Nate Coraor
e4a1d57278
Security fixes for tool shed repository browsing
2016-02-24 11:18:23 -05:00
Nate Coraor
cd8b96553f
Remove sample tracking manual external service transfer due to security concerns
2016-02-24 11:18:23 -05:00
John Chilton
ce24ec6821
Remove alert from toolbox reload.
2016-01-03 13:10:55 +00:00
John Chilton
864cc32892
Allow toolbox reloading via app, UI, and API.
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Introduce an app ToolCache to help ensure this operation remains speedy.
2016-01-03 13:10:08 +00:00
Daniel Blankenberg
30668fe534
Fix for reloading tools that have non-standard tool_ids/versions.
2015-11-10 11:58:17 -05:00
Dannon Baker
54ee8cfdc0
Update old dynatree usage to 1.0 standards, clean up some of the extra-chatty debugging and an invalid ajaxComplete attachment that we don't need.
2015-10-06 10:34:12 -04:00
Daniel Blankenberg
1e6c49b277
Allow uninstalling multiple toolshed repositories at a time within the Galaxy UI, using checkboxes with grid multi-actions.
2015-07-28 16:22:16 -04:00
Kyle Ellrott
745c777879
Clarifing naming to use 'Phase'
2015-06-09 11:08:25 -07:00
Kyle Ellrott
b904a5fddd
Adding system to log tool loading/preperation exceptions so that they can be viewed in an admin dialog
2015-06-08 22:33:01 -07:00
Dave B
f1af5c6c92
Attach the uninstall label to the checkbox.
2015-03-24 15:54:13 -04:00
Nate Coraor
23f3e479be
Remove memdump, which probably has not worked for many years.
2015-01-28 16:20:30 -05:00
Dave Bouvier
126c98031f
Remove the alert popups from the repository and tool dependency installation status pages.
2015-01-28 11:49:48 -05:00
Dannon Baker
551dfc453e
Allow cancelling of upload jobs. This won't cancel the actual upload, but it'll kill (or prevent) the processing job if it exists. This also allows one to clean up 'zombie' upload jobs that never leave 'upload' state via the admin panel.
2015-01-26 16:25:19 -05:00
John Chilton
aa86181e7c
Move ToolSection and ToolSectionLabel out of galaxy.tools directly.
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Would like to move the whole ToolBox out of galaxy.tools and into galaxy.tools.toolbox but need to separate all dependencies on galaxy.tools first.
2014-12-31 18:21:10 -05:00
John Chilton
8edced2685
Bugfix: Apply tool panel filtering in workflow editor.
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Bug originally reported by Eric here - http://dev.list.galaxyproject.org/Bug-Toolbox-filters-not-applied-in-workflows-td4662879.html (though this only fixes the superficial bug of them showing up in the workflow editor - and does not yet implement "strong" toolbox filters as requested).
This is actually a broader change that centralizes logic for listing out tool panel contents when displaying components to the user and the added filtering comes about from that. It also eliminates the last places Galaxy was accessing toolbox.tool_panel directly (in those mako templates).
2014-12-29 11:48:38 -05:00
Daniel Blankenberg
190409af3a
Do not |h escape tool dependency error message, as it is escaped and formated by tool_shed.util.basic_util.to_html_string
2014-12-15 17:01:07 -05:00
Dave Bouvier
69ff4677bc
Escape anything that could be user input in mako templates, add markupsafe.escape to username and email in users API controller.
2014-12-10 11:31:21 -05:00
Martin Cech
7f4e8140a1
propagate the commit of 795336f22d8b94b86256b1d4738ee1bf24e18b57 that is already in next-stable to the stable
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original commit msg:
none of the requests & forms controllers used escaping so I escaped the variables exclusively in the templates
2014-12-03 13:29:03 -05:00
Dannon Baker
21eb0edea3
Web helpers (${h.*}) in mako used to_json_string, now dumps.
2014-09-08 17:03:22 -04:00
Dave Bouvier
cf419552da
Add feature to download a tarball containing tool XML, tool wrapper script, test inputs and outputs, and tool data table definitions + sample .loc file.
2014-08-27 14:55:43 -04:00
Dannon Baker
600cdc5b8f
Clarify wording, explain cutoff. Add headers to better segment the page and prevent confusion between the two grids.
2014-08-26 10:48:12 -04:00
Dannon Baker
0ed6b9f4ee
Remove extra p tag from jobs admin.
2014-08-26 10:28:38 -04:00
Dannon Baker
a8d95b5a04
Merge 'recent jobs' view from PR466/467. Work in progress.
