fix: update civic test fixtures + re-run make all

schema/va-spec/aac-2017/json/VariantDiagnosticStudyStatement

@@ -6,12 +6,12 @@
    "description": "A statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/VariantDiagnosticProposition",
                "description": "A proposition about a diagnostic association between a variant and condition, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it,  may be assessed and reported by the Statement. "
             }
          }

schema/va-spec/aac-2017/json/VariantPrognosticStudyStatement

@@ -6,12 +6,12 @@
    "description": "A statement reporting a conclusion from a single study about whether a variant is associated with a disease prognosis - based on interpretation of the study's results.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/VariantPrognosticProposition",
                "description": "A proposition about a prognostic association between a variant and condition, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it,  may be assessed and reported by the Statement. "
             }
          }

schema/va-spec/aac-2017/json/VariantTherapeuticResponseStudyStatement

@@ -6,12 +6,12 @@
    "description": "A statement reporting a conclusion from a single study about whether a variant is associated with a therapeutic response (positive or negative) - based on interpretation of the study's results.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/VariantTherapeuticResponseProposition",
                "description": "A proposition about the therapeutic response associated with a variant, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it,  may be assessed and reported by the Statement. "
             }
          }

schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine

@@ -6,13 +6,13 @@
    "description": "An Evidence Line that describes how information about the functional impact of a variant on a gene or  gene product was interpreted as evidence for or against the variant's pathogenicity. ",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/EvidenceLine"
+         "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/EvidenceLine"
       },
       {
          "properties": {
             "targetProposition": {
                "description": "A Variant Pathogenicity Proposition against which functional impact information was assessed, in determining the strength and direction of support this information provides as evidence.",
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition"
+               "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/VariantPathogenicityProposition"
             },
             "strengthOfEvidenceProvided": {
                "description": "The strength of support that an Evidence Line is determined to provide for or against the proposition or the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute.     *Conditional requirement: if directionOfEvidenceProvided is either 'supports' or 'disputes', then this attribute is required. If it is 'none', then this attribute is not allowed.",

schema/va-spec/acmg-2015/json/VariantPathogenicityStatement

@@ -6,12 +6,12 @@
    "description": "A Statement describing the role of a variant in causing an inherited condition.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/VariantPathogenicityProposition",
                "description": "A proposition about the pathogenicity of a varaint, the validity of which is assessed and reported by the Statement.  A Statement can put forth the proposition as being true, false, or uncertain, and may provide an assessment of the level of confidence/evidence supporting this claim.        "
             }
          }

schema/va-spec/base/def/ClinicalVariantProposition.rst

@@ -76,7 +76,7 @@ Some ClinicalVariantProposition attributes are inherited from :ref:`SubjectVaria
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/EvidenceLine.rst

@@ -88,7 +88,7 @@ Some EvidenceLine attributes are inherited from :ref:`InformationEntity`.
                         .. 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:`StudyResult` | :ref:`Statement` | :ref:`EvidenceLine` | :ref:`iriReference`
+      - :ref:`Statement` | :ref:`EvidenceLine` | :ref:`iriReference`
       - 0..m
       - An individual piece of information that was evaluated as evidence in building the argument represented by an Evidence Line.
    *  - directionOfEvidenceProvided

schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst

@@ -71,9 +71,9 @@ Some ExperimentalVariantFunctionalImpactProposition attributes are inherited fro
       - 
       - :ref:`iriReference` | :ref:`MappableConcept`
       - 1..1
-      - The sequence feature (typically a gene or gene product) on whose function the impact  of the subject variant is reported.
+      - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is reported.
    *  - experimentalContextQualifier
       - 
       - :ref:`iriReference` | :ref:`Document` | object
       - 0..1
-      - An assay in which the reported variant functional impact was determined -  providing a specific experimental context in which this effect is asserted to hold.
+      - An assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.

