs/def/Expression.rst b/tests/data/vrs/def/Expression.rst deleted file mode 100644 index 5c46e71..0000000 --- a/tests/data/vrs/def/Expression.rst +++ /dev/null @@ -1,38 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures. - -**Information Model** - - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - syntax - - - - string - - 1..1 - - - * - value - - - - string - - 1..1 - - - * - syntax_version - - - - string - - 0..1 - - diff --git a/tests/data/vrs/def/Ga4ghIdentifiableObject.rst b/tests/data/vrs/def/Ga4ghIdentifiableObject.rst deleted file mode 100644 index 5998f87..0000000 --- a/tests/data/vrs/def/Ga4ghIdentifiableObject.rst +++ /dev/null @@ -1,67 +0,0 @@ -**Computational Definition** - -A contextual value object for which a GA4GH computed identifier can be created. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['type'] - - -**Information Model** - -Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core:Entity`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. diff --git a/tests/data/vrs/def/Haplotype.rst b/tests/data/vrs/def/Haplotype.rst deleted file mode 100644 index e6dcbf5..0000000 --- a/tests/data/vrs/def/Haplotype.rst +++ /dev/null @@ -1,88 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -An ordered set of co-occurring :ref:`variants ` on the same molecule. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - HT - - ['members', 'type'] - - -**Information Model** - -Some Haplotype attributes are inherited from :ref:`Variation`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - MUST be "Haplotype" - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - - * - members - - - .. raw:: html - - OL - - :ref:`Adjacency` | :ref:`Allele` | :ref:`IRI` - - 2..m - - A list of :ref:`Alleles ` and :ref:`Adjacencies ` that comprise a Haplotype. Members must share the same reference sequence as adjacent members. Alleles should not have overlapping or adjacent coordinates with neighboring Alleles. Neighboring alleles should be ordered by ascending coordinates, unless represented on a DNA inversion (following an Adjacency with end-defined adjoinedSequences), in which case they should be ordered in descending coordinates. Sequence references MUST be consistent for all members between and including the end of one Adjacency and the beginning of another. diff --git a/tests/data/vrs/def/LengthExpression.rst b/tests/data/vrs/def/LengthExpression.rst deleted file mode 100644 index 25f106f..0000000 --- a/tests/data/vrs/def/LengthExpression.rst +++ /dev/null @@ -1,72 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -A sequence expressed only by its length. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['length', 'type'] - - -**Information Model** - -Some LengthExpression attributes are inherited from :ref:`SequenceExpression`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 1..1 - - MUST be "LengthExpression" - * - length - - - - :ref:`Range` | integer - - 0..1 - - diff --git a/tests/data/vrs/def/LiteralSequenceExpression.rst b/tests/data/vrs/def/LiteralSequenceExpression.rst deleted file mode 100644 index f95e9ee..0000000 --- a/tests/data/vrs/def/LiteralSequenceExpression.rst +++ /dev/null @@ -1,72 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -An explicit expression of a Sequence. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['sequence', 'type'] - - -**Information Model** - -Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpression`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 1..1 - - MUST be "LiteralSequenceExpression" - * - sequence - - - - :ref:`SequenceString` - - 1..1 - - the literal sequence diff --git a/tests/data/vrs/def/Location.rst b/tests/data/vrs/def/Location.rst deleted file mode 100644 index 0d8a4a7..0000000 --- a/tests/data/vrs/def/Location.rst +++ /dev/null @@ -1,3 +0,0 @@ -**Computational Definition** - -A contiguous segment of a biological sequence. diff --git a/tests/data/vrs/def/MolecularVariation.rst b/tests/data/vrs/def/MolecularVariation.rst deleted file mode 100644 index cfebddc..0000000 --- a/tests/data/vrs/def/MolecularVariation.rst +++ /dev/null @@ -1,3 +0,0 @@ -**Computational Definition** - -A :ref:`variation` on a contiguous molecule. diff --git a/tests/data/vrs/def/Range.rst b/tests/data/vrs/def/Range.rst deleted file mode 100644 index 0c88b84..0000000 --- a/tests/data/vrs/def/Range.rst +++ /dev/null @@ -1,8 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -An inclusive range of values bounded by one or more integers. diff --git a/tests/data/vrs/def/ReferenceLengthExpression.rst b/tests/data/vrs/def/ReferenceLengthExpression.rst deleted file mode 100644 index 74d3481..0000000 --- a/tests/data/vrs/def/ReferenceLengthExpression.rst +++ /dev/null @@ -1,82 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -An expression of a length of a sequence from a repeating reference. