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fixes the event icon's twotone background color #594

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merged 7 commits into from
Aug 3, 2022
Merged

fixes the event icon's twotone background color #594

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b301bf3
replace gene/variant input on assertion add/revise forms with mp builder
susannasiebert Jul 30, 2022
1ac6764
Disallow MP creation while creating/revising assertions
susannasiebert Jul 30, 2022
c2dec31
use molecular profile segment loader
acoffman Jul 30, 2022
1e51448
remove breakpoint
acoffman Jul 30, 2022
9535d7d
Merge branch 'molecular-profiles' of github.com:griffithlab/civic-v2 …
acoffman Jul 30, 2022
df7b506
fix loader
acoffman Jul 30, 2022
510e606
corrected event-icon's twotone background hex color
mrjosh-zz Jul 30, 2022
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33 changes: 11 additions & 22 deletions client/src/app/forms/assertion-revise/assertion-revise.form.ts
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Expand Up @@ -6,7 +6,7 @@ import { AcmgCode, AmpLevel, AssertionClinicalSignificance, AssertionDetailGQL,
import { FormlyFieldConfig, FormlyFormOptions } from '@ngx-formly/core';
import { Subject } from 'rxjs';
import { AssertionState } from '../config/states/assertion.state';
import { FormDisease, FormDrug, FormEvidence, FormGene, FormPhenotype, FormVariant } from '../forms.interfaces';
import { FormDisease, FormDrug, FormEvidence, FormMolecularProfile, FormPhenotype } from '../forms.interfaces';
import * as fmt from '@app/forms/config/utilities/input-formatters';
import { takeUntil } from 'rxjs/operators';

Expand All @@ -15,8 +15,7 @@ interface FormModel {
id: number
description: string
summary: string
variant: FormVariant[]
gene: FormGene[]
molecularProfile: FormMolecularProfile,
variantOrigin: VariantOrigin
evidenceType: AssertionType
clinicalSignificance: AssertionClinicalSignificance
Expand Down Expand Up @@ -89,21 +88,15 @@ export class AssertionReviseForm implements OnDestroy, AfterViewInit {
},
fieldGroup: [
{
key: 'gene',
type: 'gene-array',
templateOptions: {
maxCount: 1,
required: true
}
},
{
key: 'variant',
type: 'variant-array',
key: 'molecularProfile',
type: 'molecular-profile-input',
templateOptions: {
label: 'Molecular Profile',
helpText: 'lorem ipsum',
required: true,
maxCount: 1,
allowCreate: false
}
nzSelectedIndex: 2,
allowCreate: false,
},
},
{
key: 'variantOrigin',
Expand Down Expand Up @@ -280,8 +273,7 @@ export class AssertionReviseForm implements OnDestroy, AfterViewInit {
fields: {
description: fmt.toNullableString(fields.description),
summary: fmt.toNullableString(fields.summary),
variantId: fields.variant[0].id!,
geneId: fields.gene[0].id!,
molecularProfileId: fields.molecularProfile.id,
variantOrigin: fields.variantOrigin,
assertionType: fields.evidenceType,
clinicalSignificance: fields.clinicalSignificance,
Expand Down Expand Up @@ -310,10 +302,7 @@ export class AssertionReviseForm implements OnDestroy, AfterViewInit {
id: fields.id,
description: fields.description,
summary: fields.summary,
//variant: [fields.variant],
//gene: [fields.gene],
gene: [],
variant: [],
molecularProfile: fields.molecularProfile,
variantOrigin: fields.variantOrigin,
evidenceType: fields.assertionType,
clinicalSignificance: fields.clinicalSignificance,
Expand Down
4 changes: 2 additions & 2 deletions client/src/app/forms/assertion-revise/assertion-revise.module.ts
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Expand Up @@ -46,6 +46,7 @@ import { CvcEvidenceInputTypeModule } from '../config/types/evidence-input/evide
import { CvcEvidenceManagerWrapperModule } from '../config/wrappers/with-evidence-manager/with-evidence-manager.module';
import { CvcCancelButtonModule } from '../config/types/cancel-button/cancel-button.module';
import { CvcClingenCodeArrayTypeModule } from '../config/types/clingen-code-array/clingen-code-array.module';
import { CvcMolecularProfileInputTypeModule } from '../config/types/molecular-profile-input/molecular-profile-input.module';

