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[WIP] Support Regulatory Fusions #1176

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[WIP] Support Regulatory Fusions #1176

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6d8e19c
schema support for regulatory fusions
acoffman Jan 3, 2025
7bd904f
add missing validator
acoffman Jan 3, 2025
c345ca1
fix typo from codespell
acoffman Jan 3, 2025
bf557ad
dump schema
acoffman Jan 3, 2025
aa8f94f
hook up forms for regulatory fusion creation
acoffman Feb 6, 2025
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1 change: 1 addition & 0 deletions client/src/app/forms/types/feature-select/feature-select.type.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,7 @@ export class CvcFeatureSelectField
nzContent: CvcFusionSelectForm,
nzData: {},
nzFooter: null,
nzWidth: '60%',
}
)

Expand Down
6 changes: 4 additions & 2 deletions client/src/app/forms/types/feature-select/fusion-select/fusion-add.query.gql
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Original file line number Diff line number Diff line change
@@ -1,13 +1,15 @@
mutation SelectOrCreateFusion($organizationId: Int, $fivePrimeGeneId: Int, $fivePrimePartnerStatus: FusionPartnerStatus!, $threePrimeGeneId: Int, $threePrimePartnerStatus: FusionPartnerStatus! ) {
mutation SelectOrCreateFusion($organizationId: Int, $fivePrimeGeneId: Int, $fivePrimeRegulatoryFusionType: RegulatoryFusionType, $fivePrimePartnerStatus: FusionPartnerStatus!, $threePrimeGeneId: Int, $threePrimeRegulatoryFusionType: RegulatoryFusionType, $threePrimePartnerStatus: FusionPartnerStatus!) {
createFusionFeature(input: {
organizationId: $organizationId
fivePrimeGene: {
geneId: $fivePrimeGeneId,
partnerStatus: $fivePrimePartnerStatus
regulatoryFusionType: $fivePrimeRegulatoryFusionType
},
threePrimeGene: {
geneId: $threePrimeGeneId,
partnerStatus: $threePrimePartnerStatus
partnerStatus: $threePrimePartnerStatus,
regulatoryFusionType: $threePrimeRegulatoryFusionType
}

}) {
Expand Down
130 changes: 114 additions & 16 deletions client/src/app/forms/types/feature-select/fusion-select/fusion-select.form.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ import {
FeatureInstanceTypes,
FusionPartnerStatus,
Maybe,
RegulatoryFusionType,
SelectOrCreateFusionGQL,
SelectOrCreateFusionMutation,
SelectOrCreateFusionMutationVariables,
Expand All @@ -28,7 +29,6 @@ import { CommonModule } from '@angular/common'
import { NzFormModule } from 'ng-zorro-antd/form'
import { NzButtonModule } from 'ng-zorro-antd/button'
import { RouterModule } from '@angular/router'
import { LetDirective, PushPipe } from '@ngrx/component'
import { NzAlertModule } from 'ng-zorro-antd/alert'
import { UntilDestroy } from '@ngneat/until-destroy'
import {
Expand All @@ -41,8 +41,10 @@ import { NZ_MODAL_DATA, NzModalModule, NzModalRef } from 'ng-zorro-antd/modal'
type FusionSelectModel = {
fivePrimeGeneId?: number
fivePrimePartnerStatus: FusionPartnerStatus
fivePrimRegulatoryFusionType?: RegulatoryFusionType
threePrimeGeneId?: number
threePrimePartnerStatus: FusionPartnerStatus
threePrimRegulatoryFusionType?: RegulatoryFusionType
}

export interface FusionSelectModalData {
Expand All @@ -58,9 +60,7 @@ export interface FusionSelectModalData {
changeDetection: ChangeDetectionStrategy.OnPush,
imports: [
CommonModule,
PushPipe,
ReactiveFormsModule,
LetDirective,
NzFormModule,
NzButtonModule,
NzAlertModule,
Expand Down Expand Up @@ -92,7 +92,7 @@ export class CvcFusionSelectForm {

constructor(
private query: SelectOrCreateFusionGQL,
private errors: NetworkErrorsService
errors: NetworkErrorsService
) {
this.selectOrCreateFusionMutator = new MutatorWithState(errors)

Expand All @@ -103,6 +103,8 @@ export class CvcFusionSelectForm {
threePrimeGeneId: undefined,
fivePrimePartnerStatus: FusionPartnerStatus.Known,
threePrimePartnerStatus: FusionPartnerStatus.Known,
fivePrimRegulatoryFusionType: undefined,
threePrimRegulatoryFusionType: undefined,
}
this.options = {}

