Multiple variant tags filtering

seqr/views/apis/summary_data_api.py

@@ -87,8 +87,11 @@ def saved_variants_page(request, tag):
     if tag == 'ALL':
         saved_variant_models = SavedVariant.objects.exclude(varianttag=None)
     else:
-        tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
-        saved_variant_models = SavedVariant.objects.filter(varianttag__variant_tag_type=tag_type)
+        tags = tag.split(';')
+        tag_type = VariantTagType.objects.filter(name__in=tags, project__isnull=True)
+        saved_variant_models = SavedVariant.objects.all()
+        for tt in tag_type:
+            saved_variant_models = saved_variant_models.filter(varianttag__variant_tag_type=tt).distinct()
 
     saved_variant_models = saved_variant_models.filter(family__project__guid__in=get_project_guids_user_can_view(request.user))
 

seqr/views/apis/summary_data_api_tests.py

@@ -134,6 +134,11 @@ def test_saved_variants_page(self):
         expected_variant_guids.add('SV0000002_1248367227_r0390_100')
         self.assertSetEqual(set(response.json()['savedVariantsByGuid'].keys()), expected_variant_guids)
 
+        multi_tag_url = reverse(saved_variants_page, args=['Review;Tier 1 - Novel gene and phenotype'])
+        response = self.client.get('{}?gene=ENSG00000135953'.format(multi_tag_url))
+        self.assertEqual(response.status_code, 200)
+        self.assertSetEqual(set(response.json()['savedVariantsByGuid'].keys()), {'SV0000001_2103343353_r0390_100'})
+
     def test_hpo_summary_data(self):
         url = reverse(hpo_summary_data, args=['HP:0002011'])
         self.check_require_login(url)
@@ -231,14 +236,18 @@ class LocalSummaryDataAPITest(AuthenticationTestCase, SummaryDataAPITest):
     MANAGER_VARIANT_GUID = 'SV0000006_1248367227_r0004_non'
 
 
-def assert_has_expected_calls(self, users, skip_group_call_idxs=None):
+def assert_has_expected_calls(self, users, skip_group_call_idxs=None, has_ws_access_level_call=False):
     calls = [mock.call(user) for user in users]
     self.mock_list_workspaces.assert_has_calls(calls)
     group_calls = [call for i, call in enumerate(calls) if i in skip_group_call_idxs] if skip_group_call_idxs else calls
     self.mock_get_groups.assert_has_calls(group_calls)
     self.mock_get_ws_acl.assert_not_called()
     self.mock_get_group_members.assert_not_called()
-    self.mock_get_ws_access_level.assert_not_called()
+    if has_ws_access_level_call:
+        self.mock_get_ws_access_level.assert_called_with(
+            self.analyst_user, 'my-seqr-billing', 'anvil-1kg project nåme with uniçøde')
+    else:
+        self.mock_get_ws_access_level.assert_not_called()
 
 # Test for permissions from AnVIL only
 class AnvilSummaryDataAPITest(AnvilAuthenticationTestCase, SummaryDataAPITest):
@@ -254,4 +263,4 @@ def test_saved_variants_page(self):
         super(AnvilSummaryDataAPITest, self).test_saved_variants_page()
         assert_has_expected_calls(self, [
             self.no_access_user, self.manager_user, self.manager_user, self.analyst_user, self.analyst_user
-        ], skip_group_call_idxs=[2])
+        ], skip_group_call_idxs=[2], has_ws_access_level_call=True)

ui/pages/Project/components/SavedVariants.jsx

@@ -15,6 +15,7 @@ import {
   VARIANT_PER_PAGE_FIELD,
   EXCLUDED_TAG_NAME,
   REVIEW_TAG_NAME,
+  TAG_URL_DELIMITER,
 } from 'shared/utils/constants'
 import UpdateButton from 'shared/components/buttons/UpdateButton'
 import { LargeMultiselect, Dropdown } from 'shared/components/form/Inputs'
@@ -142,12 +143,15 @@ class BaseProjectSavedVariants extends React.PureComponent {
       project.variantTagTypes.map(type => type.category).filter(category => category),
     )]
 
