Merge pull request #113 from ncats/development

Merge Development

apps/ramp-client/Dockerfile

@@ -31,4 +31,4 @@ COPY --from=build /var/www/app/dist/ramp-client/browser /var/www/app
 
 # Add read permissions to all files under assets directory
 RUN chmod -R o+r /var/www/app/assets/*
-RUN echo "Checkout assets file permissions" && ls -la /var/www/app/assets/*
+# RUN echo "Checkout assets file permissions" && ls -la /var/www/app/assets/*

apps/ramp-client/Jenkinsfile-ifx

@@ -102,12 +102,6 @@ pipeline {
                     """
                 }
             }
-            post {
-               always {
-                    echo " Clean up the workspace in deploy node!"
-                    cleanWs()
-                }
-            }
         }
     }
 }

apps/ramp-client/Jenkinsfile-ncats

@@ -98,12 +98,6 @@ pipeline {
                     }
                 }
             }
-            post {
-                always {
-                    echo " Clean up the workspace in deploy node!"
-                    cleanWs()
-                }
-            }
         }
     }
 }

apps/ramp-server/Jenkinsfile-ifx

@@ -120,12 +120,6 @@ pipeline {
                     """
                 }
             }
-            post {
-               always {
-                    echo " Clean up the workspace in deploy node!"
-                    cleanWs()
-                }
-            }
         } 
     }
 }

apps/ramp-server/Jenkinsfile-ncats

@@ -94,12 +94,6 @@ pipeline {
                     }
                 }
             }
-            post {
-                always {
-                    echo " Clean up the workspace in deploy node!"
-                    cleanWs()
-                }
-            }
         }
     }
 }

apps/ramp-server/install.R

@@ -1,4 +1,4 @@
 library(devtools)
-install_github("ncats/RaMP-DB", ref="pw_enrich_dev", force = TRUE, dependencies=TRUE)
+install_github("ncats/RaMP-DB", force = TRUE, dependencies=TRUE)
 library(RaMP)
 

apps/ramp-server/plumber.R

@@ -440,8 +440,8 @@ function(fishers_results,  pval_type = 'fdr', pval_cutoff = 0.1) {
 function(
   fishers_results,
   #analyte_source_id,
-  perc_analyte_overlap = 0.2,
-  perc_pathway_overlap = 0.2,
+  perc_analyte_overlap = 0.5,
+  perc_pathway_overlap = 0.5,
   min_pathway_tocluster=2
 ) {
   if (typeof(min_pathway_tocluster) == "character") {
@@ -475,8 +475,8 @@ function(
 #'
 function(
   fishers_results,
-  perc_analyte_overlap = 0.2,
-  perc_pathway_overlap = 0.2,
+  perc_analyte_overlap = 0.5,
+  perc_pathway_overlap = 0.5,
   min_pathway_tocluster=2,
   filename
 ) {

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

@@ -163,6 +163,8 @@ <h3>Cluster Results</h3>
                   matInput
                   type="number"
                   step="0.01"
+                  min=".5"
+                  max ="1"
                   [formControl]="percentAnalyteFormCtrl"
                 />
               </mat-form-field>
@@ -172,6 +174,8 @@ <h3>Cluster Results</h3>
                   matInput
                   type="number"
                   step="0.01"
+                  min=".5"
+                  max ="1"
                   [formControl]="percentPathwayFormCtrl"
                 />
               </mat-form-field>
@@ -228,9 +232,8 @@ <h3>Cluster Results</h3>
        <br>
        <br>
        <div fxLayout="row" fxLayoutAlign="end center">
-         <div fxFlex="10">
-           <button
-             mat-stroked-button
+         <div fxFlex="10" *ngIf="!tooBig">
+           <button mat-stroked-button
              class="tool-button list-download"
              (click)="fetchClusterImageFile()"
              matTooltip="Download Data"
@@ -240,7 +243,8 @@ <h3>Cluster Results</h3>
            </button>
          </div>
        </div>
-       <div [innerHTML]="image"></div>
+       <div *ngIf="tooBig">This website currently does not support clustering over 100 pathways.</div>
+       <div *ngIf="!tooBig" [innerHTML]="image"></div>
     </mat-tab>
   </mat-tab-group>
 </div>

