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Add warning banner to eid and assertion summary if entity is in an invalid state #622

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Add warning banner to eid and assertion summary if entity is in an invalid state #622

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8 changes: 6 additions & 2 deletions client/src/app/generated/civic.apollo-helpers.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ export type AdvancedSearchResultFieldPolicy = {
resultIds?: FieldPolicy<any> | FieldReadFunction<any>,
searchEndpoint?: FieldPolicy<any> | FieldReadFunction<any>
};
export type AssertionKeySpecifier = ('acceptanceEvent' | 'acmgCodes' | 'ampLevel' | 'assertionDirection' | 'assertionType' | 'clingenCodes' | 'clinicalSignificance' | 'comments' | 'description' | 'disease' | 'drugInteractionType' | 'drugs' | 'events' | 'evidenceItems' | 'evidenceItemsCount' | 'fdaCompanionTest' | 'fdaCompanionTestLastUpdated' | 'flagged' | 'flags' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'molecularProfile' | 'name' | 'nccnGuideline' | 'nccnGuidelineVersion' | 'phenotypes' | 'regulatoryApproval' | 'regulatoryApprovalLastUpdated' | 'rejectionEvent' | 'revisions' | 'status' | 'submissionEvent' | 'summary' | 'variantOrigin' | AssertionKeySpecifier)[];
export type AssertionKeySpecifier = ('acceptanceEvent' | 'acmgCodes' | 'ampLevel' | 'assertionDirection' | 'assertionType' | 'clingenCodes' | 'clinicalSignificance' | 'comments' | 'description' | 'disease' | 'drugInteractionType' | 'drugs' | 'events' | 'evidenceItems' | 'evidenceItemsCount' | 'fdaCompanionTest' | 'fdaCompanionTestLastUpdated' | 'flagged' | 'flags' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'molecularProfile' | 'name' | 'nccnGuideline' | 'nccnGuidelineVersion' | 'phenotypes' | 'regulatoryApproval' | 'regulatoryApprovalLastUpdated' | 'rejectionEvent' | 'revisions' | 'status' | 'submissionEvent' | 'summary' | 'valid' | 'validationErrors' | 'variantOrigin' | AssertionKeySpecifier)[];
export type AssertionFieldPolicy = {
acceptanceEvent?: FieldPolicy<any> | FieldReadFunction<any>,
acmgCodes?: FieldPolicy<any> | FieldReadFunction<any>,
Expand Down Expand Up @@ -84,6 +84,8 @@ export type AssertionFieldPolicy = {
status?: FieldPolicy<any> | FieldReadFunction<any>,
submissionEvent?: FieldPolicy<any> | FieldReadFunction<any>,
summary?: FieldPolicy<any> | FieldReadFunction<any>,
valid?: FieldPolicy<any> | FieldReadFunction<any>,
validationErrors?: FieldPolicy<any> | FieldReadFunction<any>,
variantOrigin?: FieldPolicy<any> | FieldReadFunction<any>
};
export type AssertionConnectionKeySpecifier = ('edges' | 'nodes' | 'pageCount' | 'pageInfo' | 'totalCount' | AssertionConnectionKeySpecifier)[];
Expand Down Expand Up @@ -603,7 +605,7 @@ export type EventSubjectWithCountFieldPolicy = {
occuranceCount?: FieldPolicy<any> | FieldReadFunction<any>,
subject?: FieldPolicy<any> | FieldReadFunction<any>
};
export type EvidenceItemKeySpecifier = ('acceptanceEvent' | 'assertions' | 'clinicalSignificance' | 'comments' | 'description' | 'disease' | 'drugInteractionType' | 'drugs' | 'events' | 'evidenceDirection' | 'evidenceLevel' | 'evidenceRating' | 'evidenceType' | 'flagged' | 'flags' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'molecularProfile' | 'name' | 'phenotypes' | 'rejectionEvent' | 'revisions' | 'source' | 'status' | 'submissionEvent' | 'variant' | 'variantHgvs' | 'variantOrigin' | EvidenceItemKeySpecifier)[];
export type EvidenceItemKeySpecifier = ('acceptanceEvent' | 'assertions' | 'clinicalSignificance' | 'comments' | 'description' | 'disease' | 'drugInteractionType' | 'drugs' | 'events' | 'evidenceDirection' | 'evidenceLevel' | 'evidenceRating' | 'evidenceType' | 'flagged' | 'flags' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'molecularProfile' | 'name' | 'phenotypes' | 'rejectionEvent' | 'revisions' | 'source' | 'status' | 'submissionEvent' | 'valid' | 'validationErrors' | 'variant' | 'variantHgvs' | 'variantOrigin' | EvidenceItemKeySpecifier)[];
export type EvidenceItemFieldPolicy = {
acceptanceEvent?: FieldPolicy<any> | FieldReadFunction<any>,
assertions?: FieldPolicy<any> | FieldReadFunction<any>,
Expand Down Expand Up @@ -633,6 +635,8 @@ export type EvidenceItemFieldPolicy = {
source?: FieldPolicy<any> | FieldReadFunction<any>,
status?: FieldPolicy<any> | FieldReadFunction<any>,
submissionEvent?: FieldPolicy<any> | FieldReadFunction<any>,
valid?: FieldPolicy<any> | FieldReadFunction<any>,
validationErrors?: FieldPolicy<any> | FieldReadFunction<any>,
variant?: FieldPolicy<any> | FieldReadFunction<any>,
variantHgvs?: FieldPolicy<any> | FieldReadFunction<any>,
variantOrigin?: FieldPolicy<any> | FieldReadFunction<any>
Expand Down
22 changes: 18 additions & 4 deletions client/src/app/generated/civic.apollo.ts
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Expand Up @@ -234,6 +234,8 @@ export type Assertion = Commentable & EventOriginObject & EventSubject & Flaggab
status: EvidenceStatus;
submissionEvent: Event;
summary: Scalars['String'];
valid: Scalars['Boolean'];
validationErrors: Array<FieldValidationError>;
variantOrigin: VariantOrigin;
};