-    const isCategory = categoryOptions.includes(newTag)
-    updateTableField('categoryFilter')(isCategory ? newTag : null)
+    const lastNewTag = newTag.length > 0 ? newTag[newTag.length - 1] : null
+    const isCategory = categoryOptions.includes(lastNewTag)
+    const [firstTag, ...otherTag] = newTag
+    const updatedTag = firstTag === ALL_FILTER || categoryOptions.includes(firstTag) ? otherTag : newTag
+    updateTableField('categoryFilter')(isCategory ? lastNewTag : null)
     return getSavedVariantsLinkPath({
       projectGuid: project.projectGuid,
       analysisGroupGuid: match.params.analysisGroupGuid,
-      tag: !isCategory && newTag !== ALL_FILTER && newTag,
+      tag: !isCategory && lastNewTag !== ALL_FILTER && (updatedTag || []).join(TAG_URL_DELIMITER),
       familyGuid: match.params.familyGuid,
     })
   }

ui/pages/SummaryData/components/SavedVariants.jsx

@@ -7,19 +7,19 @@ import { Form, Button } from 'semantic-ui-react'
 
 import { getGenesById } from 'redux/selectors'
 import {
-  REVIEW_TAG_NAME,
-  KNOWN_GENE_FOR_PHENOTYPE_TAG_NAME,
   VARIANT_SORT_FIELD,
   VARIANT_PER_PAGE_FIELD,
   VARIANT_TAGGED_DATE_FIELD,
   SHOW_ALL,
+  TAG_URL_DELIMITER,
 } from 'shared/utils/constants'
 import { StyledForm } from 'shared/components/form/FormHelpers'
 import AwesomeBar from 'shared/components/page/AwesomeBar'
 import SavedVariants from 'shared/components/panel/variants/SavedVariants'
 import { HorizontalSpacer } from 'shared/components/Spacers'
 
 import { loadSavedVariants, updateAllProjectSavedVariantTable } from '../reducers'
+import { SUMMARY_PAGE_SAVED_VARIANT_TAGS } from '../constants'
 
 const GENE_SEARCH_CATEGORIES = ['genes']
 
@@ -29,29 +29,7 @@ const FILTER_FIELDS = [
   VARIANT_PER_PAGE_FIELD,
 ]
 
-const TAG_OPTIONS = [
-  'Tier 1 - Novel gene and phenotype',
-  'Tier 1 - Novel gene for known phenotype',
-  'Tier 1 - Phenotype expansion',
-  'Tier 1 - Phenotype not delineated',
-  'Tier 1 - Novel mode of inheritance',
-  'Tier 1 - Known gene, new phenotype',
-  'Tier 2 - Novel gene and phenotype',
-  'Tier 2 - Novel gene for known phenotype',
-  'Tier 2 - Phenotype expansion',
-  'Tier 2 - Phenotype not delineated',
-  'Tier 2 - Known gene, new phenotype',
-  KNOWN_GENE_FOR_PHENOTYPE_TAG_NAME,
-  REVIEW_TAG_NAME,
-  'Send for Sanger validation',
-  'Sanger validated',
-  'Sanger did not confirm',
-  'Confident AR one hit',
-  'Analyst high priority',
-  'seqr MME (old)',
-  'Submit to Clinvar',
-  'Share with KOMP',
-].map(name => ({
+const TAG_OPTIONS = SUMMARY_PAGE_SAVED_VARIANT_TAGS.map(name => ({
   value: name,
   text: name,
   key: name,
@@ -67,8 +45,12 @@ TAG_OPTIONS.push({
 
 const PAGE_URL = '/summary_data/saved_variants'
 
-const getUpdateTagUrl =
-  (selectedTag, match) => `${PAGE_URL}/${selectedTag}${match.params.gene ? `/${match.params.gene}` : ''}`
+const getUpdateTagUrl = (selectedTag, match) => {
+  const lastTag = selectedTag.length > 0 ? selectedTag[selectedTag.length - 1] : null
+  const [firstTag, ...otherTag] = selectedTag
+  const updatedTag = firstTag === SHOW_ALL ? otherTag : lastTag !== SHOW_ALL && selectedTag
+  return `${PAGE_URL}/${(updatedTag || [SHOW_ALL]).join(TAG_URL_DELIMITER)}${match.params.gene ? `/${match.params.gene}` : ''}`
+}
 
 const getGeneHref = tag => selectedGene => `${PAGE_URL}/${tag || SHOW_ALL}/${selectedGene.key}`
 

ui/pages/SummaryData/constants.js

@@ -1,9 +1,7 @@
-/* eslint-disable import/prefer-default-export */
-
 import React from 'react'
 import { Link } from 'react-router-dom'
 
