Merge branch 'main' into serialize

ga4gh · Jul 18, 2024 · 1771675 · 1771675
2 parents 0469063 + 03425d3
commit 1771675
Show file tree

Hide file tree

Showing 12 changed files with 113 additions and 83 deletions.
diff --git a/.github/workflows/python-cqa.yml b/.github/workflows/python-cqa.yml
@@ -18,17 +18,17 @@ jobs:
       SEQREPO_ROOT_DIR: ./tests/data/seqrepo/latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
-    - uses: actions/cache@v2
+    - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
         restore-keys: |
           ${{ runner.os }}-pip-
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Update pip and setuptools

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -26,7 +26,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install pypa/build
@@ -38,7 +38,7 @@ jobs:
       - name: Build a binary wheel and a source tarball
         run: python3 -m build
       - name: Store the distribution packages
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
@@ -55,7 +55,7 @@ jobs:
       id-token: write # IMPORTANT: mandatory for trusted publishing
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: python-package-distributions
           path: dist/

diff --git a/notebooks/getting_started/3_Basic_Models.ipynb b/notebooks/getting_started/3_Basic_Models.ipynb
@@ -347,7 +347,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.1"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/getting_started/4_Exploring_the_AlleleTranslator.ipynb b/notebooks/getting_started/4_Exploring_the_AlleleTranslator.ipynb
@@ -513,7 +513,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.1"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb b/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb
@@ -170,16 +170,16 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CX.0M5VkV5v504_laQURFMEsqzZGcOF9YEw',\n",
-       " 'type': <VrsType.CN_CHANGE: 'CopyNumberChange'>,\n",
+       " 'type': 'CopyNumberChange',\n",
        " 'digest': '0M5VkV5v504_laQURFMEsqzZGcOF9YEw',\n",
        " 'location': {'id': 'ga4gh:SL.GSJAEJXFDz7Nq6VlJj5NTEku48MmteUU',\n",
-       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       "  'type': 'SequenceLocation',\n",
        "  'digest': 'GSJAEJXFDz7Nq6VlJj5NTEku48MmteUU',\n",
-       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       "  'sequenceReference': {'type': 'SequenceReference',\n",
        "   'refgetAccession': 'SQ.eK4D2MosgK_ivBkgi6FVPg5UXs1bYESm'},\n",
        "  'start': 45002866,\n",
        "  'end': 45015056},\n",
-       " 'copyChange': <CopyChange.EFO_0030067: 'efo:0030067'>}"
+       " 'copyChange': 'efo:0030067'}"
       ]
      },
      "execution_count": 4,
@@ -225,16 +225,16 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CX.0BN4vrqPrLPAZYsQEAPnG4IS8AYeBGe1',\n",
-       " 'type': <VrsType.CN_CHANGE: 'CopyNumberChange'>,\n",
+       " 'type': 'CopyNumberChange',\n",
        " 'digest': '0BN4vrqPrLPAZYsQEAPnG4IS8AYeBGe1',\n",
        " 'location': {'id': 'ga4gh:SL.tydo6UFL8Y60L5Me3k8AJfljURO9vYn9',\n",
-       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       "  'type': 'SequenceLocation',\n",
        "  'digest': 'tydo6UFL8Y60L5Me3k8AJfljURO9vYn9',\n",
-       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       "  'sequenceReference': {'type': 'SequenceReference',\n",
        "   'refgetAccession': 'SQ.KEO-4XBcm1cxeo_DIQ8_ofqGUkp4iZhI'},\n",
        "  'start': 75502957,\n",
        "  'end': 76045032},\n",
-       " 'copyChange': <CopyChange.EFO_0030070: 'efo:0030070'>}"
+       " 'copyChange': 'efo:0030070'}"
       ]
      },
      "execution_count": 5,
@@ -292,12 +292,12 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CN.O_QHImmfErh9jDFkJaypPPvUmnj7EM70',\n",
-       " 'type': <VrsType.CN_COUNT: 'CopyNumberCount'>,\n",
+       " 'type': 'CopyNumberCount',\n",
        " 'digest': 'O_QHImmfErh9jDFkJaypPPvUmnj7EM70',\n",
        " 'location': {'id': 'ga4gh:SL.hBVWalem_rNclxjmUuT9CHbEGCdlqW9L',\n",
-       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       "  'type': 'SequenceLocation',\n",
        "  'digest': 'hBVWalem_rNclxjmUuT9CHbEGCdlqW9L',\n",
-       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       "  'sequenceReference': {'type': 'SequenceReference',\n",
        "   'refgetAccession': 'SQ.HxuclGHh0XCDuF8x6yQrpHUBL7ZntAHc'},\n",
        "  'start': 85623,\n",
        "  'end': 57073230},\n",
@@ -346,12 +346,12 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CN.WDzlT9oUq4IcQrVRWGH0dZnARnFBotCS',\n",
-       " 'type': <VrsType.CN_COUNT: 'CopyNumberCount'>,\n",
+       " 'type': 'CopyNumberCount',\n",
        " 'digest': 'WDzlT9oUq4IcQrVRWGH0dZnARnFBotCS',\n",
        " 'location': {'id': 'ga4gh:SL.H1Zh5xdBqamBjwVE9orWdY_uBkpEMH1V',\n",
-       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       "  'type': 'SequenceLocation',\n",
        "  'digest': 'H1Zh5xdBqamBjwVE9orWdY_uBkpEMH1V',\n",
-       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       "  'sequenceReference': {'type': 'SequenceReference',\n",
        "   'refgetAccession': 'SQ.5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8'},\n",
        "  'start': 46111352,\n",
        "  'end': 46119948},\n",
