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add work on release notes 16.10, improve docs for webhooks

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Conflicts:
	doc/source/releases/16.10.rst
	doc/source/releases/16.10_announce.rst
This commit is contained in:
Martin Cech
2016-12-07 15:37:44 -05:00
parent d0f39ceff5
commit 3e0e96657d
4 changed files with 108 additions and 91 deletions
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doc/source/admin/index.rst
+3 -1
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@@ -11,7 +11,7 @@ documentation. These resources should be used together.
dependency_resolvers.rst
conda_faq.rst
mulled_containers.rst
interactive_environments.rst
@@ -23,3 +23,5 @@ documentation. These resources should be used together.
grt.rst
chat.rst
webhooks.rst
doc/source/admin/webhooks.rst
+21 -19
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@@ -1,5 +1,7 @@
Galaxy webhooks - tiny plugin interface to extend the Galaxy client
-------------------------------------------------------------------
Galaxy webhooks
===============
Tiny plugin interface to extend the Galaxy client.
Galaxy webhooks provides a simple way of inserting icons, links, or other HTML elements into predefined locations.
For this Galaxy provides some entry points which can be used to extend the client with content. This content
@@ -10,12 +12,12 @@ can consists out of simple HTML, JS or dynamically generated content from a pyth
Plugin activation
-----------------
All webhooks that are included in the main Galaxy distribution are located in the `config/plugins/webhooks/demo` folder
All webhooks that are included in the main Galaxy distribution are located in the ``config/plugins/webhooks/demo`` folder
and are deactivated by default.
To activate these demo webhooks make sure this path is added to `webhooks_dir` in your `galaxy.ini`. You can add as many
webhook folders as you like as a comma separated list.
Webhooks supports one additionl layer of activating/deactivating by changing the `activate: true` in each config of each webhook.
To activate these demo webhooks make sure this path is added to ``webhooks_dir`` in your ``galaxy.ini``. You can add as many
webhook folders as you like as a comma separated list.
Webhooks supports one additionAl layer of activating/deactivating by changing the ``activate: true`` in each config of each webhook.
Entry points
------------
@@ -31,7 +33,7 @@ For each type there is an example provided:
- Tool and workflow: A comic strip can be shown when a tool or a workflow is running. Right now PhD_ and XKCD_ comics are provided.
.. _PhD: http://phdcomics.com
.. _PhD: http://phdcomics.com
.. _XKCD: http://xkcd.com/
.. image:: images_webhooks/tool.png
@@ -42,11 +44,11 @@ For each type there is an example provided:
- Additional functionality can be added to the top menu. Two dummy buttons are implemented to show the idea:
- A button that links to biostars
- A button that links to biostars
.. image:: images_webhooks/masthead.png
:scale: 50 %
- A button that shows a pop-up with information about an user.
- A button that shows a pop-up with information about an user.
.. image:: images_webhooks/masthead_trans_object.png
:scale: 50 %
@@ -72,7 +74,7 @@ Each plugin has the following folder structure:
config
******
------
The configuration file is just a .yml (or .yaml) file with a few options. The following options are mandatory:
@@ -84,7 +86,7 @@ All other options can be anything used by the plugin and accessed later via *web
helper/__init__.py
******************
------------------
*__init__.py has* to have the **main()** function with the following (or similar) structure:
@@ -92,7 +94,7 @@ helper/__init__.py
import logging
log = logging.getLogger(__name__)
def main(trans, webhook):
error = ''
data = {}
@@ -103,16 +105,16 @@ helper/__init__.py
except ImportError as e:
log.exception(e)
return {}
# some processing...
# some processing...
except Exception as e:
error = str(e)
error = str(e)
return {'success': not error, 'error': error, 'data': data}
As an example please take a look at the *phdcomics* example plugin: https://github.com/bgruening/galaxy/blob/feature/plugin-system/config/plugins/webhooks/phdcomics/helper/__init__.py
static
******
------
The *static* folder contains only two files with the specified above names (otherwise, they won’t be read on Galaxy run).
@@ -139,14 +141,14 @@ Issues
------
tool/workflow
*************
-------------
If a tool or a workflow plugin has script.js and/or styles.css, the content of these files will be read as two strings and sent to the client and appended to DOM’s <head>.