@NgModule({
declarations: [
Expand Down Expand Up @@ -84,8 +85,7 @@ import { CvcClingenCodeArrayTypeModule } from '../config/types/clingen-code-arra
CvcDrugArrayTypeModule,
CvcPhenotypeArrayTypeModule,
CvcDrugInteractionSelectTypeModule,
CvcGeneArrayTypeModule,
CvcVariantArrayTypeModule,
CvcMolecularProfileInputTypeModule,
CvcSourceArrayTypeModule,
CvcAmpLevelInputTypeModule,
CvcAcmgCodeArrayTypeModule,
Expand Down
16 changes: 5 additions & 11 deletions client/src/app/forms/assertion-revise/assertion-revise.query.gql
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Expand Up @@ -8,17 +8,11 @@ fragment RevisableAssertionFields on Assertion {
id
summary
description
# variant {
# id
# name
# link
# singleVariantMolecularProfileId
# }
# gene {
# id
# name
# link
# }
molecularProfile {
id
name
link
}
variantOrigin
clinicalSignificance
disease {
Expand Down
28 changes: 9 additions & 19 deletions client/src/app/forms/assertion-submit/assertion-submit.form.ts
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Expand Up @@ -28,18 +28,16 @@ import {
FormDisease,
FormDrug,
FormEvidence,
FormGene,
FormMolecularProfile,
FormPhenotype,
FormVariant
} from '../forms.interfaces';

interface FormModel {
fields: {
id: number
description: string
summary: string
variant: FormVariant[]
gene: FormGene[]
molecularProfile: FormMolecularProfile
variantOrigin: VariantOrigin
evidenceType: AssertionType
clinicalSignificance: AssertionClinicalSignificance
Expand Down Expand Up @@ -110,21 +108,14 @@ export class AssertionSubmitForm implements OnDestroy {
},
fieldGroup: [
{
key: 'gene',
type: 'gene-array',
templateOptions: {
maxCount: 1,
required: true
}
},
{
key: 'variant',
type: 'variant-array',
key: 'molecularProfile',
type: 'molecular-profile-input',
templateOptions: {
label: 'Molecular Profile',
helpText: 'lorem ipsum',
required: true,
maxCount: 1,
allowCreate: false
}
allowCreate: false,
},
},
{
key: 'variantOrigin',
Expand Down Expand Up @@ -295,8 +286,7 @@ export class AssertionSubmitForm implements OnDestroy {
fields: {
description: fmt.toNullableString(fields.description),
summary: fmt.toNullableString(fields.summary),
variantId: fields.variant[0].id!,
geneId: fields.gene[0].id!,
molecularProfileId: fields.molecularProfile.id,
variantOrigin: fields.variantOrigin,
assertionType: fields.evidenceType,
clinicalSignificance: fields.clinicalSignificance,
Expand Down
6 changes: 2 additions & 4 deletions client/src/app/forms/assertion-submit/assertion-submit.module.ts
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Expand Up @@ -32,8 +32,6 @@ import { CvcDiseaseArrayTypeModule } from '../config/types/disease-array/disease
import { CvcDrugArrayTypeModule } from '../config/types/drugs-array/drugs-array.module';
import { CvcPhenotypeArrayTypeModule } from '../config/types/phenotypes-array/phenotypes-array.module';
import { CvcDrugInteractionSelectTypeModule } from '../config/types/drug-interaction-select/drug-interaction-select.module';
import { CvcGeneArrayTypeModule } from '../config/types/gene-array/gene-array.module';
import { CvcVariantArrayTypeModule } from '../config/types/variant-array/variant-array.module';
import { CvcSourceArrayTypeModule } from '../config/types/source-array/source-array.module';
import { CvcAmpLevelInputTypeModule } from '../config/types/amp-level-input/amp-level-input.module';
import { CvcAcmgCodeArrayTypeModule } from '../config/types/acmg-code-array/acmg-code-array.module';
Expand All @@ -49,6 +47,7 @@ import { NzCardModule } from 'ng-zorro-antd/card';
import { NzSpaceModule } from 'ng-zorro-antd/space';
import { NzTypographyModule } from 'ng-zorro-antd/typography';
import { CvcClingenCodeArrayTypeModule } from '../config/types/clingen-code-array/clingen-code-array.module';
import { CvcMolecularProfileInputTypeModule } from '../config/types/molecular-profile-input/molecular-profile-input.module';

