Skip to content

EVA-4035: Remove hard-coded accessioning job name from spring properties generator #77

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
apriltuesday merged 1 commit into from
Jan 29, 2026
Merged

EVA-4035: Remove hard-coded accessioning job name from spring properties generator #77

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions ebi_eva_internal_pyutils/spring_properties.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def _common_accessioning_clustering_properties(self, *, assembly_accession, read
merge = {**self._common_accessioning_properties(assembly_accession, read_preference, chunk_size), **props}
return merge

def get_accessioning_properties(self, *, target_assembly=None, fasta=None, assembly_report=None,
def get_accessioning_properties(self, *, 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):
"""Properties for accessioning pipeline."""
Expand All @@ -141,7 +141,7 @@ def get_accessioning_properties(self, *, target_assembly=None, fasta=None, assem
read_preference='secondaryPreferred',
chunk_size=chunk_size),
{
'spring.batch.job.names': 'CREATE_SUBSNP_ACCESSION_JOB',
'spring.batch.job.names': job_name,
'parameters.assemblyReportUrl': self._format_str('file:{0}', assembly_report),
'parameters.contigNaming': 'NO_REPLACEMENT',
'parameters.fasta': fasta,
Expand Down
5 changes: 2 additions & 3 deletions tests/internal/test_spring_prop.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -147,7 +147,7 @@ def test_get_accessioning_properties(self):
spring.datasource.username=accuser
spring.datasource.password=accpassword
spring.data.mongodb.database=eva_accession_sharded
spring.batch.job.names=CREATE_SUBSNP_ACCESSION_JOB
spring.batch.job.names=SUBSNP_ACCESSION_JOB

eva.count-stats.url=https://www.ebi.ac.uk/eva/webservices/count-stats
eva.count-stats.username=statsuser
Expand Down Expand Up @@ -179,7 +179,7 @@ def test_get_accessioning_properties(self):
recovery.cutoff.days=9999999
'''
assert self.prop.get_accessioning_properties(
target_assembly='GCA_00000001.1', fasta='/path/to/fasta.fa',
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

Expand Down Expand Up @@ -368,7 +368,6 @@ def test_get_accessioning_properties_with_none(self):
spring.datasource.username=accuser
spring.datasource.password=accpassword
spring.data.mongodb.database=eva_accession_sharded
spring.batch.job.names=CREATE_SUBSNP_ACCESSION_JOB

eva.count-stats.url=https://www.ebi.ac.uk/eva/webservices/count-stats
eva.count-stats.username=statsuser
Expand Down