Merge branch 'main' into update-pkg-deps

.github/workflows/tests.yml

@@ -44,6 +44,7 @@ jobs:
         env:
           CI_BUILD: true
           RAILS_ENV: test
+          CIVIC_API_HMAC_KEY: fakeKeyForTests
         run: bundle exec rails test
         working-directory: ./server
 

client/src/app/forms/config/fusion-variant-revise/fusion-variant-revise.form.config.ts

@@ -88,8 +88,10 @@ function formFieldConfig(
                         {
                           key: 'referenceBuild',
                           type: 'reference-build-select',
-                          props: {
-                            required: true,
+                          expressions: {
+                            'props.required': (field) =>
+                              Boolean(field.model.fivePrimeTranscript) ||
+                              Boolean(field.model.threePrimeTranscript),
                           },
                         },
                         {
@@ -107,7 +109,11 @@ function formFieldConfig(
                             label: 'Ensembl Version',
                             description:
                               'Enter a valid Ensembl database version (e.g. 75)',
-                            required: true,
+                          },
+                          expressions: {
+                            'props.required': (field) =>
+                              Boolean(field.model.fivePrimeTranscript) ||
+                              Boolean(field.model.threePrimeTranscript),
                           },
                         },
                       ],
@@ -125,11 +131,14 @@ function formFieldConfig(
                           type: 'base-input',
                           props: {
                             label: "5' Transcript",
-                            required: !fivePrimeDisabled,
                             disabled: fivePrimeDisabled,
                             tooltip:
                               "Specify a transcript ID, including version number (e.g. ENST00000348159.4) for the 5' exon you have selected",
                           },
+                          expressions: {
+                            'props.required': (field) =>
+                              Boolean(field.model.fivePrimeExonEnd),
+                          },
                           validators: {
                             isTranscriptId: {
                               expression: isEnsemblTranscript,
@@ -149,11 +158,14 @@ function formFieldConfig(
                           },
                           props: {
                             label: "5' End Exon",
-                            required: !fivePrimeDisabled,
                             disabled: fivePrimeDisabled,
                             tooltip:
                               'The exon number counted from the 5’ end of the transcript.',
                           },
+                          expressions: {
+                            'props.required': (field) =>
+                              Boolean(field.model.fivePrimeTranscript),
+                          },
                         },
                         {
                           key: 'fivePrimeOffset',
@@ -205,7 +217,6 @@ function formFieldConfig(
                           key: 'threePrimeTranscript',
                           type: 'base-input',
                           props: {
-                            required: !threePrimeDisabled,
                             disabled: threePrimeDisabled,
                             label: "3' Transcript",
                             tooltip:
@@ -218,6 +229,10 @@ function formFieldConfig(
                                 "3' Transcript must be a valid, human, versioned, Ensembl transcript ID",
                             },
                           },
+                          expressions: {
+                            'props.required': (field) =>
+                              Boolean(field.model.threePrimeExonStart),
+                          },
                         },
                         {
                           key: 'threePrimeExonStart',
@@ -232,9 +247,12 @@ function formFieldConfig(
                             label: "3' Start Exon",
                             tooltip:
                               'The exon number counted from the 3’ end of the transcript.',
-                            required: !threePrimeDisabled,
                             disabled: threePrimeDisabled,
                           },
+                          expressions: {
+                            'props.required': (field) =>
+                              Boolean(field.model.threePrimeTranscript),
+                          },
                         },
                         {
                           key: 'threePrimeOffset',

client/src/app/generated/civic.apollo-helpers.ts

@@ -735,13 +735,13 @@ export type CreateVariantPayloadFieldPolicy = {
 	new?: FieldPolicy<any> | FieldReadFunction<any>,
 	variant?: FieldPolicy<any> | FieldReadFunction<any>
 };
-export type DataReleaseKeySpecifier = ('acceptedAndSubmittedVariantsVcf' | 'acceptedVariantsVcf' | 'assertionTsv' | 'evidenceTsv' | 'geneTsv' | 'molecularProfileTsv' | 'name' | 'variantGroupTsv' | 'variantTsv' | DataReleaseKeySpecifier)[];
+export type DataReleaseKeySpecifier = ('acceptedAndSubmittedVariantsVcf' | 'acceptedVariantsVcf' | 'assertionTsv' | 'evidenceTsv' | 'featureTsv' | 'molecularProfileTsv' | 'name' | 'variantGroupTsv' | 'variantTsv' | DataReleaseKeySpecifier)[];
 export type DataReleaseFieldPolicy = {
 	acceptedAndSubmittedVariantsVcf?: FieldPolicy<any> | FieldReadFunction<any>,
 	acceptedVariantsVcf?: FieldPolicy<any> | FieldReadFunction<any>,
 	assertionTsv?: FieldPolicy<any> | FieldReadFunction<any>,
 	evidenceTsv?: FieldPolicy<any> | FieldReadFunction<any>,
-	geneTsv?: FieldPolicy<any> | FieldReadFunction<any>,
+	featureTsv?: FieldPolicy<any> | FieldReadFunction<any>,
 	molecularProfileTsv?: FieldPolicy<any> | FieldReadFunction<any>,
 	name?: FieldPolicy<any> | FieldReadFunction<any>,
 	variantGroupTsv?: FieldPolicy<any> | FieldReadFunction<any>,