@NgModule({
declarations: [
Expand Down Expand Up @@ -78,6 +77,7 @@ import { CvcClingenCodeArrayTypeModule } from '../config/types/clingen-code-arra
CvcDiseaseInputTypeModule,
CvcTextareaBaseTypeModule,
CvcCommentTextareaTypeModule,
CvcMolecularProfileInputTypeModule,
CvcVariantOriginSelectTypeModule,
CvcEvidenceTypeSelectTypeModule,
CvcClinicalSignificanceSelectModule,
Expand All @@ -87,8 +87,6 @@ import { CvcClingenCodeArrayTypeModule } from '../config/types/clingen-code-arra
CvcDrugArrayTypeModule,
CvcPhenotypeArrayTypeModule,
CvcDrugInteractionSelectTypeModule,
CvcGeneArrayTypeModule,
CvcVariantArrayTypeModule,
CvcSourceArrayTypeModule,
CvcAmpLevelInputTypeModule,
CvcAcmgCodeArrayTypeModule,
Expand Down
13 changes: 9 additions & 4 deletions ...t/src/app/forms/complex-molecular-profile-input/complex-molecular-profile-input.form.html
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Expand Up @@ -30,10 +30,15 @@
</ng-container>
<ng-template #newMp>
<cvc-mp-tag-name [nameSegments]="mpName"></cvc-mp-tag-name>
<button nz-button
nzSize="small" (click)="submitNewMp()" style="float: right">
Create Molecular Profile
</button>
<ng-container *ngIf="this.allowCreate; else createNotAllowed">
<button nz-button
nzSize="small" (click)="submitNewMp()" style="float: right">
Create Molecular Profile
</button>
</ng-container>
<ng-template #createNotAllowed>
<span style="float: right">This Molecular Profile doesn't exist yet. Only existing Molecular Profiles can be used for Assertions. </span>
</ng-template>
</ng-template>
</ng-container>
</ng-container>
Expand Down
1 change: 1 addition & 0 deletions client/src/app/forms/complex-molecular-profile-input/complex-molecular-profile-input.form.ts
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Expand Up @@ -55,6 +55,7 @@ interface WithDisplayNameAndValue {
})
export class CvcComplexMolecularProfileInputForm implements OnDestroy, OnInit {
@Input() formConfig?: FormlyFieldConfig
@Input() allowCreate: boolean = true
@Output() onMolecularProfileSelected = new EventEmitter<number>();

private destroy$ = new Subject();
Expand Down
7 changes: 5 additions & 2 deletions client/src/app/forms/config/types/molecular-profile-input/molecular-profile-input.type.html
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Expand Up @@ -8,12 +8,15 @@
(nzSelectChange)="clear()"
[nzSelectedIndex]="this.field.templateOptions?.nzSelectedIndex == undefined ? 0 : this.field.templateOptions?.nzSelectedIndex">
<nz-tab nzTitle="Simple Molecular Profile">
<cvc-variant-submit-form (onVariantSelected)="onVariantSelected($event)"></cvc-variant-submit-form>
<cvc-variant-submit-form
(onVariantSelected)="onVariantSelected($event)"
[allowCreate]="this.field.templateOptions?.allowCreate"></cvc-variant-submit-form>
</nz-tab>
<nz-tab nzTitle="Complex Molecular Profile">
<cvc-complex-molecular-profile-input-form #complexMolecularProfileInputForm
(onMolecularProfileSelected)="onMpSelected($event)"
[formConfig]="field"></cvc-complex-molecular-profile-input-form>
[formConfig]="field"
[allowCreate]="this.field.templateOptions?.allowCreate"></cvc-complex-molecular-profile-input-form>
</nz-tab>
</nz-tabset>

Expand Down
1 change: 1 addition & 0 deletions client/src/app/forms/evidence-revise/evidence-revise.form.ts
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Expand Up @@ -145,6 +145,7 @@ export class EvidenceReviseForm implements OnInit, AfterViewInit, OnDestroy {
helpText: 'lorem ipsum',
required: true,
nzSelectedIndex: 2,
allowCreate: true
},
},
{
Expand Down
1 change: 1 addition & 0 deletions client/src/app/forms/evidence-submit/evidence-submit.form.ts
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Expand Up @@ -100,6 +100,7 @@ export class EvidenceSubmitForm implements AfterViewInit, OnDestroy {
label: 'Molecular Profile',
helpText: 'lorem ipsum',
required: true,
allowCreate: true,
},
},
{
Expand Down
34 changes: 7 additions & 27 deletions client/src/app/forms/variant-submit/variant-submit.form.ts
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@@ -1,4 +1,4 @@
import { Component, EventEmitter, Input, OnDestroy, Output } from '@angular/core';
import { Component, EventEmitter, Input, OnDestroy, OnInit, Output } from '@angular/core';
import { FormGroup } from '@angular/forms';
import {
AddVariantGQL,
Expand Down Expand Up @@ -33,14 +33,15 @@ export interface SelectedVariant {
templateUrl: './variant-submit.form.html',
styleUrls: ['./variant-submit.form.less'],
})
export class VariantSubmitForm implements OnDestroy {
export class VariantSubmitForm implements OnDestroy, OnInit {
@Output() onVariantSelected = new EventEmitter<SelectedVariant>();
@Input() allowCreate: boolean = true;

