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fix: batch job ID and label prior to submission #58

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fix: batch job ID and label prior to submission #58

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579a6ca
Fix batch job ID and label prior to submission
tadasbare Mar 11, 2025
ebddb59
CI test
tadasbare Mar 11, 2025
3208f82
Revert CI change
tadasbare Mar 11, 2025
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11 changes: 9 additions & 2 deletions snakemake_executor_plugin_googlebatch/executor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ def get_labels(self, job):
"""
Derive default labels for the job (and add custom)
"""
labels = {"snakemake-job": job.name}
labels = {"snakemake-job": self.fix_job_name(job.name)}
for contender in self.get_param(job, "labels").split(","):
if not contender:
continue
Expand Down Expand Up @@ -93,7 +93,7 @@ def generate_jobid(self, job):
Generate a random jobid
"""
uid = str(uuid.uuid4())
return job.name.replace("_", "-") + "-" + uid[0:6]
return self.fix_job_name(job.name) + "-" + uid[0:6]

def get_container(self, job, entrypoint=None, commands=None):
"""
Expand Down Expand Up @@ -180,6 +180,13 @@ def get_command_writer(self, job):
resources=job.resources,
)

def fix_job_name(self, name):
"""
Replace illegal symbols and fix the job name length to adhere to
the Google Batch API job ID and label naming restrictions
"""
return name.replace("_", "-").replace(".", "")[:50]

def run_job(self, job: JobExecutorInterface):
"""
Run the Google Batch job.
Expand Down
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