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fix: Ga4gh tes bugfixes #1127

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merged 11 commits into from Aug 12, 2021
Merged

fix: Ga4gh tes bugfixes #1127

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fca3120
add py-tes
svedziok Aug 9, 2021
0c173a7
check remote log and benchmark
svedziok Aug 9, 2021
5012b63
reduce complexity
svedziok Aug 9, 2021
c67a75e
bugfix
svedziok Aug 9, 2021
3ee9c8d
Merge branch 'main' into ga4gh_tes_bugfixes
johanneskoester Aug 10, 2021
df1b971
add exception for missing tes module
svedziok Aug 10, 2021
12dc7fd
Merge branch 'ga4gh_tes_bugfixes' of github.com:snakemake/snakemake i…
svedziok Aug 10, 2021
b04b746
add install py-tes info to doc
svedziok Aug 10, 2021
5784c96
add raise exception
svedziok Aug 10, 2021
fe8e00d
formatting
svedziok Aug 10, 2021
055c873
remove py-tes
svedziok Aug 10, 2021
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1 change: 1 addition & 0 deletions setup.py
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Expand Up @@ -76,6 +76,7 @@
"filelock",
"stopit",
"tabulate",
"py-tes",
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I don't think this needs to be a required dependency. But the docs should probably say that py-tes needs to be installed.

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And the import statement here should be wrapped in a try-except with a WorkflowError("Unable to import Python package tes. TES backend requires py-tes to be installed. Please install py-tes, e.g. via Conda or Pip.")

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Ok, I added a try-except statement in the init function. I will also a note at the documentation

],
extras_require={
"reports": ["jinja2", "networkx", "pygments", "pygraphviz"],
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32 changes: 11 additions & 21 deletions snakemake/executors/ga4gh_tes.py
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Expand Up @@ -310,39 +310,29 @@ def _get_task_inputs(self, job, jobscript, checkdir):

return inputs

def _get_task_outputs(self, job, checkdir):
outputs = []
# add output files to outputs
for o in job.output:
def _append_task_outputs(self, outputs, files):
for file in files:
obj = self._prepare_file(
filename=o,
filename=file,
checkdir=checkdir,
type="Output",
)
if obj:
outputs.append(obj)
return outputs

def _get_task_outputs(self, job, checkdir):
outputs = []
# add output files to outputs
outputs = self._append_task_outputs(outputs, job.output)

# add log files to outputs
if job.log:
for log in job.log:
outputs.append(
self._prepare_file(
filename=log,
checkdir=checkdir,
type="Output",
)
)
outputs = self._append_task_outputs(outputs, job.log)

# add benchmark files to outputs
if hasattr(job, "benchmark") and job.benchmark:
for benchmark in job.benchmark:
outputs.append(
self._prepare_file(
filename=benchmark,
checkdir=checkdir,
type="Output",
)
)
outputs = self._append_task_outputs(outputs, job.benchmark)

return outputs

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