-import { successStoryTypeDisplay } from 'shared/utils/constants'
+import { successStoryTypeDisplay, KNOWN_GENE_FOR_PHENOTYPE_TAG_NAME, REVIEW_TAG_NAME } from 'shared/utils/constants'
 
 const formatIDLink =
   row => <Link to={`/project/${row.project_guid}/family_page/${row.family_guid}`} target="_blank">{row.family_id}</Link>
@@ -20,3 +18,27 @@ export const SUCCESS_STORY_COLUMNS = [
   { name: 'success_story', content: 'Success Story', style: { minWidth: '564px' } },
   { name: 'discovery_tags', content: 'Discovery Tags', format: formatDiscoveryTags, noFormatExport: true, style: { minWidth: '400px' } },
 ]
+
+export const SUMMARY_PAGE_SAVED_VARIANT_TAGS = [
+  'Tier 1 - Novel gene and phenotype',
+  'Tier 1 - Novel gene for known phenotype',
+  'Tier 1 - Phenotype expansion',
+  'Tier 1 - Phenotype not delineated',
+  'Tier 1 - Novel mode of inheritance',
+  'Tier 1 - Known gene, new phenotype',
+  'Tier 2 - Novel gene and phenotype',
+  'Tier 2 - Novel gene for known phenotype',
+  'Tier 2 - Phenotype expansion',
+  'Tier 2 - Phenotype not delineated',
+  'Tier 2 - Known gene, new phenotype',
+  KNOWN_GENE_FOR_PHENOTYPE_TAG_NAME,
+  REVIEW_TAG_NAME,
+  'Send for Sanger validation',
+  'Sanger validated',
+  'Sanger did not confirm',
+  'Confident AR one hit',
+  'Analyst high priority',
+  'seqr MME (old)',
+  'Submit to Clinvar',
+  'Share with KOMP',
+]

ui/pages/SummaryData/reducers.js

@@ -2,7 +2,7 @@ import { combineReducers } from 'redux'
 
 import { loadingReducer, createSingleValueReducer, createSingleObjectReducer } from 'redux/utils/reducerFactories'
 import { RECEIVE_DATA, REQUEST_SAVED_VARIANTS } from 'redux/utils/reducerUtils'
-import { SHOW_ALL, SORT_BY_XPOS } from 'shared/utils/constants'
+import { SHOW_ALL, SORT_BY_XPOS, TAG_URL_DELIMITER } from 'shared/utils/constants'
 import { HttpRequestHelper } from 'shared/utils/httpRequestHelper'
 
 // action creators and reducers in one file as suggested by https://github.com/erikras/ducks-modular-redux
@@ -43,8 +43,9 @@ export const loadSuccessStory = successStoryTypes => (dispatch) => {
 
 export const loadSavedVariants = ({ tag, gene = '' }) => (dispatch, getState) => {
   // Do not load if already loaded
+  const stateKey = `${tag ? tag.split(TAG_URL_DELIMITER).sort().join(TAG_URL_DELIMITER) : ''}${gene}`
   if (tag) {
-    if (getState().savedVariantTags[tag]) {
+    if (getState().savedVariantTags[stateKey]) {
       return
     }
   } else if (!gene) {
@@ -57,7 +58,7 @@ export const loadSavedVariants = ({ tag, gene = '' }) => (dispatch, getState) =>
       if (tag && !gene) {
         dispatch({
           type: RECEIVE_SAVED_VARIANT_TAGS,
-          updates: { [tag]: true },
+          updates: { [stateKey]: true },
         })
       }
       dispatch({ type: RECEIVE_DATA, updatesById: responseJson })