client/src/app/generated/civic.apollo.ts

@@ -1550,7 +1550,7 @@ export type DataRelease = {
   acceptedVariantsVcf?: Maybe<DownloadableFile>;
   assertionTsv?: Maybe<DownloadableFile>;
   evidenceTsv?: Maybe<DownloadableFile>;
-  geneTsv?: Maybe<DownloadableFile>;
+  featureTsv?: Maybe<DownloadableFile>;
   molecularProfileTsv?: Maybe<DownloadableFile>;
   name: Scalars['String']['output'];
   variantGroupTsv?: Maybe<DownloadableFile>;
@@ -9726,9 +9726,9 @@ export type PhenotypeDetailQuery = { __typename: 'Query', phenotype?: { __typena
 export type DataReleasesQueryVariables = Exact<{ [key: string]: never; }>;
 
 
-export type DataReleasesQuery = { __typename: 'Query', dataReleases: Array<{ __typename: 'DataRelease', name: string, geneTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantGroupTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, evidenceTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, molecularProfileTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, assertionTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedAndSubmittedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined }> };
+export type DataReleasesQuery = { __typename: 'Query', dataReleases: Array<{ __typename: 'DataRelease', name: string, featureTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantGroupTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, evidenceTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, molecularProfileTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, assertionTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedAndSubmittedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined }> };
 
-export type ReleaseFragment = { __typename: 'DataRelease', name: string, geneTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantGroupTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, evidenceTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, molecularProfileTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, assertionTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedAndSubmittedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined };
+export type ReleaseFragment = { __typename: 'DataRelease', name: string, featureTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, variantGroupTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, evidenceTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, molecularProfileTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, assertionTsv?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined, acceptedAndSubmittedVariantsVcf?: { __typename: 'DownloadableFile', filename: string, path: string } | undefined };
 
 export type SourceDetailQueryVariables = Exact<{
   sourceId: Scalars['Int']['input'];
@@ -13263,7 +13263,7 @@ export const OrganizationMembersFieldsFragmentDoc = gql`
 export const ReleaseFragmentDoc = gql`
     fragment Release on DataRelease {
   name
-  geneTsv {
+  featureTsv {
     filename
     path
   }

client/src/app/generated/server.model.graphql

@@ -2436,7 +2436,7 @@ type DataRelease {
   acceptedVariantsVcf: DownloadableFile
   assertionTsv: DownloadableFile
   evidenceTsv: DownloadableFile
-  geneTsv: DownloadableFile
+  featureTsv: DownloadableFile
   molecularProfileTsv: DownloadableFile
   name: String!
   variantGroupTsv: DownloadableFile

client/src/app/generated/server.schema.json

@@ -12394,7 +12394,7 @@
               "deprecationReason": null
             },
             {
-              "name": "geneTsv",
+              "name": "featureTsv",
               "description": null,
               "args": [],
               "type": {

client/src/app/views/releases/releases-main/releases-list.query.gql

@@ -6,7 +6,7 @@ query DataReleases {
 
 fragment Release on DataRelease {
   name
-  geneTsv {
+  featureTsv {
     filename
     path
   }

