Merge pull request #138 from tsheils/development

fix pathway analysis download

libs/features/ramp/pathway-enrichment/src/lib/pathway-enrichment/pathway-enrichment.component.ts

@@ -522,8 +522,9 @@ export class PathwayEnrichmentComponent
     } else {
       data = this.enrichedDataframe as unknown[]
     }
+    const fff = new FisherResult(data[0] as Partial<FisherResult>)
       this._downloadFile(
-      this._toTSV(data),
+      this._toTSV(data, fff._getFields()),
       'fetchEnrichedPathwaysFromAnalytes-download.tsv',
     );
   }

libs/features/ramp/ramp-about/src/lib/about/about.component.html

@@ -461,7 +461,7 @@ <h3>Gene Overlap</h3>
             Citation
           </div>
           <div class="section-content">
-            <p>
+           <!-- <p>
               Our most current preprint is available
               <a
                 href="https://www.biorxiv.org/content/10.1101/2022.01.19.476987v1"
@@ -470,7 +470,7 @@ <h3>Gene Overlap</h3>
                 aria-label="link to Updated RaMP-DB 2 preprint."
                 >here.</a
               >
-            </p>
+            </p>-->
             <p>If you use RaMP, please cite the following work:</p>
             <p>
               <a

libs/models/ramp-models/src/lib/_utils.ts

@@ -2,7 +2,8 @@ import { ChemicalEnrichment } from './chemical-enrichment';
 import { FisherResult, FishersDataframe } from './fisher-result';
 import { RampQuery } from './ramp-query';
 
-export class RampDataGeneric {}
+export class RampDataGeneric {
+}
 
 export interface RampAPIResponse<T extends RampDataGeneric> {
   data: Array<T>;

libs/models/ramp-models/src/lib/fisher-result.ts

@@ -26,7 +26,7 @@ export class FisherResult {
   pathwayName!: string;
   pathwaySource!: string;
   pathwayId!: string;
-  cluster_assignment?: number;
+  cluster_assignment?: string;
   metabCount!: string;
   geneCount!: string;
   pathCount!: string;
@@ -46,4 +46,8 @@ export class FisherResult {
       this.pathCount = obj.Num_In_Path + '/' + obj.Total_In_Path;
     }
   }
+
+  _getFields() {
+   return Object.keys(this).filter(field => !['Total_In_Path', 'Pval_Holm', 'Pval_FDR', 'Pval', 'Num_In_Path', 'metabCount',	'geneCount',	'pathCount'].includes(field));
+  }
 }

libs/shared/ramp/page-core/src/lib/page-core/page-core.component.ts

@@ -79,20 +79,27 @@ export class PageCoreComponent {
       .subscribe();
   }
 
-  _toTSV<T extends RampDataGeneric>(data: unknown[]): string {
+  _toTSV<T extends RampDataGeneric>(data: unknown[], fields?: string[]): string {
     if (data) {
       // grab the column headings (separated by tabs)
-      const headings: string = Object.keys(data[0] as string[]).join('\t');
+      const headings: string[] =  fields ? fields : Object.keys(data[0] as string[]);
       // iterate over the data
       const rows: string[] = <string[]>data.reduce(
         (acc: string[], c: unknown) => {
+          const ret = headings.map(field => {
+            if((c as T)[field as keyof T]) {
+              return (c as T)[<string>field as keyof T]
+            } else {
+             return
+            }
+          })
           // for each row object get its values and add tabs between them
           // then add them as a new array to the outgoing array
-          return acc.concat([Object.values(c as T).join('\t')]);
+          return acc.concat(ret.join('\t'));
 
           // finally joining each row with a line break
         },
-        [headings],
+        [headings.join('\t')],
       );
       return rows.join('\n');
     } else return '';

libs/stores/ramp-store/src/lib/+state/ramp.service.ts

@@ -562,7 +562,7 @@ export class RampService {
               (obj: unknown) => new FisherResult(obj as Partial<FisherResult>),
             ),
             query: {},
-            combinedFishersdataframe: response.data as FishersDataframe,
+            combinedFishersDataframe: response.data as FishersDataframe,
           } as RampPathwayEnrichmentResponse;
         }),
         // catchError(this.handleError('chemical enrichment', [])),