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Remove shebang lines from pre/post scripts #895

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merged 3 commits into from
Aug 27, 2024
Merged

Remove shebang lines from pre/post scripts #895

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9b26ea3
remove shebang lines from pre/post scripts after validating shell int…
kchilleri Aug 1, 2024
6b7cc16
Fix pylint errors
kchilleri Aug 1, 2024
86f3507
Merge branch 'develop' into issue890/remove-shebang
rstyd Aug 27, 2024
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7 changes: 7 additions & 0 deletions beeflow/common/parser/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,6 +305,8 @@ def _validate_prepost_shell_env(self, key, items, fname):
:type fname: str
"""
env_decl = items[key].splitlines()
# Need to remove whitespaces/newlines from list
env_decl = [x for x in env_decl if x.strip()]
# Check for shebang line in pre/post scripts
if not env_decl[0].startswith("#!"):
msg = f'No shebang line found in {fname}'
Expand All @@ -315,6 +317,11 @@ def _validate_prepost_shell_env(self, key, items, fname):
if shell_val != shebang_val:
msg = f'CWL file shell {shell_val} does not match {fname} shell {shebang_val}'
raise CwlParseError(msg) from None
# Remove shebang lines from scripts
rm_line = env_decl[1:]
# List to string format
rm_line = "\n".join(rm_line)
items.update({key: rm_line})

def parse_requirements(self, requirements, as_hints=False):
"""Parse CWL hints/requirements.
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2 changes: 1 addition & 1 deletion beeflow/tests/test_parser.py
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Expand Up @@ -165,7 +165,7 @@ def test_parse_workflow_missing_input(self):
name='clamr',
base_command='/CLAMR/clamr_cpuonly',
hints=[Hint(class_='DockerRequirement', params={'dockerFile': '# Dockerfile.clamr-ffmpeg\n# Developed on Chicoma @lanl\n# Patricia Grubel <pagrubel@lanl.gov>\n\nFROM debian:11\n\n\nRUN apt-get update && \\\n apt-get install -y wget gnupg git cmake ffmpeg g++ make openmpi-bin libopenmpi-dev libpng-dev libpng16-16 libpng-tools imagemagick libmagickwand-6.q16-6 libmagickwand-6.q16-dev\n\nRUN git clone https://github.com/lanl/CLAMR.git\nRUN cd CLAMR && cmake . && make clamr_cpuonly\n', 'beeflow:containerName': 'clamr-ffmpeg'}), #noqa
Hint(class_='beeflow:ScriptRequirement', params={'enabled': True, 'pre_script': '#!/bin/bash\n\necho "Before run"\n', 'post_script': '#!/bin/bash\n\necho "After run"\n', 'shell': '/bin/bash'})], #noqa
Hint(class_='beeflow:ScriptRequirement', params={'enabled': True, 'pre_script': 'echo "Before run"', 'post_script': 'echo "After run"', 'shell': '/bin/bash'})], #noqa
requirements=[],
inputs=[StepInput(id='graphic_steps', type='int', value=None, default=None,
source='steps_between_graphics', prefix='-g', position=None,
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