Updated organ and organ part to use specimen. Resolves #901 (#1156)

* Updated row mapper and facets to use specimen organ and speciment organ part. Resolves #901.

* Updated organ and organ part to use specimen. Resolves #901.

Author: MillenniumFalconMechanic

spa/src/app/files/hca-table-column-header-count/hca-table-column-header-count.component.ts

@@ -10,6 +10,7 @@ import { Component, Input } from "@angular/core";
 
 // App dependencies
 import { getColumnCountType } from "../table/table-methods";
+import { getColumnCountName } from "../table/table-methods";
 
 @Component({
     selector: "hca-table-column-header-count",
@@ -27,10 +28,6 @@ export class HCATableColumnHeaderCountComponent {
     // Template variables
     tooltipContentForCount = "Count of distinct values for this facet in the current search result set.";
 
-    /**
-     * Public API
-     */
-
     /**
      * Return a count of the set of values for the specified column.
      *
@@ -39,7 +36,8 @@ export class HCATableColumnHeaderCountComponent {
      */
     public getDomainCount(columnName: string): number {
 
-        return this.domainCountsByColumnName.get(columnName);
+        const columnCountName = getColumnCountName(columnName);
+        return this.domainCountsByColumnName.get(columnCountName);
     }
 
     /**

spa/src/app/files/hca-table-projects/project-row-mapper.mock.ts

@@ -528,9 +528,12 @@ export const PROJECT_ROW_VALUES_ACROSS_MULTIPLE_OBJECTS =
                     "420508_specimen"
                 ],
                 "organ": [
-                    "brain"
+                    "brain",
+                    "blood"
+                ],
+                "organPart": [
+                    "a"
                 ],
-                "organPart": [],
                 "disease": [
                     "x",
                     "y"

spa/src/app/files/shared/file-facet-display.service.ts

@@ -25,7 +25,7 @@ export class FileFacetDisplayService {
         },
         {
             facetGroupName: "Tissue Type",
-            facetNames: ["sampleEntityType", "organ", "organPart", "modelOrgan", "selectedCellType"]
+            facetNames: ["sampleEntityType", "specimenOrgan", "specimenOrganPart", "modelOrgan", "selectedCellType"]
         },
         {
             facetGroupName: "Specimen",

spa/src/app/files/shared/file-facet-name-display.model.ts

@@ -11,5 +11,7 @@ export enum FileFacetNameDisplay {
     "libraryConstructionApproach" = "Library Construction Method",
     "projectId" = "Project",
     "sampleEntityType" = "Sample Type",
+    "specimenOrgan" = "Organ",
+    "specimenOrganPart" = "Organ Part",
     "workflow" = "Analysis Protocol"
 }

spa/src/app/files/table/entity-row-mapper.spec.ts

@@ -427,7 +427,7 @@ describe("EntityRowMapper:", () => {
         dataSource.connect().subscribe((rows) => {
 
             const mappedProject = rows[0];
-            expect(mappedProject.organ).toEqual(projectToMap.samples[0].organ[0]);
+            expect(mappedProject.organ).toEqual(projectToMap.specimens[0].organ[0]);
             done();
         })
     });
@@ -442,7 +442,7 @@ describe("EntityRowMapper:", () => {
         dataSource.connect().subscribe((rows) => {
 
             const mappedProject = rows[0];
-            expect(mappedProject.organ).toEqual(projectToMap.samples[0].organ.join(", "));
+            expect(mappedProject.organ).toEqual(projectToMap.specimens[0].organ.join(", "));
             done();
         })
     });
@@ -457,7 +457,7 @@ describe("EntityRowMapper:", () => {
         dataSource.connect().subscribe((rows) => {
 
             const mappedProject = rows[0];
-            const expectedValue = mapMultipleValues(projectToMap.samples, "organ");
+            const expectedValue = mapMultipleValues(projectToMap.specimens, "organ");
             expect(mappedProject.organ).toEqual(expectedValue);
             done();
         })
@@ -590,7 +590,7 @@ describe("EntityRowMapper:", () => {
         dataSource.connect().subscribe((rows) => {
 
