Merge pull request #4457 from broadinstitute/dev

Dev
broadinstitute · Oct 28, 2024 · 424715b · 424715b
2 parents 77e8464 + 5b5551a
commit 424715b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,9 @@
 
 ## dev
 
+## 10/28/24
+* Update RNA Tissue Type choices (REQUIRES DB MIGRATION)
+
 ## 9/19/24
 * Update Biosample choices (REQUIRES DB MIGRATION)
 * Add support for Azure OAuth

diff --git a/seqr/migrations/0077_alter_rnasample_tissue_type.py b/seqr/migrations/0077_alter_rnasample_tissue_type.py
@@ -0,0 +1,18 @@
+# Generated by Django 4.2.16 on 2024-10-27 17:48
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('seqr', '0076_alter_individual_sex'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='rnasample',
+            name='tissue_type',
+            field=models.CharField(choices=[('WB', 'whole_blood'), ('F', 'fibroblasts'), ('M', 'muscle'), ('L', 'lymphocytes'), ('A', 'airway_cultured_epithelium'), ('B', 'brain')], max_length=2),
+        ),
+    ]
diff --git a/seqr/models.py b/seqr/models.py
@@ -762,6 +762,7 @@ class RnaSample(ModelWithGUID):
         ('M', 'muscle'),
         ('L', 'lymphocytes'),
         ('A', 'airway_cultured_epithelium'),
+        ('B', 'brain'),
     )
 
     individual = models.ForeignKey('Individual', on_delete=models.PROTECT)

diff --git a/seqr/views/apis/project_api.py b/seqr/views/apis/project_api.py
@@ -187,7 +187,7 @@ def project_page_data(request, project_guid):
     'parental_ids': {
         'agg': ArrayAgg(JSONObject(**{k: k for k in ['id', 'guid', 'father_id', 'mother_id']})),
         'format': lambda parental_ids, id_guid_map: [
-            {'paternalGuid': id_guid_map.get(p['father_id']), 'maternalGuid': id_guid_map.get(p['mother_id'])}
+            {'paternalGuid': id_guid_map.get(p['father_id']), 'maternalGuid': id_guid_map.get(p['mother_id']), 'individualGuid': p['guid']}
             for p in parental_ids if p['father_id'] or p['mother_id']
         ],
         'response_key': 'parents',

diff --git a/seqr/views/apis/project_api_tests.py b/seqr/views/apis/project_api_tests.py
@@ -402,7 +402,7 @@ def test_project_families(self):
         self.assertTrue(family_1['hasRequiredMetadata'])
         self.assertFalse(family_3['hasRequiredMetadata'])
         self.assertFalse(empty_family['hasRequiredMetadata'])
-        self.assertListEqual(family_1['parents'], [{'maternalGuid': 'I000003_na19679', 'paternalGuid': 'I000002_na19678'}])
+        self.assertListEqual(family_1['parents'], [{'maternalGuid': 'I000003_na19679', 'paternalGuid': 'I000002_na19678', 'individualGuid': 'I000001_na19675'}])
         self.assertListEqual(family_3['parents'], [])
         self.assertListEqual(empty_family['parents'], [])
         self.assertEqual(family_1['hasPhenotypePrioritization'], True)

diff --git a/ui/pages/Project/components/FamilyTable/IndividualRow.jsx b/ui/pages/Project/components/FamilyTable/IndividualRow.jsx
@@ -495,9 +495,9 @@ const EDIT_INDIVIDUAL_FIELDS = [INDIVIDUAL_FIELD_SEX, INDIVIDUAL_FIELD_AFFECTED]
 )))
 
 const mapIgvOptionsStateToProps = (state) => {
-  const { namespace, name } = getCurrentProject(state)
+  const { workspaceNamespace, workspaceName } = getCurrentProject(state)
   return {
-    url: `/api/anvil_workspace/${namespace}/${name}/get_igv_options`,
+    url: `/api/anvil_workspace/${workspaceNamespace}/${workspaceName}/get_igv_options`,
   }
 }
 