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['length', 'repeatSubunitLength', 'type'] - - -**Information Model** - -Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpression`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 1..1 - - MUST be "ReferenceLengthExpression" - * - length - - - - integer | :ref:`Range` - - 1..1 - - The number of residues in the expressed sequence. - * - sequence - - - - :ref:`SequenceString` - - 0..1 - - the :ref:`Sequence` encoded by the Reference Length Expression. - * - repeatSubunitLength - - - - integer - - 1..1 - - The number of residues in the repeat subunit. diff --git a/tests/data/vrs/def/Residue.rst b/tests/data/vrs/def/Residue.rst deleted file mode 100644 index 8469465..0000000 --- a/tests/data/vrs/def/Residue.rst +++ /dev/null @@ -1,8 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -A character representing a specific residue (i.e., molecular species) or groupings of these ("ambiguity codes"), using `one-letter IUPAC abbreviations `_ for nucleic acids and amino acids. diff --git a/tests/data/vrs/def/SequenceExpression.rst b/tests/data/vrs/def/SequenceExpression.rst deleted file mode 100644 index 32b74d1..0000000 --- a/tests/data/vrs/def/SequenceExpression.rst +++ /dev/null @@ -1,62 +0,0 @@ -**Computational Definition** - -An expression describing a :ref:`Sequence`. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['type'] - - -**Information Model** - -Some SequenceExpression attributes are inherited from :ref:`gks.core:Entity`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 1..1 - - The SequenceExpression class type. MUST match child class type. diff --git a/tests/data/vrs/def/SequenceLocation.rst b/tests/data/vrs/def/SequenceLocation.rst deleted file mode 100644 index 4d78a42..0000000 --- a/tests/data/vrs/def/SequenceLocation.rst +++ /dev/null @@ -1,87 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -A :ref:`Location` defined by an interval on a referenced :ref:`Sequence`. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - SL - - ['end', 'sequenceReference', 'start', 'type'] - - -**Information Model** - -Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObject`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - MUST be "SequenceLocation" - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - sequenceReference - - - - :ref:`IRI` | :ref:`SequenceReference` - - 0..1 - - A :ref:`SequenceReference`. - * - start - - - - integer | :ref:`Range` - - 0..1 - - The start coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than or equal to the value of `end`. - * - end - - - - integer | :ref:`Range` - - 0..1 - - The end coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than or equal to the value of `start`. diff --git a/tests/data/vrs/def/SequenceReference.rst b/tests/data/vrs/def/SequenceReference.rst deleted file mode 100644 index 55abef2..0000000 --- a/tests/data/vrs/def/SequenceReference.rst +++ /dev/null @@ -1,77 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -A sequence of nucleic or amino acid character codes. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - [] - - -**Information Model** - -Some SequenceReference attributes are inherited from :ref:`gks.core:Entity`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - - * - refgetAccession - - - - string - - 1..1 - - A `GA4GH RefGet ` identifier for the referenced sequence, using the sha512t24u digest. - * - residueAlphabet - - - - string - - 0..1 - - The interpretation of the character codes referred to by the refget accession, where "aa" specifies an amino acid character set, and "na" specifies a nucleic acid character set. diff --git a/tests/data/vrs/def/SequenceString.rst b/tests/data/vrs/def/SequenceString.rst deleted file mode 100644 index 7f84f69..0000000 --- a/tests/data/vrs/def/SequenceString.rst +++ /dev/null @@ -1,8 +0,0 @@ -.. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in - the :ref:`maturity-model`. - - -**Computational Definition** - -A character string of :ref:`Residues ` that represents a biological sequence using the conventional sequence order (5’-to-3’ for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings. diff --git a/tests/data/vrs/def/SystemicVariation.rst b/tests/data/vrs/def/SystemicVariation.rst deleted file mode 100644 index e5cb71d..0000000 --- a/tests/data/vrs/def/SystemicVariation.rst +++ /dev/null @@ -1,3 +0,0 @@ -**Computational Definition** - -A Variation of multiple molecules in the context of a system, e.g. a genome, sample, or homologous chromosomes. diff --git a/tests/data/vrs/def/ValueObject.rst b/tests/data/vrs/def/ValueObject.rst deleted file mode 100644 index 0f1de8b..0000000 --- a/tests/data/vrs/def/ValueObject.rst +++ /dev/null @@ -1,3 +0,0 @@ -**Computational