Such approach is a possible bottleneck if the two files are big (however, this shouldn’t ever happen because plugins are supposed to be small and simple).
masthead
********
--------
Topbar buttons are hard coded, so they’re rendered only after *make client*.
@@ -167,7 +169,7 @@ I found a not very optimal way to add buttons to the topbar (masthead):
});
history-menu
************
------------
History Panel items are again hard coded, but in the current implementation they’re rendered as html elements (so, they’re not even stored in a collection or any other object).
doc/source/releases/16.10.rst
+60 -62
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@@ -6,28 +6,11 @@
.. announce_start
Enhancements
-------------------------------
Highlighted Enhancements
------------------------
.. major_feature
* Introduce Galaxy Webhooks - plugins for the web UI
(including work from `@bgruening <https://github.com/bgruening>`__,
and `@anatskiy <https://github.com/anatskiy>`__).
`Pull Request 3040`_, `Pull Request 3102`_
* The workflow run form has been replaced by one backed by the new tool form and the API.
`Pull Request 2669`_, `Pull Request 2720`_, `Pull Request 2766`_,
`Pull Request 2776`_, `Pull Request 2770`_, `Pull Request 2895`_,
`Pull Request 2935`_, `Pull Request 3007`_, `Pull Request 2969`_,
`Pull Request 2799`_, `Pull Request 3082`_, `Pull Request 2672`_,
`Pull Request 2920`_, `Pull Request 2777`_, `Pull Request 2902`_
* Overhaul of charts visualization - more visualizations, more options, and better user interface.
`Pull Request 2875`_, `Pull Request 2820`_
* Paginate contents of large histories.
`Pull Request 2588`_
* Reload tools automatically without restarting Galaxy during tool shed installs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 2840`_, `Pull Request 3025`_
* Implement a collection operation tool for merging collections
(thanks to `@Takadonet <https://github.com/Takadonet>`__).
`Pull Request 2771`_
@@ -44,7 +27,7 @@ Enhancements
* Add "Save as" as an option in the workflow editor
(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
`Pull Request 3035`_
* Replace `reference documentation <https://docs.galaxyproject.org/en/latest/dev/schema.html>`__
* Replace `reference documentation <https://docs.galaxyproject.org/en/latest/dev/schema.html>`__
for tool XML files with automatically generated
documentation from a now official Galaxy XSD documentation (with help from many).
`Pull Request 2923`_, `Pull Request 2936`_, `Pull Request 3086`_,
@@ -53,6 +36,19 @@ Enhancements
* Allow naming input datasets and collections during workflow extraction.
`Pull Request 2943`_
* Various enhancements for API driven installation of tool shed repositories.
Enhancements
-------------------------------
* Add "Save as" as an option in the workflow editor
(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
`Pull Request 3035`_
* Allow '.' and '_' for public names
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 2947`_
* Allow naming input datasets and collections during workflow extraction.
`Pull Request 2943`_
* Various enhancements for API driven installation of Tool Shed repositories.
`Pull Request 2769`_
* Implement beta support for discovering biocontainer Docker containers automatically for tool dependencies.
`Pull Request 2986`_
@@ -75,9 +71,6 @@ Enhancements
collection workflows
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 2978`_
* Allow '.' and '_' for public names
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 2947`_
* Add CEL datatype
(thanks to `@nturaga <https://github.com/nturaga>`__).
`Pull Request 3073`_
@@ -96,8 +89,6 @@ Enhancements
on library dataset import
(thanks to `@SANBI-SA <https://github.com/SANBI-SA>`__).
`Pull Request 2819`_
* Fix dataset selector update when deleting history items.
`Pull Request 2677`_
* Add a tutorial on building job runners to the documentation
(thanks to `@varunshankar <https://github.com/varunshankar>`__).
`Pull Request 2700`_
@@ -114,11 +105,6 @@ Enhancements
`Pull Request 2857`_, `Pull Request 2858`_, `Pull Request 2689`_,
`Pull Request 2865`_, `Pull Request 2952`_, `Pull Request 2695`_,
`Pull Request 2991`_, `Pull Request 3232`_
* Various datatypes fixes and enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 2690`_
* Various fixes and improvements for galaxy.json.
`Pull Request 2697`_
* Improve samtools usage with ``--version-only`` check
(thanks to `@remimarenco <https://github.com/remimarenco>`__).