diff --git a/ui/pages/Project/components/ProjectOverview.jsx b/ui/pages/Project/components/ProjectOverview.jsx
@@ -26,8 +26,8 @@ import { updateProjectMmeContact, loadMmeSubmissions, updateAnvilWorkspace } fro
 import {
   getCurrentProject,
   getAnalysisStatusCounts,
-  getProjectAnalysisGroupFamilyIndividualCounts,
-  getProjectAnalysisGroupDataLoadedFamilyIndividualCounts,
+  getProjectAnalysisGroupFamilySizeHistogram,
+  getProjectAnalysisGroupDataLoadedFamilySizeHistogram,
   getProjectAnalysisGroupSamplesByTypes,
   getProjectAnalysisGroupMmeSubmissionDetails,
   getMmeSubmissionsLoading,
@@ -46,17 +46,15 @@ const FAMILY_SIZE_LABELS = {
 }
 
 const FAMILY_STRUCTURE_SIZE_LABELS = {
-  2: plural => ` duo${plural ? 's' : ''}`,
-  3: plural => ` trio${plural ? 's' : ''}`,
-  4: plural => ` quad${plural ? 's' : ''}`,
-  5: plural => ` trio${plural ? 's' : ''}+`,
+  2: 'duo',
+  3: 'trio',
+  4: 'quad',
 }
 
 const FAMILY_STRUCTURE_HOVER = {
   2: 'A family with one parent and one child',
   3: 'A family with two parents and one child',
   4: 'A family with two parents and two children',
-  5: 'A family with two parents and three or more other family members',
 }
 
 const SAMPLE_TYPE_LOOKUP = SAMPLE_TYPE_OPTIONS.reduce(
@@ -160,19 +158,24 @@ const MatchmakerSubmissionOverview = connect(
   mapMatchmakerSubmissionsStateToProps, mapDispatchToProps,
 )(BaseMatchmakerSubmissionOverview)
 
-const FamiliesIndividuals = React.memo(({ canEdit, hasCaseReview, familyCounts, user, title }) => {
-  const familySizeHistogram = familyCounts.reduce((acc, { size, numParents }) => {
-    const familySize = Math.min(size, 5)
-    const sizeAcc = acc[familySize] || { total: 0, withParents: 0 }
-    sizeAcc.total += 1
-    if (familySize === 2 && numParents) {
-      sizeAcc.withParents += 1
-    } else if (familySize > 2 && numParents === 2) {
-      sizeAcc.withParents += 1
+const MAX_FAMILY_HIST_SIZE = 5
+
+const FamiliesIndividuals = React.memo(({ canEdit, hasCaseReview, familySizes, user, title }) => {
+  const familiesCount = Object.values(familySizes).reduce((acc, { total }) => acc + total, 0)
+  const individualsCount = Object.entries(familySizes).reduce((acc, [size, { total }]) => acc + (size * total), 0)
+  const familySizeHistogram = Object.entries(familySizes).reduce((acc, [size, counts]) => {
+    if (size <= MAX_FAMILY_HIST_SIZE) {
+      return { ...acc, [size]: counts }
+    }
+    if (!acc[MAX_FAMILY_HIST_SIZE]) {
+      acc[MAX_FAMILY_HIST_SIZE] = { total: 0, withParents: 0, trioPlus: 0, quadPlus: 0 }
     }
-    return { ...acc, [familySize]: sizeAcc }
+    acc[MAX_FAMILY_HIST_SIZE].total += counts.total
+    acc[MAX_FAMILY_HIST_SIZE].trioPlus += counts.trioPlus
+    acc[MAX_FAMILY_HIST_SIZE].quadPlus += acc[MAX_FAMILY_HIST_SIZE].withParents + counts.withParents + counts.quadPlus
+    acc[MAX_FAMILY_HIST_SIZE].withParents = 0
+    return acc
   }, {})
-  const individualsCount = familyCounts.reduce((acc, { size }) => acc + size, 0)
 
