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show RNAseq type in sample hover #4171

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merged 16 commits into from
Jul 1, 2024
Merged

show RNAseq type in sample hover #4171

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73875fb
show RNA type in sample hover
jklugherz Jun 17, 2024
9c6f2a6
remove hasRnaOutlierData
jklugherz Jun 17, 2024
d6dfb8f
additional values and post processing
jklugherz Jun 21, 2024
88c86c5
extra
jklugherz Jun 21, 2024
c73e3f6
test
jklugherz Jun 21, 2024
a539726
unused
jklugherz Jun 21, 2024
065a8d3
Merge remote-tracking branch 'origin/dev' into rnatypes
jklugherz Jun 24, 2024
e2d52f1
with isnull
jklugherz Jun 24, 2024
6268b10
with outerref
jklugherz Jun 24, 2024
50213d9
changes
jklugherz Jun 25, 2024
6602382
lint stuff
jklugherz Jun 25, 2024
a28272a
key from project api tests?
jklugherz Jun 25, 2024
41ffb9b
fix the last test
jklugherz Jun 25, 2024
50c4951
Merge remote-tracking branch 'origin/dev' into rnatypes
jklugherz Jun 27, 2024
c1fdc78
fix individualrow
jklugherz Jun 27, 2024
af46542
isactive
jklugherz Jun 27, 2024
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22 changes: 14 additions & 8 deletions seqr/views/apis/family_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
from seqr.views.utils.project_context_utils import add_families_context, families_discovery_tags, add_project_tag_types, \
MME_TAG_NAME
from seqr.models import Family, FamilyAnalysedBy, Individual, FamilyNote, Sample, VariantTag, AnalysisGroup, RnaSeqTpm, \
PhenotypePrioritization, Project
PhenotypePrioritization, Project, RnaSeqOutlier, RnaSeqSpliceOutlier
from seqr.views.utils.permissions_utils import check_project_permissions, get_project_and_check_pm_permissions, \
login_and_policies_required, user_is_analyst, has_case_review_permissions
from seqr.views.utils.variant_utils import get_phenotype_prioritization, get_omim_intervals_query, DISCOVERY_CATEGORY
Expand All @@ -43,10 +43,21 @@ def family_page_data(request, family_guid):
has_case_review_perm = has_case_review_permissions(project, request.user)

sample_models = Sample.objects.filter(individual__family=family)
samples = get_json_for_samples(sample_models, project_guid=project.guid, family_guid=family_guid, skip_nested=True, is_analyst=is_analyst)
samples = get_json_for_samples(
sample_models, project_guid=project.guid, family_guid=family_guid, skip_nested=True, is_analyst=is_analyst
)
response = {
'samplesByGuid': {s['sampleGuid']: s for s in samples},
'samplesByGuid': {s['sampleGuid']: s for s in samples}
}
rna_type_samples = {
'TPM': set(RnaSeqTpm.objects.filter(sample__in=sample_models).values_list('sample__guid', flat=True)),
'Expression Outlier': set(RnaSeqOutlier.objects.filter(sample__in=sample_models).values_list('sample__guid', flat=True)),
'Splice Outlier': set(RnaSeqSpliceOutlier.objects.filter(sample__in=sample_models).values_list('sample__guid', flat=True)),
}
for sample in response['samplesByGuid'].values():
sample['rnaSeqTypes'] = [
rnaseq_type for rnaseq_type, sample_ids in rna_type_samples.items() if sample['sampleGuid'] in sample_ids
]

add_families_context(response, families, project.guid, request.user, is_analyst, has_case_review_perm)
family_response = response['familiesByGuid'][family_guid]
Expand Down Expand Up @@ -77,11 +88,6 @@ def family_page_data(request, family_guid):
'postDiscoveryOmimOptions': omim_map,
})

outlier_individual_guids = sample_models.filter(sample_type=Sample.SAMPLE_TYPE_RNA, is_active=True)\
.exclude(rnaseqoutlier__isnull=True, rnaseqspliceoutlier__isnull=True).values_list('individual__guid', flat=True)
for individual_guid in outlier_individual_guids:
response['individualsByGuid'][individual_guid]['hasRnaOutlierData'] = True

tools_by_indiv = {}
tools_agg = PhenotypePrioritization.objects.filter(individual__family=family).values('individual__guid').annotate(
phenotypePrioritizationTools=ArrayAgg(
Expand Down
17 changes: 10 additions & 7 deletions seqr/views/apis/family_api_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,10 @@

INDIVIDUAL_GUIDS = [INDIVIDUAL_GUID, INDIVIDUAL2_GUID, INDIVIDUAL3_GUID]

FAMILY_API_SAMPLE_FIELDS = {*SAMPLE_FIELDS, 'rnaSeqTypes'}
SAMPLE_GUIDS = ['S000129_na19675', 'S000130_na19678', 'S000131_na19679', 'S000151_na19675_1', 'S000152_na19675_d2', 'S000153_na19679']


class FamilyAPITest(AuthenticationTestCase):
fixtures = ['users', '1kg_project', 'reference_data']

