Merge branch 'beta'

Author: Nestor Diaz

src/app/pages/submission/submission-direct/direct-submit-file.component.html

@@ -18,26 +18,25 @@
         </div>
         <h5 class="st-direct-submit-file-name m-0">{{file.name}}</h5>
       </div>
-      <span *ngIf="!hasSubmitFailed && isStudy">
-        {{project ? project : 'No project'}}
-      </span>
+      <div *ngIf="hasSubmitPassed">
+        <p class="card-title">
+          <strong>{{accno}}</strong>
+        </p>
+        <dl class="row mb-0">
+          <dt class="col-sm-6" *ngIf="releaseDate">Release Date</dt>
+          <dd class="col-sm-6" *ngIf="releaseDate">{{releaseDate | date: 'dd MMM yyyy'}}</dd>
+          <dd class="col-sm-6" *ngIf="!releaseDate">No release date</dd>
+
+          <dt class="col-sm-6" *ngIf="isStudy">Project</dt>
+          <dd class="col-sm-6" *ngIf="isStudy">{{project ? project : 'No project'}}</dd>
+        </dl>
+      </div>
       <span class="text-danger" *ngIf="hasSubmitFailed">
         {{error}}
       </span>
       <div class="overflow-auto" *ngIf="hasSubmitFailed">
         <st-subm-results-tree [log]="errorLog"></st-subm-results-tree>
       </div>
-      <div *ngIf="hasSubmitPassed" class="text-right">
-        <p class="card-title">
-          <strong>{{accno}}</strong>
-        </p>
-        <span *ngIf="releaseDate">
-          <i class="fa fa-bullhorn"></i>&nbsp; {{releaseDate | date: 'dd MMM yyyy'}}
-        </span>
-        <span *ngIf="!releaseDate">
-          No release date
-        </span>
-      </div>
     </div>
     <div *ngIf="!hasSubmitFailed && !hasSubmitPassed" class="card-footer text-muted"
       (click)="handleOnIsStudyChange(!isStudy, fileName)">

src/app/pages/submission/submission-direct/direct-submit.component.html

@@ -117,10 +117,9 @@ <h4>{{pluralise('Study')}} {{sidebar.submitType + 'd'}}</h4>
                   <i class="fa fa-fw fa-external-link-square"></i>
                 </a>
               </strong>
-              <p>
-                McEntyre J, Sarkans U, Brazma A (2015) The
-                BioStudies database. <i>Mol. Syst. Biol.</i> 11(12):847.
-                https://doi.org/10.15252/msb.20156658.
+              <p>Sarkans U, Gostev M, Athar A, et al. <a href="http://doi.org/10.1093/nar/gkx965">The BioStudies
+                database-one stop shop for all data supporting a life sciences study.</a>
+                <i>Nucleic Acids Res.</i> 2018;46(D1):D1266-D1270. doi:10.1093/nar/gkx965
               </p>
             </ng-container>
           </div>

src/app/pages/submission/submission-direct/direct-submit.service.ts

@@ -89,6 +89,25 @@ export class DirectSubmitRequest {
     return this.directSubmissionReleaseDate;
   }
 
+  private extractReleaseDate(res: SubmitResponse): string {
+    const { attributes = [], section } = res;
+    let releaseDate;
+
+    if (attributes.length > 0) {
+      const releaseDateAttribute = attributes.find((attribute) => attribute.name === 'ReleaseDate');
+
+      releaseDate = releaseDateAttribute ? releaseDateAttribute.value : null;
+    }
+
+    if (!releaseDate && section && section.attributes && section.attributes.length > 0) {
+      const releaseDateAttribute = section.attributes.find((attribute) => attribute.name === 'ReleaseDate');
+
+      releaseDate = releaseDateAttribute ? releaseDateAttribute.value : null;
+    }
+
+    return releaseDate;
+  }
+
   /**
    * Handler for responses from conversion or final submission, updating request status accordingly.
    * @param res - Data object representative of response to the request.
@@ -110,6 +129,7 @@ export class DirectSubmitRequest {
 
