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Merge remote-tracking branch 'origin/main' into release
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@susannasiebert
susannasiebert committed Apr 13, 2022
2 parents 8bb90fe + 1f924c5 commit 75c7a06
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Showing 15 changed files with 170 additions and 173 deletions.
32 changes: 16 additions & 16 deletions client/src/app/forms/variant-revise/variant-revise.form.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,8 @@ interface FormModel {
ensemblVersion?: number;
hgvsDescriptions: string[];
variantTypes: FormVariantType[];
fivePrimeCoordinates?: CoordinateFieldsFragment;
threePrimeCoordinates?: CoordinateFieldsFragment;
primaryCoordinates?: CoordinateFieldsFragment;
secondaryCoordinates?: CoordinateFieldsFragment;
referenceBases: Maybe<string>;
variantBases: Maybe<string>;
comment?: string;
Expand Down Expand Up @@ -286,7 +286,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
type: 'cvc-ensembl-input',
},
{
key: 'threePrimeCoordinates.referenceBases',
key: 'referenceBases',
type: 'input',
defaultValue: undefined,
templateOptions: {
Expand All @@ -299,7 +299,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
}
},
{
key: 'threePrimeCoordinates.variantBases',
key: 'variantBases',
type: 'input',
defaultValue: undefined,
templateOptions: {
Expand All @@ -312,7 +312,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
}
},
{
key: 'threePrimeCoordinates.chromosome',
key: 'primaryCoordinates.chromosome',
type: 'select',
defaultValue: undefined,
templateOptions: {
Expand All @@ -323,7 +323,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
},
},
{
key: 'threePrimeCoordinates.start',
key: 'primaryCoordinates.start',
type: 'input',
templateOptions: {
label: 'Start',
Expand All @@ -335,7 +335,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
}
},
{
key: 'threePrimeCoordinates.stop',
key: 'primaryCoordinates.stop',
type: 'input',
templateOptions: {
label: 'Stop',
Expand All @@ -347,7 +347,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
}
},
{
key: 'threePrimeCoordinates.representativeTranscript',
key: 'primaryCoordinates.representativeTranscript',
type: 'input',
templateOptions: {
label: 'Representative Transcript',
Expand All @@ -358,7 +358,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
template: '<h3>Secondary Coordinates</h3>',
},
{
key: 'fivePrimeCoordinates.chromosome',
key: 'secondaryCoordinates.chromosome',
type: 'select',
defaultValue: undefined,
templateOptions: {
Expand All @@ -370,7 +370,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
},
},
{
key: 'fivePrimeCoordinates.start',
key: 'secondaryCoordinates.start',
type: 'input',
templateOptions: {
label: 'Start',
Expand All @@ -381,7 +381,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
}
},
{
key: 'fivePrimeCoordinates.stop',
key: 'secondaryCoordinates.stop',
type: 'input',
templateOptions: {
label: 'Stop',
Expand All @@ -392,7 +392,7 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
}
},
{
key: 'fivePrimeCoordinates.representativeTranscript',
key: 'secondaryCoordinates.representativeTranscript',
type: 'input',
templateOptions: {
label: 'Representative Transcript',
Expand Down Expand Up @@ -487,8 +487,8 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
...variant,
clinvarStatus: this.getClinvarStatus(variant.clinvarIds),
clinvarIds: this.getClinvarIds(variant.clinvarIds),
referenceBases: variant.fivePrimeCoordinates?.referenceBases,
variantBases: variant.fivePrimeCoordinates?.variantBases,
referenceBases: variant.referenceBases,
variantBases: variant.variantBases,
comment: this.formModel?.fields.comment,
organization: this.formModel?.fields.organization,
},
Expand Down Expand Up @@ -534,8 +534,8 @@ export class VariantReviseForm implements AfterViewInit, OnDestroy {
ensemblVersion: fmt.toNullableInput(fields.ensemblVersion),
description: fmt.toNullableString(fields.description),
clinvarIds: fmt.toClinvarInput(fields.clinvarIds, fields.clinvarStatus),
primaryCoordinates: fmt.toCoordinateInput(fields.threePrimeCoordinates),
secondaryCoordinates: fmt.toCoordinateInput(fields.fivePrimeCoordinates),
primaryCoordinates: fmt.toCoordinateInput(fields.primaryCoordinates),
secondaryCoordinates: fmt.toCoordinateInput(fields.secondaryCoordinates),
referenceBases: fmt.toNullableString(fields.referenceBases),
variantBases: fmt.toNullableString(fields.variantBases),
referenceBuild: fmt.toNullableReferenceBuildInput(fields.referenceBuild),
Expand Down
8 changes: 4 additions & 4 deletions client/src/app/forms/variant-revise/variant-revise.query.gql
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Original file line number Diff line number Diff line change
Expand Up @@ -29,21 +29,21 @@ fragment RevisableVariantFields on Variant {
name
soid
}
fivePrimeCoordinates {
primaryCoordinates {
... CoordinateFields
}
threePrimeCoordinates {
secondaryCoordinates {
... CoordinateFields
}
referenceBases
variantBases
}