ui/shared/components/panel/variants/SavedVariants.jsx

@@ -8,6 +8,7 @@ import { getSavedVariantsIsLoading, getSavedVariantsLoadingError } from 'redux/s
 import {
   DISCOVERY_CATEGORY_NAME,
   VARIANT_PAGINATION_FIELD,
+  TAG_URL_DELIMITER,
 } from 'shared/utils/constants'
 
 import ExportTableButton from '../../buttons/ExportTableButton'
@@ -65,7 +66,7 @@ class SavedVariants extends React.PureComponent {
 
   navigateToTag = (e, data) => {
     const { history, getUpdateTagUrl, match } = this.props
-    history.push(getUpdateTagUrl(data.value, match))
+    history.push(getUpdateTagUrl(data.value.length > 0 ? data.value : [ALL_FILTER], match))
   }
 
   showAllFilters = () => {
@@ -81,9 +82,10 @@ class SavedVariants extends React.PureComponent {
     const { showAllFilters } = this.state
     const { familyGuid, variantGuid, tag } = match.params
 
-    const appliedTagCategoryFilter = tag || (variantGuid ? null : (tableState.categoryFilter || ALL_FILTER))
+    const tags = tag ? tag.split(TAG_URL_DELIMITER) : tag
+    const appliedTagCategoryFilter = tags || (variantGuid ? [] : [(tableState.categoryFilter || ALL_FILTER)])
 
-    let shownFilters = (discoveryFilters && appliedTagCategoryFilter === DISCOVERY_CATEGORY_NAME) ?
+    let shownFilters = (discoveryFilters && appliedTagCategoryFilter === [DISCOVERY_CATEGORY_NAME]) ?
       discoveryFilters : filters
     const hasHiddenFilters = !showAllFilters && shownFilters.length > MAX_FILTERS
     if (hasHiddenFilters) {
@@ -111,6 +113,7 @@ class SavedVariants extends React.PureComponent {
               {`Showing ${shownSummary} ${filteredVariantsCount}  `}
               <Dropdown
                 inline
+                multiple
                 options={tagOptions}
                 value={appliedTagCategoryFilter}
                 onChange={this.navigateToTag}

ui/shared/components/panel/variants/selectors.js

@@ -12,6 +12,7 @@ import {
   VARIANT_SORT_LOOKUP,
   SHOW_ALL,
   VARIANT_EXPORT_DATA,
+  TAG_URL_DELIMITER,
 } from 'shared/utils/constants'
 import {
   getVariantTagsByGuid, getVariantNotesByGuid, getSavedVariantsByGuid, getAnalysisGroupsByGuid, getGenesById, getUser,
@@ -135,8 +136,12 @@ export const getPairedSelectedSavedVariants = createSelector(
     } else if (tag === MME_TAG_NAME) {
       pairedVariants = matchingVariants(pairedVariants, ({ mmeSubmissions = [] }) => mmeSubmissions.length)
     } else if (tag && tag !== SHOW_ALL) {
+      const tags = tag.split(TAG_URL_DELIMITER)
       pairedVariants = matchingVariants(
-        pairedVariants, ({ tagGuids }) => tagGuids.some(tagGuid => tagsByGuid[tagGuid].name === tag),
+        pairedVariants, ({ tagGuids }) => {
+          const tagNames = tagGuids.map(tagGuid => tagsByGuid[tagGuid].name)
+          return tags.every(tagName => tagNames.includes(tagName))
+        },
       )
     } else if (!(familyGuid || analysisGroupGuid)) {
       pairedVariants = matchingVariants(pairedVariants, ({ tagGuids }) => tagGuids.length)

ui/shared/utils/constants.js

@@ -1042,6 +1042,8 @@ export const KNOWN_GENE_FOR_PHENOTYPE_TAG_NAME = 'Known gene for phenotype'
 export const DISCOVERY_CATEGORY_NAME = 'CMG Discovery Tags'
 export const MME_TAG_NAME = 'MME Submission'
 
+export const TAG_URL_DELIMITER = ';'
+
 export const SORT_BY_FAMILY_GUID = 'FAMILY_GUID'
 export const SORT_BY_XPOS = 'XPOS'
 const SORT_BY_PATHOGENICITY = 'PATHOGENICITY'