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DSERV-1315 reading simple_sample_summaries from AnalysisSet obj #733

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DSERV-1315 reading simple_sample_summaries from AnalysisSet obj #733

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46 changes: 3 additions & 43 deletions data/adapters/file_fileset_adapter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -488,49 +488,6 @@ def parse_sample_donor_treatment_igvf(
treatment_object['treatment_term_id'])
# Add support for treatment vs. untreated analyses later

# special case STARR-seq for inclusion of 1000 Genomes donors in the simple sample summary
if method == 'STARR-seq':
thousand_genomes_ids = set()
construct_library_set_accessions = set()
integrated_content_files_accessions = set()
curated_set_accessions = set()
donors_accessions = set()

for construct_library_set in sample_object.get('construct_library_sets', []):
construct_library_set_accessions.add(
construct_library_set['accession'])
construct_library_set_objects = FileFileSet.get_batch_objects(
list(construct_library_set_accessions), ['integrated_content_files'], api_url=FileFileSet.IGVF_API)

for construct_library_set_object in construct_library_set_objects:
integrated_content_files = construct_library_set_object.get(
'integrated_content_files', [])
for integrated_content_file in integrated_content_files:
integrated_content_files_accessions.add(
integrated_content_file['accession'])
integrated_content_files_objects = FileFileSet.get_batch_objects(
list(integrated_content_files_accessions), ['file_set'], api_url=FileFileSet.IGVF_API)
for integrated_content_file_object in integrated_content_files_objects:
curated_set = integrated_content_file_object['file_set']
curated_set_accessions.add(curated_set['accession'])
curated_sets_objects = FileFileSet.get_batch_objects(
list(curated_set_accessions), ['donors'], api_url=FileFileSet.IGVF_API)
for curated_set_object in curated_sets_objects:
for donor in curated_set_object.get('donors', []):
donors_accessions.add(donor['accession'])
donors_objects = FileFileSet.get_batch_objects(
list(donors_accessions), ['dbxrefs'], api_url=FileFileSet.IGVF_API)
for donor_object in donors_objects:
dbxrefs = donor_object.get('dbxrefs', [])
for dbxref in dbxrefs:
if dbxref.startswith('IGSR'):
thousand_genomes_id = dbxref.split(':')[1]
thousand_genomes_ids.add(thousand_genomes_id)
if thousand_genomes_ids:
thousand_genomes_ids = ', '.join(
sorted(thousand_genomes_ids))
simple_sample_summary = f'{simple_sample_summary} with variants from 1000 Genomes donors: {thousand_genomes_ids}'

simple_sample_summaries.add(simple_sample_summary)
if len(crispr_modalities) > 1:
raise ValueError(
Expand Down Expand Up @@ -808,6 +765,9 @@ def query_fileset_files_props_igvf(file_object):
samples,
method)

if fileset_object_type == 'AnalysisSet':
simple_sample_summaries = [fileset_object['sample_summary']]

sample_term_ids = [sample_term_id.replace(
':', '_') for sample_term_id in sample_term_ids]

Expand Down