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41d7155fb6defa3ec83fdaaa93182b9935b6f53d
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21210 Commits
Author SHA1 Message Date
Daniel Blankenberg 41d7155fb6 Add requires_domain to entry_point. Default is False. Currently only True works. 2019-08-20 16:20:48 -04:00
Daniel Blankenberg ab6e934fd3 minor typo 2019-08-20 15:58:13 -04:00
Daniel Blankenberg 4bda4c92bd Make InteractiveTools enable-able. 2019-08-20 14:57:45 -04:00
Daniel Blankenberg c3c4aefcbd Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-20 13:44:44 -04:00
John Chilton b179c72412 Merge pull request #8078 from mvdbeek/single_task_scheduler 
Delegate config file watching to single handler
 2019-08-20 10:35:13 -04:00
jvanbraekel 87d9a0d1a8 Handle the auto registration conflict error 
Catch and display to the user (as message) any conflict error raised by
the authentication providers in case of autoregistration.
 2019-08-20 01:23:03 +01:00
Julien Van Braekel 6b17aaf9b1 Fix the not logged exeption during AD authentication, now log and reraise it properly 2019-08-20 01:22:05 +01:00
Marius van den Beek 2d6e87b986 Merge pull request #8409 from bernt-matthias/topic/argument-dashes 
argument tag: automatically replace dashes by underscores
 2019-08-19 16:56:45 +02:00
Marius van den Beek 9eabc9c65f Merge pull request #8315 from natefoo/installable-config 
Config updates for installable Galaxy
 2019-08-19 16:54:37 +02:00
Marius van den Beek ce61509122 Merge pull request #8473 from nsoranzo/restore_mysql 
Fix MySQL database creation and migrations
 2019-08-19 16:52:59 +02:00
M BerntandNicola Soranzo 92b4c80b6f documentation improvements 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-19 11:33:41 +02:00
M BerntandNicola Soranzo 6169b692b0 fix apparent copy paste error 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-19 10:52:36 +02:00
M BerntandNicola Soranzo 779fabeadf argument tag: move name+argument parsing 
- to tool_util.parser.util
- make ToolParameter.build work with InputSource
  instead of plain XML as commonly done in tests
- refactor stdio related function to tool_util.parser.stdio
  to avoid circular import

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-19 10:52:36 +02:00
M BerntMarius van den BeekNicola Soranzo
 		63436d9233 add linting of input and output names 
checks if input and output names are valid cheetah placeholders

Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-19 10:46:56 +02:00
M Bernt a7e49048e6 argument tag: replace dashes by underscores 2019-08-19 10:46:56 +02:00
Nicola Soranzo fa1b4ce5db Reimplement MetadataSpecCollection as subclass of OrderedDict 2019-08-18 19:40:20 +01:00
Dannon Baker 29b9a7c7eb Fix symlink busted in rebase. 2019-08-18 19:25:45 +01:00
Dannon Baker 36b2067066 Swap another non-insert-necessary odict usage. 2019-08-18 19:25:45 +01:00
Dannon Baker 74c56ff14e Retain odict module for use in tool panel and metadata extensions, note 
that it likely should not be used *unless* insert functionality is
specifically required.
 2019-08-18 19:25:44 +01:00
Dannon Baker b191003626 Add suggestions/fixes from @nsoranzo -- thanks! 2019-08-18 19:25:44 +01:00
Nicola Soranzo e007cc928f Fix `items() and keys()` not supporting indexing on Py3 2019-08-18 19:25:44 +01:00
Dannon Baker 9c9d3e31c9 Namespace conflict; force absolute import. 2019-08-18 19:25:44 +01:00
Dannon Baker b27daadad0 Attempt to fix a TODO in cwl/representation since OrderedDict is json serializable. 2019-08-18 19:25:44 +01:00
Dannon Baker d6cf262ffe Swap all odicts for OrderedDicts, remove galaxy.util.odict 2019-08-18 19:25:44 +01:00
Dannon Baker 95ff5ac381 Testing the waters (i.e. the full suite) swapping our odict for real OrderedDicts 2019-08-18 19:25:44 +01:00
Björn Grüning 98ceb835d2 Merge pull request #8456 from selten/data-libraries-file-extension 
Add file extensions when downloading from data libraries
 2019-08-18 17:18:10 +02:00
mvdbeek f3276bf1db Always use send_control_task via queue_worker 2019-08-18 16:01:32 +02:00
mvdbeek 30027a094b Rename instances of GalaxyQueueWorker from control_worker to queue_worker 
It just seems more logical, and I repeatedly was using the queue_worker
instead of control_worker and wondering why things didn't work.
 2019-08-18 16:01:32 +02:00
mvdbeek a05abc41f5 Add task sending to GalaxyQueueWorker class 
Resolves import issues in app package and overall seems more coherent.
 2019-08-18 16:01:32 +02:00
mvdbeek 523eb860ff Fix restarting ToolConfWatcher 2019-08-18 16:01:32 +02:00
mvdbeek c75d884fe5 No need for register_postfork_function in ToolConfWatcher, watchers will always be started after forking 2019-08-18 16:01:32 +02:00
mvdbeek e73a20db02 Require explicit thread start 2019-08-18 16:01:32 +02:00
mvdbeek 2046303079 Remove unused NullToolConfWatcher, use NullWatcher from galaxy.util 
I couldn't find a single use of NullToolConfWatcher on github,
so I'm going to assume this has never been used.
 2019-08-18 16:01:32 +02:00
mvdbeek 14a8507ce0 Drop ToolDataWatcher and LocFileEventHandler 
The very neat `get_watcher` and `EventHandler` classes
can do the same thing.
 2019-08-18 16:01:32 +02:00
mvdbeek 5791ea17af No mutable default args 2019-08-18 16:01:32 +02:00
mvdbeek b99fa24e36 Move up control queue shutdown 
We don't want to start reconfiguring the watcher while shutting
down.
 2019-08-18 16:01:32 +02:00
mvdbeek 3abaf24ba3 Share start/stop logic in Watcher classes 2019-08-18 16:01:32 +02:00
mvdbeek d158c1b150 Use send_control_task to reload job rules 2019-08-18 16:01:32 +02:00
mvdbeek b0dd3a1652 Allow sending control task that reloads a data table by path 2019-08-18 16:01:32 +02:00
mvdbeek 1fd283309d Remove process from worker processes on shutdown 
When shutting down process remove process from WorkerProcess table and
let remaining handler pick a new config watcher. Reduces the time during
which config changes would go unnoticed to a couple of milliseconds.
 2019-08-18 16:01:32 +02:00
mvdbeek f65ed9b43d Delegate config file watching to single handler 
This should reduce IO especially on instances that use a lot of
handlers and/or on a remote file system.