Expand Down Expand Up @@ -1448,6 +1450,8 @@ export type EvidenceItem = Commentable & EventOriginObject & EventSubject & Flag
source: Source;
status: EvidenceStatus;
submissionEvent: Event;
valid: Scalars['Boolean'];
validationErrors: Array<FieldValidationError>;
variant: Variant;
variantHgvs: Scalars['String'];
variantOrigin: VariantOrigin;
Expand Down Expand Up @@ -6103,9 +6107,9 @@ export type AssertionDetailQueryVariables = Exact<{
}>;


export type AssertionDetailQuery = { __typename: 'Query', assertion?: { __typename: 'Assertion', id: number, name: string, status: EvidenceStatus, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } } | undefined };
export type AssertionDetailQuery = { __typename: 'Query', assertion?: { __typename: 'Assertion', id: number, name: string, status: EvidenceStatus, valid: boolean, validationErrors: Array<{ __typename: 'FieldValidationError', fieldName: string, error: string }>, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } } | undefined };

export type AssertionDetailFieldsFragment = { __typename: 'Assertion', id: number, name: string, status: EvidenceStatus, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } };
export type AssertionDetailFieldsFragment = { __typename: 'Assertion', id: number, name: string, status: EvidenceStatus, valid: boolean, validationErrors: Array<{ __typename: 'FieldValidationError', fieldName: string, error: string }>, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } };

export type AssertionSummaryQueryVariables = Exact<{
assertionId: Scalars['Int'];
Expand Down Expand Up @@ -6167,9 +6171,9 @@ export type EvidenceDetailQueryVariables = Exact<{
}>;


export type EvidenceDetailQuery = { __typename: 'Query', evidenceItem?: { __typename: 'EvidenceItem', id: number, name: string, status: EvidenceStatus, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, assertions: Array<{ __typename: 'Assertion', id: number, name: string, link: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } } | undefined };
export type EvidenceDetailQuery = { __typename: 'Query', evidenceItem?: { __typename: 'EvidenceItem', id: number, name: string, status: EvidenceStatus, valid: boolean, validationErrors: Array<{ __typename: 'FieldValidationError', fieldName: string, error: string }>, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, assertions: Array<{ __typename: 'Assertion', id: number, name: string, link: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } } | undefined };