private destroy$ = new Subject();

formModel!: FormModel;
formGroup: FormGroup = new FormGroup({});
formFields: FormlyFieldConfig[];
formFields: FormlyFieldConfig[] = [];
formOptions: FormlyFormOptions = { formState: new EvidenceState() };

submitVariantMutator: MutatorWithState<AddVariantGQL, AddVariantMutation, AddVariantMutationVariables>
Expand All @@ -61,7 +62,9 @@ export class VariantSubmitForm implements OnDestroy {
) {

this.submitVariantMutator = new MutatorWithState(networkErrorService);
}

ngOnInit() {
this.formFields = [
{
key: 'fields',
Expand All @@ -87,33 +90,10 @@ export class VariantSubmitForm implements OnDestroy {
type: 'variant-array',
templateOptions: {
required: false,
canCreate: false,
maxCount: 1,
allowCreate: this.allowCreate,
}
},
/* {
key: 'variant',
type: 'cvc-textarea',
templateOptions: {
label: 'Variant Name',
helpText: 'The name of the variant to add',
placeholder: 'Enter variant name',
required: true,
autosize: {
minRows: 1,
maxRows: 1
}
},
validation: {
messages: {
required: 'Variant name is required to add a new variant.'
}
}
}, */
/* {
key: 'submit',
type: 'submit-button'
}, */
]
}
];
Expand Down
15 changes: 9 additions & 6 deletions client/src/app/generated/civic.apollo.ts
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Expand Up @@ -363,8 +363,8 @@ export type AssertionFields = {
fdaCompanionTest: NullableBooleanInput;
/** Does the Assertion have FDA regulatory approval. */
fdaRegulatoryApproval: NullableBooleanInput;
/** The ID of the Gene to which this Assertion belongs */
geneId: Scalars['Int'];
/** The ID of the Molecular Profile to which this Assertion belongs */
molecularProfileId: Scalars['Int'];
/** The internal CIViC ID of the NCCN guideline associated with this Assertion */
nccnGuidelineId: NullableIntInput;
/** The version of the NCCN Guideline specified */
Expand All @@ -373,8 +373,6 @@ export type AssertionFields = {
phenotypeIds: Array<Scalars['Int']>;
/** A brief single sentence statement summarizing the clinical significance of this Assertion. */
summary: NullableStringInput;
/** The ID of the Variant to which this Assertion belongs */
variantId: Scalars['Int'];
/** The Variant Origin for this Assertion. */
variantOrigin: VariantOrigin;
};
Expand Down Expand Up @@ -5570,9 +5568,9 @@ export type AssertionRevisableFieldsQueryVariables = Exact<{
}>;


