Allow Browse Table Contents to be downloaded

client/src/app/components/assertions/assertions-table/assertions-table.component.html

@@ -392,5 +392,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="assertions"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/assertions/assertions-table/assertions-table.module.ts

@@ -8,6 +8,7 @@ import { CvcMolecularProfileTagModule } from '@app/components/molecular-profiles
 import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-input-filter/clearable-input-filter.module';
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcTagListModule } from '@app/components/shared/tag-list/tag-list.module';
 import { CvcTagOverflowModule } from '@app/components/shared/tag-overflow/tag-overflow.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
@@ -61,6 +62,7 @@ import { CvcAssertionsTableComponent } from './assertions-table.component';
     CvcTagListModule,
     CvcTagOverflowModule,
     CvcMolecularProfileTagModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcAssertionsTableComponent]
 })

client/src/app/components/clinical-trials/clinical-trials-table/clinical-trials-table.component.html

@@ -141,5 +141,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="clinical_trials"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/clinical-trials/clinical-trials-table/clinical-trials-table.module.ts

@@ -3,6 +3,7 @@ import { NgModule } from '@angular/core';
 import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-input-filter/clearable-input-filter.module';
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
 import { CvcAutoHeightCardModule } from '@app/directives/auto-height-card/auto-height-card.module';
 import { CvcAutoHeightTableModule } from '@app/directives/auto-height-table/auto-height-table.module';
@@ -40,6 +41,7 @@ import { CvcClinicalTrialsTableComponent } from './clinical-trials-table.compone
     CvcNoMoreRowsModule,
     CvcTableCountsModule,
     CvcTableScrollModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcClinicalTrialsTableComponent]
 })

client/src/app/components/diseases/diseases-table/diseases-table.component.html

@@ -193,5 +193,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="diseases"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/diseases/diseases-table/diseases-table.module.ts

@@ -4,6 +4,7 @@ import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-
 import { CvcLinkTagModule } from '@app/components/shared/link-tag/link-tag.module';
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
 import { CvcAutoHeightCardModule } from '@app/directives/auto-height-card/auto-height-card.module';
 import { CvcAutoHeightTableModule } from '@app/directives/auto-height-table/auto-height-table.module';
@@ -43,6 +44,7 @@ import { CvcDiseasesTableComponent } from './diseases-table.component';
     CvcNoMoreRowsModule,
     CvcTableCountsModule,
     CvcTableScrollModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcDiseasesTableComponent]
 })

client/src/app/components/drugs/drugs-table/drugs-table.component.html

@@ -141,5 +141,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="drugs"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/drugs/drugs-table/drugs-table.module.ts

@@ -18,6 +18,7 @@ import { CvcTableScrollModule } from '@app/directives/table-scroll/table-scroll.
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 
 @NgModule({
   declarations: [CvcDrugsTableComponent],
@@ -43,6 +44,7 @@ import { CvcPipesModule } from '@app/core/pipes/pipes.module';
     CvcNoMoreRowsModule,
     CvcTableCountsModule,
     CvcTableScrollModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcDrugsTableComponent]
 })

client/src/app/components/evidence/evidence-table/evidence-table.component.html

@@ -489,5 +489,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="evidence"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/evidence/evidence-table/evidence-table.component.ts

@@ -133,7 +133,7 @@ export class CvcEvidenceTableComponent implements OnInit {
         first: this.initialPageSize,
         organizationId: this.organizationId,
         phenotypeId: this.phenotypeId,
-        rating: this.evidenceRatingInput ? this.evidenceRatingInput : undefined,
+        evidenceRating: this.evidenceRatingInput ? this.evidenceRatingInput : undefined,
         sourceId: this.sourceId,
         status: this.status,
         userId: this.userId,
@@ -258,7 +258,7 @@ export class CvcEvidenceTableComponent implements OnInit {
         variantOrigin: this.variantOriginInput
           ? this.variantOriginInput
           : undefined,
-        rating: this.evidenceRatingInput ? this.evidenceRatingInput : undefined,
+        evidenceRating: this.evidenceRatingInput ? this.evidenceRatingInput : undefined,
         molecularProfileName: this.molecularProfileNameInput ? this.molecularProfileNameInput : undefined,
       })
       .then(() => this.scrollIndex$.next(0));