`Pull Request 2705`_
@@ -163,8 +149,6 @@ Enhancements
`Pull Request 2832`_
* Filter disposable mail blacklist on the first domain level only.
`Pull Request 2839`_
* Fix link target in admin view of tool lineages.
`Pull Request 2862`_
* Refactor duplicated back-end code to create a new ``trans`` method for
getting the most recently touched history.
`Pull Request 2870`_
@@ -181,9 +165,6 @@ Enhancements
`Pull Request 3016`_
* Add documentation on optional ``multiple="true"`` data parameters.
`Pull Request 3024`_
* Fix tool XSD to accept a help attribute for ``section``s
(thanks to `@joachimwolff <https://github.com/joachimwolff>`__).
`Pull Request 3131`_
* In Trackster, read numerical data directly from bigWig files.
`Pull Request 2880`_
* Improve wording of tool installation forms
@@ -200,8 +181,6 @@ Enhancements
* Extend ``PUT /api/workflows/{id}`` with additional workflow properties
(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
`Pull Request 3080`_
* Update the copyright year in the LICENSE.txt.
`Pull Request 2926`_
* Remove unnecessary use of binascii
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 2946`_
@@ -224,19 +203,15 @@ Enhancements
* Pass dependency shell command errors to log
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3129`_
* Fix for bioconda recipes depending on conda-forge.
`Pull Request 3023`_
* Increase min number of columns for pileup sniffing to 5
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3033`_
* Remove outdated warning on ID_SECRET
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 3046`_
* Always display text
`Pull Request 3052`_
* Add Galaxy architecture slides documentation to project.
`Pull Request 3060`_, `Pull Request 3091`_
* Add tool XML reload to tool run page - for admins only
* Add tool XML reload to tool run page - for admins only
(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
`Pull Request 3070`_, `Issue 943 <https://github.com/galaxyproject/galaxy/issues/943>`__
* Move thumbnail list view to shared UI elements, revise tabs, add test cases
@@ -255,53 +230,71 @@ Enhancements
`Pull Request 3169`_, `Pull Request 2888`_
* Add links to local tours to sample welcome.
`Pull Request 3176`_
* Fix history deletion bug when using impersonation.
`Pull Request 2654`_
* Fix dataset selector update when deleting history items.
`Pull Request 2677`_
* Refactor upload dialog to use local CSS classes and avoid model listeners.
`Pull Request 2711`_
* Rework tool shed middleware
* Rework Tool Shed middleware
`Pull Request 2782`_, `Pull Request 2753`_
* Refactor - move filelock.py to galaxy.util.
`Pull Request 2879`_
* Use requests in driver_util for better proxy handling
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3013`_
* Add ``download_to_file`` function to ``galaxy.util``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3100`_
* Quote all paths in converter tool XML files
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3165`_
* Add routes to get genomes indexes and sequences
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
`Pull Request 3109`_
* Admin installation UX wording fixes.
`Pull Request 3226`_
Fixes
-------------------------------
* Fix for bioconda recipes depending on conda-forge.
`Pull Request 3023`_
* Fix history deletion bug when using impersonation.
`Pull Request 2654`_
* Fix workflow extraction API tests on PostgreSQL
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3039`_
* Fix link target in admin view of tool lineages.
`Pull Request 2862`_
* Avoid pointless lambda function
(thanks to `@peterjc <https://github.com/peterjc>`__).
`Pull Request 3097`_
* Remove unnecessary ``set_output_history`` parameter
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3155`_
* Various code fixes for object store and docs
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3119`_
* Fix BLAST database *.loc files inconsistency
(thanks to `@peterjc <https://github.com/peterjc>`__).
`Pull Request 3098`_
* Add ``download_to_file`` function to ``galaxy.util``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3100`_
* Log invalid XML filename
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3124`_
* Quote all paths in converter tool XML files
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3165`_
Fixes
-------------------------------
* Various code fixes for object store and docs
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3119`_
* Use default job history on ``build_for_rerun`` if current history is unavailable.
`Pull Request 2668`_
* Fixing button width on composite upload dialog
* Always display text
`Pull Request 3052`_
* Fixing button width on composite upload dialog
(thanks to `@sszakony <https://github.com/sszakony>`__).
`Pull Request 2703`_, `Issue 2591 <https://github.com/galaxyproject/galaxy/issues/2591>`__
* Fix for splitting dataset collections
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
`Pull Request 2708`_
* Various datatypes fixes and enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 2690`_
* Various fixes and improvements for galaxy.json.