Expand All @@ -119,8 +121,27 @@ export class CvcFusionSelectForm {
label: 'Multiple',
value: FusionPartnerStatus.Multiple,
},
{
label: 'Regulatory',
value: FusionPartnerStatus.Regulatory,
},
]

const regulatoryOptions = Object.keys(RegulatoryFusionType)
.map((x) => {
const val = RegulatoryFusionType[x as keyof typeof RegulatoryFusionType]
return { label: val.toLowerCase(), value: val }
})
.sort((a, b) => {
if (a.label == 'reg_e') {
return -1
} else if (a.label == 'reg_p') {
return -1
} else {
return a.label.localeCompare(b.label)
}
})

this.config = [
{
wrappers: ['form-layout'],
Expand All @@ -129,13 +150,18 @@ export class CvcFusionSelectForm {
},
validators: {
partnerStatus: {
message: "At least one of 5' or 3' partner status must be Known",
message:
"At least one of 5' or 3' partner status must be Known or Regulatory",
expression: (x: AbstractControl) => {
const model = x.value
if (model) {
if (
model.fivePrimePartnerStatus == FusionPartnerStatus.Known ||
model.threePrimePartnerStatus == FusionPartnerStatus.Known
model.fivePrimePartnerStatus ==
FusionPartnerStatus.Regulatory ||
model.threePrimePartnerStatus == FusionPartnerStatus.Known ||
model.threePrimePartnerStatus ==
FusionPartnerStatus.Regulatory
) {
return true
}
Expand All @@ -144,6 +170,24 @@ export class CvcFusionSelectForm {
},
errorPath: 'fivePrimePartnerStatus',
},
regulatoryStatus: {
message: "At most one of 5' or 3' partner status can be Regulatory",
expression: (x: AbstractControl) => {
const model = x.value
if (model) {
if (
model.fivePrimePartnerStatus ==
FusionPartnerStatus.Regulatory &&
model.threePrimePartnerStatus ==
FusionPartnerStatus.Regulatory
) {
return false
}
}
return true
},
errorPath: 'fivePrimePartnerStatus',
},
sameGene: {
message: "5' and 3' Genes must be different",
expression: (x: AbstractControl) => {
Expand Down Expand Up @@ -171,7 +215,7 @@ export class CvcFusionSelectForm {
wrappers: ['form-row'],
props: {
formRowOptions: {
span: 12,
span: 8,
},
},
fieldGroup: [
Expand All @@ -181,13 +225,33 @@ export class CvcFusionSelectForm {
props: {
label: "5' Partner Status",
tooltip:
"Select Known if the specific 5' Gene partner is known, Unknown if not. Select Multiple if there are multiple potential 5' Gene partners",
"Select Known if the specific 5' Gene partner is known, Unknown if not. Select Multiple if there are multiple potential 5' Gene partners. Select Regulatory if this partner is a Regulatory fusion partner.",
required: true,
placeholder: "5' Partner Status",
options: selectOptions,
multiple: false,
},
},
{
key: 'fivePrimeRegulatoryFusionType',
type: 'base-select',
props: {
label: "5' Regulatory Element Type",
tooltip: '',
required: true,
placeholder: "5' Regulatory Element",
options: regulatoryOptions,
multiple: false,
},
expressions: {
'props.required': (field) =>
field.model.fivePrimePartnerStatus ==
FusionPartnerStatus.Regulatory,
'props.disabled': (field) =>
field.model.fivePrimePartnerStatus !=
FusionPartnerStatus.Regulatory,
},
},
{
key: 'fivePrimeGeneId',
type: 'feature-select',
Expand All @@ -202,10 +266,14 @@ export class CvcFusionSelectForm {
expressions: {
'props.disabled': (field) =>
field.model.fivePrimePartnerStatus !=
FusionPartnerStatus.Known,
FusionPartnerStatus.Known &&
field.model.fivePrimePartnerStatus !=
FusionPartnerStatus.Regulatory,
'props.required': (field) =>
field.model.fivePrimePartnerStatus ==
FusionPartnerStatus.Known,
FusionPartnerStatus.Known ||
field.model.fivePrimePartnerStatus ==
FusionPartnerStatus.Regulatory,
},
},
],
Expand All @@ -214,7 +282,7 @@ export class CvcFusionSelectForm {
wrappers: ['form-row'],
props: {
formRowOptions: {
span: 12,
span: 8,
},
},
fieldGroup: [
Expand All @@ -226,11 +294,31 @@ export class CvcFusionSelectForm {
placeholder: "3' Partner Status",
label: "3' Partner Status",
tooltip:
"Select Known if the specific 3' Gene partner is known, Unknown if not. Select Multiple if there are multiple potential 3' Gene partners",
"Select Known if the specific 3' Gene partner is known, Unknown if not. Select Multiple if there are multiple potential 3' Gene partners. Select Regulatory if this partner is a Regulatory fusion partner.",
options: selectOptions,
multiple: false,
},
},
{
key: 'threePrimeRegulatoryFusionType',
type: 'base-select',
props: {
label: "3' Regulatory Element Type",
tooltip: '',
required: true,
placeholder: "3' Regulatory Element",
options: regulatoryOptions,
multiple: false,
},
expressions: {
'props.required': (field) =>
field.model.threePrimePartnerStatus ==
FusionPartnerStatus.Regulatory,
'props.disabled': (field) =>
field.model.threePrimePartnerStatus !=
FusionPartnerStatus.Regulatory,
},
},
{
key: 'threePrimeGeneId',
type: 'feature-select',
Expand All @@ -245,10 +333,14 @@ export class CvcFusionSelectForm {
expressions: {
'props.disabled': (field) =>
field.model.threePrimePartnerStatus !=
FusionPartnerStatus.Known,
FusionPartnerStatus.Known &&
field.model.threePrimePartnerStatus !=
FusionPartnerStatus.Regulatory,
'props.required': (field) =>
field.model.threePrimePartnerStatus ==
FusionPartnerStatus.Known,
FusionPartnerStatus.Known ||
field.model.threePrimePartnerStatus ==
FusionPartnerStatus.Regulatory,
},
},
],
Expand Down Expand Up @@ -280,13 +372,19 @@ export class CvcFusionSelectForm {