Definition** - -A contextual value whose equality is based on value, not identity. See https://en.wikipedia.org/wiki/Value_object for more on Value Objects. diff --git a/tests/data/vrs/def/Variation.rst b/tests/data/vrs/def/Variation.rst deleted file mode 100644 index 1793ae1..0000000 --- a/tests/data/vrs/def/Variation.rst +++ /dev/null @@ -1,75 +0,0 @@ -**Computational Definition** - -A representation of the state of one or more biomolecules. - -**GA4GH Digest** - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Prefix - - Keys - - * - None - - ['type'] - - -**Information Model** - -Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description - * - id - - - - string - - 0..1 - - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). - * - label - - - - string - - 0..1 - - A primary label for the entity. - * - description - - - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - - .. raw:: html - - OL - - :ref:`Extension` - - 0..m - - - * - type - - - - string - - 0..1 - - - * - digest - - - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - expressions - - - .. raw:: html - - UL - - :ref:`Expression` - - 0..m - - diff --git a/tests/data/vrs/json/Adjacency b/tests/data/vrs/json/Adjacency deleted file mode 100644 index dc9bf64..0000000 --- a/tests/data/vrs/json/Adjacency +++ /dev/null @@ -1,91 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Adjacency", - "title": "Adjacency", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "prefix": "AJ", - "keys": [ - "adjoinedSequences", - "linker", - "type" - ] - }, - "description": "The `Adjacency` class can represent either the termination of a sequence or the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "Adjacency", - "default": "Adjacency", - "description": "MUST be \"Adjacency\"." - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" - } - }, - "adjoinedSequences": { - "type": "array", - "uniqueItems": false, - "ordered": true, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" - }, - { - "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" - } - ] - }, - "description": "The terminal sequence or pair of adjoined sequences that defines in the adjacency.", - "minItems": 1, - "maxItems": 2 - }, - "linker": { - "description": "The sequence found between adjoined sequences.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/LengthExpression" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/LiteralSequenceExpression" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/ReferenceLengthExpression" - } - ] - } - }, - "required": [ - "adjoinedSequences" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/Allele b/tests/data/vrs/json/Allele deleted file mode 100644 index b25d4ad..0000000 --- a/tests/data/vrs/json/Allele +++ /dev/null @@ -1,85 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Allele", - "title": "Allele", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "prefix": "VA", - "keys": [ - "location", - "state", - "type" - ] - }, - "description": "The state of a molecule at a Location.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "Allele", - "default": "Allele", - "description": "MUST be \"Allele\"" - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" - } - }, - "location": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" - }, - { - "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" - } - ], - "description": "The location of the Allele" - }, - "state": { - "description": "An expression of the sequence state", - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/LengthExpression" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/LiteralSequenceExpression" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/ReferenceLengthExpression" - } - ] - } - }, - "required": [ - "location", - "state" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/CopyNumberChange b/tests/data/vrs/json/CopyNumberChange deleted file mode 100644 index f5d3465..0000000 --- a/tests/data/vrs/json/CopyNumberChange +++ /dev/null @@ -1,85 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/CopyNumberChange", - "title": "CopyNumberChange", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "keys": [ - "copyChange", - "location", - "type" - ], - "prefix": "CX" - }, - "description": "An assessment of the copy number of a Location or a Gene within a system (e.g. genome, cell, etc.) relative to a baseline ploidy.