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EVA-4059 Add property for QC duplicate SS acc in accessioning pipeline properties #79

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Merged
nitin-ebi merged 1 commit into from
Feb 5, 2026
Merged

EVA-4059 Add property for QC duplicate SS acc in accessioning pipeline properties #79

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6 changes: 4 additions & 2 deletions ebi_eva_internal_pyutils/spring_properties.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,8 @@ def _common_accessioning_clustering_properties(self, *, assembly_accession, read

def get_accessioning_properties(self, *, read_preference='primary', job_name=None, target_assembly=None, fasta=None,
assembly_report=None, project_accession=None, aggregation='BASIC',
taxonomy_accession=None, vcf_file='', output_vcf='', chunk_size=100):
taxonomy_accession=None, vcf_file='', output_vcf='', duplicate_ss_acc_file='',
chunk_size=100):
"""Properties for accessioning pipeline."""
return self._format(
self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
Expand All @@ -150,7 +151,8 @@ def get_accessioning_properties(self, *, read_preference='primary', job_name=Non
'parameters.taxonomyAccession': taxonomy_accession,
'parameters.vcfAggregation': aggregation,
'parameters.vcf': vcf_file,
'parameters.outputVcf': output_vcf
'parameters.outputVcf': output_vcf,
'parameters.duplicateSSAccFile': duplicate_ss_acc_file
},
)

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15 changes: 9 additions & 6 deletions tests/internal/test_spring_prop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,8 @@ def test_get_accessioning_properties(self):
parameters.taxonomyAccession=9906
parameters.vcfAggregation=BASIC
parameters.vcf=/path/to/vcf_file.vcf
parameters.outputVcf=
parameters.outputVcf=/path/to/output_vcf.vcf
parameters.duplicateSSAccFile=/path/to/duplicate_ss_acc_file.vcf

accessioning.submitted.categoryId=ss
accessioning.clustered.categoryId=rs
Expand All @@ -181,7 +182,8 @@ def test_get_accessioning_properties(self):
assert self.prop.get_accessioning_properties(
job_name='SUBSNP_ACCESSION_JOB', target_assembly='GCA_00000001.1', fasta='/path/to/fasta.fa',
assembly_report='/path/to/assembly_report.txt', project_accession='PRJEB0001', aggregation='BASIC',
taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf') == expected
taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf', output_vcf='/path/to/output_vcf.vcf',
duplicate_ss_acc_file='/path/to/duplicate_ss_acc_file.vcf') == expected

def test_get_variant_load_properties(self):
expected = '''spring.data.mongodb.uri=mongodb://mongouser:mongop%40ssword@mongos-host1.example.com:27017,mongos-host2.example.com:27017/?retryWrites=true&authSource=admin
Expand Down Expand Up @@ -383,7 +385,8 @@ def test_get_accessioning_properties_with_none(self):
parameters.taxonomyAccession=9906
parameters.vcfAggregation=BASIC
parameters.vcf=/path/to/vcf_file.vcf
parameters.outputVcf=
parameters.outputVcf=/path/to/output_vcf.vcf
parameters.duplicateSSAccFile=/path/to/duplicate_ss_acc_file.vcf

accessioning.submitted.categoryId=ss
accessioning.clustered.categoryId=rs
Expand All @@ -397,9 +400,9 @@ def test_get_accessioning_properties_with_none(self):
recovery.cutoff.days=9999999
'''
assert self.prop.get_accessioning_properties(
target_assembly='GCA_00000001.1', fasta=None,
assembly_report=None, project_accession='PRJEB0001', aggregation='BASIC',
taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf') == expected
target_assembly='GCA_00000001.1', fasta=None, assembly_report=None, project_accession='PRJEB0001',
aggregation='BASIC', taxonomy_accession='9906', vcf_file='/path/to/vcf_file.vcf',
output_vcf='/path/to/output_vcf.vcf', duplicate_ss_acc_file='/path/to/duplicate_ss_acc_file.vcf') == expected

def test_get_release_properties(self):
expected = '''spring.data.mongodb.uri=mongodb://mongouser:mongop%40ssword@mongos-host1.example.com:27017,mongos-host2.example.com:27017/?retryWrites=true&authSource=admin
Expand Down