   let editIndividualsButton = null
   if (user && (user.isPm || (hasCaseReview && canEdit))) {
@@ -185,25 +188,29 @@ const FamiliesIndividuals = React.memo(({ canEdit, hasCaseReview, familyCounts,
     <DetailSection
       title={(
         <span>
-          {`${Object.keys(familyCounts).length} Families${title || ''},`}
+          {`${familiesCount} Families${title || ''},`}
           <br />
           {`${individualsCount} Individuals${title || ''}`}
         </span>
       )}
       content={
-        sortBy(Object.entries(familySizeHistogram)).map(([size, { total, withParents }]) => (
+        sortBy(Object.entries(familySizeHistogram)).map(([size, { total, withParents, trioPlus, quadPlus }]) => (
           <div key={size}>
             {`${total} famil${total === 1 ? 'y' : 'ies'} with ${FAMILY_SIZE_LABELS[size] || size} individual${size === '1' ? '' : 's'}`}
-            {withParents > 0 && (
-              <div>
+            {[
+              [withParents, FAMILY_STRUCTURE_SIZE_LABELS[size], FAMILY_STRUCTURE_HOVER[size], total > 1],
+              [trioPlus, 'trio+', 'A family with two parents, one child, and other family members'],
+              [quadPlus, 'quad+', 'A family with two parents, at least two children, and other family members'],
+            ].filter(([count]) => count > 0).map(([count, label, hover, plural]) => (
+              <div key="label">
                 &nbsp;&nbsp;&nbsp;&nbsp;
-                {withParents}
+                {count}
                 <Popup
-                  trigger={<span>{FAMILY_STRUCTURE_SIZE_LABELS[size](total > 1)}</span>}
-                  content={FAMILY_STRUCTURE_HOVER[size]}
+                  trigger={<span>{` ${label}${plural ? 's' : ''}`}</span>}
+                  content={hover}
                 />
               </div>
-            )}
+            ))}
           </div>
         ))
       }
@@ -213,7 +220,7 @@ const FamiliesIndividuals = React.memo(({ canEdit, hasCaseReview, familyCounts,
 })
 
 FamiliesIndividuals.propTypes = {
-  familyCounts: PropTypes.arrayOf(PropTypes.object).isRequired,
+  familySizes: PropTypes.object.isRequired,
   canEdit: PropTypes.bool,
   hasCaseReview: PropTypes.bool,
   user: PropTypes.object,
@@ -222,12 +229,12 @@ FamiliesIndividuals.propTypes = {
 
 const mapFamiliesStateToProps = (state, ownProps) => ({
   user: getUser(state),
-  familyCounts: getProjectAnalysisGroupFamilyIndividualCounts(state, ownProps),
+  familySizes: getProjectAnalysisGroupFamilySizeHistogram(state, ownProps),
 })
 
 const mapDataLoadedFamiliesStateToProps = (state, ownProps) => ({
   title: ' With Data',
-  familyCounts: getProjectAnalysisGroupDataLoadedFamilyIndividualCounts(state, ownProps),
+  familySizes: getProjectAnalysisGroupDataLoadedFamilySizeHistogram(state, ownProps),
 })
 
 const FamiliesIndividualsOverview = connect(mapFamiliesStateToProps)(FamiliesIndividuals)

diff --git a/ui/pages/Project/selectors.js b/ui/pages/Project/selectors.js
@@ -97,30 +97,65 @@ export const getProjectAnalysisGroupFamiliesByGuid = createSelector(
   },
 )
 
-export const getProjectAnalysisGroupFamilyIndividualCounts = createSelector(
+const getFamilySizeHistogram = familyCounts => familyCounts.reduce((acc, { size, parents }) => {
+  const parentCounts = Object.values(parents.reduce(
+    (parentAcc, { maternalGuid, paternalGuid }) => {
+      const parentKey = `${maternalGuid || ''}-${paternalGuid || ''}`
+      const parent = parentAcc[parentKey] || {
+        numParents: [maternalGuid, paternalGuid].filter(g => g).length,
+        numChildren: 0,
+      }
+      parent.numChildren += 1
+      return { ...parentAcc, [parentKey]: parent }
+    }, {},
+  ))
+  const sizeAcc = acc[size] || { total: 0, withParents: 0, trioPlus: 0, quadPlus: 0 }
+  sizeAcc.total += 1
+  const mainParentCount = parentCounts.find(({ numParents }) => numParents === (size === 2 ? 1 : 2))
+  const mainFamilySize = mainParentCount ? mainParentCount.numChildren + mainParentCount.numParents : 0
+  if (mainFamilySize === size) {
+    sizeAcc.withParents += 1
+  } else if (mainFamilySize === 3) {
+    sizeAcc.trioPlus += 1
+  } else if (mainFamilySize > 3) {
+    sizeAcc.quadPlus += 1
+  }
+  return { ...acc, [size]: sizeAcc }
+}, {})
+
+export const getProjectAnalysisGroupFamilySizeHistogram = createSelector(
   getProjectAnalysisGroupFamiliesByGuid,
-  familiesByGuid => Object.values(familiesByGuid).map(family => ({
+  familiesByGuid => getFamilySizeHistogram(Object.values(familiesByGuid).map(family => ({
     size: (family.individualGuids || []).length,
-    numParents: (family.parents || []).length === 1 ?
-      [family.parents[0].maternalGuid, family.parents[0].paternalGuid].filter(g => g).length : 0,
-  })),
+    parents: family.parents || [],
+  }))),
 )
 