fragment CoordinateFields on Coordinate {
chromosome
referenceBases
representativeTranscript
start
stop
variantBases
}

mutation SuggestVariantRevision($input: SuggestVariantRevisionInput!) {
Expand Down
44 changes: 21 additions & 23 deletions client/src/app/generated/civic.apollo.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -963,11 +963,9 @@ export type Contribution = {
export type Coordinate = {
__typename: 'Coordinate';
chromosome?: Maybe<Scalars['String']>;
referenceBases?: Maybe<Scalars['String']>;
representativeTranscript?: Maybe<Scalars['String']>;
start?: Maybe<Scalars['Int']>;
stop?: Maybe<Scalars['Int']>;
variantBases?: Maybe<Scalars['String']>;
};

export type CoordinateInput = {
Expand Down Expand Up @@ -4096,7 +4094,6 @@ export type Variant = Commentable & EventOriginObject & EventSubject & Flaggable
events: EventConnection;
evidenceItems: EvidenceItemConnection;
evidenceScore: Scalars['Float'];
fivePrimeCoordinates?: Maybe<Coordinate>;
flagged: Scalars['Boolean'];
/** List and filter flags. */
flags: FlagConnection;
Expand All @@ -4109,12 +4106,15 @@ export type Variant = Commentable & EventOriginObject & EventSubject & Flaggable
link: Scalars['String'];
myVariantInfo?: Maybe<MyVariantInfo>;
name: Scalars['String'];
primaryCoordinates?: Maybe<Coordinate>;
referenceBases: Scalars['String'];
referenceBuild?: Maybe<ReferenceBuild>;
/** List and filter revisions. */
revisions: RevisionConnection;
secondaryCoordinates?: Maybe<Coordinate>;
sources: Array<Source>;
threePrimeCoordinates?: Maybe<Coordinate>;
variantAliases: Array<Scalars['String']>;
variantBases: Scalars['String'];
variantTypes: Array<VariantType>;
};

Expand Down Expand Up @@ -6961,7 +6961,7 @@ export type VariantRevisableFieldsQuery = (

export type RevisableVariantFieldsFragment = (
{ __typename: 'Variant' }
& Pick<Variant, 'id' | 'name' | 'description' | 'variantAliases' | 'alleleRegistryId' | 'clinvarIds' | 'ensemblVersion' | 'hgvsDescriptions' | 'referenceBuild'>
& Pick<Variant, 'id' | 'name' | 'description' | 'variantAliases' | 'alleleRegistryId' | 'clinvarIds' | 'ensemblVersion' | 'hgvsDescriptions' | 'referenceBuild' | 'referenceBases' | 'variantBases'>
& { sources: Array<(
{ __typename: 'Source' }
& Pick<Source, 'id' | 'sourceType' | 'citation' | 'citationId'>
Expand All @@ -6971,18 +6971,18 @@ export type RevisableVariantFieldsFragment = (
), variantTypes: Array<(
{ __typename: 'VariantType' }
& Pick<VariantType, 'id' | 'name' | 'soid'>
)>, fivePrimeCoordinates?: Maybe<(
)>, primaryCoordinates?: Maybe<(
{ __typename: 'Coordinate' }
& CoordinateFieldsFragment
)>, threePrimeCoordinates?: Maybe<(
)>, secondaryCoordinates?: Maybe<(
{ __typename: 'Coordinate' }
& CoordinateFieldsFragment
)> }
);

export type CoordinateFieldsFragment = (
{ __typename: 'Coordinate' }
& Pick<Coordinate, 'chromosome' | 'referenceBases' | 'representativeTranscript' | 'start' | 'stop' | 'variantBases'>
& Pick<Coordinate, 'chromosome' | 'representativeTranscript' | 'start' | 'stop'>
);

export type SuggestVariantRevisionMutationVariables = Exact<{
Expand Down Expand Up @@ -7936,7 +7936,7 @@ export type VariantSummaryQuery = (

