Merge pull request #3502 from broadinstitute/multiple-variant-tag-fil…

…tering

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_types = VariantTagType.objects.filter(name__in=tags, project__isnull=True)
+        saved_variant_models = SavedVariant.objects.all()
+        for tt in tag_types:
+            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)
@@ -238,7 +243,7 @@ def assert_has_expected_calls(self, users, skip_group_call_idxs=None):
     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()
+
 
 # Test for permissions from AnVIL only
 class AnvilSummaryDataAPITest(AnvilAuthenticationTestCase, SummaryDataAPITest):
@@ -249,9 +254,12 @@ class AnvilSummaryDataAPITest(AnvilAuthenticationTestCase, SummaryDataAPITest):
     def test_mme_details(self, *args):
         super(AnvilSummaryDataAPITest, self).test_mme_details(*args)
         assert_has_expected_calls(self, [self.no_access_user, self.manager_user, self.analyst_user])
+        self.mock_get_ws_access_level.assert_not_called()
 
     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])
+        self.mock_get_ws_access_level.assert_called_with(
+            self.analyst_user, 'my-seqr-billing', 'anvil-1kg project nåme with uniçøde')

ui/pages/Project/components/SavedVariants.jsx

@@ -15,6 +15,8 @@ import {
   VARIANT_PER_PAGE_FIELD,
   EXCLUDED_TAG_NAME,
   REVIEW_TAG_NAME,
+  DISCOVERY_CATEGORY_NAME,
+  SHOW_ALL,
 } from 'shared/utils/constants'
 import UpdateButton from 'shared/components/buttons/UpdateButton'
 import { LargeMultiselect, Dropdown } from 'shared/components/form/Inputs'
@@ -24,7 +26,7 @@ import { TAG_FORM_FIELD } from '../constants'
 import { loadSavedVariants, updateSavedVariantTable } from '../reducers'
 import {
   getCurrentProject, getProjectTagTypeOptions, getTaggedVariantsByFamily, getProjectVariantSavedByOptions,
-  getSavedVariantTagTypeCounts, getSavedVariantTagTypeCountsByFamily,
+  getSavedVariantTagTypeCounts, getSavedVariantTagTypeCountsByFamily, getSavedVariantTableState,
 } from '../selectors'
 import VariantTagTypeBar, { getSavedVariantsLinkPath } from './VariantTagTypeBar'
 import SelectSavedVariantsTable, { TAG_COLUMN, VARIANT_POS_COLUMN, GENES_COLUMN } from './SelectSavedVariantsTable'
@@ -37,8 +39,6 @@ const LabelLink = styled(Link)`
   }
 `
 
-const ALL_FILTER = 'ALL'
-
 const mapSavedByInputStateToProps = state => ({
   options: getProjectVariantSavedByOptions(state),
 })
@@ -134,6 +134,7 @@ class BaseProjectSavedVariants extends React.PureComponent {
     tagTypeCounts: PropTypes.object,
     updateTableField: PropTypes.func,
     loadProjectSavedVariants: PropTypes.func,
+    categoryFilter: PropTypes.string,
   }
 
   getUpdateTagUrl = (newTag) => {
@@ -147,7 +148,7 @@ class BaseProjectSavedVariants extends React.PureComponent {
     return getSavedVariantsLinkPath({
       projectGuid: project.projectGuid,
       analysisGroupGuid: match.params.analysisGroupGuid,
-      tag: !isCategory && newTag !== ALL_FILTER && newTag,
+      tag: !isCategory && newTag !== SHOW_ALL && newTag,
       familyGuid: match.params.familyGuid,
     })
   }
@@ -191,7 +192,7 @@ class BaseProjectSavedVariants extends React.PureComponent {
       })
       return acc
     }, [{
-      value: ALL_FILTER,
+      value: SHOW_ALL,
       text: 'All Saved',
       content: (
         <LabelLink
@@ -234,14 +235,15 @@ class BaseProjectSavedVariants extends React.PureComponent {
   }
 