-export const getProjectAnalysisGroupDataLoadedFamilyIndividualCounts = createSelector(
+export const getProjectAnalysisGroupDataLoadedFamilySizeHistogram = createSelector(
   getProjectAnalysisGroupFamiliesByGuid,
   getSamplesByFamily,
-  (familiesByGuid, samplesByFamily) => Object.values(familiesByGuid).map(((family) => {
+  (familiesByGuid, samplesByFamily) => getFamilySizeHistogram(Object.values(familiesByGuid).map(((family) => {
     const sampleIndividuals = new Set((samplesByFamily[family.familyGuid] || []).filter(
       sample => sample.isActive,
     ).map(sample => sample.individualGuid))
-    const hasSampleParentCounts = (family.parents || []).map(
-      ({ maternalGuid, paternalGuid }) => [maternalGuid, paternalGuid].filter(guid => sampleIndividuals.has(guid)),
-    ).filter(parents => parents.length > 0)
+    const hasSampleParents = (family.parents || []).reduce(
+      (acc, { individualGuid, maternalGuid, paternalGuid }) => {
+        const hasSampleMaternal = sampleIndividuals.has(maternalGuid)
+        const hasSamplePaternal = sampleIndividuals.has(paternalGuid)
+        if (sampleIndividuals.has(individualGuid) && (hasSampleMaternal || hasSamplePaternal)) {
+          acc.push({
+            maternalGuid: hasSampleMaternal ? maternalGuid : null,
+            paternalGuid: hasSamplePaternal ? paternalGuid : null,
+          })
+        }
+        return acc
+      }, [],
+    )
     return {
       size: sampleIndividuals.size,
-      numParents: hasSampleParentCounts.length === 1 ? hasSampleParentCounts[0].length : 0,
+      parents: hasSampleParents,
     }
-  })).filter(({ size }) => size > 0),
+  })).filter(({ size }) => size > 0)),
 )
 
 export const getProjectAnalysisGroupIndividualsByGuid = createSelector(

diff --git a/ui/shared/utils/constants.js b/ui/shared/utils/constants.js
@@ -396,6 +396,7 @@ export const CATEGORY_FAMILY_FILTERS = {
 // INDIVIDUAL FIELDS
 const SEX_MALE = 'M'
 const SEX_FEMALE = 'F'
+const SEX_UNKNOWN = 'U'
 const MALE_ANEUPLOIDIES = ['XXY', 'XYY']
 const FEMALE_ANEUPLOIDIES = ['XXX', 'X0']
 export const SEX_OPTIONS = [
@@ -409,6 +410,7 @@ export const SEX_OPTIONS = [
 export const SIMPLIFIED_SEX_LOOKUP = {
   ...[SEX_MALE, ...MALE_ANEUPLOIDIES].reduce((acc, val) => ({ ...acc, [val]: SEX_MALE }), {}),
   ...[SEX_FEMALE, ...FEMALE_ANEUPLOIDIES].reduce((acc, val) => ({ ...acc, [val]: SEX_FEMALE }), {}),
+  [SEX_UNKNOWN]: SEX_UNKNOWN,
 }
 
 export const SEX_LOOKUP = SEX_OPTIONS.reduce(
@@ -2004,6 +2006,8 @@ export const TISSUE_DISPLAY = {
   F: 'Fibroblast',
   M: 'Muscle',
   L: 'Lymphocyte',
+  A: 'Airway Cultured Epithelium',
+  B: 'Brain',
 }
 
 export const RNASEQ_JUNCTION_PADDING = 200