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "CopyNumberChange", - "default": "CopyNumberChange", - "description": "MUST be \"CopyNumberChange\"" - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" - } - }, - "location": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" - }, - { - "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" - } - ], - "description": "A location for which the number of systemic copies is described." - }, - "copyChange": { - "type": "string", - "enum": [ - "efo:0030069", - "efo:0020073", - "efo:0030068", - "efo:0030067", - "efo:0030064", - "efo:0030070", - "efo:0030071", - "efo:0030072" - ], - "description": "MUST be one of \"efo:0030069\" (complete genomic loss), \"efo:0020073\" (high-level loss), \"efo:0030068\" (low-level loss), \"efo:0030067\" (loss), \"efo:0030064\" (regional base ploidy), \"efo:0030070\" (gain), \"efo:0030071\" (low-level gain), \"efo:0030072\" (high-level gain)." - } - }, - "required": [ - "copyChange", - "location" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/CopyNumberCount b/tests/data/vrs/json/CopyNumberCount deleted file mode 100644 index 6bb8b9e..0000000 --- a/tests/data/vrs/json/CopyNumberCount +++ /dev/null @@ -1,82 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/CopyNumberCount", - "title": "CopyNumberCount", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "keys": [ - "copies", - "location", - "type" - ], - "prefix": "CN" - }, - "description": "The absolute count of discrete copies of a Location or Gene, within a system (e.g. genome, cell, etc.).", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "CopyNumberCount", - "default": "CopyNumberCount", - "description": "MUST be \"CopyNumberCount\"" - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" - } - }, - "location": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" - }, - { - "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" - } - ], - "description": "A location for which the number of systemic copies is described." - }, - "copies": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" - }, - { - "type": "integer" - } - ], - "description": "The integral number of copies of the subject in a system" - } - }, - "required": [ - "copies", - "location" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/Expression b/tests/data/vrs/json/Expression deleted file mode 100644 index bf3b5fd..0000000 --- a/tests/data/vrs/json/Expression +++ /dev/null @@ -1,36 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Expression", - "title": "Expression", - "type": "object", - "privateTo": "Variation", - "maturity": "draft", - "description": "Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures.", - "properties": { - "syntax": { - "type": "string", - "enum": [ - "hgvs.c", - "hgvs.p", - "hgvs.g", - "hgvs.m", - "hgvs.n", - "hgvs.r", - "iscn", - "gnomad", - "spdi" - ] - }, - "value": { - "type": "string" - }, - "syntax_version": { - "type": "string" - } - }, - "required": [ - "syntax", - "value" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/Haplotype b/tests/data/vrs/json/Haplotype deleted file mode 100644 index dadcc11..0000000 --- a/tests/data/vrs/json/Haplotype +++ /dev/null @@ -1,78 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Haplotype", - "title": "Haplotype", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "prefix": "HT", - "keys": [ - "members", - "type" - ] - }, - "description": "An ordered set of co-occurring variants on the same molecule.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "Haplotype", - "default": "Haplotype", - "description": "MUST be \"Haplotype\"" - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/vrs/2.x/json/Expression" - } - }, - "members": { - "type": "array", - "ordered": true, - "minItems": 2, - "uniqueItems": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Adjacency" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" - }, - { - "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" - } - ] - }, - "description": "A list of Alleles that comprise a Haplotype. Members must share the same reference sequence as adjacent members. Alleles should not have overlapping or adjacent coordinates with neighboring Alleles. Neighboring alleles should be ordered by ascending coordinates, unless represented on a DNA inversion (following an Adjacency with end-defined adjoinedSequences), in which case they should be ordered in descending coordinates. Sequence references MUST be consistent for all members between and including the end of one Adjacency and the beginning of another." - } - }, - "required": [ - "members" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/LengthExpression b/tests/data/vrs/json/LengthExpression deleted file mode 100644 index 397c48c..0000000 --- a/tests/data/vrs/json/LengthExpression +++ /dev/null @@ -1,55 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/LengthExpression", - "title": "LengthExpression", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "keys": [ - "length", - "type" - ] - }, - "description": "A sequence expressed only by its length.