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untangle Analysis.create and build_analysis_files #3496

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Merged
lucaspatel merged 2 commits into from
Dec 10, 2025
Merged

untangle Analysis.create and build_analysis_files #3496

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c5d338d
untangle Analysis.create and build_analysis_files
antgonza Dec 9, 2025
3d6f6c3
add TRN
antgonza Dec 9, 2025
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32 changes: 23 additions & 9 deletions qiita_db/analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -147,21 +147,31 @@ def create(
description : str
Description of the analysis
from_default : bool, optional
If True, use the default analysis to populate selected samples.
If True, use the default analysis to populate selected samples;
when True, we will create a `build_analysis_files` job.
Default False.
merge_duplicated_sample_ids : bool, optional
If the duplicated sample ids in the selected studies should be
merged or prepended with the artifact ids. False (default) prepends
the artifact id
categories : list of str, optional
If not None, use _only_ these categories for the metaanalysis
reservation : str
reservation : str, optional
The slurm reservation to asign to the analysis

Returns
-------
qdb.analysis.Analysis
The newly created analysis

Notes
-----
Before 12.09.25 this method was fully tangled with `build_analysis_files`, which
meant that we couldn't create a stand alone analysis; additionally, this method
had the intrinsic assumption that we can create an analysis not from default but not
pass any sample/artifact information - which will create an empty analysis but still submit
a build_analysis_files file. Thus, we are using this assumption to define if we should
create the `build_analysis_files` job
"""
with qdb.sql_connection.TRN:
portal_id = qdb.util.convert_to_id(
Expand Down Expand Up @@ -199,6 +209,7 @@ def create(
if reservation is not None:
instance.slurm_reservation = reservation

if from_default:
# Once the analysis is created, we can create the mapping file and
# the initial set of artifacts
plugin = qdb.software.Software.from_name_and_version("Qiita", "alpha")
Expand All @@ -211,15 +222,18 @@ def create(
"categories": categories,
},
)

job = qdb.processing_job.ProcessingJob.create(owner, params, True)
sql = """INSERT INTO qiita.analysis_processing_job
(analysis_id, processing_job_id)
VALUES (%s, %s)"""
qdb.sql_connection.TRN.add(sql, [a_id, job.id])
qdb.sql_connection.TRN.execute()

# Doing the submission outside of the transaction
job.submit()
with qdb.sql_connection.TRN:
sql = """INSERT INTO qiita.analysis_processing_job
(analysis_id, processing_job_id)
VALUES (%s, %s)"""
qdb.sql_connection.TRN.add(sql, [a_id, job.id])
qdb.sql_connection.TRN.execute()

job.submit()

return instance

@classmethod
Expand Down
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