export type EvidenceDetailFieldsFragment = { __typename: 'EvidenceItem', id: number, name: string, status: EvidenceStatus, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, assertions: Array<{ __typename: 'Assertion', id: number, name: string, link: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } };
export type EvidenceDetailFieldsFragment = { __typename: 'EvidenceItem', id: number, name: string, status: EvidenceStatus, valid: boolean, validationErrors: Array<{ __typename: 'FieldValidationError', fieldName: string, error: string }>, submissionEvent: { __typename: 'Event', originatingUser: { __typename: 'User', id: number } }, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, assertions: Array<{ __typename: 'Assertion', id: number, name: string, link: string }>, flags: { __typename: 'FlagConnection', totalCount: number }, revisions: { __typename: 'RevisionConnection', totalCount: number }, comments: { __typename: 'CommentConnection', totalCount: number } };

export type EvidenceSummaryQueryVariables = Exact<{
evidenceId: Scalars['Int'];
Expand Down Expand Up @@ -7803,6 +7807,11 @@ export const AssertionDetailFieldsFragmentDoc = gql`
id
name
status
valid
validationErrors {
fieldName
error
}
submissionEvent {
originatingUser {
id
Expand Down Expand Up @@ -7943,6 +7952,11 @@ export const EvidenceDetailFieldsFragmentDoc = gql`
id
name
status
valid
validationErrors {
fieldName
error
}
submissionEvent {
originatingUser {
id
Expand Down
4 changes: 4 additions & 0 deletions client/src/app/generated/server.model.graphql
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Expand Up @@ -498,6 +498,8 @@ type Assertion implements Commentable & EventOriginObject & EventSubject & Flagg
status: EvidenceStatus!
submissionEvent: Event!
summary: String!
valid: Boolean!
validationErrors: [FieldValidationError!]!
variantOrigin: VariantOrigin!
}

Expand Down Expand Up @@ -2384,6 +2386,8 @@ type EvidenceItem implements Commentable & EventOriginObject & EventSubject & Fl
source: Source!
status: EvidenceStatus!
submissionEvent: Event!
valid: Boolean!
validationErrors: [FieldValidationError!]!
variant: Variant!
variantHgvs: String!
variantOrigin: VariantOrigin!
Expand Down
80 changes: 80 additions & 0 deletions client/src/app/generated/server.schema.json
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Expand Up @@ -1886,6 +1886,46 @@
"isDeprecated": false,
"deprecationReason": null
},
{
"name": "valid",
"description": null,
"args": [],
"type": {
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "SCALAR",
"name": "Boolean",
"ofType": null
}
},
"isDeprecated": false,
"deprecationReason": null
},
{
"name": "validationErrors",
"description": null,
"args": [],
"type": {
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "LIST",
"name": null,
"ofType": {
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "OBJECT",
"name": "FieldValidationError",
"ofType": null
}
}
}
},
"isDeprecated": false,
"deprecationReason": null
},
{
"name": "variantOrigin",
"description": null,
Expand Down Expand Up @@ -11443,6 +11483,46 @@
"isDeprecated": false,
"deprecationReason": null
},
{
"name": "valid",
"description": null,
"args": [],
"type": {
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "SCALAR",
"name": "Boolean",
"ofType": null
}
},
"isDeprecated": false,
"deprecationReason": null
},
{
"name": "validationErrors",
"description": null,
"args": [],
"type": {
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "LIST",
"name": null,
"ofType": {
"kind": "NON_NULL",
"name": null,
"ofType": {
"kind": "OBJECT",
"name": "FieldValidationError",
"ofType": null
}
}
}
},
"isDeprecated": false,
"deprecationReason": null
},
{
"name": "variant",
"description": null,
Expand Down
45 changes: 25 additions & 20 deletions client/src/app/views/assertions/assertions-detail/assertions-detail.query.gql
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Expand Up @@ -7,26 +7,31 @@ query AssertionDetail(
}

