| bbbd1b4 | Daniel Blankenberg | 10 January 2013, 19:57:37 UTC | Fixes for Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes an issue where rurun would select the wrong input dataset. | 10 January 2013, 19:57:37 UTC |
| 979c1a6 | Daniel Blankenberg | 07 January 2013, 16:45:30 UTC | Pack scripts. | 07 January 2013, 16:45:30 UTC |
| fce8cce | Daniel Blankenberg | 07 January 2013, 16:45:26 UTC | Fix for workflow editor when a missing tool is connected to a valid tool. Javascript error would cause the 'Loading worflow editor...' modal window to spin indefinitely. | 07 January 2013, 16:45:26 UTC |
| c7da7da | Daniel Blankenberg | 07 January 2013, 16:07:52 UTC | Enhance Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes issue where a server error would occur within workflows when parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input. | 07 January 2013, 16:07:52 UTC |
| 0ea7786 | Greg Von Kuster | 04 January 2013, 21:10:26 UTC | Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy. | 04 January 2013, 21:10:26 UTC |
| 092fa9f | James Taylor | 04 January 2013, 19:42:28 UTC | remove trailing comma | 04 January 2013, 19:42:28 UTC |
| ab977b3 | James Taylor | 04 January 2013, 19:38:06 UTC | Fix for scrolling on iOS (thanks Carrie Ganote!) | 04 January 2013, 19:38:06 UTC |
| 99c12fb | Jeremy Goecks | 04 January 2013, 17:07:38 UTC | Improve wording for item sharing. | 04 January 2013, 17:07:38 UTC |
| 06158e1 | Dave Bouvier | 04 January 2013, 16:30:11 UTC | Tool shed functional tests for repositories with invalid tools, functional test enhancement for repositories with workflows. | 04 January 2013, 16:30:11 UTC |
| fc4ca70 | Carl Eberhard | 04 January 2013, 15:57:18 UTC | history panel: panel was not showing deleted datasets when a dataset was purged (even when set to 'include deleted datasets') - fix by using purge_async; history panel: fix history-options menu checkbox with new font awesome class format; pack scripts | 04 January 2013, 15:57:18 UTC |
| 9d3a386 | Greg Von Kuster | 04 January 2013, 14:17:47 UTC | Make sure metata is set for repositories in the tool shed that contain only invalid tools. | 04 January 2013, 14:17:47 UTC |
| 0a3faf8 | Jeremy Goecks | 04 January 2013, 03:07:55 UTC | Fix bugs that prevented creating a Circster visualization from a dataset. | 04 January 2013, 03:07:55 UTC |
| 21eab42 | Nate Coraor | 03 January 2013, 21:34:40 UTC | merge | 03 January 2013, 21:34:40 UTC |
| 9dc85b4 | Nate Coraor | 03 January 2013, 21:32:55 UTC | backout ab827b2c7907 | 03 January 2013, 21:32:55 UTC |
| 7ba75c4 | Nate Coraor | 03 January 2013, 21:32:43 UTC | backout 8c6cf637058a | 03 January 2013, 21:32:43 UTC |
| 3e7629f | Nate Coraor | 03 January 2013, 21:32:29 UTC | backout e6676636cfe7 | 03 January 2013, 21:32:29 UTC |
| 5666982 | Nate Coraor | 03 January 2013, 21:32:17 UTC | backout e4adc9ad0bb7 | 03 January 2013, 21:32:17 UTC |
| 7974c92 | Nate Coraor | 03 January 2013, 21:32:06 UTC | backout 93dd6202175a | 03 January 2013, 21:32:06 UTC |
| 3c37615 | Nate Coraor | 03 January 2013, 21:30:42 UTC | backout 50c1edba7fe0 | 03 January 2013, 21:30:42 UTC |
| 9b09226 | Nate Coraor | 03 January 2013, 21:30:32 UTC | backout 5822038f8c96 | 03 January 2013, 21:30:32 UTC |
| 45b733a | Nate Coraor | 03 January 2013, 21:30:21 UTC | backout 6265bf3f27ad | 03 January 2013, 21:30:21 UTC |
| 2bb7102 | Nate Coraor | 03 January 2013, 21:30:07 UTC | Backout 875ac898df00 | 03 January 2013, 21:30:07 UTC |