   render() {
-    const { project, analysisGroup, loadProjectSavedVariants, ...props } = this.props
-    const { familyGuid } = props.match.params
+    const { project, analysisGroup, loadProjectSavedVariants, categoryFilter, ...props } = this.props
+    const { familyGuid, tag, variantGuid } = props.match.params
+    const appliedTagCategoryFilter = tag || (variantGuid ? null : (categoryFilter || SHOW_ALL))
 
     return (
       <SavedVariants
         tagOptions={this.tagOptions()}
-        filters={NON_DISCOVERY_FILTER_FIELDS}
-        discoveryFilters={FILTER_FIELDS}
+        filters={appliedTagCategoryFilter === DISCOVERY_CATEGORY_NAME ? FILTER_FIELDS : NON_DISCOVERY_FILTER_FIELDS}
+        selectedTag={appliedTagCategoryFilter}
         additionalFilter={
           (project.canEdit && familyGuid) ? <LinkSavedVariants familyGuid={familyGuid} {...props} /> : null
         }
@@ -262,6 +264,7 @@ const mapStateToProps = (state, ownProps) => ({
   tagTypeCounts: ownProps.match.params.familyGuid ?
     getSavedVariantTagTypeCountsByFamily(state)[ownProps.match.params.familyGuid] :
     getSavedVariantTagTypeCounts(state, ownProps),
+  categoryFilter: getSavedVariantTableState(state)?.categoryFilter,
 })
 
 const mapDispatchToProps = dispatch => ({

ui/pages/Project/reducers.js

@@ -86,7 +86,7 @@ export const loadSavedVariants = ({ familyGuids, variantGuid, tag }) => (dispatc
   // Do not load if already loaded
   let expectedFamilyGuids
   if (variantGuid) {
-    if (state.savedVariantsByGuid[variantGuid]) {
+    if (variantGuid.split(',').every(g => state.savedVariantsByGuid[g])) {
       return
     }
     url = `${url}/${variantGuid}`

ui/pages/Project/selectors.js

@@ -63,6 +63,7 @@ export const getMmeSubmissionsLoading = state => state.mmeSubmissionsLoading.isL
 export const getSamplesLoading = state => state.samplesLoading.isLoading
 export const getTagTypesLoading = state => state.tagTypesLoading.isLoading
 export const getFamilyTagTypeCounts = state => state.familyTagTypeCounts
+export const getSavedVariantTableState = state => state.savedVariantTableState
 const getFamiliesTableFiltersByProject = state => state.familyTableFilterState
 
 export const getCurrentProject = createSelector(

ui/pages/SummaryData/components/SavedVariants.jsx

@@ -58,17 +58,10 @@ const TAG_OPTIONS = [
   label: { empty: true, circular: true, style: { backgroundColor: 'white' } },
 }))
 
-TAG_OPTIONS.push({
-  value: SHOW_ALL,
-  text: 'All',
-  key: 'all',
-  label: { empty: true, circular: true, style: { backgroundColor: 'white' } },
-})
-
 const PAGE_URL = '/summary_data/saved_variants'
 
 const getUpdateTagUrl =
-  (selectedTag, match) => `${PAGE_URL}/${selectedTag}${match.params.gene ? `/${match.params.gene}` : ''}`
+  (selectedTag, match) => `${PAGE_URL}/${(selectedTag || []).join(';') || SHOW_ALL}${match.params.gene ? `/${match.params.gene}` : ''}`
 
 const getGeneHref = tag => selectedGene => `${PAGE_URL}/${tag || SHOW_ALL}/${selectedGene.key}`
 