       // exposes the accession number
       this.directSubmissionAccno = res.accno;
+      this.directSubmissionReleaseDate = this.extractReleaseDate(res);
     }
   }
 }

src/app/pages/submission/submission-edit/subm-form/field/subm-field.component.ts

@@ -60,6 +60,10 @@ export class SubmFieldComponent {
   }
 
   get isEmpty(): boolean {
+    if (Array.isArray(this.fieldControl!.control.value)) {
+      return this.fieldControl!.control.value.length === 0;
+    }
+
     return isStringEmpty(this.fieldControl!.control.value as string);
   }
 

src/app/pages/submission/submission-shared/model/pagetab/pagetab-attributes.utils.ts

@@ -22,6 +22,10 @@ export function mergeAttributes(attrs1: PtAttribute[], attrs2: PtAttribute[]): P
   return merged.filter((attr) => !isAttributeEmpty(attr));
 }
 
+export function findAttributesByName(name: string, attributes: PtAttribute[]): PtAttribute[] {
+  return attributes.filter((attribute) => attribute.name === name);
+}
+
 export function extractKeywordsFromAttributes(attributes: PtAttribute[]): PtAttribute[] {
   return attributes.filter((attribute) => attribute.name === 'Keyword');
 }

src/app/pages/submission/submission-shared/model/submission/submission.model.ts

@@ -182,7 +182,7 @@ export class Feature {
         const rowValue = rowMap.valueFor(pair[1].id);
 
         if (rowValue) {
-          rowValue.value = pair[0].value || '';
+          rowValue.value = (pair[0].value || '') as string;
         }
       });
     });
@@ -628,7 +628,7 @@ export interface AttributeData {
   name: string;
   reference?: boolean;
   terms?: NameAndValue[];
-  value?: string;
+  value?: string | string[];
 }
 
 export interface FeatureData {

src/app/pages/submission/submission-shared/model/templates/bia.template.ts

@@ -54,6 +54,7 @@ export const biaTemplate = {
         display: 'required',
         valueType: {
           name: 'select',
+          multiple: true,
           values: [
             'Homo sapiens (human)',
             'Mus musculus (mouse)',

src/app/pages/submission/submission-shared/model/templates/default.template.ts

@@ -40,6 +40,7 @@ export const defaultTemplate = {
         display: 'required',
         valueType: {
           name: 'select',
+          multiple: true,
           values: [
             'Homo sapiens (human)',
             'Mus musculus (mouse)',

src/app/pages/submission/submission-shared/pagetab-to-submission.service.ts

@@ -7,17 +7,19 @@ import {
   PageTabSection,
   PtAttribute,
   authorsToContacts,
-  extractKeywordsFromAttributes,
   mergeAttributes,
   pageTabToSubmissionProtocols,
   PtLink,
-  PtFile
+  PtFile,
+  findAttributesByName
 } from './model/pagetab';
 import { AttributeData, FeatureData, SectionData, Submission, SubmissionData } from './model/submission';
 import { DEFAULT_TEMPLATE_NAME, READONLY_TEMPLATE_NAME, SubmissionType } from './model/templates';
 import { NameAndValue, PAGE_TAG, Tag } from './model/model.common';
 import { findAttribute } from './utils/pagetab.utils';
 
+const multiValueAttributeNames = ['Organism'];
+
 @Injectable()
 export class PageTabToSubmissionService {
   pageTab2Submission(pageTab: PageTab): Submission {
@@ -66,16 +68,37 @@ export class PageTabToSubmissionService {
     return hasSubsection || hasLinks || hasFiles || hasLibraryFile || hasPageTag;
   }
 
+  private attributeToAttributeData(attr: PtAttribute): AttributeData {
+    return {
+      name: attr.name || '',
+      reference: attr.reference || attr.isReference,
+      terms: (attr.valqual || []).map((t) => new NameAndValue(t.name, t.value)),
+      value: attr.value
+    };
+  }
+
   private pageTabAttributesToAttributeData(attrs: PtAttribute[]): AttributeData[] {
-    return attrs.map(
-      (at) =>
-        ({
-          name: at.name,
-          reference: at.reference || at.isReference,
-          terms: (at.valqual || []).map((t) => new NameAndValue(t.name, t.value)),
-          value: at.value
-        } as AttributeData)
-    );
+    const attributesData: AttributeData[] = [];
+    const otherAttributes = attrs.filter((attr) => !multiValueAttributeNames.includes(attr.name || ''));
+
+    multiValueAttributeNames.forEach((multiValueAttributeName) => {
+      const multiValueAttributes = attrs.filter(
+        (attr) => attr.name === multiValueAttributeName && attr.value !== undefined
+      );
+
+      if (multiValueAttributes.length > 0) {
+        const firstAttribute = multiValueAttributes[0];
+        const values = multiValueAttributes.map((attr) => attr.value) as string[];
+
+        attributesData.push(this.attributeToAttributeData({ ...firstAttribute, value: values }));
+      }
+    });
+
+    otherAttributes.forEach((attr) => {
+      attributesData.push(this.attributeToAttributeData(attr));
+    });
+
+    return attributesData;
   }
 