modelChange(model: Maybe<FusionSelectModel>) {
if (model) {
if (this.model.fivePrimePartnerStatus != FusionPartnerStatus.Known) {
if (
this.model.fivePrimePartnerStatus != FusionPartnerStatus.Known &&
this.model.fivePrimePartnerStatus != FusionPartnerStatus.Regulatory
) {
this.model = {
...this.model,
fivePrimeGeneId: undefined,
}
}
if (this.model.threePrimePartnerStatus != FusionPartnerStatus.Known) {
if (
this.model.threePrimePartnerStatus != FusionPartnerStatus.Known &&
this.model.threePrimePartnerStatus != FusionPartnerStatus.Regulatory
) {
this.model = {
...this.model,
threePrimeGeneId: undefined,
Expand Down
3 changes: 2 additions & 1 deletion client/src/app/generated/civic.apollo-helpers.ts
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Expand Up @@ -1185,7 +1185,7 @@ export type FlaggableFieldPolicy = {
link?: FieldPolicy<any> | FieldReadFunction<any>,
name?: FieldPolicy<any> | FieldReadFunction<any>
};
export type FusionKeySpecifier = ('comments' | 'creationActivity' | 'deprecated' | 'deprecationActivity' | 'deprecationReason' | 'description' | 'events' | 'featureAliases' | 'featureInstance' | 'featureType' | 'fivePrimeGene' | 'fivePrimePartnerStatus' | 'flagged' | 'flags' | 'fullName' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'name' | 'openRevisionCount' | 'revisions' | 'sources' | 'threePrimeGene' | 'threePrimePartnerStatus' | 'variants' | FusionKeySpecifier)[];
export type FusionKeySpecifier = ('comments' | 'creationActivity' | 'deprecated' | 'deprecationActivity' | 'deprecationReason' | 'description' | 'events' | 'featureAliases' | 'featureInstance' | 'featureType' | 'fivePrimeGene' | 'fivePrimePartnerStatus' | 'flagged' | 'flags' | 'fullName' | 'id' | 'lastAcceptedRevisionEvent' | 'lastCommentEvent' | 'lastSubmittedRevisionEvent' | 'link' | 'name' | 'openRevisionCount' | 'regulatoryFusionType' | 'revisions' | 'sources' | 'threePrimeGene' | 'threePrimePartnerStatus' | 'variants' | FusionKeySpecifier)[];
export type FusionFieldPolicy = {
comments?: FieldPolicy<any> | FieldReadFunction<any>,
creationActivity?: FieldPolicy<any> | FieldReadFunction<any>,
Expand All @@ -1209,6 +1209,7 @@ export type FusionFieldPolicy = {
link?: FieldPolicy<any> | FieldReadFunction<any>,
name?: FieldPolicy<any> | FieldReadFunction<any>,
openRevisionCount?: FieldPolicy<any> | FieldReadFunction<any>,
regulatoryFusionType?: FieldPolicy<any> | FieldReadFunction<any>,
revisions?: FieldPolicy<any> | FieldReadFunction<any>,
sources?: FieldPolicy<any> | FieldReadFunction<any>,
threePrimeGene?: FieldPolicy<any> | FieldReadFunction<any>,
Expand Down
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