             const mappedProject = rows[0];
-            expect(mappedProject.organPart).toEqual(projectToMap.samples[0].organPart[0]);
+            expect(mappedProject.organPart).toEqual(projectToMap.specimens[0].organPart[0]);
             done();
         })
     });
@@ -605,7 +605,7 @@ describe("EntityRowMapper:", () => {
         dataSource.connect().subscribe((rows) => {
 
             const mappedProject = rows[0];
-            expect(mappedProject.organPart).toEqual(projectToMap.samples[0].organPart.join(", "));
+            expect(mappedProject.organPart).toEqual(projectToMap.specimens[0].organPart.join(", "));
             done();
         })
     });
@@ -620,7 +620,7 @@ describe("EntityRowMapper:", () => {
         dataSource.connect().subscribe((rows) => {
 
             const mappedProject = rows[0];
-            const expectedValue = mapMultipleValues(projectToMap.samples, "organPart");
+            const expectedValue = mapMultipleValues(projectToMap.specimens, "organPart");
             expect(mappedProject.organPart).toEqual(expectedValue);
             done();
         })

spa/src/app/files/table/entity-row-mapper.ts

@@ -30,11 +30,11 @@ export class EntityRowMapper {
         this.cellSuspensions = rollUpMetadata(row.cellSuspensions);
         this.donorOrganisms = rollUpMetadata(row.donorOrganisms);
         this.samples = rollUpMetadata(row.samples);
-        this.organs = this.samples.organ;
+        this.specimens = rollUpMetadata(row.specimens);
+        this.organs = this.specimens.organ;
         this.projects = rollUpMetadata(row.projects);
         this.protocols = rollUpMetadata(row.protocols);
         this.row = row;
-        this.specimens = rollUpMetadata(row.specimens);
     }
 
     /**
@@ -75,7 +75,7 @@ export class EntityRowMapper {
             libraryConstructionApproach: mappedLibraryConstructionApproach,
             organ: getUnspecifiedIfNullValue(this.organs),
             organismAge: getUnspecifiedIfNullValue(this.donorOrganisms.organismAge),
-            organPart: getUnspecifiedIfNullValue(this.samples.organPart),
+            organPart: getUnspecifiedIfNullValue(this.specimens.organPart),
             modelOrgan: modelOrgan,
             pairedEnd: getUnspecifiedIfNullValue(this.protocols.pairedEnd),
             projectTitle: getUnspecifiedIfNullValue(this.projects.projectTitle),

spa/src/app/files/table/table-column.model.ts

@@ -18,6 +18,7 @@ export interface TableColumn {
     columnSortKey?: string;
     columnTitleWidth?: number;
     countType: CountType;
+    countName?: string;
     description?: string;
     descriptionFiles?: string;
     descriptionProjects?: string;

spa/src/app/files/table/table-methods.ts

@@ -35,6 +35,7 @@ let tableColumns: TableColumn[] = [
         alignment: ColumnAlignment.LEFT,
         columnMinWidth: 88,
         columnSort: true,
+        countName: "specimenDisease",
         countType: CountType.DOMAIN_COUNT
 
     },
@@ -151,6 +152,7 @@ let tableColumns: TableColumn[] = [
         columnFlexDirection: ColumnFlexDirection.COLUMN,
         columnMinWidth: 100,
         columnSort: true,
+        countName: "specimenOrgan",
         countType: CountType.DOMAIN_COUNT
     },
     {
@@ -159,6 +161,7 @@ let tableColumns: TableColumn[] = [
         description: "A term for a specific part of the organ that the biomaterial came from.",
         alignment: ColumnAlignment.LEFT,
         columnSort: true,
+        countName: "specimenOrganPart",
         countType: CountType.DOMAIN_COUNT
     },
     {
@@ -307,6 +310,17 @@ export function getColumnCountType(column: string): string {
     return CountType[tableColumn.get(column).countType];
 }
 
+/**
+ * Returns count name for specified column if specified, otherwise returns the column name.
+ *
+ * @param {string} columnName
+ * @returns {string}
+ */
+export function getColumnCountName(columnName: string): string {
+
+    return tableColumn.get(columnName).countName || columnName;
+}
+
 /**
  * Returns the column description.
  * Used by table header tooltip.