export type VariantSummaryFieldsFragment = (
{ __typename: 'Variant' }
& Pick<Variant, 'id' | 'name' | 'description' | 'variantAliases' | 'alleleRegistryId' | 'hgvsDescriptions' | 'clinvarIds' | 'evidenceScore' | 'referenceBuild' | 'ensemblVersion'>
& Pick<Variant, 'id' | 'name' | 'description' | 'variantAliases' | 'alleleRegistryId' | 'hgvsDescriptions' | 'clinvarIds' | 'evidenceScore' | 'referenceBuild' | 'ensemblVersion' | 'referenceBases' | 'variantBases'>
& { gene: (
{ __typename: 'Gene' }
& Pick<Gene, 'id' | 'name'>
Expand All @@ -7946,12 +7946,12 @@ export type VariantSummaryFieldsFragment = (
)>, variantTypes: Array<(
{ __typename: 'VariantType' }
& Pick<VariantType, 'id' | 'link' | 'soid' | 'name'>
)>, fivePrimeCoordinates?: Maybe<(
)>, primaryCoordinates?: Maybe<(
{ __typename: 'Coordinate' }
& Pick<Coordinate, 'representativeTranscript' | 'chromosome' | 'start' | 'stop' | 'referenceBases' | 'variantBases'>
)>, threePrimeCoordinates?: Maybe<(
& Pick<Coordinate, 'representativeTranscript' | 'chromosome' | 'start' | 'stop'>
)>, secondaryCoordinates?: Maybe<(
{ __typename: 'Coordinate' }
& Pick<Coordinate, 'representativeTranscript' | 'chromosome' | 'start' | 'stop' | 'referenceBases' | 'variantBases'>
& Pick<Coordinate, 'representativeTranscript' | 'chromosome' | 'start' | 'stop'>
)>, flags: (
{ __typename: 'FlagConnection' }
& Pick<FlagConnection, 'totalCount'>
Expand Down Expand Up @@ -9146,11 +9146,9 @@ export const SubmittableVariantGroupFieldsFragmentDoc = gql`
export const CoordinateFieldsFragmentDoc = gql`
fragment CoordinateFields on Coordinate {
chromosome
referenceBases
representativeTranscript
start
stop
variantBases
}
`;
export const RevisableVariantFieldsFragmentDoc = gql`
Expand Down Expand Up @@ -9179,12 +9177,14 @@ export const RevisableVariantFieldsFragmentDoc = gql`
name
soid
}
fivePrimeCoordinates {
primaryCoordinates {
...CoordinateFields
}
threePrimeCoordinates {
secondaryCoordinates {
...CoordinateFields
}
referenceBases
variantBases
}
${CoordinateFieldsFragmentDoc}`;
export const AssertionDetailFieldsFragmentDoc = gql`
Expand Down Expand Up @@ -9878,22 +9878,20 @@ export const VariantSummaryFieldsFragmentDoc = gql`
evidenceScore
referenceBuild
ensemblVersion
fivePrimeCoordinates {
primaryCoordinates {
representativeTranscript
chromosome
start
stop
referenceBases
variantBases
}
threePrimeCoordinates {
secondaryCoordinates {
representativeTranscript
chromosome
start
stop
referenceBases
variantBases
}
referenceBases
variantBases
flags(state: OPEN) {
totalCount
}
Expand Down
14 changes: 7 additions & 7 deletions client/src/app/generated/server.field-policies.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -431,14 +431,12 @@ export type ContributionFieldPolicy = {
action?: FieldPolicy<any> | FieldReadFunction<any>,
count?: FieldPolicy<any> | FieldReadFunction<any>
};
export type CoordinateKeySpecifier = ('chromosome' | 'referenceBases' | 'representativeTranscript' | 'start' | 'stop' | 'variantBases' | CoordinateKeySpecifier)[];
export type CoordinateKeySpecifier = ('chromosome' | 'representativeTranscript' | 'start' | 'stop' | CoordinateKeySpecifier)[];
export type CoordinateFieldPolicy = {
chromosome?: FieldPolicy<any> | FieldReadFunction<any>,
referenceBases?: FieldPolicy<any> | FieldReadFunction<any>,
representativeTranscript?: FieldPolicy<any> | FieldReadFunction<any>,
start?: FieldPolicy<any> | FieldReadFunction<any>,
stop?: FieldPolicy<any> | FieldReadFunction<any>,
variantBases?: FieldPolicy<any> | FieldReadFunction<any>
stop?: FieldPolicy<any> | FieldReadFunction<any>
};
export type CountryKeySpecifier = ('id' | 'iso' | 'name' | CountryKeySpecifier)[];
export type CountryFieldPolicy = {
Expand Down Expand Up @@ -1274,7 +1272,7 @@ export type ValidationErrorsFieldPolicy = {
genericErrors?: FieldPolicy<any> | FieldReadFunction<any>,
validationErrors?: FieldPolicy<any> | FieldReadFunction<any>
};
export type VariantKeySpecifier = ('alleleRegistryId' | 'clinvarIds' | 'comments' | 'description' | 'ensemblVersion' | 'events' | 'evidenceItems' | 'evidenceScore' | 'fivePrimeCoordinates' | 'flagged' | 'flags' | 'gene' | 'hgvsDescriptions' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'myVariantInfo' | 'name' | 'referenceBuild' | 'revisions' | 'sources' | 'threePrimeCoordinates' | 'variantAliases' | 'variantTypes' | VariantKeySpecifier)[];
export type VariantKeySpecifier = ('alleleRegistryId' | 'clinvarIds' | 'comments' | 'description' | 'ensemblVersion' | 'events' | 'evidenceItems' | 'evidenceScore' | 'flagged' | 'flags' | 'gene' | 'hgvsDescriptions' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'myVariantInfo' | 'name' | 'primaryCoordinates' | 'referenceBases' | 'referenceBuild' | 'revisions' | 'secondaryCoordinates' | 'sources' | 'variantAliases' | 'variantBases' | 'variantTypes' | VariantKeySpecifier)[];
export type VariantFieldPolicy = {
alleleRegistryId?: FieldPolicy<any> | FieldReadFunction<any>,
clinvarIds?: FieldPolicy<any> | FieldReadFunction<any>,
Expand All @@ -1284,7 +1282,6 @@ export type VariantFieldPolicy = {
events?: FieldPolicy<any> | FieldReadFunction<any>,
evidenceItems?: FieldPolicy<any> | FieldReadFunction<any>,
evidenceScore?: FieldPolicy<any> | FieldReadFunction<any>,
fivePrimeCoordinates?: FieldPolicy<any> | FieldReadFunction<any>,
flagged?: FieldPolicy<any> | FieldReadFunction<any>,
flags?: FieldPolicy<any> | FieldReadFunction<any>,
gene?: FieldPolicy<any> | FieldReadFunction<any>,
Expand All @@ -1296,11 +1293,14 @@ export type VariantFieldPolicy = {
link?: FieldPolicy<any> | FieldReadFunction<any>,
myVariantInfo?: FieldPolicy<any> | FieldReadFunction<any>,
name?: FieldPolicy<any> | FieldReadFunction<any>,
primaryCoordinates?: FieldPolicy<any> | FieldReadFunction<any>,
referenceBases?: FieldPolicy<any> | FieldReadFunction<any>,
referenceBuild?: FieldPolicy<any> | FieldReadFunction<any>,
revisions?: FieldPolicy<any> | FieldReadFunction<any>,
secondaryCoordinates?: FieldPolicy<any> | FieldReadFunction<any>,
sources?: FieldPolicy<any> | FieldReadFunction<any>,
threePrimeCoordinates?: FieldPolicy<any> | FieldReadFunction<any>,
variantAliases?: FieldPolicy<any> | FieldReadFunction<any>,
variantBases?: FieldPolicy<any> | FieldReadFunction<any>,
variantTypes?: FieldPolicy<any> | FieldReadFunction<any>
};
export type VariantAliasKeySpecifier = ('name' | VariantAliasKeySpecifier)[];
Expand Down
10 changes: 5 additions & 5 deletions client/src/app/generated/server.model.graphql
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Original file line number Diff line number Diff line change
Expand Up @@ -1543,11 +1543,9 @@ type Contribution {