| 5129f63 | Nate Coraor | 03 January 2013, 21:29:41 UTC | backout 2f5544be71d1 | 03 January 2013, 21:29:41 UTC |
| ad4ddad | Nate Coraor | 03 January 2013, 21:29:11 UTC | Backed out 9ec94e5d6a28 | 03 January 2013, 21:29:11 UTC |
| 65bf4b8 | James Taylor | 03 January 2013, 21:21:57 UTC | workflow: tool search always on, fix tool menu padding, using cog icon for options menu | 03 January 2013, 21:21:57 UTC |
| c6f1df0 | Jeremy Goecks | 03 January 2013, 20:12:51 UTC | Add missing import to visualization controller. | 03 January 2013, 20:12:51 UTC |
| db7e355 | Jeremy Goecks | 03 January 2013, 19:54:50 UTC | Enable BBI data provider to work even when chromosome naming conventions are mixed. | 03 January 2013, 19:54:50 UTC |
| 3c5027c | Greg Von Kuster | 03 January 2013, 19:48:26 UTC | Restrict discovery of repository dependencies to those occasions where the user chose to install them. | 03 January 2013, 19:48:26 UTC |
| 2eace29 | James Taylor | 03 January 2013, 19:28:41 UTC | styles: remove old font-awesome svg fonts | 03 January 2013, 19:28:41 UTC |
| d69e971 | James Taylor | 03 January 2013, 19:25:48 UTC | admin: fix scrolling for admin left menu | 03 January 2013, 19:25:48 UTC |
| 28ed3d0 | James Taylor | 03 January 2013, 19:17:59 UTC | styles: update to latest boostrap (2.2.2) and Font-Awesome (3.0) | 03 January 2013, 19:17:59 UTC |
| c8be616 | Dave Bouvier | 03 January 2013, 19:31:09 UTC | Functional tests for installing a repository that contains a workflow. | 03 January 2013, 19:31:09 UTC |
| c53aaf7 | Dave Bouvier | 03 January 2013, 18:28:12 UTC | Fix for installing repository without repository dependencies. | 03 January 2013, 18:28:12 UTC |
| 801fd54 | Greg Von Kuster | 03 January 2013, 16:29:01 UTC | Fix for discovering repository dependencies for a tool shed repository being installed into Galaxy. | 03 January 2013, 16:29:01 UTC |
| 5a7dbec | Jeremy Goecks | 03 January 2013, 14:43:53 UTC | Make Galaxy Q&A URL optional and disable by default. | 03 January 2013, 14:43:53 UTC |
| e3fc87f | Greg Von Kuster | 02 January 2013, 22:02:25 UTC | Fix for discovering all repository dependencies for a tool shed repository being installed into Galaxy. | 02 January 2013, 22:02:25 UTC |
| 727b98e | Greg Von Kuster | 02 January 2013, 21:35:02 UTC | Fix for displaying an installed tool shed repository in an error state. | 02 January 2013, 21:35:02 UTC |
| 0eafc2e | Carl Eberhard | 02 January 2013, 21:30:24 UTC | history_contents, index & show: add force_history_refresh key/value; history panel: fix broken addHdas when used via the updater, add force_history_refresh to reload the history panel when an hda/tool requests it; pack scripts | 02 January 2013, 21:30:24 UTC |
| e7ffb76 | Dave Bouvier | 02 January 2013, 21:20:14 UTC | Fix additional exception in shutdown method of LWR. | 02 January 2013, 21:20:14 UTC |
| cb0be06 | Greg Von Kuster | 02 January 2013, 21:05:08 UTC | Fixes for rendering tool dependencies and repository dependencies for tool shed repositories being installed into Galaxy. | 02 January 2013, 21:05:08 UTC |
| 839a574 | Daniel Blankenberg | 02 January 2013, 20:25:28 UTC | When listing GenomeSpace directories in GenomeSpace export tool, if an API-discovered URL is invalid, skip gracefully. | 02 January 2013, 20:25:28 UTC |
| cff7b32 | Dave Bouvier | 02 January 2013, 20:02:08 UTC | Tool shed functional test enhancements - verify datatype repository install/uninstall/deactivate/reactivate. | 02 January 2013, 20:02:08 UTC |
