add contact field list support (#1789, #2033)

CHANGELOG.rst

@@ -31,6 +31,7 @@ Added
     - Study plugin override via ISA-Tab comments (#1885)
     - Token auth support in study plugin IGV XML serving views (#1999, #2021)
     - Support for newlines in altamISA error messages (#2033)
+    - Support for performer and contact field values as list (#1789, #2033)
 - **Taskflowbackend**
     - ``TaskflowAPI.raise_submit_api_exception()`` helper (#1847)
 
@@ -65,7 +66,7 @@ Changed
     - Refactor ``SampleSheetAssayPluginPoint.get_assay_path()`` (#2016)
     - Return ``503`` in ``IrodsCollsCreateAPIView`` if project is locked (#1847)
     - Return ``503`` in ``IrodsDataRequestAcceptAPIView`` if project is locked (#1847)
-    - Remove length limitation from ``Process.performer`` (#1789, #1942, #2033)
+    - Remove length limit from ``Process.performer`` (#1789, #1942, #2033)
 - **Taskflowbackend**
     - Refactor task tests (#2002)
     - Unify user name parameter naming in flows (#1653)

docs_manual/source/app_samplesheets_edit.rst

@@ -103,7 +103,9 @@ Node Names
     orphaned files.
 Contacts
     Contact cells act as string cells with the following expected syntax:
-    ``Contact Name <[email protected]>``. The email can be omitted.
+    ``Contact Name <[email protected]>``. The email can be omitted. Multiple
+    contacts can be provided using the semicolon character as a delimter. For
+    example: ``Contact1 <c1.example.com>;Contact1 <c2.example.com>``.
 Dates
     Date cells also provide standard string editing but enforce the ISO 8601
     ``YYYY-MM-DD`` syntax.

docs_manual/source/sodar_release_notes.rst

@@ -19,6 +19,7 @@ Release for SODAR Core v1.0 upgrade, iRODS v4.3 upgrade and feature updates.
 - Add study plugin override via ISA-Tab comments
 - Add session control in Django settings and environment variables
 - Add token-based iRODS/IGV basic auth support for OIDC users
+- Add support for performer and contact field values as list
 - Update minimum supported iRODS version to v4.3.3
 - Update REST API versioning
 - Update REST API views for OpenAPI support

samplesheets/rendering.py

@@ -527,16 +527,22 @@ def _is_num(value):
 
             col_type = self._field_header[i]['col_type']
             if col_type == 'CONTACT':
+                contact_vals = []
+                for x in self._table_data:
+                    if not x[i].get('value'):
+                        contact_vals.append('')
+                    elif isinstance(x[i]['value'], list):
+                        contact_vals.append('; '.join(x[i]['value']))
+                    else:
+                        contact_vals.append(x[i]['value'])
                 max_cell_len = max(
                     [
                         (
-                            _get_length(
-                                re.findall(link_re, x[i]['value'])[0][0]
-                            )
-                            if re.findall(link_re, x[i].get('value'))
-                            else len(x[i].get('value') or '')
+                            _get_length(re.findall(link_re, x)[0][0])
+                            if re.findall(link_re, x)
+                            else len(x or '')
                         )
-                        for x in self._table_data
+                        for x in contact_vals
                     ]
                 )
             elif col_type == 'EXTERNAL_LINKS':  # Special case, count elements

samplesheets/tests/test_views_ajax.py

@@ -774,6 +774,35 @@ def test_post_performer(self):
         obj.refresh_from_db()
         self.assertEqual(obj.performer, value)
 
+    def test_post_performer_list(self):
+        """Test POST with process performer and list value"""
+        obj = Process.objects.filter(study=self.study, assay=None).first()
+        value = [
+            'Alice Example <[email protected]>',
+            'Bob Example <[email protected]>',
+        ]
+        self.values['updated_cells'].append(
+            {
+                'uuid': str(obj.sodar_uuid),
+                'header_name': 'Performer',
+                'header_type': 'performer',
+                'obj_cls': 'Process',
+                'value': value,
+            }
+        )
+        with self.login(self.user):
+            response = self.client.post(
+                reverse(
+                    'samplesheets:ajax_edit_cell',
+                    kwargs={'project': self.project.sodar_uuid},
+                ),
+                json.dumps(self.values),
+                content_type='application/json',
+            )
+        self.assertEqual(response.status_code, 200)
+        obj.refresh_from_db()
+        self.assertEqual(obj.performer, ';'.join(value))
+
     def test_post_perform_date(self):
         """Test POST with process perform date"""
         obj = Process.objects.filter(study=self.study, assay=None).first()

samplesheets/views_ajax.py

@@ -913,7 +913,10 @@ def _update_cell(self, node_obj, cell, save=False):
 