type Coordinate {
chromosome: String
referenceBases: String
representativeTranscript: String
start: Int
stop: Int
variantBases: String
}

input CoordinateInput {
Expand Down Expand Up @@ -3094,7 +3092,7 @@ type Mutation {
): AddDrugPayload

"""
Add a stub record for an external source that is not yet in CiVIC.
Add a stub record for an external source that is not yet in CIViC.
This is for adding a new Source inline while performing other curation activities
such as adding new evidence items and is distinct from suggesting a source for curation.
"""
Expand Down Expand Up @@ -6760,7 +6758,6 @@ type Variant implements Commentable & EventOriginObject & EventSubject & Flaggab
last: Int
): EvidenceItemConnection!
evidenceScore: Float!
fivePrimeCoordinates: Coordinate
flagged: Boolean!

"""
Expand Down Expand Up @@ -6816,6 +6813,8 @@ type Variant implements Commentable & EventOriginObject & EventSubject & Flaggab
link: String!
myVariantInfo: MyVariantInfo
name: String!
primaryCoordinates: Coordinate
referenceBases: String!
referenceBuild: ReferenceBuild

"""
Expand Down Expand Up @@ -6867,9 +6866,10 @@ type Variant implements Commentable & EventOriginObject & EventSubject & Flaggab
"""
status: RevisionStatus
): RevisionConnection!
secondaryCoordinates: Coordinate
sources: [Source!]!
threePrimeCoordinates: Coordinate
variantAliases: [String!]!
variantBases: String!
variantTypes: [VariantType!]!
}

Expand Down
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