Expand Down Expand Up @@ -69,8 +73,7 @@ def test_family_page_data(self):

self.assertEqual(len(response_json['individualsByGuid']), 3)
individual = response_json['individualsByGuid'][INDIVIDUAL_GUID]
individual_fields = {'sampleGuids', 'igvSampleGuids', 'mmeSubmissionGuid', 'hasRnaOutlierData',
'phenotypePrioritizationTools'}
individual_fields = {'sampleGuids', 'igvSampleGuids', 'mmeSubmissionGuid', 'phenotypePrioritizationTools'}
individual_fields.update(INDIVIDUAL_FIELDS)
self.assertSetEqual(set(individual.keys()), individual_fields)
self.assertListEqual([
Expand All @@ -83,19 +86,19 @@ def test_family_page_data(self):
],
[response_json['individualsByGuid'][guid].get('phenotypePrioritizationTools') for guid in INDIVIDUAL_GUIDS]
)
self.assertListEqual(
[True, False, True],
[response_json['individualsByGuid'][guid].get('hasRnaOutlierData', False) for guid in INDIVIDUAL_GUIDS]
)
self.assertSetEqual({PROJECT_GUID}, {i['projectGuid'] for i in response_json['individualsByGuid'].values()})
self.assertSetEqual({FAMILY_GUID}, {i['familyGuid'] for i in response_json['individualsByGuid'].values()})

self.assertEqual(len(response_json['samplesByGuid']), 6)
self.assertSetEqual(set(next(iter(response_json['samplesByGuid'].values())).keys()), SAMPLE_FIELDS)
self.assertSetEqual(set(next(iter(response_json['samplesByGuid'].values())).keys()), FAMILY_API_SAMPLE_FIELDS)
self.assertSetEqual({PROJECT_GUID}, {s['projectGuid'] for s in response_json['samplesByGuid'].values()})
self.assertSetEqual({FAMILY_GUID}, {s['familyGuid'] for s in response_json['samplesByGuid'].values()})
self.assertEqual(len(individual['sampleGuids']), 3)
self.assertTrue(set(individual['sampleGuids']).issubset(set(response_json['samplesByGuid'].keys())))
self.assertListEqual(
[[], [], [], ['TPM', 'Splice Outlier'], ['TPM', 'Expression Outlier', 'Splice Outlier'], ['Splice Outlier']],
[response_json['samplesByGuid'][guid].get('rnaSeqTypes', {}) for guid in SAMPLE_GUIDS]
)

self.assertEqual(len(response_json['igvSamplesByGuid']), 1)
self.assertSetEqual(set(next(iter(response_json['igvSamplesByGuid'].values())).keys()), IGV_SAMPLE_FIELDS)
Expand Down
2 changes: 1 addition & 1 deletion ui/pages/Project/components/FamilyTable/IndividualRow.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ const DataDetails = React.memo(({ loadedSamples, individual, mmeSubmission }) =>
/>
) : <MmeStatusLabel title="Submitted to MME" dateField="lastModifiedDate" color="violet" individual={individual} mmeSubmission={mmeSubmission} />
)}
{individual.hasRnaOutlierData && (
{loadedSamples.some(sample => sample.isActive && (sample.rnaSeqTypes.includes('Expression Outlier') || sample.rnaSeqTypes.includes('Splice Outlier'))) && (
<div>
<Link
target="_blank"
Expand Down
17 changes: 12 additions & 5 deletions ui/shared/components/panel/sample.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ import PropTypes from 'prop-types'
import styled from 'styled-components'
import { Popup, Icon } from 'semantic-ui-react'

import { HorizontalSpacer } from '../Spacers'
import { DATASET_TYPE_SNV_INDEL_CALLS } from '../../utils/constants'
import { HorizontalSpacer, VerticalSpacer } from '../Spacers'
import { DATASET_TYPE_SNV_INDEL_CALLS, SAMPLE_TYPE_RNA } from '../../utils/constants'

const Detail = styled.span`
font-size: 11px;
Expand Down Expand Up @@ -33,9 +33,16 @@ const Sample = React.memo(({ loadedSample, isOutdated, hoverDetails }) => (
}
</span>
}
content={loadedSample ?
`data was${isOutdated ? ' previously ' : ''} ${hoverDetails ? `${hoverDetails} on ${new Date(loadedSample.loadedDate).toLocaleDateString()}` : 'loaded'}` :
'no data available'}
content={
<div>
{loadedSample ?
`data was${isOutdated ? ' previously ' : ''} ${hoverDetails ? `${hoverDetails} on ${new Date(loadedSample.loadedDate).toLocaleDateString()}` : 'loaded'}` :
'no data available'}
<VerticalSpacer height={5} />
{loadedSample.sampleType && loadedSample.sampleType === SAMPLE_TYPE_RNA &&
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rnaSeqTypes will only have values for RNA samples so you can remove this part of the condition check

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@jklugherz jklugherz Jun 27, 2024 •
edited
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Without this part of the check some old(?) rna samples which do not have any matches in the 3 rnaseqtype tables will display like this:
image

There are 76 of these samples all created on 2016-12-05

WITH sample_rnaseq as (
    select s.guid, s.id, s.created_date,
           seqr_rnaseqtpm.id as tpm_id, seqr_rnaseqoutlier.id as outlier_id, sr.id as splice_outlier_id
    from seqr_sample s
    left join seqr_rnaseqtpm on s.id = seqr_rnaseqtpm.sample_id
    left join seqr_rnaseqoutlier on s.id = seqr_rnaseqoutlier.sample_id
    left join public.seqr_rnaseqspliceoutlier sr on s.id = sr.sample_id
    where s.sample_type in ('RNA')
)
SELECT * FROM sample_rnaseq
WHERE tpm_id is null
and outlier_id is null
and splice_outlier_id is null

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they're all probably from the R0246_rna_seq_bc project, I've been using that for testing since I was certain it would have rna samples given the name

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Oh we should only be showing this for active samples, not inactive sample

loadedSample.isActive && `RNAseq methods: ${loadedSample.rnaSeqTypes.join(', ')}`}
</div>
}
position="left center"
/>
))
Expand Down
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