export type AssertionRevisableFieldsQuery = { __typename: 'Query', assertion?: { __typename: 'Assertion', id: number, summary: string, description: string, variantOrigin: VariantOrigin, clinicalSignificance: AssertionClinicalSignificance, drugInteractionType?: DrugInteraction | undefined, assertionDirection: AssertionDirection, assertionType: AssertionType, ampLevel?: AmpLevel | undefined, nccnGuidelineVersion?: string | undefined, regulatoryApproval?: boolean | undefined, fdaCompanionTest?: boolean | undefined, disease?: { __typename: 'Disease', id: number, doid?: number | undefined, name: string, displayName: string, link: string } | undefined, drugs: Array<{ __typename: 'Drug', id: number, ncitId?: string | undefined, name: string, link: string }>, phenotypes: Array<{ __typename: 'Phenotype', id: number, hpoId: string, name: string }>, acmgCodes: Array<{ __typename: 'AcmgCode', id: number, code: string, description: string }>, clingenCodes: Array<{ __typename: 'ClingenCode', id: number, code: string, description: string }>, nccnGuideline?: { __typename: 'NccnGuideline', id: number, name: string } | undefined, evidenceItems: Array<{ __typename: 'EvidenceItem', id: number, name: string, link: string, status: EvidenceStatus }> } | undefined };
export type AssertionRevisableFieldsQuery = { __typename: 'Query', assertion?: { __typename: 'Assertion', id: number, summary: string, description: string, variantOrigin: VariantOrigin, clinicalSignificance: AssertionClinicalSignificance, drugInteractionType?: DrugInteraction | undefined, assertionDirection: AssertionDirection, assertionType: AssertionType, ampLevel?: AmpLevel | undefined, nccnGuidelineVersion?: string | undefined, regulatoryApproval?: boolean | undefined, fdaCompanionTest?: boolean | undefined, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, disease?: { __typename: 'Disease', id: number, doid?: number | undefined, name: string, displayName: string, link: string } | undefined, drugs: Array<{ __typename: 'Drug', id: number, ncitId?: string | undefined, name: string, link: string }>, phenotypes: Array<{ __typename: 'Phenotype', id: number, hpoId: string, name: string }>, acmgCodes: Array<{ __typename: 'AcmgCode', id: number, code: string, description: string }>, clingenCodes: Array<{ __typename: 'ClingenCode', id: number, code: string, description: string }>, nccnGuideline?: { __typename: 'NccnGuideline', id: number, name: string } | undefined, evidenceItems: Array<{ __typename: 'EvidenceItem', id: number, name: string, link: string, status: EvidenceStatus }> } | undefined };

export type RevisableAssertionFieldsFragment = { __typename: 'Assertion', id: number, summary: string, description: string, variantOrigin: VariantOrigin, clinicalSignificance: AssertionClinicalSignificance, drugInteractionType?: DrugInteraction | undefined, assertionDirection: AssertionDirection, assertionType: AssertionType, ampLevel?: AmpLevel | undefined, nccnGuidelineVersion?: string | undefined, regulatoryApproval?: boolean | undefined, fdaCompanionTest?: boolean | undefined, disease?: { __typename: 'Disease', id: number, doid?: number | undefined, name: string, displayName: string, link: string } | undefined, drugs: Array<{ __typename: 'Drug', id: number, ncitId?: string | undefined, name: string, link: string }>, phenotypes: Array<{ __typename: 'Phenotype', id: number, hpoId: string, name: string }>, acmgCodes: Array<{ __typename: 'AcmgCode', id: number, code: string, description: string }>, clingenCodes: Array<{ __typename: 'ClingenCode', id: number, code: string, description: string }>, nccnGuideline?: { __typename: 'NccnGuideline', id: number, name: string } | undefined, evidenceItems: Array<{ __typename: 'EvidenceItem', id: number, name: string, link: string, status: EvidenceStatus }> };
export type RevisableAssertionFieldsFragment = { __typename: 'Assertion', id: number, summary: string, description: string, variantOrigin: VariantOrigin, clinicalSignificance: AssertionClinicalSignificance, drugInteractionType?: DrugInteraction | undefined, assertionDirection: AssertionDirection, assertionType: AssertionType, ampLevel?: AmpLevel | undefined, nccnGuidelineVersion?: string | undefined, regulatoryApproval?: boolean | undefined, fdaCompanionTest?: boolean | undefined, molecularProfile: { __typename: 'MolecularProfile', id: number, name: string, link: string }, disease?: { __typename: 'Disease', id: number, doid?: number | undefined, name: string, displayName: string, link: string } | undefined, drugs: Array<{ __typename: 'Drug', id: number, ncitId?: string | undefined, name: string, link: string }>, phenotypes: Array<{ __typename: 'Phenotype', id: number, hpoId: string, name: string }>, acmgCodes: Array<{ __typename: 'AcmgCode', id: number, code: string, description: string }>, clingenCodes: Array<{ __typename: 'ClingenCode', id: number, code: string, description: string }>, nccnGuideline?: { __typename: 'NccnGuideline', id: number, name: string } | undefined, evidenceItems: Array<{ __typename: 'EvidenceItem', id: number, name: string, link: string, status: EvidenceStatus }> };

export type SuggestAssertionRevisionMutationVariables = Exact<{
input: SuggestAssertionRevisionInput;
Expand Down Expand Up @@ -7346,6 +7344,11 @@ export const RevisableAssertionFieldsFragmentDoc = gql`
id
summary
description
molecularProfile {
id
name
link
}
variantOrigin
clinicalSignificance
disease {
Expand Down
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