@@ -82,6 +75,9 @@ const BaseSavedVariants = React.memo(({ loadVariants, geneDetail, ...props }) =>
       filters={FILTER_FIELDS}
       getUpdateTagUrl={getUpdateTagUrl}
       loadVariants={loadVariants}
+      summaryFullWidth
+      multiple
+      selectedTag={tag && tag.split(';').filter(t => t !== SHOW_ALL)}
       additionalFilter={
         <StyledForm inline>
           <Form.Field

ui/pages/SummaryData/reducers.js

@@ -43,8 +43,9 @@ export const loadSuccessStory = successStoryTypes => (dispatch) => {
 
 export const loadSavedVariants = ({ tag, gene = '' }) => (dispatch, getState) => {
   // Do not load if already loaded
-  if (tag) {
-    if (getState().savedVariantTags[tag]) {
+  if (tag && tag !== SHOW_ALL) {
+    const loadedTags = getState().savedVariantTags
+    if (loadedTags[tag] || tag.split(';').some(t => loadedTags[t])) {
       return
     }
   } else if (!gene) {
@@ -86,7 +87,6 @@ export const reducers = {
   savedVariantTags: createSingleObjectReducer(RECEIVE_SAVED_VARIANT_TAGS),
   externalAnalysisUploadStats: createSingleValueReducer(RECEIVE_EXTERNAL_ANALYSIS_UPLOAD_STATS, {}),
   allProjectSavedVariantTableState: createSingleObjectReducer(UPDATE_ALL_PROJECT_SAVED_VARIANT_TABLE_STATE, {
-    categoryFilter: SHOW_ALL,
     sort: SORT_BY_XPOS,
     page: 1,
     recordsPerPage: 25,

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

@@ -5,10 +5,7 @@ import { Grid, Dropdown, Message } from 'semantic-ui-react'
 import styled from 'styled-components'
 
 import { getSavedVariantsIsLoading, getSavedVariantsLoadingError } from 'redux/selectors'
-import {
-  DISCOVERY_CATEGORY_NAME,
-  VARIANT_PAGINATION_FIELD,
-} from 'shared/utils/constants'
+import { VARIANT_PAGINATION_FIELD } from 'shared/utils/constants'
 
 import ExportTableButton from '../../buttons/ExportTableButton'
 import StateChangeForm from '../../form/StateChangeForm'
@@ -22,7 +19,6 @@ import {
   getVisibleSortedSavedVariants,
 } from './selectors'
 
-const ALL_FILTER = 'ALL'
 const MAX_FILTERS = 4
 
 const ControlsRow = styled(Grid.Row)`
@@ -43,8 +39,8 @@ class SavedVariants extends React.PureComponent {
     match: PropTypes.object,
     history: PropTypes.object,
     tagOptions: PropTypes.arrayOf(PropTypes.object),
+    selectedTag: PropTypes.any, // eslint-disable-line react/forbid-prop-types
     filters: PropTypes.arrayOf(PropTypes.object),
-    discoveryFilters: PropTypes.arrayOf(PropTypes.object),
     loading: PropTypes.bool,
     error: PropTypes.string,
     variantsToDisplay: PropTypes.arrayOf(PropTypes.any),
@@ -59,6 +55,8 @@ class SavedVariants extends React.PureComponent {
     loadVariants: PropTypes.func,
     additionalFilter: PropTypes.node,
     tableSummaryComponent: PropTypes.elementType,
+    multiple: PropTypes.bool,
+    summaryFullWidth: PropTypes.bool,
   }
 
   state = { showAllFilters: false }
@@ -74,17 +72,14 @@ class SavedVariants extends React.PureComponent {
 
   render() {
     const {
-      match, tableState, filters, discoveryFilters, totalPages, variantsToDisplay, totalVariantsCount, firstRecordIndex,
+      match, tableState, filters, totalPages, variantsToDisplay, totalVariantsCount, firstRecordIndex,
       tableSummaryComponent, loading, filteredVariantsCount, tagOptions, additionalFilter, updateTableField,
-      variantExportConfig, loadVariants, error,
+      variantExportConfig, loadVariants, error, multiple, summaryFullWidth, selectedTag,
     } = this.props
     const { showAllFilters } = this.state
-    const { familyGuid, variantGuid, tag } = match.params
-
-    const appliedTagCategoryFilter = tag || (variantGuid ? null : (tableState.categoryFilter || ALL_FILTER))
+    const { familyGuid, variantGuid } = match.params
 