2014-08-26 10:28:00 -04:00
Dannon Baker
946dfb74ff
Re-enable administrative job lock, works with multiple handler processes using the internal message queue
2014-08-20 09:48:19 -04:00
Dave Bouvier
da73ca12e7
Remove deprecated "data admin" code, since the functionality was implemented better with Dan's data manager framework.
2014-07-08 13:17:22 -04:00
Greg Von Kuster
02c71550da
Add a confirmation page when purging installed repositories and include a fix for purging an installed repository that has a tool version lineage chain.
2014-06-26 13:54:51 -04:00
Greg Von Kuster
37eabda30b
Eliminate the use of the common_install_util module for Galaxy installs from the Tool Shed.
2014-06-18 22:08:00 -04:00
Greg Von Kuster
f34f8877de
Eliminate the use of trans in most functions in the Tool Shed's shed_util_common utility module.
2014-06-12 15:43:38 -04:00
Greg Von Kuster
b2f3d6a551
Continued down-sizing of the Tool Shed's shed_util_common module by moving certain functions to more appropriate locations. Some fixes for adding and removing entries to the Tool Shed's repository registry.
2014-05-28 11:17:50 -04:00
Daniel Blankenberg
421e88cd05
Display line errors in data table registry display encountered when loading a location file.
2014-05-13 16:10:27 -04:00
Daniel Blankenberg
f5d2c1eb7d
When viewing tool data table registry in admin interface, provide link to manage data table interface for each tool data table.
2014-05-13 12:35:35 -04:00
Dave Bouvier
b18b1cb5f3
Merge fix from stable.
2014-04-28 13:20:00 -04:00
Dave Bouvier
53cc897047
Fix server error when attempting to update a repository that defines set_environment tool dependency types.
2014-04-23 16:24:11 -04:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Greg Von Kuster
27e60943bf
The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
2014-04-09 10:11:48 -04:00
Daniel Blankenberg
ba7a5c7b08
When a tool dependency has failed to install, display the error message as pretty escaped html.
2014-04-02 15:15:00 -04:00
Greg Von Kuster
7bdb8a06fb
Handle combinations of newly defined tool dependencies and repository dependencies that are included in updates being pulled to tool shed repositories installed into Galaxy.
2014-03-26 14:58:08 -04:00
Dannon Baker
558d002bd2
Select2 dynamic loading now uses non-static URL (Should fix main's prefixed URL issue)
2014-02-11 11:59:38 -05:00
Greg Von Kuster
7e883fb968
Eliminate the recently introduced restriction on uninstalling repositories that are dependencies of other installed items, but keep the beneficial feature that displays dependent items that will be affected if a repository is uninstalled.
2014-01-20 16:07:08 -05:00
Dave Bouvier
37eb8a5b39
Fix tool configuration reload for changes in 5f6c670.
2014-01-15 08:54:33 -05:00
Dave Bouvier
4663aace4b
Don't try to fetch the nonexistent status element from the dependency tuples.
2013-12-13 11:02:33 -05:00
Greg Von Kuster
0132d1ae0a
Use tuples to define objects in Galaxy's installed_repository_manager.
2013-12-13 10:35:49 -05:00
Greg Von Kuster
b411625e42
Use dependent repositories rather than repository dependencies to define restriction rules allowing for uninstalling repositories.
2013-12-12 10:45:30 -05:00
Greg Von Kuster
430506351e
Allow a tool dependency to be uninstalled from Galaxy only if it is in an error state. Allow an installed repository to be uninstalled from Galaxy only if it has no dependent repositories and none of its contents are dependencies of other repository contents.
2013-12-11 16:36:32 -05:00
Greg Von Kuster
08cc737dd5
Send only a tool panel section id if selecting and existing section or a new tool panel section label when installing repositories that contain tools for display in the Galaxy tool panel from the tool shed. ToolSection objects are not passed at all, so the parameter names have been corrected for better identification.
2013-12-05 16:49:11 -05:00
John Chilton
5984bbe10c
Models: Introduce app.install_model.
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All references to galaxy.model.tool_shed_install models should go through this instance. Right now it is a reference to the same ModelMapping instance, but the goal is to allow them to be two different mappings.
2013-12-05 00:20:54 -06:00
Aysam Guerler
7fbe750594
Grids: Unify operation handling, use new popups, refactor, bug fixes
2013-11-23 16:14:59 -05:00
Dannon Baker
2a91e276b4
Swap impersonate to select2 deferred load w/ filter. This adds a 'f_email' filter parameter to the Users api collection -- we should revisit this before the next stable release to decide how we want API filtering to actually work down the road.
2013-11-20 16:59:01 -08:00
Greg Von Kuster
a9b52453be
Move pass-through params from the request to the form data when reselecting a tool panel section when reinstalling an uninstalled tool shed repository that contains tools.
2013-10-31 10:23:46 -04:00
Nate Coraor