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Merge branch '2.x' into traversal-block-components
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@ahwagner
ahwagner authored Oct 23, 2024
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13 changes: 9 additions & 4 deletions CONTRIBUTING.md
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Expand Up @@ -5,10 +5,15 @@ The additional information presented here are guidelines for issues,
branches, commits, and pull requests. Before adding documentation,
please also review the [docs style guide](docs/source/style.rst).

## Discussions
[Discussions](https://github.com/ga4gh/vrs/discussions) are for feature
requests, release candidate discussions, and questions.

## Issues
[Issues](https://github.com/ga4gh/vrs/issues) are for discussion, bug
reports, and feature requests. When creating an issue, use sentence case
for the issue title and avoid the use of periods at the end of titles.
[Issues](https://github.com/ga4gh/vrs/issues) are for bug
reports, and planned feature descriptions. When creating an issue, use
sentence casefor the issue title and avoid the use of periods at the end
of titles.

## Branches
[Branches](https://github.com/ga4gh/vrs/branches) are used for
Expand All @@ -28,4 +33,4 @@ be merged. PR titles must reflect the issue associated with the PR. For
example, the associated PR title for
[issue 250](https://github.com/ga4gh/vrs/issues/250) would be
`#250: Add CONTRIBUTING.md`, as seen in
[PR #253](https://github.com/ga4gh/vrs/pull/253).
[PR #253](https://github.com/ga4gh/vrs/pull/253).
25 changes: 0 additions & 25 deletions LICENSE
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Expand Up @@ -174,28 +174,3 @@
of your accepting any such warranty or additional liability.

END OF TERMS AND CONDITIONS

APPENDIX: How to apply the Apache License to your work.

To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "{}"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.

Copyright {yyyy} {name of copyright owner}

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
2 changes: 1 addition & 1 deletion docs/source/concepts/AdditionalDataTypes/Code.rst
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Code
!!!!

.. include:: ../../def/gks.common/data-types/Code.rst
.. include:: ../../def/gks.common/core-im/Code.rst
2 changes: 1 addition & 1 deletion docs/source/concepts/AdditionalDataTypes/Coding.rst
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Expand Up @@ -3,4 +3,4 @@
Coding
!!!!!!

.. include:: ../../def/gks.common/data-types/Coding.rst
.. include:: ../../def/gks.common/core-im/Coding.rst
2 changes: 1 addition & 1 deletion docs/source/concepts/AdditionalDataTypes/Extension.rst
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Expand Up @@ -3,4 +3,4 @@
Extension
!!!!!!!!!

.. include:: ../../def/gks.common/data-types/Extension.rst
.. include:: ../../def/gks.common/core-im/Extension.rst
2 changes: 1 addition & 1 deletion docs/source/concepts/AdditionalDataTypes/IRI.rst
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IRI
!!!

.. include:: ../../def/gks.common/data-types/IRI.rst
.. include:: ../../def/gks.common/core-im/IRI.rst
2 changes: 1 addition & 1 deletion docs/source/concepts/MolecularVariation/index.rst
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Expand Up @@ -9,7 +9,7 @@ rearrangements that form derivative molecules.

Collectively, these types of variation are called molecular variation.

.. include:: ../../def/MolecularVariation.rst
.. include:: ../../def/vrs/MolecularVariation.rst

**Subclasses**

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2 changes: 1 addition & 1 deletion docs/source/concepts/SequenceExpression/index.rst
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Expand Up @@ -9,7 +9,7 @@ representation of :ref:`Variation` state.
Unlike :ref:`SequenceReference`, a sequence expression represents the
content of a sequence, instead of representing a sequence by reference.

.. include:: ../../def/SequenceExpression.rst
.. include:: ../../def/vrs/SequenceExpression.rst

**Subclasses**

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2 changes: 1 addition & 1 deletion docs/source/concepts/SystemicVariation/index.rst
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Expand Up @@ -9,7 +9,7 @@ rearrangements that form derivative molecules.

Collectively, these types of variation are called molecular variation.

.. include:: ../../def/SystemicVariation.rst
.. include:: ../../def/vrs/SystemicVariation.rst

**Subclasses**

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1 change: 0 additions & 1 deletion schema/data-types
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This file was deleted.

4 changes: 2 additions & 2 deletions schema/vrs/json/Adjacency
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Expand Up @@ -39,7 +39,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand Down Expand Up @@ -72,7 +72,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
]
},
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4 changes: 2 additions & 2 deletions schema/vrs/json/Allele
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Expand Up @@ -39,7 +39,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand Down Expand Up @@ -68,7 +68,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
],
"description": "The location of the Allele"
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4 changes: 2 additions & 2 deletions schema/vrs/json/CisPhasedBlock
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Expand Up @@ -38,7 +38,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand Down Expand Up @@ -72,7 +72,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/Allele"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
]
},
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8 changes: 4 additions & 4 deletions schema/vrs/json/CopyNumberChange
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Expand Up @@ -39,7 +39,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand All @@ -62,7 +62,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
],
"description": "A location for which the number of systemic copies is described."
Expand All @@ -74,8 +74,8 @@
"description": "MUST be \"CopyNumberChange\""
},
"copyChange": {
"description": "MUST be a Coding representing 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).",
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
"description": "MUST be a Coding representing 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": [
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4 changes: 2 additions & 2 deletions schema/vrs/json/CopyNumberCount
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Expand Up @@ -39,7 +39,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand All @@ -62,7 +62,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
],
"description": "A location for which the number of systemic copies is described."
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4 changes: 2 additions & 2 deletions schema/vrs/json/DerivativeMolecule
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Expand Up @@ -38,7 +38,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand Down Expand Up @@ -80,7 +80,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/TraversalBlock"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
]
},
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2 changes: 1 addition & 1 deletion schema/vrs/json/LengthExpression
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Expand Up @@ -37,7 +37,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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2 changes: 1 addition & 1 deletion schema/vrs/json/LiteralSequenceExpression
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Expand Up @@ -37,7 +37,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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2 changes: 1 addition & 1 deletion schema/vrs/json/ReferenceLengthExpression
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Expand Up @@ -38,7 +38,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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4 changes: 2 additions & 2 deletions schema/vrs/json/SequenceLocation
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Expand Up @@ -40,7 +40,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand All @@ -62,7 +62,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceReference"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
],
"description": "A reference to a Sequence on which the location is defined."
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2 changes: 1 addition & 1 deletion schema/vrs/json/SequenceReference
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Expand Up @@ -37,7 +37,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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4 changes: 2 additions & 2 deletions schema/vrs/json/Terminus
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Expand Up @@ -38,7 +38,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand Down Expand Up @@ -67,7 +67,7 @@
"$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
},
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
}
],
"description": "The location of the terminus."
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2 changes: 1 addition & 1 deletion schema/vrs/json/TraversalBlock
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Expand Up @@ -38,7 +38,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
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