The process that watches the tool conf files will now
be the active process that alphabetially compares highest.
If that process goes away or is superseded by a process that
compares higher now that process will take over.
If a change has been found a control task will be sent via
the kombu messaging system.

Overall this works nicely, but while stopping the current
config watcher there is a small break during which changes
to the config don't trigger a reload, this could be handled
more gracefully.
 2019-08-18 16:01:32 +02:00
Nicola Soranzo d80687a8db Fix MySQL database creation and migrations 
Fix https://github.com/galaxyproject/galaxy/issues/6401 .
Fix https://github.com/galaxyproject/galaxy/issues/8400 .

Remove `index=True` from some `Column()` definitions in
lib/galaxy/model/mapping.py when the index was not part of any migration.
 2019-08-18 11:17:35 +01:00
Nicola Soranzo 1f45e54daf Handle better an SQLAlchemy Migrate issue 
when adding a column with both a ForeignKey and an index in SQLite.
 2019-08-18 11:17:35 +01:00
Nicola Soranzo 4ece752ebe Another round of migration refactoring 
Allow `table` to be a string in `drop_table()`.

Sync definition of `form_definition` and `form_definition_current` tables
between migration 8 and `mapping.py` .

Drop unnecessary logging configurations.
 2019-08-18 11:17:35 +01:00
Nicola Soranzo 6de82ed531 Fix create_db.sh 
Broken in commit d34142e420 .

Traceback:

```
$ rm -f database/universe.sqlite && sqlite3 database/universe.sqlite 'VACUUM;' && ./create_db.sh
Activating virtualenv at .venv
Traceback (most recent call last):
  File "./scripts/create_db.py", line 44, in <module>
    invoke_create()
  File "./scripts/create_db.py", line 36, in invoke_create
    create_db(config['db_url'], config['config_file'])
  File "/opt/galaxy/lib/galaxy/model/migrate/check.py", line 74, in create_or_verify_database
    elif getattr(app.config, 'database_auto_migrate', False):
AttributeError: 'NoneType' object has no attribute 'config'
```
 2019-08-18 11:17:34 +01:00
John Chilton f82e5e9186 Don't cleanup integration tests twice. 2019-08-15 13:31:06 -04:00
John Chilton 2a20de3848 Merge pull request #8462 from ic4f/dev_config_properties 
Refactor reading config properties from a file
 2019-08-15 11:04:24 -04:00
John Chilton b3a030378a Merge pull request #8450 from guerler/config_visualizations 
Allow admins to disable the visualizations tab in the masthead
 2019-08-15 10:56:36 -04:00
Sergey Golitsynskiy ec74687d12 Refactor reading config properties from a file 2019-08-14 19:11:04 -04:00
Peter Selten ebb4572bd8 Update to set the extension by default 2019-08-14 20:54:17 +02:00