client/src/app/components/evidence/evidence-table/evidence-table.module.ts

@@ -7,6 +7,7 @@ import { CvcMolecularProfileTagModule } from '@app/components/molecular-profiles
 import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-input-filter/clearable-input-filter.module';
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcTagListModule } from '@app/components/shared/tag-list/tag-list.module';
 import { CvcTagOverflowModule } from '@app/components/shared/tag-overflow/tag-overflow.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
@@ -63,6 +64,7 @@ import { CvcEvidenceTableComponent } from './evidence-table.component';
     CvcTagListModule,
     CvcTagOverflowModule,
     CvcMolecularProfileTagModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcEvidenceTableComponent]
 })

client/src/app/components/evidence/evidence-table/evidence-table.query.gql

@@ -11,7 +11,7 @@ query EvidenceBrowse(
   $evidenceDirection: EvidenceDirection
   $clinicalSignificance: EvidenceClinicalSignificance
   $evidenceType: EvidenceType
-  $rating: Int
+  $evidenceRating: Int
   $variantOrigin: VariantOrigin
   $variantId: Int
   $molecularProfileId: Int
@@ -40,7 +40,7 @@ query EvidenceBrowse(
     evidenceDirection: $evidenceDirection
     clinicalSignificance: $clinicalSignificance
     evidenceType: $evidenceType
-    evidenceRating: $rating
+    evidenceRating: $evidenceRating
     variantOrigin: $variantOrigin
     variantId: $variantId
     molecularProfileId: $molecularProfileId

client/src/app/components/genes/genes-table/genes-table.component.html

@@ -173,5 +173,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="genes"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/genes/genes-table/genes-table.module.ts

@@ -6,6 +6,7 @@ import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcPlainTagOverflowModule } from '@app/components/shared/plain-tag-overflow/plain-tag-overflow.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcTagOverflowModule } from '@app/components/shared/tag-overflow/tag-overflow.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
 import { CvcAutoHeightCardModule } from '@app/directives/auto-height-card/auto-height-card.module';
@@ -50,6 +51,7 @@ import { CvcGenesTableComponent } from './genes-table.component';
     CvcTableCountsModule,
     CvcTableScrollModule,
     CvcTagOverflowModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcGenesTableComponent]
 })

client/src/app/components/molecular-profiles/molecular-profile-table/molecular-profile-table.component.html

@@ -200,5 +200,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="molecular_profiles"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/molecular-profiles/molecular-profile-table/molecular-profile-table.module.ts

@@ -5,6 +5,7 @@ import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcPlainTagOverflowModule } from '@app/components/shared/plain-tag-overflow/plain-tag-overflow.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcTagOverflowModule } from '@app/components/shared/tag-overflow/tag-overflow.module';
 import { CvcVariantTagModule } from '@app/components/variants/variant-tag/variant-tag.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
@@ -46,7 +47,8 @@ import { CvcMolecularProfilesTableComponent } from './molecular-profile-table.co
     CvcTableScrollModule,
     CvcTagOverflowModule,
     CvcMolecularProfileTagModule,
-    CvcPlainTagOverflowModule
+    CvcPlainTagOverflowModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcMolecularProfilesTableComponent]
 })

client/src/app/components/shared/table-downloader/table-downloader.component.html