| 837c8b4 | Dave Bouvier | 02 January 2013, 20:00:50 UTC | Fix for installing repositories with conflicting datatype definitions. | 02 January 2013, 20:00:50 UTC |
| 20655c8 | Dave Bouvier | 02 January 2013, 20:00:21 UTC | Fix exception in shutdown method of LWR. | 02 January 2013, 20:00:21 UTC |
| 89f6d56 | Dannon Baker | 02 January 2013, 16:40:41 UTC | Fix tabular dataset download for cols > 50. | 02 January 2013, 16:40:41 UTC |
| 5a2a236 | Dave Bouvier | 02 January 2013, 16:24:51 UTC | Fix for reactivating a deactivated repository that includes proprietary datatypes. | 02 January 2013, 16:24:51 UTC |
| 2cf0bf7 | Greg Von Kuster | 01 January 2013, 15:07:46 UTC | Fix for viewing tool metadata for tools contained in repositories in the tool shed that have been reviewed by the IUC. | 01 January 2013, 15:07:46 UTC |
| 3f91f66 | Jeremy Goecks | 01 January 2013, 01:52:07 UTC | Merged in kellrott/galaxy-central (pull request #103: Fixing missing imports in page controller) | 01 January 2013, 01:52:07 UTC |
| da7a479 | Kyle Ellrott | 01 January 2013, 00:26:25 UTC | Fixing missing imports in page controller | 01 January 2013, 00:26:25 UTC |
| fb634be | Greg Von Kuster | 31 December 2012, 23:39:02 UTC | Tool shed utility import fixes. | 31 December 2012, 23:39:02 UTC |
| 8dc1795 | Greg Von Kuster | 31 December 2012, 23:34:42 UTC | Tool shed utility refactoring fix. | 31 December 2012, 23:34:42 UTC |
| 5424a5a | Greg Von Kuster | 31 December 2012, 16:59:36 UTC | Fix status color when monitoring tool shed repositories being installed that end in a missing repository dependencies status. | 31 December 2012, 16:59:36 UTC |
| 616fec0 | Greg Von Kuster | 30 December 2012, 17:00:14 UTC | Fixes for reinstalling an uninstalled tool shed repository but choosing to noe handle repository dependencies. | 30 December 2012, 17:00:14 UTC |
| af78911 | Greg Von Kuster | 29 December 2012, 22:17:19 UTC | Fixes for reinstalling repository dependencies for tool shed repositories that are being reinstalled. | 29 December 2012, 22:17:19 UTC |
| 7e24010 | Greg Von Kuster | 28 December 2012, 21:15:59 UTC | Add exception handling when checking for updates for an installed tool shed repository. | 28 December 2012, 21:15:59 UTC |
| a171182 | Greg Von Kuster | 28 December 2012, 20:52:15 UTC | Fixes and improvements for importing a workflow contained in an installed tool shed repository into the Galaxy instance. | 28 December 2012, 20:52:15 UTC |
| 3276d61 | Dannon Baker | 28 December 2012, 16:21:49 UTC | Admin: Select all checkbox added for job management. See card: https://trello.com/card/select-all-option-for-admin-jobs/50686d0302dfa79d13d90c45/338 | 28 December 2012, 16:21:49 UTC |
| 33181b9 | Dannon Baker | 28 December 2012, 15:51:03 UTC | Admin UI: Make left panel scroll. | 28 December 2012, 15:51:03 UTC |
| 746fbd0 | Greg Von Kuster | 27 December 2012, 21:00:16 UTC | Add the ability to view an SVG image of a workflow contained in a tool shed repository installed into a Galaxy instance. This feature is the same as the feature that has been available in the tool shed for some time. | 27 December 2012, 21:00:16 UTC |
