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olink_dag_taskflow_params_fix #176

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Merged
avikdatta merged 3 commits into from
Mar 9, 2026
Merged

olink_dag_taskflow_params_fix #176

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574b237
change taskflow parms
avikdatta Mar 9, 2026
0b012fb
updated unit test
avikdatta Mar 9, 2026
ef8e08a
updated unit test for bash task
avikdatta Mar 9, 2026
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13 changes: 7 additions & 6 deletions igf_airflow/utils/dag50_olink_reveal_nextflow_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
retry_delay=timedelta(minutes=5),
retries=4,
queue='hpc_4G',
multiple_outputs=False)
multiple_outputs=True)
def prepare_olink_nextflow_script(
design_dict: dict,
work_dir: str,
Expand Down Expand Up @@ -138,7 +138,7 @@ def prepare_olink_nextflow_script(
WORKDIR=work_dir
)
)
return nf_script_file.as_posix()
return {"run_script": nf_script_file.as_posix()}
except Exception as e:
log.error(e)
send_airflow_failed_logs_to_channels(
Expand All @@ -153,13 +153,14 @@ def prepare_olink_nextflow_script(
queue='hpc_8G4t72hr',
pool='batch_job',
retries=4)
def run_olink_nextflow_script(run_script: str):
def run_olink_nextflow_script(run_script: str) -> str:
try:
script_dir = os.path.dirname(run_script)
bash_cmd = f"""set -eo pipefail;
cd {script_dir};
chmod u+x {run_script};
bash {run_script}"""
## Move to the script dir
cd {script_dir} ;
chmod u+x {run_script} ;
bash {run_script} ;"""
return bash_cmd
except Exception as e:
log.error(e)
Expand Down
9 changes: 7 additions & 2 deletions test/igf_airflow/test_dag50_olink_reveal_nextflow_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,10 +54,11 @@ def test_prepare_olink_nextflow_script(self, *args):
with open(design_yaml_file, "w") as fp:
fp.write(design_yaml)
design_dict = {"analysis_design": design_yaml_file}
analysis_script = prepare_olink_nextflow_script.function(
analysis_script_conf = prepare_olink_nextflow_script.function(
design_dict=design_dict,
work_dir=self.temp_dir
)
analysis_script = analysis_script_conf["run_script"]
assert os.path.exists(analysis_script)
with open(analysis_script, "r") as fp:
script_data = fp.read() ## small file
Expand All @@ -84,7 +85,11 @@ def test_run_olink_nextflow_script(self):
analysis_cmd = run_olink_nextflow_script.function(
script_file
)
assert analysis_cmd == f"set -eo pipefail;\ncd {os.path.dirname(script_file)};\nchmod u+x {script_file};\nbash {script_file}"
assert analysis_cmd == f"""set -eo pipefail;
## Move to the script dir
cd {os.path.dirname(script_file)} ;
chmod u+x {script_file} ;
bash {script_file} ;"""

if __name__=='__main__':
unittest.main()