-    let shownFilters = (discoveryFilters && appliedTagCategoryFilter === DISCOVERY_CATEGORY_NAME) ?
-      discoveryFilters : filters
+    let shownFilters = filters
     const hasHiddenFilters = !showAllFilters && shownFilters.length > MAX_FILTERS
     if (hasHiddenFilters) {
       shownFilters = shownFilters.slice(0, MAX_FILTERS)
@@ -107,18 +102,19 @@ class SavedVariants extends React.PureComponent {
         })}
         {!loading && (
           <ControlsRow>
-            <Grid.Column width={4}>
+            <Grid.Column width={summaryFullWidth ? 16 : 4}>
               {`Showing ${shownSummary} ${filteredVariantsCount}  `}
               <Dropdown
                 inline
+                multiple={multiple}
                 options={tagOptions}
-                value={appliedTagCategoryFilter}
+                value={selectedTag}
                 onChange={this.navigateToTag}
               />
               {` variants ${allShown ? '' : `(${totalVariantsCount} total)`}`}
 
             </Grid.Column>
-            <Grid.Column width={12} floated="right" textAlign="right">
+            <Grid.Column width={summaryFullWidth ? 16 : 12} floated="right" textAlign="right">
               {additionalFilter}
               {!variantGuid && (
                 <StateChangeForm

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

@@ -65,29 +65,78 @@ const matchingVariants = (variants, matchFunc) => variants.filter(o => (Array.is
 // sorts manual variants to top of list, as manual variants are missing all populations
 const sortCompHet = (a, b) => (a.populations ? 1 : 0) - (b.populations ? 1 : 0)
 
-export const getPairedSelectedSavedVariants = createSelector(
-  getSavedVariantsByGuid,
+const getProjectSavedVariantsSelection = createSelector(
   (state, props) => props.match.params,
   getFamiliesByGuid,
   getAnalysisGroupsByGuid,
-  (state, props) => (props.project || {}).projectGuid,
+  state => state.currentProjectGuid,
   getVariantTagsByGuid,
-  getVariantNotesByGuid,
-  (savedVariants, { tag, gene, familyGuid, analysisGroupGuid, variantGuid }, familiesByGuid, analysisGroupsByGuid,
-    projectGuid, tagsByGuid, notesByGuid) => {
-    let variants = Object.values(savedVariants)
-    if (variantGuid) {
-      variants = variants.filter(o => variantGuid.split(',').includes(o.variantGuid))
-      return variants.length > 1 ? [variants] : variants
+  ({ tag, familyGuid, analysisGroupGuid, variantGuid }, familiesByGuid, analysisGroupsByGuid,
+    projectGuid, tagsByGuid) => {
+    if (!projectGuid) {
+      return null
     }
 
