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fix(htcondorcern): unpacked images and multiline commands #474

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merged 2 commits into from
Nov 22, 2024
Merged

fix(htcondorcern): unpacked images and multiline commands #474

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9cda591
fix(htcondorcern): run provided command in unpacked image (#474)
mdonadoni Nov 20, 2024
eb07aa9
fix(htcondorcern): support multiline commands (#474)
mdonadoni Nov 20, 2024
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8 changes: 5 additions & 3 deletions reana_job_controller/htcondorcern_job_manager.py
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Original file line number Diff line number Diff line change
@@ -9,6 +9,7 @@
import base64
import logging
import os
import shlex
import threading
from shutil import copyfile

@@ -163,7 +164,7 @@ def _format_arguments(self):
# Take only the user's command, removes the change directory to workflow workspace
# added by RWE-Serial/Snakemake since HTCondor implementation does not need it.
# E.g. "cd /path/to/workspace ; user-command" -> "user-command"
base_cmd = " ".join(self.cmd.split()[3:])
base_cmd = self.cmd.split(maxsplit=3)[3]
if self.workflow.type_ == "snakemake":
# For Snakemake workflows, also remove the workspace path from
# `jobfinished` and `jobfailed` touch commands.
@@ -235,9 +236,10 @@ def _copy_wrapper_file(self):
"--bind $PWD:/srv "
"--bind /cvmfs "
"--bind /eos "
"{DOCKER_IMG} {CMD}".format(
"{DOCKER_IMG} "
"bash -c {CMD}".format(
DOCKER_IMG=self.docker_img,
CMD=self._format_arguments() + " | bash",
CMD=shlex.quote(self._format_arguments() + " | bash"),
)
)
f = open("job_singularity_wrapper.sh", "w")
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