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "LengthExpression", - "default": "LengthExpression", - "description": "MUST be \"LengthExpression\"" - }, - "length": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" - }, - { - "type": "integer" - } - ] - } - }, - "required": [ - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/LiteralSequenceExpression b/tests/data/vrs/json/LiteralSequenceExpression deleted file mode 100644 index d958b3d..0000000 --- a/tests/data/vrs/json/LiteralSequenceExpression +++ /dev/null @@ -1,50 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/LiteralSequenceExpression", - "title": "LiteralSequenceExpression", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "keys": [ - "sequence", - "type" - ] - }, - "description": "An explicit expression of a Sequence.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "LiteralSequenceExpression", - "default": "LiteralSequenceExpression", - "description": "MUST be \"LiteralSequenceExpression\"" - }, - "sequence": { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceString", - "description": "the literal sequence" - } - }, - "required": [ - "sequence", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/Location b/tests/data/vrs/json/Location deleted file mode 100644 index 4612118..0000000 --- a/tests/data/vrs/json/Location +++ /dev/null @@ -1,11 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Location", - "title": "Location", - "type": "object", - "description": "A contiguous segment of a biological sequence.", - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation", - "discriminator": { - "propertyName": "type" - } -} \ No newline at end of file diff --git a/tests/data/vrs/json/MolecularVariation b/tests/data/vrs/json/MolecularVariation deleted file mode 100644 index f2de4e1..0000000 --- a/tests/data/vrs/json/MolecularVariation +++ /dev/null @@ -1,18 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/MolecularVariation", - "title": "MolecularVariation", - "type": "object", - "description": "A variation on a contiguous molecule.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Haplotype" - } - ], - "discriminator": { - "propertyName": "type" - } -} \ No newline at end of file diff --git a/tests/data/vrs/json/Range b/tests/data/vrs/json/Range deleted file mode 100644 index 5ae7fda..0000000 --- a/tests/data/vrs/json/Range +++ /dev/null @@ -1,21 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Range", - "title": "Range", - "type": "array", - "maturity": "draft", - "description": "An inclusive range of values bounded by one or more integers.", - "ordered": true, - "items": { - "oneOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ] - }, - "maxItems": 2, - "minItems": 2 -} \ No newline at end of file diff --git a/tests/data/vrs/json/ReferenceLengthExpression b/tests/data/vrs/json/ReferenceLengthExpression deleted file mode 100644 index b4687a9..0000000 --- a/tests/data/vrs/json/ReferenceLengthExpression +++ /dev/null @@ -1,67 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/ReferenceLengthExpression", - "title": "ReferenceLengthExpression", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "keys": [ - "length", - "repeatSubunitLength", - "type" - ] - }, - "description": "An expression of a length of a sequence from a repeating reference.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "ReferenceLengthExpression", - "default": "ReferenceLengthExpression", - "description": "MUST be \"ReferenceLengthExpression\"" - }, - "length": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" - }, - { - "type": "integer" - } - ], - "description": "The number of residues in the expressed sequence." - }, - "sequence": { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceString", - "description": "the Sequence encoded by the Reference Length Expression." - }, - "repeatSubunitLength": { - "type": "integer", - "description": "The number of residues in the repeat subunit." - } - }, - "required": [ - "length", - "repeatSubunitLength", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/Residue b/tests/data/vrs/json/Residue deleted file mode 100644 index d96de64..0000000 --- a/tests/data/vrs/json/Residue +++ /dev/null @@ -1,9 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Residue", - "title": "Residue", - "type": "string", - "maturity": "draft", - "description": "A character representing a specific residue (i.e., molecular species) or groupings of these (\"ambiguity codes\"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids.", - "pattern": "[A-Z*\\-]" -} \ No newline at end of file diff --git a/tests/data/vrs/json/SequenceExpression b/tests/data/vrs/json/SequenceExpression deleted file mode 100644 index 4150c3f..0000000 --- a/tests/data/vrs/json/SequenceExpression +++ /dev/null @@ -1,18 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/SequenceExpression", - "title": "SequenceExpression", - "type": "object", - "description": "An expression describing a Sequence.