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Add ability to test data manager tools#912

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jmchilton merged 3 commits intogalaxyproject:masterfrom
mvdbeek:test_data_managers
May 9, 2019
Merged

Add ability to test data manager tools#912
jmchilton merged 3 commits intogalaxyproject:masterfrom
mvdbeek:test_data_managers

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@mvdbeek mvdbeek commented Feb 7, 2019

xref galaxyproject/galaxy#7331, needs at least a single test

@mvdbeek mvdbeek force-pushed the test_data_managers branch 2 times, most recently from a70ec1d to e932bc9 Compare February 8, 2019 09:23
@mvdbeek mvdbeek changed the title WIP: Add ability to test data manager tools Add ability to test data manager tools Feb 8, 2019
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mvdbeek commented Feb 8, 2019

Alright, this works nicely, but we'll need to wait for galaxyproject/galaxy#7331 and a new galaxy-lib release.

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New galaxy-lib released, is this ready to go? I triggered a Travis rebuild. Sorry for the delay @mvdbeek.

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nsoranzo commented Mar 2, 2019

We need to update requirements.txt to require galaxy-lib>=19.5.0

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Hmm... we need to add some sort of fallback for interface compatibility or update Planemo. I'll see if I can figure this out today...

Exception [verify() got an unexpected keyword argument 'get_filename'], Traceback [['Traceback (most recent call last):\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/testing.py", line 326, in invoke\n cli.main(args=args or (), prog_name=prog_name, **extra)\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/core.py", line 717, in main\n rv = self.invoke(ctx)\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/core.py", line 1137, in invoke\n return _process_result(sub_ctx.command.invoke(sub_ctx))\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/core.py", line 956, in invoke\n return ctx.invoke(self.callback, **ctx.params)\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/core.py", line 555, in invoke\n return callback(*args, **kwargs)\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/decorators.py", line 64, in new_func\n return ctx.invoke(f, obj, *args, **kwargs)\n', ' File "/home/travis/build/galaxyproject/planemo/.tox/py36-quick/lib/python3.6/site-packages/click/core.py", line 555, in invoke\n return callback(*args, **kwargs)\n', ' File "/home/travis/build/galaxyproject/planemo/planemo/cli.py", line 195, in handle_blended_options\n return f(*args, **kwds)\n', ' File "/home/travis/build/galaxyproject/planemo/planemo/commands/cmd_test.py", line 87, in cli\n test_data = engine.test(runnables)\n', ' File "/home/travis/build/galaxyproject/planemo/planemo/engine/interface.py", line 82, in test\n test_case_data = test_case.structured_test_data(run_response)\n', ' File "/home/travis/build/galaxyproject/planemo/planemo/runnable.py", line 256, in structured_test_data\n self._check_output(output_id, output_value, output_test)\n', ' File "/home/travis/build/galaxyproject/planemo/planemo/runnable.py", line 314, in _check_output\n output_test,\n', ' File "/home/travis/build/galaxyproject/planemo/planemo/test/_check_output.py", line 43, in check_output\n verify_extra_files=None,\n', "TypeError: verify() got an unexpected keyword argument 'get_filename'\n"]]

@mvdbeek mvdbeek force-pushed the test_data_managers branch from b30913d to a2ccfe7 Compare April 9, 2019 12:44
@mvdbeek mvdbeek force-pushed the test_data_managers branch 2 times, most recently from aab0967 to 35b0f4c Compare May 8, 2019 21:12
@mvdbeek mvdbeek force-pushed the test_data_managers branch from 35b0f4c to 05c0e5a Compare May 8, 2019 21:22
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mvdbeek commented May 9, 2019

Alright, it's green!

@mvdbeek mvdbeek requested a review from jmchilton May 9, 2019 09:25
@jmchilton jmchilton merged commit f633e08 into galaxyproject:master May 9, 2019
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Amazing! Of course as always, but still just incredible and so essential. Thanks so much!

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nsoranzo commented May 9, 2019

@mvdbeek
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mvdbeek commented May 9, 2019

We'll also need a new planemo release, but maybe we can wait for #931

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We have got to get that gemini data manager PR merged and pushed - I'm going to just release as is right now, hope that is okay.

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mvdbeek commented May 9, 2019

Of course!

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Planemo 0.59.0 has been released - thanks all! This is incredible.

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3 participants