client/src/app/views/releases/releases-main/releases-main.component.html

@@ -65,7 +65,7 @@ <h2>Data Releases</h2>
       <nz-row *nzSpaceItem>
         <p nz-typography>
           The CIViC server produces nightly and monthly releases that include a
-          subset of all primary entity records (Genes, Variants, Molecular
+          subset of all primary entity records (Features, Variants, Molecular
           Profiles, Evidence, Variant Groups, and Assertions). Both TSV and VCF
           versions are provided below - just locate the specific entity type and
           data format you wish to obtain, then click on the relevant button to
@@ -128,7 +128,7 @@ <h2>Data Releases</h2>
                 <thead>
                   <tr>
                     <th>Date</th>
-                    <th>Genes</th>
+                    <th>Features</th>
                     <th>Variants</th>
                     <th>Molecular Profiles</th>
                     <th>Evidence</th>
@@ -141,11 +141,11 @@ <h2>Data Releases</h2>
                 <tbody>
                   <tr *ngFor="let release of releasesTable.data">
                     <td>{{ release.name }}</td>
-                    <td *ngIf="release.geneTsv; else noData">
+                    <td *ngIf="release.featureTsv; else noData">
                       <cvc-link-tag
-                        [href]="release.geneTsv.path"
+                        [href]="release.featureTsv.path"
                         iconName="download">
-                        Genes TSV
+                        Features TSV
                       </cvc-link-tag>
                     </td>
                     <td *ngIf="release.variantTsv; else noData">

server/app/graphql/mutations/suggest_fusion_variant_revision.rb

@@ -86,7 +86,11 @@ def resolve(fields:, id:, organization_id: nil, comment: nil)
     updated_variant.single_variant_molecular_profile_id = variant.single_variant_molecular_profile_id
     updated_variant.feature = variant.feature
     updated_variant.fusion = variant.feature.feature_instance
-    updated_variant.name = updated_variant.generate_name
+    if variant.name == 'Fusion'
+      updated_variant.name = 'Fusion'
+    else
+      updated_variant.name = updated_variant.generate_name
+    end
     updated_variant.vicc_compliant_name = updated_variant.generate_vicc_name
 
     variant_revisions_obj = Activities::RevisedObjectPair.new(existing_obj: variant, updated_obj: updated_variant)

server/app/graphql/types/data_release_type.rb

@@ -10,7 +10,7 @@ def filename
 
   class DataReleaseType < Types::BaseObject
     field :name, String, null: false 
-    field :gene_tsv, DownloadableFile, null: true
+    field :feature_tsv, DownloadableFile, null: true
     field :variant_tsv, DownloadableFile, null: true
     field :variant_group_tsv, DownloadableFile, null: true
     field :evidence_tsv, DownloadableFile, null: true

server/app/graphql/types/queries/data_release_query.rb

@@ -13,7 +13,7 @@ def data_releases
             release_name = File.basename(release)
             {
               name: release_name,
-              gene_tsv: file_or_nil(release, release_name, 'GeneSummaries.tsv'),
+              feature_tsv: file_or_nil(release, release_name, 'FeatureSummaries.tsv'),
               variant_tsv: file_or_nil(release, release_name, 'VariantSummaries.tsv'),
               variant_group_tsv: file_or_nil(release, release_name, 'VariantGroupSummaries.tsv'),
               evidence_tsv: file_or_nil(release, release_name, 'ClinicalEvidenceSummaries.tsv'),
@@ -34,7 +34,7 @@ def data_releases
 
         end
       end
-      
+
       def file_or_nil(path, release, filename)
         full_path = File.join(path, "#{release}-#{filename}")
         if File.exist?(full_path)

server/app/jobs/generate_tsvs.rb

@@ -14,6 +14,15 @@ def perform
         public_path = public_file_path(e.file_name)
         FileUtils.cp(tmp_file.path, public_path)
         File.chmod(0644, public_path)
+
+        #symlink in legacy TSV names for backwards compatibility
+        if e.respond_to?(:file_aliases)
+          e.file_aliases.each do |fa|
+            link_path = public_file_path(fa)
+            FileUtils.ln_s(public_path, link_path, force: true)
+            File.chmod(0644, link_path)
+          end
+        end
       ensure
         tmp_file.unlink
       end
@@ -22,7 +31,7 @@ def perform
 
   def tsvs_to_generate
     [
-      GeneTsvFormatter,
+      FeatureTsvFormatter,
       VariantTsvFormatter,
       EvidenceItemTsvFormatter,
       VariantGroupTsvFormatter,