@@ -0,0 +1,8 @@
+<button nz-button
+  nzSize="small"
+  (click)="this.downloadTable()"
+  [disabled]="this.downloading | async">
+  <span *ngIf="!(this.downloading | async)"nz-icon nzType="download" nzTheme="outline"></span>
+  <span *ngIf="this.downloading | async" nz-icon nzType="sync" [nzSpin]="true"></span>
+  Download Table
+</button>

client/src/app/components/shared/table-downloader/table-downloader.component.ts

@@ -0,0 +1,42 @@
+import { Component, Output, EventEmitter, OnDestroy, Input } from "@angular/core";
+import { HttpClient } from "@angular/common/http";
+import { Query } from "apollo-angular";
+import { EmptyObject } from "apollo-angular/types";
+import { BehaviorSubject } from "rxjs";
+
+@Component({
+  selector: 'cvc-table-downloader',
+  templateUrl: './table-downloader.component.html',
+  styleUrls: ['./table-downloader.component.less'],
+})
+export class CvcTableDownloaderComponent<V extends EmptyObject> {
+
+  @Input() tableName?: string
+  @Input() vars?: V
+
+  downloading = new BehaviorSubject<boolean>(false)
+
+  constructor(private http: HttpClient) {}
+
+  downloadTable() {
+    if(this.vars) {
+      let payload = {
+        variables: this.vars
+      }
+      this.downloading.next(true);
+      this.http.post(`/api/download_table/${this.tableName}`, payload, {responseType: 'blob', observe: 'response'}).subscribe((resp: any) => {
+        const a = document.createElement("a");
+        document.body.append(a);
+        a.style.display = 'none';
+        const blob = new Blob([resp.body], {type: 'text/csv'});
+        const url = window.URL.createObjectURL(blob);
+        a.href = url;
+        a.download = `${this.tableName}-${new Date().toLocaleString().split(',')[0]}.tsv`
+        a.click();
+        this.downloading.next(false);
+        setTimeout(() => { window.URL.revokeObjectURL(url); }, 400)
+      })
+    }
+
+  }
+}

client/src/app/components/shared/table-downloader/table-downloader.module.ts

@@ -0,0 +1,16 @@
+import { NgModule } from '@angular/core';
+import { CommonModule } from '@angular/common';
+import { NzButtonModule } from 'ng-zorro-antd/button';
+import { NzIconModule } from 'ng-zorro-antd/icon';
+import { CvcTableDownloaderComponent } from './table-downloader.component';
+
+@NgModule({
+  declarations: [CvcTableDownloaderComponent],
+  imports: [
+    CommonModule,
+    NzButtonModule,
+    NzIconModule
+  ],
+  exports: [CvcTableDownloaderComponent]
+})
+export class CvcTableDownloaderModule { }

client/src/app/components/sources/sources-table/sources-table.component.html

@@ -202,5 +202,6 @@
       nzSpin></i>
     <span>Loading…</span>
   </nz-tag>
+  <cvc-table-downloader [vars]="this.queryRef.variables" tableName="sources"></cvc-table-downloader>
   <cvc-no-more-rows [cvcShowTag]="noMoreRows$ | ngrxPush"></cvc-no-more-rows>
 </ng-template>

client/src/app/components/sources/sources-table/sources-table.module.ts

@@ -5,6 +5,7 @@ import { CvcClearableInputFilterModule } from '@app/components/shared/clearable-
 import { CvcNoMoreRowsModule } from '@app/components/shared/no-more-rows/no-more-rows.module';
 import { CvcPlainTagOverflowModule } from '@app/components/shared/plain-tag-overflow/plain-tag-overflow.module';
 import { CvcTableCountsModule } from '@app/components/shared/table-counts/table-counts.module';
+import { CvcTableDownloaderModule } from '@app/components/shared/table-downloader/table-downloader.module';
 import { CvcPipesModule } from '@app/core/pipes/pipes.module';
 import { CvcAutoHeightCardModule } from '@app/directives/auto-height-card/auto-height-card.module';
 import { CvcAutoHeightTableModule } from '@app/directives/auto-height-table/auto-height-table.module';
@@ -46,6 +47,7 @@ import { CvcSourcesTableComponent } from './sources-table.component';
     CvcSourceTagModule,
     CvcTableCountsModule,
     CvcTableScrollModule,
+    CvcTableDownloaderModule
   ],
   exports: [CvcSourcesTableComponent]
 })