fragment AssertionDetailFields on Assertion {
id
name
status
submissionEvent {
originatingUser {
id
}
}
molecularProfile {
id
name
status
valid
validationErrors {
fieldName
error
}
submissionEvent {
originatingUser {
id
name
link
}
flags(state: OPEN) {
totalCount
}
revisions(status: NEW) {
totalCount
}
comments {
totalCount
}
}
molecularProfile {
id
name
link
}
flags(state: OPEN) {
totalCount
}
revisions(status: NEW) {
totalCount
}
comments {
totalCount
}
}
12 changes: 12 additions & 0 deletions client/src/app/views/assertions/assertions-detail/assertions-detail.view.html
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Expand Up @@ -105,6 +105,18 @@
nzMessage="This Assertion has been rejected."
nzType="error">
</nz-alert>
<nz-alert *ngIf="!this.assertion.valid"
nzBanner
[nzMessage]="validationErrorTpl"
nzType="warning">
</nz-alert>
<ng-template #validationErrorTpl>
This Assertion is in an invalid state.
<br/>
<span nzTypographq *ngFor="let error of this.assertion.validationErrors">
<strong>Field</strong>: {{error.fieldName}}. <strong>Error</strong>: {{error.error}}<br/>
</span>
</ng-template>
<cvc-tab-navigation [tabs]="this.tabs$ | ngrxPush">
<ng-template #tabBarExtraContent>
<nz-col id="contributors-col">
Expand Down
5 changes: 5 additions & 0 deletions client/src/app/views/evidence/evidence-detail/evidence-detail.query.gql
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Expand Up @@ -8,6 +8,11 @@ fragment EvidenceDetailFields on EvidenceItem {
id
name
status
valid
validationErrors {
fieldName
error
}
submissionEvent {
originatingUser {
id
Expand Down
12 changes: 12 additions & 0 deletions client/src/app/views/evidence/evidence-detail/evidence-detail.view.html
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Expand Up @@ -100,6 +100,18 @@
nzMessage="This Evidence Item has been rejected."
nzType="error">
</nz-alert>
<nz-alert *ngIf="!this.evidence.valid"
nzBanner
[nzMessage]="validationErrorTpl"
nzType="warning">
</nz-alert>
<ng-template #validationErrorTpl>
This Evidence Item is in an invalid state.
<br/>
<span nzTypographq *ngFor="let error of this.evidence.validationErrors">
<strong>Field</strong>: {{error.fieldName}}. <strong>Error</strong>: {{error.error}}<br/>
</span>
</ng-template>
<cvc-tab-navigation [tabs]="this.tabs$ | ngrxPush">
<ng-template #tabBarExtraContent>
<nz-col id="contributors-col">
Expand Down
23 changes: 23 additions & 0 deletions server/app/graphql/types/entities/assertion_type.rb
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Expand Up @@ -8,6 +8,8 @@ class AssertionType < Types::BaseObject
implements Types::Interfaces::EventOriginObject

field :id, Int, null: false
field :valid, Boolean, null: false
field :validation_errors, [Types::FieldValidationErrorType], null: false
field :name, String, null: false
field :molecular_profile, Types::Entities::MolecularProfileType, null: false
field :clinical_significance, Types::AssertionClinicalSignificanceType, null: false
Expand Down Expand Up @@ -36,6 +38,27 @@ class AssertionType < Types::BaseObject
field :evidence_items, [Types::Entities::EvidenceItemType], null: false
field :evidence_items_count, Integer, null: false

def valid
object.valid?
end

def validation_errors
if !object.valid?
object.errors.map do |attribute, message|
attribute = attribute.to_s
if attribute.ends_with?("_ids")
formatted_attribute = attribute.singularize.humanize.pluralize
else
formatted_attribute = attribute.humanize
end
{ 'field_name': formatted_attribute, 'error': message }
end
else
[]
end
end


def disease
Loaders::RecordLoader.for(Disease).load(object.disease_id)
end
Expand Down
22 changes: 22 additions & 0 deletions server/app/graphql/types/entities/evidence_item_type.rb
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Expand Up @@ -8,6 +8,8 @@ class EvidenceItemType < Types::BaseObject
implements Types::Interfaces::EventOriginObject

field :id, Int, null: false
field :valid, Boolean, null: false
field :validation_errors, [Types::FieldValidationErrorType], null: false
field :name, String, null: false
field :molecular_profile, Types::Entities::MolecularProfileType, null: false
field :clinical_significance, Types::EvidenceClinicalSignificanceType, null: false
Expand All @@ -31,6 +33,26 @@ class EvidenceItemType < Types::BaseObject
field :rejection_event, Types::Entities::EventType, null: true
field :assertions, [Types::Entities::AssertionType], null: false

def valid
object.valid?
end

def validation_errors
if !object.valid?
object.errors.map do |attribute, message|
attribute = attribute.to_s
if attribute.ends_with?("_ids")
formatted_attribute = attribute.singularize.humanize.pluralize
else
formatted_attribute = attribute.humanize
end
{ 'field_name': formatted_attribute, 'error': message }
end
else
[]
end
end

def disease
Loaders::RecordLoader.for(Disease).load(object.disease_id)
end
Expand Down