`Pull Request 2697`_
* Fix tours pasting content into text area.
`Pull Request 2715`_
* Slight styling tweak to prevent overflow on the right edge in composite upload dialog.
@@ -380,6 +373,9 @@ Fixes
`Pull Request 3049`_
* Remove incorrect communication server check.
`Pull Request 3053`_
* Fix tool XSD to accept a help attribute for ``section``s
(thanks to `@joachimwolff <https://github.com/joachimwolff>`__).
`Pull Request 3131`_
* Fix import orders for updates to flake8_import_order.
`Pull Request 3059`_
* Dataset metadata should not be cached when building chart visualizations.
@@ -388,9 +384,6 @@ Fixes
`Pull Request 3074`_
* Fix qunit local testing install -- now runs on modern node (v6.9.1).
`Pull Request 3089`_
* Add routes to get genomes indexes and sequences
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
`Pull Request 3109`_
* Escape section name when writing to XML
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3122`_
@@ -433,6 +426,10 @@ Fixes
conda environments and API to manage them
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 3227`_
* Update the copyright year in the LICENSE.txt.
`Pull Request 2926`_
* Fix for ToolShed install when copied sample data target exists, but is broken symlink.
`Pull Request 3279`_
.. _Issue 2375: https://github.com/galaxyproject/galaxy/issues/2375
.. github_links
@@ -676,4 +673,5 @@ Fixes
.. _Pull Request 3227: https://github.com/galaxyproject/galaxy/pull/3227
.. _Pull Request 3232: https://github.com/galaxyproject/galaxy/pull/3232
.. _Pull Request 3262: https://github.com/galaxyproject/galaxy/pull/3262
.. _Pull Request 3279: https://github.com/galaxyproject/galaxy/pull/3279
doc/source/releases/16.10_announce.rst
+24 -9
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@@ -6,19 +6,28 @@ October 2016 Galaxy Release (v 16.10)
.. include:: _header.rst
Highlights
===========================================================
==========
**Feature1**
Feature description.
**Galaxu UI plugins - Webhooks**
We introduce Galaxy Webhooks - optiuonal plugins for the web UI that allow for better customization of your instance. See the `documentation <https://docs.galaxyproject.org/en/master/admin/webhooks.html>`__.
Includes work from `@bgruening <https://github.com/bgruening>`__, `@anatskiy <https://github.com/anatskiy>`__, and Joachim Wolff `@joachimwolff <https://github.com/joachimwolff>`__.
Implemented in `Pull Request 3040`_.
**Feature2**
Feature description.
**Workflow run form replaced**
The workflow run form has been replaced by one backed by the new tool form and the API. Nicer, faster, standardized.
Implemented in `Pull Request 2669`_, `Pull Request 2720`_, `Pull Request 2766`_,
`Pull Request 2776`_, `Pull Request 2770`_, `Pull Request 2895`_,
`Pull Request 2935`_, `Pull Request 3007`_, `Pull Request 2969`_,
`Pull Request 2799`_, `Pull Request 3082`_, `Pull Request 2672`_,
`Pull Request 2920`_, `Pull Request 2777`_, `Pull Request 2902`_.
**Feature3**
Feature description.
**Automatic tool reload after installation**
Galaxy does not need to be restarted after tool installation anymore. This provides a smoother experience for your users. Yay!
Thanks to `@mvdbeek <https://github.com/mvdbeek>`__.
Implemented in `Pull Request 2840`_, `Pull Request 3025`_.
`Github <https://github.com/galaxyproject/galaxy>`__
===========================================================
=====================================================
New Galaxy repository
.. code-block:: shell
@@ -32,8 +41,14 @@ Update of existing Galaxy repository
See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
Deprecation Notices
===================
* API-like endpoints (returning JSON) that start with ``<galaxy>/root/`` in the URL are now deprecated and will be removed in future releases. Please use proper API (e.g. ``/api/histories`` or ``/api/tools``) to replace your implementations.
* The ``jsonp`` parameter for search API endpoints in Tool Shed is deprecated and will be removed in the future. Instead the presence of a ``callback`` argument will trigger the JSONP format to be returned.
Release Notes
===========================================================
=============
.. include:: 16.10.rst
:start-after: announce_start