@@ -385,7 +385,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.1"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/getting_started/6_Upcoming_features.ipynb b/notebooks/getting_started/6_Upcoming_features.ipynb
@@ -146,17 +146,16 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:VA.LK_4rOVxyEwrEpaOVd-BDFV0ocbO5vgV',\n",
-       " 'type': <VrsType.ALLELE: 'Allele'>,\n",
+       " 'type': 'Allele',\n",
        " 'digest': 'LK_4rOVxyEwrEpaOVd-BDFV0ocbO5vgV',\n",
        " 'location': {'id': 'ga4gh:SL.nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
-       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       "  'type': 'SequenceLocation',\n",
        "  'digest': 'nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
-       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       "  'sequenceReference': {'type': 'SequenceReference',\n",
        "   'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'},\n",
        "  'start': 80656509,\n",
        "  'end': 80656510},\n",
-       " 'state': {'type': <VrsType.LIT_SEQ_EXPR: 'LiteralSequenceExpression'>,\n",
-       "  'sequence': 'TT'}}"
+       " 'state': {'type': 'LiteralSequenceExpression', 'sequence': 'TT'}}"
       ]
      },
      "execution_count": 4,
@@ -226,9 +225,9 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:SL.nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
-       " 'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       " 'type': 'SequenceLocation',\n",
        " 'digest': 'nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
-       " 'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       " 'sequenceReference': {'type': 'SequenceReference',\n",
        "  'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'},\n",
        " 'start': 80656509,\n",
        " 'end': 80656510}"
@@ -261,7 +260,7 @@
     {
      "data": {
       "text/plain": [
-       "{'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       "{'type': 'SequenceReference',\n",
        " 'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'}"
       ]
      },
@@ -293,7 +292,7 @@
      "data": {
       "text/plain": [
        "{'id': None,\n",
-       " 'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
+       " 'type': 'SequenceReference',\n",
        " 'label': None,\n",
        " 'description': None,\n",
        " 'alternativeLabels': None,\n",
@@ -399,9 +398,9 @@
      "data": {
       "text/plain": [
        "{'id': 'refseq:NC_000005.10',\n",
-       " 'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
-       " 'label': 'GRCh38:chr5',\n",
-       " 'alternativeLabels': ['GRCh38:5'],\n",
+       " 'type': 'SequenceReference',\n",
+       " 'label': 'GRCh38:5',\n",
+       " 'alternativeLabels': ['GRCh38:chr5'],\n",
        " 'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'}"
       ]
      },
@@ -435,12 +434,12 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:SL.nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
-       " 'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       " 'type': 'SequenceLocation',\n",
        " 'digest': 'nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
        " 'sequenceReference': {'id': 'refseq:NC_000005.10',\n",
-       "  'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
-       "  'label': 'GRCh38:chr5',\n",
-       "  'alternativeLabels': ['GRCh38:5'],\n",
+       "  'type': 'SequenceReference',\n",
+       "  'label': 'GRCh38:5',\n",
+       "  'alternativeLabels': ['GRCh38:chr5'],\n",
        "  'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'},\n",
        " 'start': 80656509,\n",
        " 'end': 80656510}"
@@ -465,20 +464,19 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:VA.LK_4rOVxyEwrEpaOVd-BDFV0ocbO5vgV',\n",
-       " 'type': <VrsType.ALLELE: 'Allele'>,\n",
+       " 'type': 'Allele',\n",
        " 'digest': 'LK_4rOVxyEwrEpaOVd-BDFV0ocbO5vgV',\n",
        " 'location': {'id': 'ga4gh:SL.nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
-       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
+       "  'type': 'SequenceLocation',\n",
        "  'digest': 'nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n",
        "  'sequenceReference': {'id': 'refseq:NC_000005.10',\n",
-       "   'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
-       "   'label': 'GRCh38:chr5',\n",
-       "   'alternativeLabels': ['GRCh38:5'],\n",
+       "   'type': 'SequenceReference',\n",
+       "   'label': 'GRCh38:5',\n",
+       "   'alternativeLabels': ['GRCh38:chr5'],\n",
        "   'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'},\n",
        "  'start': 80656509,\n",
        "  'end': 80656510},\n",
-       " 'state': {'type': <VrsType.LIT_SEQ_EXPR: 'LiteralSequenceExpression'>,\n",
-       "  'sequence': 'TT'}}"
+       " 'state': {'type': 'LiteralSequenceExpression', 'sequence': 'TT'}}"
       ]
      },
      "execution_count": 11,
@@ -507,7 +505,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.1"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,

diff --git a/src/ga4gh/core/__init__.py b/src/ga4gh/core/__init__.py
@@ -15,6 +15,7 @@
 from .pydantic import (
     is_pydantic_instance, is_curie_type, pydantic_copy
 )
+from .domain_models import CommonDomainType
 from . import entity_models, domain_models
 
