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Do not skip Galaxy client build for ``planemo serve`` #895

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merged 11 commits into from Nov 24, 2018

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nsoranzo commented Nov 18, 2018

Fix #845 .

Also, convert an existing gx_repo git repository from bare to mirror before doing a git remote update.

@nsoranzo nsoranzo requested a review from mvdbeek Nov 18, 2018

@nsoranzo nsoranzo changed the title Do not skip client build for planemo serve Do not skip Galaxy client build for ``planemo serve`` Nov 18, 2018

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bgruening commented Nov 18, 2018

I requested an increased max build time from travis, let's see if they grant it.

Show resolved Hide resolved planemo/galaxy/serve.py Outdated

@nsoranzo nsoranzo force-pushed the nsoranzo:serve_rebuild_client branch 3 times, most recently from baddf30 to 0caa8dc Nov 20, 2018

nsoranzo added some commits Nov 18, 2018

Install Galaxy when the directory specified with ``--galaxy_root` doe…
…s not exist

or is empty.

Raise an `Exception` if `--galaxy_root` specifies an existing directory and
`--install_galaxy` is set.

Remove unused `_shed_tool_conf()` function and
`FAILED_TO_FIND_GALAXY_EXCEPTION` constant.
Run all ServeTestCase tests with the same ``galaxy_root`` directory
to not rebuild the Galaxy client every time.
Fix broken shell command
Various tests produced the following error:
```
Set $GALAXY_VIRTUAL_ENV to /home/travis/.planemo/gx_venv
/bin/sh: 1: if [ -e "$GALAXY_VIRTUAL_ENV" ]; : not found
run command exited with return code 127
```

Introduced in commit 434099e .
Remove unneeded `--galaxy_branch` option in 4 tests
Fix wrong tool version in workflow.
Set ``server_name`` before using it
Otherwise the `pid_file` is set to the wrong filename, preventing
`LocalGalaxyConfig.kill()` from working when running Galaxy under Python 3.

Follow-up to #874 .

@nsoranzo nsoranzo force-pushed the nsoranzo:serve_rebuild_client branch from 0caa8dc to e71791c Nov 23, 2018

nsoranzo added some commits Nov 23, 2018

Update ``random_lines1`` tool from galaxy repo
for Python 3 compatibility.
Default host to 127.0.0.1
Fix the following traceback:

```
Problem serving Galaxy
Traceback (most recent call last):
  File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/serve.py", line 22, in serve
    return _serve(ctx, runnables, **kwds)
  File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/serve.py", line 43, in _serve
    cmd = config.startup_command(ctx, **kwds)
  File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/config.py", line 963, in startup_command
    host=kwds['host'],
KeyError: 'host'
```
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nsoranzo commented Nov 23, 2018

Finally green!! 🎉

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mvdbeek left a comment

Awesome! Thanks a lot @nsoranzo !

@bgruening bgruening merged commit 3ab358e into galaxyproject:master Nov 24, 2018

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bgruening commented Nov 24, 2018

Thanks all!

@nsoranzo nsoranzo deleted the nsoranzo:serve_rebuild_client branch Nov 25, 2018

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nsoranzo commented Nov 25, 2018

Time for a new Planemo release supporting Galaxy 18.09?

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jmchilton commented Jan 1, 2019

I let you all down on this - sorry :(. Just released this.

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