Merge branch 'main' into release

griffithlab · Mar 7, 2024 · 747853b · 747853b
2 parents 0feb1e3 + e629a86
commit 747853b
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Showing 27 changed files with 2,128 additions and 4,964 deletions.
diff --git a/.github/workflows/build_frontend.yml b/.github/workflows/build_frontend.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ inputs.branch }}
 
@@ -24,9 +24,9 @@ jobs:
           ruby-version: '3.0'
 
       - name: Setup node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: 16
+          node-version: 20
 
       - run: npm install -g yarn
         working-directory: ./client

diff --git a/client/src/app/forms/config/assertion-revise/assertion-revise.form.ts b/client/src/app/forms/config/assertion-revise/assertion-revise.form.ts
@@ -1,22 +1,47 @@
-import { AfterViewInit, ChangeDetectionStrategy, ChangeDetectorRef, Component, Input, OnDestroy, OnInit } from '@angular/core'
+import {
+  AfterViewInit,
+  ChangeDetectionStrategy,
+  ChangeDetectorRef,
+  Component,
+  Input,
+  OnDestroy,
+  OnInit,
+} from '@angular/core'
 import { UntypedFormGroup } from '@angular/forms'
 import { NetworkErrorsService } from '@app/core/services/network-errors.service'
-import { MutationState, MutatorWithState } from '@app/core/utilities/mutation-state-wrapper'
-import { assertionReviseFormInitialModel, AssertionReviseModel } from '@app/forms/models/assertion-revise.model'
+import {
+  MutationState,
+  MutatorWithState,
+} from '@app/core/utilities/mutation-state-wrapper'
+import {
+  assertionReviseFormInitialModel,
+  AssertionReviseModel,
+} from '@app/forms/models/assertion-revise.model'
 import { AssertionState } from '@app/forms/states/assertion.state'
-import { AssertionRevisableFieldsGQL, Maybe, SuggestAssertionRevisionGQL, SuggestAssertionRevisionMutation, SuggestAssertionRevisionMutationVariables } from '@app/generated/civic.apollo'
+import {
+  AssertionRevisableFieldsGQL,
+  Maybe,
+  SuggestAssertionRevisionGQL,
+  SuggestAssertionRevisionMutation,
+  SuggestAssertionRevisionMutationVariables,
+} from '@app/generated/civic.apollo'
 import { UntilDestroy, untilDestroyed } from '@ngneat/until-destroy'
 import { FormlyFieldConfig, FormlyFormOptions } from '@ngx-formly/core'
 import { assertionReviseFields } from './assertion-revise.form.config'
-import { assertionFormModelToReviseInput, assertionToModelFields } from '@app/forms/utilities/assertion-to-model-fields'
+import {
+  assertionFormModelToReviseInput,
+  assertionToModelFields,
+} from '@app/forms/utilities/assertion-to-model-fields'
 
 @UntilDestroy()
 @Component({
   selector: 'cvc-assertion-revise-form',
   templateUrl: './assertion-revise.form.html',
   changeDetection: ChangeDetectionStrategy.OnPush,
 })
-export class CvcAssertionReviseForm implements OnInit, AfterViewInit, OnDestroy {
+export class CvcAssertionReviseForm
+  implements OnInit, AfterViewInit, OnDestroy
+{
   @Input() assertionId!: number
 
   model?: AssertionReviseModel
@@ -40,20 +65,25 @@ export class CvcAssertionReviseForm implements OnInit, AfterViewInit, OnDestroy
     private submitRevisionsGQL: SuggestAssertionRevisionGQL,
     private networkErrorService: NetworkErrorsService,
     private cdr: ChangeDetectorRef
-
   ) {
     this.form = new UntypedFormGroup({})
     this.fields = assertionReviseFields
     this.state = new AssertionState()
-    this.options = { formState: this.state}
+    this.state.formMode = 'revise'
+    this.options = { formState: this.state }
     this.reviseAssertionMutator = new MutatorWithState(networkErrorService)
   }
 
   onSubmit(model: AssertionReviseModel) {
-    if(!this.assertionId) { return }
+    if (!this.assertionId) {
+      return
+    }
     let input = assertionFormModelToReviseInput(this.assertionId, model)
     if (input) {
-      this.mutationState = this.reviseAssertionMutator.mutate(this.submitRevisionsGQL, {input: input })
+      this.mutationState = this.reviseAssertionMutator.mutate(
+        this.submitRevisionsGQL,
+        { input: input }
+      )
     }
   }
 