         # Performer (special case)
         elif header_type == 'performer':
-            node_obj.performer = cell['value']
+            if isinstance(cell['value'], list):
+                node_obj.performer = ';'.join(cell['value'])
+            else:
+                node_obj.performer = cell['value']
 
         # Perform date (special case)
         elif header_type == 'perform_date':

samplesheets/vueapp/src/components/renderers/DataCellRenderer.vue

@@ -22,16 +22,23 @@
         <span v-if="!params.app.editMode">
           <a :href="term.accession"
              :title="term.ontology_name"
-             target="_blank">{{ term.name }}</a><span v-if="termIndex + 1 < value.value.length">; </span>
+             target="_blank">{{ term.name }}</a><span v-if="termIndex < value.value.length - 1">; </span>
         </span>
         <span v-else>
-          {{ term.name }}<span v-if="termIndex + 1 < value.value.length">; </span>
+          {{ term.name }}<span v-if="termIndex < value.value.length - 1">; </span>
         </span>
       </span>
     </span>
     <!-- Contacts with email -->
     <span v-else-if="colType === 'CONTACT' && renderData">
-      <a :href="'mailto:' + renderData.email">{{ renderData.name }}</a>
+      <span v-for="(contact, index) in renderData" :key="index">
+        <span v-if="contact.email !== null">
+          <a :href="'mailto:' + contact.email">{{ contact.name }}</a><span v-if="index < renderData.length - 1">; </span>
+        </span>
+        <span v-else>
+          {{ contact.name }}<span v-if="index < renderData.length - 1">; </span>
+        </span>
+      </span>
     </span>
     <!-- External links -->
     <span v-else-if="colType === 'EXTERNAL_LINKS' && renderData">
@@ -121,11 +128,25 @@ export default Vue.extend({
       return this.params.colDef.headerName.toLowerCase()
     },
     getContact () {
-      // Return contact name and email
-      if (contactRegex.test(this.value.value) === true) {
-        const contactGroup = contactRegex.exec(this.value.value)
-        return { name: contactGroup[1], email: contactGroup[2] }
-      } else this.colType = null // Fall back to standard field
+      // Return contact name(s) and email(s)
+      const ret = []
+      if (this.value.value) {
+        // console.debug('value type = ' + typeof this.value.value)
+        let splitVal
+        if (typeof this.value.value === 'string') {
+          splitVal = this.value.value.split(';')
+        } else {
+          splitVal = this.value.value
+        }
+        for (let i = 0; i < splitVal.length; i++) {
+          if (contactRegex.test(splitVal[i]) === true) {
+            const contactGroup = contactRegex.exec(splitVal[i])
+            ret.push({ name: contactGroup[1].trim(), email: contactGroup[2] })
+          } else ret.push({ name: splitVal[i].trim(), email: null })
+        }
+      }
+      if (ret.length === 0) this.colType = null // Fall back to standard field
+      return ret
     },
     getExternalLinks () {
       // Return external links

samplesheets/vueapp/tests/unit/DataCellRenderer.spec.js

@@ -296,6 +296,25 @@ describe('DataCellRenderer.vue', () => {
     expect(cell.classes()).not.toContain('text-muted')
   })
 
+  it('renders contact cell with list value', async () => {
+    const table = copy(studyTablesOneCol).tables.study
+    table.field_header[0] = studyTables.tables.study.field_header[5]
+    table.table_data[0][0] = studyTables.tables.study.table_data[0][5]
+    table.table_data[0][0].value = 'John Doe <[email protected]>;Jane Doe'
+    const wrapper = mountSheetTable({ table: table })
+    await waitAG(wrapper)
+    await waitRAF()
+
+    const cell = wrapper.find('.sodar-ss-data-cell')
+    const cellData = cell.find('.sodar-ss-data')
+    expect(cellData.text()).toContain('John Doe;')
+    expect(cellData.text()).toContain('Jane Doe')
+    expect(cellData.find('a').exists()).toBe(true)
+    expect(cellData.find('a').attributes().href).toBe('mailto:[email protected]')
+    expect(cell.classes()).not.toContain('text-right')
+    expect(cell.classes()).not.toContain('text-muted')
+  })
+
   it('renders contact cell with bracket syntax', async () => {
     const table = copy(studyTablesOneCol).tables.study
     table.field_header[0] = studyTables.tables.study.field_header[5]