server/app/jobs/upload_tsvs_to_aws.rb

@@ -26,7 +26,7 @@ def perform
   def absolute_local_path(file)
     File.join(TsvRelease.downloads_path, file)
   end
-                      
+
   def bucket_name
     'civic-aws-opendata'
   end
@@ -61,7 +61,7 @@ def expected_files
     {
       "AssertionSummaries/date=#{date_string}/AssertionSummaries.tsv" => "#{date_string}/#{date_string}-AssertionSummaries.tsv",
       "ClinicalEvidenceSummaries/date=#{date_string}/ClinicalEvidenceSummaries.tsv" => "#{date_string}/#{date_string}-ClinicalEvidenceSummaries.tsv",
-      "GeneSummaries/date=#{date_string}/GeneSummaries.tsv" => "#{date_string}/#{date_string}-GeneSummaries.tsv",
+      "FeatureSummaries/date=#{date_string}/FeatureSummaries.tsv" => "#{date_string}/#{date_string}-FeatureSummaries.tsv",
       "VariantGroupSummaries/date=#{date_string}/VariantGroupSummaries.tsv"=> "#{date_string}/#{date_string}-VariantGroupSummaries.tsv",
       "VariantSummaries/date=#{date_string}/VariantSummaries.tsv" => "#{date_string}/#{date_string}-VariantSummaries.tsv",
       "MolecularProfileSummaries/date=#{date_string}/MolecularProfileSummaries.tsv" => "#{date_string}/#{date_string}-MolecularProfileSummaries.tsv",

server/app/tsv_formatters/feature_tsv_formatter.rb

@@ -0,0 +1,111 @@
+class FeatureTsvFormatter
+  def self.objects
+    Feature.joins(variants: { molecular_profiles: [:evidence_items]})
+      .includes(:feature_instance)
+      .distinct
+  end
+
+  def self.headers
+    shared_headers = [
+      'feature_id',
+      'feature_civic_url',
+      'feature_type',
+      'name',
+      'feature_aliases',
+      'description',
+      'last_review_date',
+      'is_flagged'
+    ]
+    shared_headers + gene_headers + factor_headers + fusion_headers
+  end
+
+  def self.gene_headers
+    ['entrez_id']
+  end
+
+  def self.factor_headers
+    ['ncit_id']
+  end
+
+  def self.fusion_headers
+    [
+      'five_prime_partner_status',
+      'three_prime_partner_status',
+      'five_prime_gene_id',
+      'five_prime_gene_name',
+      'five_prime_gene_entrez_id',
+      'three_prime_gene_id',
+      'three_prime_gene_name',
+      'three_prime_gene_entrez_id',
+    ]
+  end
+
+  def self.create_gene_row(feature)
+    row = [
+      feature.feature_instance.entrez_id
+    ]
+    row += Array.new(factor_headers.size)
+    row += Array.new(fusion_headers.size)
+    return row
+  end
+
+  def self.create_factor_row(feature)
+    row = Array.new(gene_headers.size)
+    row += [
+      feature.feature_instance.ncit_id
+    ]
+    row += Array.new(fusion_headers.size)
+  end
+
+  def self.create_fusion_row(feature)
+    feature_instance = feature.feature_instance
+    row = Array.new(gene_headers.size)
+    row += Array.new(factor_headers.size)
+    row += [
+      feature_instance.five_prime_partner_status,
+      feature_instance.three_prime_partner_status,
+      feature_instance.five_prime_gene_id,
+      feature_instance.five_prime_gene&.name,
+      feature_instance.five_prime_gene&.entrez_id,
+      feature_instance.three_prime_gene_id,
+      feature_instance.three_prime_gene&.name,
+      feature_instance.three_prime_gene&.entrez_id,
+    ]
+  end
+
+  def self.row_from_object(feature)
+    shared_cols = [
+      feature.id,
+      LinkAdaptors::Feature.new(feature).permalink_path(include_domain: true),
+      feature.feature_instance_type.demodulize,
+      feature.name,
+      feature.feature_aliases.map(&:name).join(","),
+      feature.description&.squish,
+      feature.updated_at,
+      feature.flagged
+    ]
+
+    feature_cols = case feature.feature_instance
+                   when Features::Gene
+                     create_gene_row(feature)
+                   when Features::Factor
+                     create_factor_row(feature)
+                   when Features::Fusion
+                     create_fusion_row(feature)
+                   else
+                     raise StandardError.new("Unknown feature type for TSV export: #{feature.feature_instance_type}")
+                   end
+    shared_cols + feature_cols
+  end
+
+  def self.file_name
+    'FeatureSummaries.tsv'
+  end
+
+  def self.file_aliases
+    [
+      'GeneSummaries.tsv'
+    ]
+  end
+end
+