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Enable beeflow submit from working directory #854

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merged 2 commits into from
Jun 26, 2024
Merged

Enable beeflow submit from working directory #854

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84a5dcf
Allow submitting workflows from within workflow dir
jtronge Jun 11, 2024
5c3bc06
Ensure that workdir is a Path object in integration tests
jtronge Jun 12, 2024
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21 changes: 11 additions & 10 deletions beeflow/client/bee_client.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,9 @@ def is_parent(parent, path):
path = os.path.abspath(path)
return os.path.commonpath([parent]) == os.path.commonpath([parent, path])

wf_path = wf_path.resolve()
workdir = workdir.resolve()

tarball_path = ""
if os.path.exists(wf_path):
# Check to see if the wf_path is a tarball or a directory. Package if directory
Expand All @@ -222,17 +225,15 @@ def is_parent(parent, path):
# Packaging in temp dir, after copying alternate cwl_main or yaml file
cwl_indir = is_parent(wf_path, main_cwl_path)
yaml_indir = is_parent(wf_path, yaml_path)
# Always create temp dir for the workflow
tempdir_path = pathlib.Path(tempfile.mkdtemp())
if cwl_indir and yaml_indir:
package_path = package(wf_path, tempdir_path)
else:
tempdir_wf_path = pathlib.Path(tempdir_path / wf_path.name)
shutil.copytree(wf_path, tempdir_wf_path, dirs_exist_ok=False)
if not cwl_indir:
shutil.copy2(main_cwl, tempdir_wf_path)
if not yaml_indir:
shutil.copy2(yaml, tempdir_wf_path)
package_path = package(tempdir_wf_path, tempdir_path)
tempdir_wf_path = pathlib.Path(tempdir_path / wf_name)
shutil.copytree(wf_path, tempdir_wf_path, dirs_exist_ok=False)
if not cwl_indir:
shutil.copy2(main_cwl, tempdir_wf_path)
if not yaml_indir:
shutil.copy2(yaml, tempdir_wf_path)
package_path = package(tempdir_wf_path, tempdir_path)
else:
package_path = wf_path
# Untar and parse workflow
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2 changes: 1 addition & 1 deletion beeflow/common/integration/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ def __init__(self, name, path, main_cwl, job_file, workdir, containers):
self.path = path
self.main_cwl = main_cwl
self.job_file = job_file
self.workdir = workdir
self.workdir = Path(workdir)
self.containers = containers
self.wf_id = None
self.tarball = None
Expand Down