Skip to content

remove unused, problematic galaxy_paths var collections in testing... #882

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jmchilton merged 1 commit into from
Oct 30, 2018
Merged

remove unused, problematic galaxy_paths var collections in testing... #882

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 2 additions & 22 deletions planemo/galaxy/activity.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ def _execute(ctx, config, runnable, job_path, **kwds):

history_id = _history_id(user_gi, **kwds)

galaxy_paths, job_dict, _ = stage_in(ctx, runnable, config, user_gi, history_id, job_path, **kwds)
job_dict, _ = stage_in(ctx, runnable, config, user_gi, history_id, job_path, **kwds)

if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]:
response_class = GalaxyToolRunResponse
Expand Down Expand Up @@ -163,7 +163,6 @@ def _execute(ctx, config, runnable, job_path, **kwds):
runnable=runnable,
user_gi=user_gi,
history_id=history_id,
galaxy_paths=galaxy_paths,
log=log_contents_str(config),
**response_kwds
)
Expand Down Expand Up @@ -281,19 +280,7 @@ def create_collection_func(element_identifiers, collection_type):
f.write(log_contents_str(config))
raise Exception(msg)

galaxy_paths = []
for (dataset, upload_target) in datasets:
if isinstance(upload_target, FileUploadTarget):
local_path = upload_target.path
ctx.vlog("fetching full dataset for %s, %s" % (dataset, local_path))
dataset_full = user_gi.datasets.show_dataset(dataset["id"])
galaxy_path = dataset_full["file_name"]
ctx.vlog("galaxy_path is %s" % galaxy_path)
job_path = os.path.join(job_dir, local_path)
galaxy_paths.append((job_path, galaxy_path))

ctx.vlog("galaxy_paths are %s" % galaxy_paths)
return galaxy_paths, job_dict, datasets
return job_dict, datasets


class GalaxyBaseRunResponse(SuccessfulRunResponse):
Expand All @@ -304,7 +291,6 @@ def __init__(
runnable,
user_gi,
history_id,
galaxy_paths,
log,
):
self._ctx = ctx
Expand All @@ -315,8 +301,6 @@ def __init__(

self._job_info = None

self.galaxy_paths = galaxy_paths

self._outputs_dict = None

def to_galaxy_output(self, output):
Expand Down Expand Up @@ -467,7 +451,6 @@ def __init__(
runnable,
user_gi,
history_id,
galaxy_paths,
log,
job_info,
api_run_response,
Expand All @@ -477,7 +460,6 @@ def __init__(
runnable=runnable,
user_gi=user_gi,
history_id=history_id,
galaxy_paths=galaxy_paths,
log=log,
)
self._job_info = job_info
Expand Down Expand Up @@ -513,7 +495,6 @@ def __init__(
runnable,
user_gi,
history_id,
galaxy_paths,
log,
workflow_id,
invocation_id,
Expand All @@ -523,7 +504,6 @@ def __init__(
runnable=runnable,
user_gi=user_gi,
history_id=history_id,
galaxy_paths=galaxy_paths,
log=log,
)
self._workflow_id = workflow_id
Expand Down
⚡