| a927af1 | John Chilton | 26 December 2012, 18:42:31 UTC | Rework job_id handling in LWR runner allowing remote LWR server to assign a job_id during setup, save this will serve as the job's external id. This change allows multiple Galaxy instances to submit jobs to the same LWR backend server and will prove useful when implementing additional backends (pbs/drmaa/etc...) for the LWR server. --- lib/galaxy/jobs/runners/lwr.py | 5 +++-- lib/galaxy/jobs/runners/lwr_client/__init__.py | 22 ++++++++++++++++------ 2 files changed, 19 insertions(+), 8 deletions(-) | 26 December 2012, 18:42:31 UTC |
| 61fed0b | John Chilton | 26 December 2012, 18:42:31 UTC | Implement optimization attempting to not transfer unneeded inputs to remote LWR server. More general refactoring and testing of lwr client code. --- lib/galaxy/jobs/runners/lwr_client/__init__.py | 170 +++++++++++++++++++----- 1 file changed, 136 insertions(+), 34 deletions(-) | 26 December 2012, 18:42:31 UTC |
| 36b4719 | John Chilton | 26 December 2012, 18:42:31 UTC | Extend lwr to allow execution of jobs with outputs specified using 'from_work_dir'. --- lib/galaxy/jobs/runners/__init__.py | 72 +++++++++++++----------- lib/galaxy/jobs/runners/lwr.py | 7 ++- lib/galaxy/jobs/runners/lwr_client/__init__.py | 31 ++++++++-- 3 files changed, 72 insertions(+), 38 deletions(-) | 26 December 2012, 18:42:31 UTC |
| 56b5610 | John Chilton | 26 December 2012, 18:42:31 UTC | Documentation and PEP8 fixes for lwr client code. --- lib/galaxy/jobs/runners/lwr_client/__init__.py | 206 +++++++++++++++++++----- 1 file changed, 164 insertions(+), 42 deletions(-) | 26 December 2012, 18:42:31 UTC |
| 686e5b9 | John Chilton | 26 December 2012, 18:42:31 UTC | Refactor much of the lwr client code out into its own module. This will make it easier to keep content insync with client code from lwr source. --- lib/galaxy/jobs/runners/lwr.py | 256 +----------------------- lib/galaxy/jobs/runners/lwr_client/__init__.py | 246 +++++++++++++++++++++++ 2 files changed, 249 insertions(+), 253 deletions(-) create mode 100644 lib/galaxy/jobs/runners/lwr_client/__init__.py | 26 December 2012, 18:42:31 UTC |
| 1851c71 | John Chilton | 26 December 2012, 18:42:31 UTC | Extend LWR job runner to stage an input's extra_files_path (if present). --- lib/galaxy/jobs/runners/lwr.py | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) | 26 December 2012, 18:42:31 UTC |
| 203c9d1 | John Chilton | 26 December 2012, 18:42:31 UTC | Allow execution of jobs created by task splitting via the LWR job runner. --- lib/galaxy/jobs/runners/lwr.py | 62 +++++++++++++++++++++++++++++++--------- 1 file changed, 49 insertions(+), 13 deletions(-) | 26 December 2012, 18:42:31 UTC |
| ce99b55 | John Chilton | 26 December 2012, 18:42:31 UTC | Refactor the LWRJobRunner to be a ClusterJobRunner and implement a recover method for this runner, the upshot of this is that LWR jobs can now survive Galaxy restarts. Downside is that jobs are no longer queued on Galaxy server, so LWR server should be updated (to changeset 5213f6d or newer) to queue jobs on the remote server. This is not manidatory however, this will still work it is just more jobs may run simultaneously than is desired. --- lib/galaxy/jobs/runners/lwr.py | 211 ++++++++++++++++++++++++---------------- 1 file changed, 128 insertions(+), 83 deletions(-) | 26 December 2012, 18:42:31 UTC |