@@ -62,26 +92,27 @@ export class CvcAssertionReviseForm implements OnInit, AfterViewInit, OnDestroy
   }
 
   ngAfterViewInit(): void {
-    this.revisableFieldsGQL.fetch({assertionId: this.assertionId})
-    .pipe(untilDestroyed(this))
-    .subscribe({
-      next: ({data: { assertion }}) => {
-        if (assertion) {
-          this.model = {
-            id: assertion.id,
-            fields: assertionToModelFields(assertion)
+    this.revisableFieldsGQL
+      .fetch({ assertionId: this.assertionId })
+      .pipe(untilDestroyed(this))
+      .subscribe({
+        next: ({ data: { assertion } }) => {
+          if (assertion) {
+            this.model = {
+              id: assertion.id,
+              fields: assertionToModelFields(assertion),
+            }
+            this.cdr.detectChanges()
           }
-          this.cdr.detectChanges()
-        }
-      },
-      error: (error) => {
-        console.log("Error retrieving Assertion")
-        console.log(error)
-      },
-      complete: () => {
-        this.state.formReady$.next(true)
-      }
-    })
+        },
+        error: (error) => {
+          console.log('Error retrieving Assertion')
+          console.log(error)
+        },
+        complete: () => {
+          this.state.formReady$.next(true)
+        },
+      })
   }
 
   ngOnDestroy(): void {

diff --git a/client/src/app/forms/config/molecular-profile-revise/molecular-profile-revise.form.config.ts b/client/src/app/forms/config/molecular-profile-revise/molecular-profile-revise.form.config.ts
@@ -59,8 +59,18 @@ const formFieldConfig: FormlyFieldConfig[] = [
                 wrappers: ['form-field'],
                 props: {
                   label: 'Aliases',
-                  description:
-                    'List any aliases commonly used to refer to this Molecular Profile',
+                },
+                expressions: {
+                  'props.disabled': (field: FormlyFieldConfig) => {
+                    return field.options?.formState.isSimpleMp
+                  },
+                  'props.description': (field: FormlyFieldConfig) => {
+                    if (field.options?.formState.isSimpleMp) {
+                      return 'Simple Molecular Profiles inherit their Aliases from the corresponding Variant.'
+                    } else {
+                      return 'List any aliases commonly used to refer to this Molecular Profile'
+                    }
+                  },
                 },
               },
               {

diff --git a/client/src/app/forms/config/molecular-profile-revise/molecular-profile-revise.form.ts b/client/src/app/forms/config/molecular-profile-revise/molecular-profile-revise.form.ts
@@ -4,15 +4,27 @@ import {
   ChangeDetectorRef,
   Component,
   Input,
-  OnInit, } from '@angular/core'
+  OnInit,
+} from '@angular/core'
 import { UntypedFormGroup } from '@angular/forms'
-import { MolecularProfileRevisableFieldsGQL, SuggestMolecularProfileRevisionGQL, SuggestMolecularProfileRevisionMutation, SuggestMolecularProfileRevisionMutationVariables } from '@app/generated/civic.apollo'
+import {
+  MolecularProfileRevisableFieldsGQL,
+  SuggestMolecularProfileRevisionGQL,
+  SuggestMolecularProfileRevisionMutation,
+  SuggestMolecularProfileRevisionMutationVariables,
+} from '@app/generated/civic.apollo'
 import { UntilDestroy, untilDestroyed } from '@ngneat/until-destroy'
 import { FormlyFieldConfig, FormlyFormOptions } from '@ngx-formly/core'
-import { MutationState, MutatorWithState } from '@app/core/utilities/mutation-state-wrapper'
+import {
+  MutationState,
+  MutatorWithState,
+} from '@app/core/utilities/mutation-state-wrapper'
 import { NetworkErrorsService } from '@app/core/services/network-errors.service'
 import { MolecularProfileReviseModel } from '@app/forms/models/molecular-profile-revise.model'
-import { molecularProfileFormModelToReviseInput, molecularProfileToModelFields } from '@app/forms/utilities/molecular-profile-to-model-fields'
+import {
+  molecularProfileFormModelToReviseInput,
+  molecularProfileToModelFields,
+} from '@app/forms/utilities/molecular-profile-to-model-fields'
 import { molecularProfileReviseFields } from './molecular-profile-revise.form.config'
 