-    if (analysisGroupGuid && analysisGroupsByGuid[analysisGroupGuid]) {
+    let variantFilter
+    if (variantGuid) {
+      variantFilter = o => variantGuid.split(',').includes(o.variantGuid)
+    } else if (analysisGroupGuid && analysisGroupsByGuid[analysisGroupGuid]) {
       const analysisGroupFamilyGuids = analysisGroupsByGuid[analysisGroupGuid].familyGuids
-      variants = variants.filter(o => o.familyGuids.some(fg => analysisGroupFamilyGuids.includes(fg)))
+      variantFilter = o => o.familyGuids.some(fg => analysisGroupFamilyGuids.includes(fg))
     } else if (familyGuid) {
-      variants = variants.filter(o => o.familyGuids.includes(familyGuid))
-    } else if (projectGuid) {
-      variants = variants.filter(o => o.familyGuids.some(fg => familiesByGuid[fg].projectGuid === projectGuid))
+      variantFilter = o => o.familyGuids.includes(familyGuid)
+    } else {
+      variantFilter = o => o.familyGuids.some(fg => familiesByGuid[fg].projectGuid === projectGuid)
+    }
+
+    const pairedFilters = []
+    if (tag === NOTE_TAG_NAME) {
+      pairedFilters.push(({ noteGuids }) => noteGuids.length)
+    } else if (tag === MME_TAG_NAME) {
+      pairedFilters.push(({ mmeSubmissions = [] }) => mmeSubmissions.length)
+    } else if (tag && tag !== SHOW_ALL) {
+      pairedFilters.push(({ tagGuids }) => tagGuids.some(tagGuid => tagsByGuid[tagGuid].name === tag))
+    } else if (!(familyGuid || analysisGroupGuid)) {
+      pairedFilters.push(({ tagGuids }) => tagGuids.length)
+    }
+
+    return [variantFilter, pairedFilters]
+  },
+)
+
+const getSummaryDataSavedVariantsSelection = createSelector(
+  (state, props) => props.match.params,
+  state => state.currentProjectGuid,
+  getVariantTagsByGuid,
+  ({ tag, gene }, projectGuid, tagsByGuid) => {
+    if (projectGuid) {
+      return null
+    }
+    const pairedFilters = []
+    if (gene) {
+      pairedFilters.push(({ transcripts }) => gene in (transcripts || {}))
+    } if (tag && tag !== SHOW_ALL) {
+      const tags = tag.split(';')
+      pairedFilters.push(({ tagGuids }) => tags.every(t => tagGuids.some(tagGuid => tagsByGuid[tagGuid].name === t)))
+    }
+
+    const variantFilter = tag || gene ? null : () => false
+    return [variantFilter, pairedFilters]
+  },
+)
+
+export const getPairedSelectedSavedVariants = createSelector(
+  getProjectSavedVariantsSelection,
+  getSummaryDataSavedVariantsSelection,
+  getSavedVariantsByGuid,
+  getVariantTagsByGuid,
+  getVariantNotesByGuid,
+  (projectVariants, summaryDataVariants, savedVariants, tagsByGuid, notesByGuid) => {
+    const [variantFilter, pairedFilters] = projectVariants || summaryDataVariants
+
+    let variants = Object.values(savedVariants)
+    if (variantFilter) {
+      variants = variants.filter(variantFilter)
     }
 
     const selectedVariantsByGuid = variants.reduce((acc, variant) => ({ ...acc, [variant.variantGuid]: variant }), {})
@@ -130,21 +179,9 @@ export const getPairedSelectedSavedVariants = createSelector(
       return acc
     }, [])
 
-    if (tag === NOTE_TAG_NAME) {
-      pairedVariants = matchingVariants(pairedVariants, ({ noteGuids }) => noteGuids.length)
-    } else if (tag === MME_TAG_NAME) {
-      pairedVariants = matchingVariants(pairedVariants, ({ mmeSubmissions = [] }) => mmeSubmissions.length)
-    } else if (tag && tag !== SHOW_ALL) {
-      pairedVariants = matchingVariants(
-        pairedVariants, ({ tagGuids }) => tagGuids.some(tagGuid => tagsByGuid[tagGuid].name === tag),
-      )
-    } else if (!(familyGuid || analysisGroupGuid)) {
-      pairedVariants = matchingVariants(pairedVariants, ({ tagGuids }) => tagGuids.length)
-    }
-
-    if (gene) {
-      pairedVariants = matchingVariants(pairedVariants, ({ transcripts }) => gene in (transcripts || {}))
-    }
+    pairedFilters.forEach((pairedFilter) => {
+      pairedVariants = matchingVariants(pairedVariants, pairedFilter)
+    })
 
     return pairedVariants
   },