| 62dab1f | John Chilton | 26 December 2012, 18:42:31 UTC | Implement new job runner super class ClusterJobRunner intended to reduce amount of duplicated code between drmaa, pbs, and lwr job runners (also I guess cli and condor classes seem like they could benefit from this as well). This super class will manage the monitor and worker threads and queues. I am submitting only changes to the LWR that use this class, but I would encourage the Galaxy team to refactor the drmaa and pbs runners to use this class as well (or I would be happy to make these changes if given access or a promise the changes will be accepted quickly). A variant of the drmaa runner that has been refactored to use this class can be found here: https://bitbucket.org/jmchilton/galaxy-central-lwr-enhancement-1/src/tip/lib/galaxy/jobs/runners/drmaa.py from the now defunct pull request 80. --- lib/galaxy/jobs/runners/__init__.py | 160 +++++++++++++++++++++++++++++++++++ 1 file changed, 160 insertions(+) | 26 December 2012, 18:42:31 UTC |
| b25d750 | Greg Von Kuster | 25 December 2012, 16:49:39 UTC | Display installed repository dependencies in a separate container from missing repository dependencies. | 25 December 2012, 16:49:39 UTC |
| b7ff94e | Greg Von Kuster | 22 December 2012, 20:12:41 UTC | Slight enhancements for managing simple repository dependencies. | 22 December 2012, 20:12:41 UTC |
| cc6a8e8 | James Taylor | 21 December 2012, 21:43:30 UTC | Fix shutdown on python >= 2.6.2 by calling setDaemon when creating threads (these are still cleanly shutdown by atexit). Also add descriptive names to most job worker threads | 21 December 2012, 21:43:30 UTC |
| fd3c113 | Jeremy Goecks | 21 December 2012, 21:08:16 UTC | Fixes for sorting and merging genomic regions during visual analysis. | 21 December 2012, 21:08:16 UTC |
| f6e343d | Dave Bouvier | 21 December 2012, 17:47:30 UTC | Tool shed functional test enhancements. Functional tests for uninstalling, deactivating, reinstalling, and reactivating installed repositories. | 21 December 2012, 17:47:30 UTC |
| df074cf | Greg Von Kuster | 21 December 2012, 17:35:28 UTC | Fixes and enhancemensts for rendering simple repository dependencies for tools hed repository installed into a Galaxy instance. | 21 December 2012, 17:35:28 UTC |
| 35471d2 | Dave Bouvier | 21 December 2012, 15:33:18 UTC | Make functional tests explicitly specify which shed tool config to use. | 21 December 2012, 15:33:18 UTC |
| 831231a | Dave Bouvier | 21 December 2012, 15:32:45 UTC | Fix handling of repository tools and tool dependencies. Fix issue with functional tests altering the integrated tool panel. | 21 December 2012, 15:32:45 UTC |
| 7c62a35 | Greg Von Kuster | 21 December 2012, 14:00:34 UTC | Fix for setting tool versions for tools contained in tool shed repositories installed into a Galaxy instance. | 21 December 2012, 14:00:34 UTC |
| a06ce9f | Greg Von Kuster | 21 December 2012, 01:48:11 UTC | Fixes for administering tool dependencies associated with tool shed repositories installe dinto a Galaxy instance. | 21 December 2012, 01:48:11 UTC |
| afd764e | Greg Von Kuster | 20 December 2012, 22:39:31 UTC | Enhancements to tool shed containers to enable features when tool shed repositories are installed in Galaxy. | 20 December 2012, 22:39:31 UTC |
| a6e1e5e | Dave Bouvier | 20 December 2012, 21:33:19 UTC | Fix server error when attempting to install a repository that has already been installed. | 20 December 2012, 21:33:19 UTC |
| c9605d1 | Carl Eberhard | 20 December 2012, 20:20:42 UTC | functional tests, tags: fix test_005_add_tag_to_history to check for tag using get_tagging_elt_async; twilltestcase: add get_tags (get_tagging_elt_async) | 20 December 2012, 20:20:42 UTC |