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

@@ -35,8 +35,8 @@ export class PathwayEnrichmentComponent
   @ViewChild('resultsTabs') resultsTabs!: MatTabGroup;
   @ViewChild('fileUpload') fileUpload!: ElementRef;
   minPathWayFormCtrl: UntypedFormControl = new UntypedFormControl(2);
-  percentPathwayFormCtrl: UntypedFormControl = new UntypedFormControl(0.2);
-  percentAnalyteFormCtrl: UntypedFormControl = new UntypedFormControl(0.2);
+  percentPathwayFormCtrl: UntypedFormControl = new UntypedFormControl(0.5);
+  percentAnalyteFormCtrl: UntypedFormControl = new UntypedFormControl(0.5);
 
   pValueFormCtrl: UntypedFormControl = new UntypedFormControl(0.2);
   pValueTypeFormCtrl: UntypedFormControl = new UntypedFormControl('fdr');
@@ -143,6 +143,7 @@ export class PathwayEnrichmentComponent
   pathwayDataAsDataProperty!: { [key: string]: DataProperty }[];
   image: any;
   enrichedDataframe: any;
+  tooBig = false;
 
   constructor(
     private ref: ChangeDetectorRef,
@@ -229,7 +230,10 @@ export class PathwayEnrichmentComponent
       .subscribe(
       (res: any | undefined) => {
         if (res && res.length> 0) {
-             this.image = this.sanitizer.bypassSecurityTrustHtml(res);
+          this.tooBig = false;
+          this.image = this.sanitizer.bypassSecurityTrustHtml(res);
+        } else {
+          this.tooBig = true;
         }
         this.imageLoading = false;
         this.ref.markForCheck();

libs/features/ramp/properties-from-metabolites/src/lib/properties-from-metabolites/properties-from-metabolites.component.ts

@@ -123,9 +123,15 @@ export class PropertiesFromMetabolitesComponent
           value: value[1],
         });
       });
+
+      console.log(obj.iso_smiles)
       newObj.imageUrl.url = `${
         this.route.snapshot.data.renderUrl
       }(${encodeURIComponent(obj.iso_smiles)})?size=150`;
+      console.log(newObj.imageUrl.url)
+      console.log(`${
+        this.route.snapshot.data.renderUrl
+      }(${encodeURI(obj.iso_smiles)})?size=150`)
       newObj.imageUrl.label = newObj.common_name.value;
       return newObj;
     });

libs/shared/ui/filter-panel/src/lib/filter-panel/filter-panel.component.scss

@@ -13,6 +13,7 @@
   grid-auto-rows: max-content;
   grid-template-columns: 0.2fr 2.1fr 0.7fr;
   grid-template-areas: 'checkbox label count';
+  align-items: center;
 }
 .count {
   grid-area: count;

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

@@ -73,7 +73,7 @@ describe('RampFacade', () => {
       isLoaded = await readFirst(facade.loading$);
 
       //  expect(list.length).toBe(0);
-      expect(isLoaded).toBe(true);
+      expect(isLoaded).toBe(false);
     });
 
     /**

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

@@ -110,9 +110,16 @@ const rampReducer = createReducer(
     rampAdapter.setAll(rampStore, { ...state, loading: false })
   ),
 
-  on(
+  on (
     RampActions.init,
     RampActions.initAbout,
+    (state) => ({
+      ...state,
+      error: null,
+    })
+  ),
+
+  on(
     RampActions.fetchOntologiesFromMetabolites,
     RampActions.fetchAnalytesFromPathways,
     RampActions.fetchPathwaysFromAnalytes,

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

@@ -500,23 +500,27 @@ export class RampService {
     min_pathway_tocluster?: number,
     perc_pathway_overlap?: number
   ){
+    if(!dataframe.fishresults || dataframe.fishresults.length >= 10) {
+      return ""
+    } else {
       const body = {
         fishers_results: dataframe,
         text_size: 8,
-        perc_analyte_overlap:  perc_analyte_overlap,
+        perc_analyte_overlap: perc_analyte_overlap,
         min_pathway_tocluster: min_pathway_tocluster,
         perc_pathway_overlap: perc_pathway_overlap,
         filename: Date.now() + '.svg'
       }
-      const options: Object = {responseType: 'text' as const};
+      const options: Object = { responseType: 'text' as const };
       return this.http
-        .post<string[]>(`${this.url}cluster-plot`,body, options)
+        .post<string[]>(`${this.url}cluster-plot`, body, options)
         .pipe(
           map((response: any) => {
-            return  response.toString();
+            return response.toString();
           }),
           catchError(this.handleError('chemical enrichment', []))
-        );
+        )
+    }
   }
 
   fetchClusterImageFile(data: any) {