 __all__ = [
@@ -36,6 +37,7 @@
     "is_pydantic_instance",
     "is_curie_type",
     "pydantic_copy",
+    "CommonDomainType",
     "entity_models",
     "domain_models"
 ]

diff --git a/src/ga4gh/core/domain_models.py b/src/ga4gh/core/domain_models.py
@@ -10,8 +10,8 @@
   * `import ga4gh.core`, and refer to models using the fully-qualified
     module name, e.g., `ga4gh.core.domain_models.Gene`
 """
-from typing import Literal, Union, List
 from enum import Enum
+from typing import Literal, Union, List
 
 from pydantic import Field, RootModel
 
@@ -33,8 +33,8 @@ class CommonDomainType(str, Enum):
 class Phenotype(DomainEntity):
     """An observable characteristic or trait of an organism."""
 
-    type: Literal[CommonDomainType.PHENOTYPE] = Field(
-        CommonDomainType.PHENOTYPE,
+    type: Literal["Phenotype"] = Field(
+        CommonDomainType.PHENOTYPE.value,
         description=f'MUST be "{CommonDomainType.PHENOTYPE.value}".'
     )
 
@@ -44,17 +44,17 @@ class Disease(DomainEntity):
     of all or part of an organism and is not immediately due to any external injury.
     """
 
-    type: Literal[CommonDomainType.DISEASE] = Field(
-        CommonDomainType.DISEASE,
+    type: Literal["Disease"] = Field(
+        CommonDomainType.DISEASE.value,
         description=f'MUST be "{CommonDomainType.DISEASE.value}".'
     )
 
 
 class TraitSet(DomainEntity):
     """A set of phenotype and/or disease concepts that together constitute a condition."""
 
-    type: Literal[CommonDomainType.TRAIT_SET] = Field(
-        CommonDomainType.TRAIT_SET,
+    type: Literal["TraitSet"] = Field(
+        CommonDomainType.TRAIT_SET.value,
         description=f'MUST be "{CommonDomainType.TRAIT_SET.value}".'
     )
     traits: List[Union[Disease, Phenotype]] = Field(
@@ -76,26 +76,26 @@ class Condition(RootModel):
 class TherapeuticAction(DomainEntity):
     """A therapeutic action taken that is intended to alter or stop a pathologic process."""
 
-    type: Literal[CommonDomainType.TR_ACTION] = Field(
-        CommonDomainType.TR_ACTION,
+    type: Literal["TherapeuticAction"] = Field(
+        CommonDomainType.TR_ACTION.value,
         description=f'MUST be "{CommonDomainType.TR_ACTION.value}".'
     )
 
 
 class TherapeuticAgent(DomainEntity):
     """An administered therapeutic agent that is intended to alter or stop a pathologic process."""
 
-    type: Literal[CommonDomainType.TR_AGENT] = Field(
-        CommonDomainType.TR_AGENT,
+    type: Literal["TherapeuticAgent"] = Field(
+        CommonDomainType.TR_AGENT.value,
         description=f'MUST be "{CommonDomainType.TR_AGENT.value}".'
     )
 
 
 class TherapeuticSubstituteGroup(DomainEntity):
     """A group of therapeutic procedures that may be treated as substitutes for one another."""
 
-    type: Literal[CommonDomainType.TR_SUB] = Field(
-        CommonDomainType.TR_SUB,
+    type: Literal["TherapeuticSubstituteGroup"] = Field(
+        CommonDomainType.TR_SUB.value,
         description=f'MUST be "{CommonDomainType.TR_SUB.value}".'
     )
     substitutes: List[Union[TherapeuticAction, TherapeuticAgent]] = Field(
@@ -110,8 +110,8 @@ class CombinationTherapy(DomainEntity):
     performed in combination.
     """
 
-    type: Literal[CommonDomainType.TR_COMB] = Field(
-        CommonDomainType.TR_COMB,
+    type: Literal["CombinationTherapy"] = Field(
+        CommonDomainType.TR_COMB.value,
         description=f'MUST be "{CommonDomainType.TR_COMB.value}".'
     )
     components: List[Union[TherapeuticSubstituteGroup, TherapeuticAction, TherapeuticAgent]] = Field(
@@ -136,7 +136,7 @@ class TherapeuticProcedure(RootModel):
 class Gene(DomainEntity):
     """A basic physical and functional unit of heredity."""
 
-    type: Literal[CommonDomainType.GENE] = Field(
-        CommonDomainType.GENE,
+    type: Literal["Gene"] = Field(
+        CommonDomainType.GENE.value,
         description=f'MUST be "{CommonDomainType.GENE.value}".'
     )