 @UntilDestroy()
@@ -46,22 +58,6 @@ export class CvcMolecularProfileReviseForm implements OnInit, AfterViewInit {
     this.form = new UntypedFormGroup({})
     this.options = { formState: { isSimpleMp: undefined } }
 
-    const aliasField = molecularProfileReviseFields[0]?.fieldGroup?.find(f => f.key == 'fields')?.fieldGroup?.find(f => f.key == "aliases")
-    if (aliasField) {
-      const originalDescription = aliasField.props?.description
-      aliasField.expressions = {
-        'props.disabled': (field: FormlyFieldConfig) => {
-          return field.options?.formState.isSimpleMp
-        },
-        'props.description': (field: FormlyFieldConfig) => {
-          if(field.options?.formState.isSimpleMp) {
-            return 'Simple Molecular Profiles inherit their Aliases from the corresponding Variant.'
-          } else {
-            return originalDescription
-          }
-        },
-      }
-    }
     this.fields = molecularProfileReviseFields
     this.reviseEvidenceMutator = new MutatorWithState(networkErrorService)
   }
@@ -77,7 +73,6 @@ export class CvcMolecularProfileReviseForm implements OnInit, AfterViewInit {
       .subscribe({
         next: ({ data: { molecularProfile } }) => {
           if (molecularProfile) {
-
             this.options.formState.isSimpleMp = !molecularProfile.isComplex
 
             this.model = {
@@ -91,16 +86,23 @@ export class CvcMolecularProfileReviseForm implements OnInit, AfterViewInit {
           console.error('Error retrieving MolecularProfile.')
           console.error(error)
         },
-        complete: () => {
-        },
+        complete: () => {},
       })
   }
 
   onSubmit(model: MolecularProfileReviseModel) {
-    if(!this.molecularProfileId) {return}
-    let input = molecularProfileFormModelToReviseInput(this.molecularProfileId, model)
+    if (!this.molecularProfileId) {
+      return
+    }
+    let input = molecularProfileFormModelToReviseInput(
+      this.molecularProfileId,
+      model
+    )
     if (input) {
-      this.mutationState = this.reviseEvidenceMutator.mutate(this.submitRevisionsGQL, { input: input })
+      this.mutationState = this.reviseEvidenceMutator.mutate(
+        this.submitRevisionsGQL,
+        { input: input }
+      )
     }
   }
 }
diff --git a/server/.browserslistrc b/server/.browserslistrc
diff --git a/server/Gemfile b/server/Gemfile
@@ -12,7 +12,7 @@ gem 'puma', '5.6.8'
 # Use SCSS for stylesheets
 gem 'sass-rails', '>= 6'
 # Transpile app-like JavaScript. Read more: https://github.com/rails/webpacker
-gem 'webpacker', '~> 5.0'
+gem 'webpacker', '6.0.0.rc.6'
 
 gem 'rack-cors', '~> 1.1.1'
 
@@ -50,8 +50,6 @@ gem 'typhoeus', '~>1.4.0'
 
 gem 'audited', '~> 5.3'
 
-gem 'graphiql-rails', '~> 1.8.0'
-
 #user comment rendering
 gem 'rinku', '~> 2.0.6'
 gem 'sanitize', '~> 6.0.2'