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/LiteralSequenceExpression" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/ReferenceLengthExpression" - } - ], - "discriminator": { - "propertyName": "type" - } -} \ No newline at end of file diff --git a/tests/data/vrs/json/SequenceLocation b/tests/data/vrs/json/SequenceLocation deleted file mode 100644 index 6aa9252..0000000 --- a/tests/data/vrs/json/SequenceLocation +++ /dev/null @@ -1,84 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/SequenceLocation", - "title": "SequenceLocation", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "keys": [ - "end", - "sequenceReference", - "start", - "type" - ], - "prefix": "SL" - }, - "description": "A Location defined by an interval on a referenced Sequence.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "SequenceLocation", - "default": "SequenceLocation", - "description": "MUST be \"SequenceLocation\"" - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "sequenceReference": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceReference" - }, - { - "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" - } - ], - "description": "A SequenceReference." - }, - "start": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" - }, - { - "type": "integer" - } - ], - "description": "The start coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than or equal to the value of `end`." - }, - "end": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" - }, - { - "type": "integer" - } - ], - "description": "The end coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than or equal to the value of `start`." - } - }, - "required": [], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/SequenceReference b/tests/data/vrs/json/SequenceReference deleted file mode 100644 index 3b0a932..0000000 --- a/tests/data/vrs/json/SequenceReference +++ /dev/null @@ -1,53 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/SequenceReference", - "title": "SequenceReference", - "type": "object", - "maturity": "draft", - "ga4ghDigest": { - "assigned": true - }, - "description": "A sequence of nucleic or amino acid character codes.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" - } - }, - "type": { - "type": "string", - "const": "SequenceReference" - }, - "refgetAccession": { - "description": "A `GA4GH RefGet ` identifier for the referenced sequence, using the sha512t24u digest.", - "type": "string", - "pattern": "^SQ.[0-9A-Za-z_\\-]{32}$" - }, - "residueAlphabet": { - "type": "string", - "description": "The interpretation of the character codes referred to by the refget accession, where \"aa\" specifies an amino acid character set, and \"na\" specifies a nucleic acid character set.", - "enum": [ - "aa", - "na" - ] - } - }, - "required": [ - "refgetAccession" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/tests/data/vrs/json/SequenceString b/tests/data/vrs/json/SequenceString deleted file mode 100644 index 40c5158..0000000 --- a/tests/data/vrs/json/SequenceString +++ /dev/null @@ -1,9 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/SequenceString", - "title": "SequenceString", - "type": "string", - "maturity": "draft", - "description": "A character string of Residues that represents a biological sequence using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.", - "pattern": "^[A-Z*\\-]*$" -} \ No newline at end of file diff --git a/tests/data/vrs/json/SystemicVariation b/tests/data/vrs/json/SystemicVariation deleted file mode 100644 index d7e4d61..0000000 --- a/tests/data/vrs/json/SystemicVariation +++ /dev/null @@ -1,18 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/SystemicVariation", - "title": "SystemicVariation", - "type": "object", - "description": "A Variation of multiple molecules in the context of a system, e.g. a genome, sample, or homologous chromosomes.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/CopyNumberChange" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/CopyNumberCount" - } - ], - "discriminator": { - "propertyName": "type" - } -} \ No newline at end of file diff --git a/tests/data/vrs/json/Variation b/tests/data/vrs/json/Variation deleted file mode 100644 index 65add7a..0000000 --- a/tests/data/vrs/json/Variation +++ /dev/null @@ -1,27 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Variation", - "title": "Variation", - "type": "object", - "description": "A representation of the state of one or more biomolecules.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Adjacency" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/CopyNumberChange" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/CopyNumberCount" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Haplotype" - } - ], - "discriminator": { - "propertyName": "type" - } -} \ No newline at end of file