test and update CAF to TU

ga4gh · Nov 26, 2024 · 606004c · 606004c
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diff --git a/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml b/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml
@@ -11,7 +11,7 @@ imports:
 $defs:
   CohortAlleleFrequencyStudyResult:
     inherits: va-core:StudyResult
-    maturity: draft
+    maturity: trial use
     type: object
     description: >-
       A StudyResult that reports measures related to the frequency of an Allele in a cohort

diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst
@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**

diff --git a/schema/va-spec/base/def/DataSet.rst b/schema/va-spec/base/def/DataSet.rst
@@ -67,11 +67,8 @@ Some DataSet attributes are inherited from :ref:`gks-core:Entity`.
       - A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', a 'genome annotation data set')
    *  - reportedIn
       - 
-                        .. raw:: html
-
-                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Document` | :ref:`iriReference`
-      - 0..m
+      - 0..1
       - A document in which the the Method is reported.
    *  - releaseDate
       - 

diff --git a/schema/va-spec/base/def/Method.rst b/schema/va-spec/base/def/Method.rst
@@ -64,9 +64,6 @@ Some Method attributes are inherited from :ref:`gks-core:Entity`.
       - A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol').
    *  - reportedIn
       - 
-                        .. raw:: html
-
-                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Document` | :ref:`iriReference`
-      - 0..m
+      - 0..1
       - A document in which the the Method is reported.
diff --git a/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult b/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult
@@ -2,7 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/CohortAlleleFrequencyStudyResult",
    "title": "CohortAlleleFrequencyStudyResult",
-   "maturity": "draft",
+   "maturity": "trial use",
    "type": "object",
    "description": "A StudyResult that reports measures related to the frequency of an Allele in a cohort",
    "properties": {

diff --git a/schema/va-spec/base/json/DataSet b/schema/va-spec/base/json/DataSet
@@ -51,18 +51,14 @@
          "description": "A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', a 'genome annotation data set')"
       },
       "reportedIn": {
-         "type": "array",
-         "ordered": false,
-         "items": {
-            "oneOf": [
-               {
-                  "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
-               },
-               {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
-               }
-            ]
-         },
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+            }
+         ],
          "description": "A document in which the the Method is reported."
       },
       "releaseDate": {

diff --git a/schema/va-spec/base/json/Method b/schema/va-spec/base/json/Method
@@ -47,21 +47,17 @@
       "subtype": {
          "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept",
          "description": "A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol').",
-         "$comment": "This attribute can be used to report a specific type for the Method, in cases where a model does not define Method subclasses for this purpose.  Implementers can define their own set of method type codes/terms, to match the needs of their application.\n  reportedIn:"
+         "$comment": "This attribute can be used to report a specific type for the Method, in cases where a model does not define Method subclasses for this purpose.  Implementers can define their own set of method type codes/terms, to match the needs of their application."
       },
       "reportedIn": {
-         "type": "array",
-         "ordered": false,
-         "items": {
-            "oneOf": [
-               {
-                  "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
-               },
-               {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
-               }
-            ]
-         },
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+            }
+         ],
          "description": "A document in which the the Method is reported."
       }
    },

diff --git a/schema/va-spec/base/va-core-source.yaml b/schema/va-spec/base/va-core-source.yaml
@@ -274,12 +274,8 @@ $defs:
           This attribute can be used to report a specific type for the Method, in cases where a model
           does not define Method subclasses for this purpose.  Implementers can define their own set
           of method type codes/terms, to match the needs of their application.
-            reportedIn:
       reportedIn:
-        type: array
-        ordered: false
-        items:
-          oneOf:
+        oneOf:
           - $ref: "#/$defs/Document"
           - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference"
         description: A document in which the the Method is reported.
@@ -660,10 +656,7 @@ $defs:
           Implementers can define their own set of data set type codes/terms, to match
           the needs of the domain or application.
       reportedIn:
-        type: array
-        ordered: false
-        items:
-          oneOf:
+        oneOf:
           - $ref: "#/$defs/Document"
           - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference"
         description: A document in which the the Method is reported.

diff --git a/tests/fixtures/Exp-Var-Func-Impact-Statement-01.yaml b/tests/fixtures/Exp-Var-Func-Impact-Statement-01.yaml
@@ -144,4 +144,5 @@ specifiedBy:
   subtype:
     primaryCode: variant interpretation guideline
   reportedIn: 
-    - https://pubmed.ncbi.nlm.nih.gov/29785012/
+    type: Document
+    pmid: 29785012
diff --git a/tests/fixtures/Exp-Var-Func-Impact-Study-Result-01.yaml b/tests/fixtures/Exp-Var-Func-Impact-Study-Result-01.yaml
@@ -22,14 +22,14 @@ specifiedBy:
   subtype:
     label: Experimental protocol
   reportedIn:
-  - type: Document
+    type: Document
     pmid: 29785012
 sourceDataSet:
     type: DataSet
     label: variant effect data set
     license:
       primaryCode: "CC0"
     reportedIn:
-      - type: Document
-        urls:
-          - https://mavedb.org/score-sets/urn:mavedb:00000013-a-1
+      type: Document
+      urls:
+        - "https://mavedb.org/score-sets/urn:mavedb:00000013-a-1"
diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml
@@ -75,11 +75,11 @@ specifiedBy:
   type: Method
   label: ClinGen HL ACMG Specifications v1
   reportedIn:
-    - id: https://submit.ncbi.nlm.nih.gov/ft/byid/vroiax8b/hearing_loss_acmg_specifications_v1_2018.pdf
-      urls:
-      - https://submit.ncbi.nlm.nih.gov/ft/byid/vroiax8b/hearing_loss_acmg_specifications_v1_2018.pdf
-      type: Document
-      label: ClinGen HL ACMG Specifications v1
+    id: https://submit.ncbi.nlm.nih.gov/ft/byid/vroiax8b/hearing_loss_acmg_specifications_v1_2018.pdf
+    urls:
+    - https://submit.ncbi.nlm.nih.gov/ft/byid/vroiax8b/hearing_loss_acmg_specifications_v1_2018.pdf
+    type: Document
+    label: ClinGen HL ACMG Specifications v1
 extensions:
 - name: clinvarMethodCategory
   value: curation

diff --git a/tests/fixtures/civic-curation-sop-method.yaml b/tests/fixtures/civic-curation-sop-method.yaml
@@ -1,13 +1,13 @@
 id: civic.methods:2019
 label: CIViC Curation SOP (2019)
 reportedIn:
-  - id: pmid:31779674
-    type: Document
-    label: Danos et al., 2019, Genome Med.
-    title: Standard operating procedure for curation and clinical interpretation of
-      variants in cancer
-    doi: 10.1186/s13073-019-0687-x
-    pmid: 31779674
+  id: pmid:31779674
+  type: Document
+  label: Danos et al., 2019, Genome Med.
+  title: Standard operating procedure for curation and clinical interpretation of
+    variants in cancer
+  doi: 10.1186/s13073-019-0687-x
+  pmid: 31779674
 type: Method
 subtype:
   primaryCode: variant curation standard operating procedure