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More expressive workflow inputs.#1029

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jmchilton merged 1 commit intogalaxyproject:masterfrom
jmchilton:rework_workflow_staging
Aug 3, 2020
Merged

More expressive workflow inputs.#1029
jmchilton merged 1 commit intogalaxyproject:masterfrom
jmchilton:rework_workflow_staging

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@jmchilton jmchilton commented Jul 22, 2020 •
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Synchronizes the code with Galaxy and implements tagged inputs, nested collections, utilization of newer upload mode - data fetch API.

Fixes #1018

@jmchilton jmchilton force-pushed the rework_workflow_staging branch 5 times, most recently from d695e68 to e6f17ac Compare July 27, 2020 02:12
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jmchilton commented Jul 27, 2020 

galaxy.tools ERROR 2020-07-27 02:18:56,427 Exception caught while attempting to execute tool with id 'upload1':
Traceback (most recent call last):
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/__init__.py", line 1601, in handle_single_execution
    collection_info=collection_info,
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/__init__.py", line 1685, in execute
    return self.tool_action.execute(self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs)
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/actions/upload.py", line 29, in execute
    rval = self._setup_job(tool, trans, incoming, dataset_upload_inputs, history)
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/actions/upload.py", line 47, in _setup_job
    uploaded_datasets = upload_common.get_uploaded_datasets(trans, '', incoming, dataset_upload_inputs, history=history)
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/actions/upload_common.py", line 311, in get_uploaded_datasets
    uploaded_datasets.extend(dataset_upload_input.get_uploaded_datasets(trans, params))
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/parameters/grouping.py", line 625, in get_uploaded_datasets
    datasets = get_filenames(file_contexts)
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/parameters/grouping.py", line 486, in get_filenames
    for file_bunch in get_url_paste_urls_or_filename(context, override_name=name, override_info=info):
  File "/tmp/tmp8igla_0x/galaxy-dev/lib/galaxy/tools/parameters/grouping.py", line 374, in get_url_paste_urls_or_filename
    raise AdminRequiredException()
galaxy.exceptions.AdminRequiredException: Action requires admin account.

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jmchilton commented Jul 27, 2020

Well clearly this is just already broken in Planemo - https://github.com/galaxyproject/planemo/pull/1040/checks?check_run_id=915526962 - how did I miss this ugh. It will attempt to upload by path paste even for non-admin accounts.

@jmchilton jmchilton force-pushed the rework_workflow_staging branch 14 times, most recently from 76b003a to d9fac8d Compare July 29, 2020 18:32
@jmchilton jmchilton mentioned this pull request Jul 31, 2020
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@jmchilton jmchilton force-pushed the rework_workflow_staging branch 5 times, most recently from 1bd0ea1 to 3d7f563 Compare August 3, 2020 01:47
@jmchilton jmchilton changed the title [WIP] More expressive workflow inputs. More expressive workflow inputs. Aug 3, 2020
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Rev galaxy-tool-util for staging of workflow inputs...
01c0716 
Synchronizes the code with Galaxy and implements tagged inputs, nested collections, utilization of newer upload mode - data fetch API.
@jmchilton jmchilton force-pushed the rework_workflow_staging branch from 3d7f563 to 01c0716 Compare August 3, 2020 03:20
@jmchilton jmchilton mentioned this pull request Aug 3, 2020
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@jmchilton jmchilton merged commit 2cbbfde into galaxyproject:master Aug 3, 2020
@bgruening bgruening mentioned this pull request Aug 3, 2020
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Accept inputs for collection_type: list:paired for workflow testing

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