schema/va-spec/base/def/Statement.rst

@@ -82,7 +82,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
       - 
       - :ref:`Proposition`
       - 1..1
-      - A possible fact, the validity of which is assessed and reported by the Statement. A Statement can put forth the proposition as being true, false, or uncertain, and may provide an assessment of the level of confidence/evidence supporting this claim. 
+      - A possible fact, the validity of which is assessed and reported by the Statement. A Statement can put forth the proposition as being true, false, or uncertain, and may provide an assessment of the level of confidence/evidence supporting this claim.
    *  - direction
       - 
       - string
@@ -100,7 +100,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
                             <span style="background-color: #D3D3D3; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Draft Maturity Level">D</span>
       - number
       - 0..1
-      - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. Instructions for how to interpret the menaing of a given score may be gleaned from the method or document referenced in 'specifiedBy' attribute. 
+      - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. Instructions for how to interpret the menaing of a given score may be gleaned from the method or document referenced in 'specifiedBy' attribute.
    *  - classification
       - 
       - :ref:`MappableConcept`

schema/va-spec/base/def/VariantDiagnosticProposition.rst

@@ -61,7 +61,7 @@ Some VariantDiagnosticProposition attributes are inherited from :ref:`ClinicalVa
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/VariantOncogenicityProposition.rst

@@ -61,7 +61,7 @@ Some VariantOncogenicityProposition attributes are inherited from :ref:`Clinical
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/VariantPathogenicityProposition.rst

@@ -61,7 +61,7 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Clinica
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
@@ -86,7 +86,7 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Clinica
       - 
       - :ref:`MappableConcept`
       - 0..1
-      - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. 
+      - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition.
    *  - modeOfInheritanceQualifier
       - 
       - :ref:`MappableConcept`

schema/va-spec/base/def/VariantPrognosticProposition.rst

@@ -61,7 +61,7 @@ Some VariantPrognosticProposition attributes are inherited from :ref:`ClinicalVa
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst

@@ -61,7 +61,7 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`C
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
@@ -86,4 +86,4 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`C
       - 
       - :ref:`Condition` | :ref:`iriReference`
       - 1..1
-      - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response propositions. 
+      - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response propositions.

schema/va-spec/base/json/CohortAlleleFrequencyStudyResult

@@ -46,7 +46,7 @@
             }
          ],
          "description": "A specification that describes all or part of the process that led to creation of the Information Entity",
-         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a  method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
+         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
       },
       "contributions": {
          "type": "array",

schema/va-spec/base/json/EvidenceLine

@@ -47,7 +47,7 @@
             }
          ],
          "description": "A specification that describes all or part of the process that led to creation of the Information Entity",
-         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a  method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
+         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
       },
       "contributions": {
          "type": "array",
@@ -108,9 +108,6 @@
          "ordered": false,
          "items": {
             "anyOf": [
-               {
-                  "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/StudyResult"
-               },
                {
                   "$ref": "/ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/Statement"
                },

schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition

@@ -49,7 +49,7 @@
             }
          ],
          "description": "A variant that is the subject of the Proposition.",
-         "$comment": "In profiles for most VA-Spec implementations, the subject will be a some type of genetic  variation. However, the Core VA model is domain-agnostic, and supports Propositions about any type of Entity. Some data providers may want to make statements about other entities or concepts that represent evidence for a Propositions about genetic variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)."
+         "$comment": "In profiles for most VA-Spec implementations, the subject will be a some type of genetic variation. However, the Core VA model is domain-agnostic, and supports Propositions about any type of Entity. Some data providers may want to make statements about other entities or concepts that represent evidence for a Propositions about genetic variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)."
       },
       "type": {
          "type": "string",
@@ -73,11 +73,11 @@
                "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/iriReference"
             }
          ],
-         "description": "The sequence feature (typically a gene or gene product) on whose function the impact  of the subject variant is reported.",
+         "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is reported.",
          "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject. When the subject is a genetic variation, the object is often a disease, phenotype, therapeutic intervention, or gene."
       },
       "experimentalContextQualifier": {
-         "description": "An assay in which the reported variant functional impact was determined -  providing a specific experimental context in which this effect is asserted to hold.",
+         "description": "An assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.",
          "anyOf": [
             {
                "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/iriReference"
@@ -88,7 +88,7 @@
             {
                "type": "object",
                "additionalProperties": true,
-               "$comment": "It is expected that non-Document objects will conform to externally-maintained  community schemas for representing experimental context data."
+               "$comment": "It is expected that non-Document objects will conform to externally-maintained community schemas for representing experimental context data."
             }
          ]
       }