| ad44bb6 | Dave Bouvier | 20 December 2012, 20:16:56 UTC | Tool shed functional tests for reinstalling repositories and installing repositories with invalid tools. | 20 December 2012, 20:16:56 UTC |
| 2795328 | Dave Bouvier | 20 December 2012, 20:14:13 UTC | Fix error reinstalling a repository when repo_info_dict is missing from the parameters. | 20 December 2012, 20:14:13 UTC |
| 7cc1c70 | Greg Von Kuster | 20 December 2012, 19:26:27 UTC | Fixes for handling tool dependency installation into a Galaxy instance. | 20 December 2012, 19:26:27 UTC |
| b0a4a61 | Carl Eberhard | 20 December 2012, 18:42:45 UTC | expose_api: add Cache-Control response headers to prevent some browsers from caching api calls | 20 December 2012, 18:42:45 UTC |
| 52fb3b1 | Carl Eberhard | 20 December 2012, 17:35:09 UTC | pack scripts | 20 December 2012, 17:35:09 UTC |
| dbf4343 | Carl Eberhard | 20 December 2012, 17:25:09 UTC | base-mvc: fix to handle IE console methods being objects; history panel: handle workflow hide on finish using state:ready event | 20 December 2012, 17:25:09 UTC |
| ab2f4cd | Greg Von Kuster | 20 December 2012, 15:44:45 UTC | Fixes for handling tool dependencies and missing tool dependencies for installed tool shed repositories and tose being installed. | 20 December 2012, 15:44:45 UTC |
| 0659e09 | Greg Von Kuster | 20 December 2012, 00:39:50 UTC | Fix for resintalling a single tool shed repository and fix for displaying the contents of an installed tool shed repository in Galaxy. | 20 December 2012, 00:39:50 UTC |
| acb0164 | Greg Von Kuster | 19 December 2012, 23:59:07 UTC | Fix for retrieving tool dependencies and missing tool dependencies for display in Galaxy. | 19 December 2012, 23:59:07 UTC |
| eec1010 | Carl Eberhard | 19 December 2012, 22:08:21 UTC | history_panel: do not re-render panel when an hda is deleted | 19 December 2012, 22:08:21 UTC |
| e39ca0f | Dave Bouvier | 19 December 2012, 21:48:09 UTC | Fix for displaying an installed repository that includes one or more readme files. | 19 December 2012, 21:48:09 UTC |
| 5960802 | Greg Von Kuster | 19 December 2012, 20:57:09 UTC | Add support for installing and administering simple repository dependencies for tool shed repositories installed into a Galaxy instance. | 19 December 2012, 20:57:09 UTC |
| a869f9a | Carl Eberhard | 19 December 2012, 20:49:03 UTC | pack scripts | 19 December 2012, 20:49:03 UTC |
| cc190d7 | Carl Eberhard | 19 December 2012, 20:46:55 UTC | history panel: fix delete function to use show_deleted | 19 December 2012, 20:46:55 UTC |
| 765eeea | Carl Eberhard | 19 December 2012, 17:01:57 UTC | .hgignore: ignore test/selenium related jar and html | 19 December 2012, 17:01:57 UTC |
| cc22e80 | Dave Bouvier | 19 December 2012, 16:14:44 UTC | Merged changes from galaxy-dist-central. | 19 December 2012, 16:14:44 UTC |
| ea7fba5 | Dave Bouvier | 19 December 2012, 16:08:26 UTC | Fix for reinstalling tool shed repository with readme files. | 19 December 2012, 16:08:26 UTC |
| 8bda406 | Jeremy Goecks | 19 December 2012, 13:43:57 UTC | Qualifier fix. | 19 December 2012, 13:43:57 UTC |
| a3dac95 | Dave Clements | 18 December 2012, 21:27:20 UTC | First iteration of updating Sphinx RST files. These describe classes and modules (and ...) and are used to generate the Sphinx code documentation. However, they are not updated automatically. Add the patch.py to automate some of the RST update process, but it is still pretty brutal. Look for cleanup in the next few releases. | 18 December 2012, 21:27:20 UTC |
