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Add InteractiveTools. #7494

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merged 153 commits into from Aug 22, 2019
Merged

Add InteractiveTools. #7494

merged 153 commits into from Aug 22, 2019

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blankenberg
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Basic idea: launch a container-backed Galaxy Tool and get access to content inside in real time.

  • Give user access via uwsgi (inspired by [wip] Dynamic proxy using uWSGI.  #2385), or another proxy.
  • Access is based upon a key, key_type, token mapping to a host, port. You can have and access any number of RealTimeTools at a time.
  • Port and entry url-path snippet are specified in standard tool.xml files.
  • You can specify any number of ports, so a single RealTimeTool can give access to multiple running applications.
  • RealTimeTools can be added to and installed from the ToolShed.
  • Currently working for docker in local runner.

@nsoranzo @blankenberg
Update lib/galaxy/datatypes/realtime.py
22f6d48 
Co-Authored-By: blankenberg <dan.blankenberg@gmail.com>
@galaxybot galaxybot added this to the 19.05 milestone Mar 8, 2019
@blankenberg blankenberg changed the title Add RealTimeTools. [WIP] Add RealTimeTools. Mar 9, 2019
@jxtx jxtx assigned jxtx and unassigned jxtx Mar 11, 2019
@jxtx jxtx self-requested a review March 11, 2019 15:45
jmchilton
jmchilton reviewed Aug 14, 2019
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test/functional/tools/interactive_tool_juypter_notebook.xml Outdated
#end if
</environment_variable>
<environment_variable name="REMOTE_HOST">TODO</environment_variable>
<environment_variable name="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable>
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We really need a way to inject this and something comparable to galaxy_infrastructure_url without __app__. Willing to implement higher-level primitives for encoded history ID and inject galaxy_infrastructure_url with a per-job destination override option (81b5ca5). Or at least a warning in every sample that uses __app__ that we will break backward compatibility in the near future

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Added warning in 7250162 and 34ec3bf

@blankenberg
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Can you add requires_domain (defaulting to False) or something like that to the tools (entry_point) to keep a path-base proxy approach (instead of sub-domain based proxy) a potential default requirement for the future?

Added in 41d7155

@jmchilton
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jmchilton commented Aug 21, 2019 •
edited

We should use false not False in XML probably (https://www.w3schools.com/xml/schema_dtypes_misc.asp), but yeah - looks great, thanks for adding requires_domain!

This and the warnings and them being off by default really assuage a lot of my fears. I think I'm very close to being +1 on this for 19.09. I really am sorry for saying I would merge it sooner when I wasn't ready to and didn't have the time I thought I did to put into it.

Update: Trying to figure out the tests - are they transient problems?

Update 2: Last laugh is yours though because you cause me physical pain when you demo these being used in workflows or tell people to put them on the ToolShed. If I could somehow make my +1 contingent on you not doing those two things - I would - but I don't think that would be feasible. Despite that though - really fantastic work - I think many people are really excited for these.

@jmchilton jmchilton merged commit 8b2eaba into galaxyproject:dev Aug 22, 2019
@bgruening
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Thanks John for merging.

@jmchilton jmchilton mentioned this pull request Aug 27, 2019
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@lizhi16
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lizhi16 commented Aug 29, 2019

The Interactive Tool is an amazing function. Our team is very interested in it. But we don't find any tutorial about how to deploy the InteractiveTools or how to use it. Could you please provide some advice for us to instruct how to use it. Thanks!

@bgruening
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@lizhi16 we added some initial docs here: https://github.com/blankenberg/galaxy/blob/aea9ed2a219f35ac8b94d11b51ca52ec73cdcb48/doc/source/admin/special_topics/realtimetools.rst

Let us know if this does not help.

This was referenced Oct 17, 2019
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nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Dec 19, 2019
@nsoranzo
Add implementation of parse_interactivetool to CwlToolSource class
3a914e4 
In galaxyproject#7494 and
galaxyproject#8574 , the abstract
`parse_interactivetool()` method was added to the `ToolSource` class
without a corresponding implementation in its `CwlToolSource` subclass,
leading to the following error:

```
In [4]: from galaxy.tool_util.parser.cwl import CwlToolSource
In [5]: cts = CwlToolSource('path')
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-6-2f94370fb293> in <module>()
----> 1 cts = CwlToolSource('path')

TypeError: Can't instantiate abstract class CwlToolSource with abstract methods parse_interactivetool
```
@nsoranzo nsoranzo mentioned this pull request Dec 19, 2019
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@kozbo kozbo mentioned this pull request Feb 4, 2020
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@jmchilton jmchilton mentioned this pull request Feb 10, 2020
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@mvdbeek mvdbeek mentioned this pull request Jul 22, 2021
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