server/app/controllers/concerns/with_graphql_variables.rb

@@ -0,0 +1,22 @@
+module WithGraphqlVariables
+  extend ActiveSupport::Concern
+  # Handle variables in form data, JSON body, or a blank value
+  def prepare_variables(variables_param)
+    case variables_param
+    when String
+      if variables_param.present?
+        JSON.parse(variables_param) || {}
+      else
+        {}
+      end
+    when Hash
+      variables_param
+    when ActionController::Parameters
+      variables_param.to_unsafe_hash # GraphQL-Ruby will validate name and type of incoming variables.
+    when nil
+      {}
+    else
+      raise ArgumentError, "Unexpected parameter: #{variables_param}"
+    end
+  end
+end

server/app/controllers/graphql_controller.rb

@@ -1,4 +1,5 @@
 class GraphqlController < ApplicationController
+  include WithGraphqlVariables
   # If accessing from outside this domain, nullify the session
   # This allows for outside API access while preventing CSRF attacks,
   # but you'll have to authenticate your user separately
@@ -23,27 +24,6 @@ def execute
   end
 
   private
-
-  # Handle variables in form data, JSON body, or a blank value
-  def prepare_variables(variables_param)
-    case variables_param
-    when String
-      if variables_param.present?
-        JSON.parse(variables_param) || {}
-      else
-        {}
-      end
-    when Hash
-      variables_param
-    when ActionController::Parameters
-      variables_param.to_unsafe_hash # GraphQL-Ruby will validate name and type of incoming variables.
-    when nil
-      {}
-    else
-      raise ArgumentError, "Unexpected parameter: #{variables_param}"
-    end
-  end
-
   def handle_error_in_development(e)
     logger.error e.message
     logger.error e.backtrace.join("\n")

server/app/controllers/table_download_controller.rb

@@ -0,0 +1,49 @@
+require 'csv'
+
+class TableDownloadController < ApplicationController
+  include WithGraphqlVariables
+
+  @@table_resolvers = {
+    genes: Resolvers::BrowseGenes,
+    evidence: Resolvers::TopLevelEvidenceItems,
+    drugs: Resolvers::TopLevelDrugs,
+    sources: Resolvers::BrowseSources,
+    diseases: Resolvers::BrowseDiseases,
+    molecular_profiles: Resolvers::BrowseMolecularProfiles,
+    clinical_trials: Resolvers::TopLevelClinicalTrials,
+    assertions: Resolvers::TopLevelAssertions
+  }
+
+  def download
+    if res = @@table_resolvers[params[:table_name].to_sym]
+      stream_table(resolver: res)
+    else
+      head :bad_request
+    end
+  end
+
+  private
+  def stream_table(resolver: )
+
+    variables = prepare_variables(params[:variables])
+    variables.delete('sortBy')
+    variables.transform_keys! { |k| GraphQL::Schema::Member::BuildType.underscore(k) }
+
+    headers.delete("Content-Length")
+    headers["Cache-Control"] = "no-cache"
+    headers["Content-Type"] = "text/csv"
+    headers["Content-Disposition"] = "attachment; filename=\"#{params[:action]}-#{Date.today}.tsv\""
+    headers["X-Accel-Buffering"] = "no"
+
+    response.status = 200
+
+
+    self.response_body = Enumerator.new do |collection|
+      collection << CSV.generate_line(resolver.table_headers, col_sep: "\t")
+
+      resolver.new(filters: variables).results.find_each do |result|
+        collection << CSV.generate_line( resolver.to_row(object: result), col_sep: "\t")
+      end
+    end
+  end
+end