   private pageTabSectionToSectionData(ptSection: PageTabSection, parentAttributes: PtAttribute[] = []): SectionData {
@@ -91,7 +114,7 @@ export class PageTabToSubmissionService {
     const subsections = flatArray(ptSection.subsections || []);
     const contacts = authorsToContacts(subsections.filter((section) => !this.hasSubsections(section)));
     const featureSections = pageTabToSubmissionProtocols(contacts);
-    const keywords = extractKeywordsFromAttributes(ptSection.attributes || []);
+    const keywords = findAttributesByName('Keywords', ptSection.attributes || []);
 
     const features: FeatureData[] = [];
     const hasLinks = links.length > 0;

src/app/pages/submission/submission-shared/submission-to-pagetab.service.ts

@@ -14,7 +14,7 @@ import {
   submissionToPageTabProtocols
 } from './model/pagetab';
 import { isArrayEmpty, isStringDefined, isEqualIgnoringCase, isAttributeEmpty, isDefinedAndNotEmpty } from 'app/utils';
-import { AttributeData, Feature, Section, Submission } from './model/submission';
+import { AttributeData, Feature, Field, Fields, Section, Submission } from './model/submission';
 import { DEFAULT_TEMPLATE_NAME, SubmissionType } from './model/templates';
 import { Injectable } from '@angular/core';
 
@@ -192,24 +192,38 @@ export class SubmissionToPageTabService {
     return protocolSections.concat(section.sections.list().map((s) => this.sectionToPtSection(s, isSanitize)));
   }
 
-  private fieldsAsAttributes(section: Section, isSanitise: boolean): any[] {
-    return section.fields
-      .list()
-      .map((field) => {
-        if (field.valueType.isRich()) {
-          const fieldValue: string = field.value || '';
-          const [richValue] = fieldValue.split('@');
-
-          return {
-            name: field.name,
-            value: richValue,
-            valqual: [{ name: 'display', value: 'html' }]
-          } as PtAttribute;
-        }
+  private fieldAsAttribute(field: Field, displayType?: string): PtAttribute {
+    if (displayType) {
+      return {
+        name: field.name,
+        value: field.value,
+        valqual: [{ name: 'display', value: displayType }]
+      } as PtAttribute;
+    }
+
+    return { name: field.name, value: field.value } as PtAttribute;
+  }
+
+  private fieldsAsAttributes(section: Section, isSanitise: boolean): PtAttribute[] {
+    const fields: Field[] = section.fields.list();
+    const attributes: PtAttribute[] = [];
+
+    fields.forEach((field) => {
+      if (field.valueType.isRich()) {
+        const fieldValue: string = field.value || '';
+        const [richValue] = fieldValue.split('@');
+
+        attributes.push(this.fieldAsAttribute({ name: field.name, value: richValue } as Field, 'html'));
+      } else if (Array.isArray(field.value)) {
+        field.value.forEach((value) => {
+          attributes.push(this.fieldAsAttribute({ name: field.name, value } as Field));
+        });
+      } else {
+        attributes.push({ name: field.name, value: field.value } as Field);
+      }
+    });
 
-        return { name: field.name, value: field.value } as PtAttribute;
-      })
-      .filter((attr) => (isSanitise && !isAttributeEmpty(attr)) || !isSanitise);
+    return attributes.filter((attr) => (isSanitise && !isAttributeEmpty(attr)) || !isSanitise);
   }
 
   private sectionToPtSection(section: Section, isSanitise: boolean = false): PageTabSection {