| 1c9aded | Nate Coraor | 06 October 2014, 16:58:53 UTC | Merge next-stable to stable for release_2014.10.06 | 06 October 2014, 16:58:53 UTC |
| 6f4252a | Nate Coraor | 06 October 2014, 16:58:28 UTC | Close next-stable branch for release_2014.10.06 | 06 October 2014, 16:58:28 UTC |
| cb4e0b2 | Daniel Blankenberg | 06 October 2014, 15:49:09 UTC | Remove deprecation warnings from util.json methods. | 06 October 2014, 15:49:09 UTC |
| e60df50 | John Chilton | 06 October 2014, 01:36:27 UTC | Backport Kyle's fix to docker's host argument from default. See https://bitbucket.org/galaxy/galaxy-central/pull-request/515/fixing-how-docker_utils__docker_prefix/diff. | 06 October 2014, 01:36:27 UTC |
| 502041d | John Chilton | 06 October 2014, 01:20:05 UTC | Back port Kyle's tool download fixes from default. | 06 October 2014, 01:20:05 UTC |
| 01a9e91 | John Chilton | 03 October 2014, 05:34:42 UTC | Another fix for galaxy.ini being conditionally existent. Update scripts/check_eggs.py and scripts/fetch_eggs.py with logic to find the correct config file. These files should be refactored so they can share some of this code the way I refactored the database management scripts I guess. | 03 October 2014, 05:34:42 UTC |
| d7208e7 | John Chilton | 03 October 2014, 02:05:50 UTC | Merge stable into next-stable. | 03 October 2014, 02:05:50 UTC |
| 728c5ce | John Chilton | 03 October 2014, 01:52:34 UTC | Fix failing unit tests in lib/galaxy/model/orm/scripts.py. | 03 October 2014, 01:52:34 UTC |
| 182ab55 | John Chilton | 03 October 2014, 01:52:34 UTC | Elminate invalid jstree examples that are causing doctest failures. | 03 October 2014, 01:52:34 UTC |
| 1a77753 | James Johnson | 02 October 2014, 18:34:49 UTC | SQlite needs to import re and sqlite in order to set metadata | 02 October 2014, 18:34:49 UTC |
| caba81c | Martin Cech | 30 September 2014, 17:22:10 UTC | force qualified URL for tool sharing within the toolform | 30 September 2014, 17:22:10 UTC |
| c11e61a | Jeremy Goecks | 30 September 2014, 17:20:52 UTC | Trackster: make comparisons explicit when testing for track statistical data. | 30 September 2014, 17:20:52 UTC |
| aa5111d | John Chilton | 28 September 2014, 00:37:21 UTC | Fix tool migrations to respect GALAXY_CONFIG_* environment variables. Thanks to Bjoern for the bug report. | 28 September 2014, 00:37:21 UTC |
| 85f89f3 | Martin Cech | 26 September 2014, 19:17:35 UTC | select2 fixes and impl. of missing feature import from path | 26 September 2014, 19:17:35 UTC |
| 625cd31 | Nate Coraor | 25 September 2014, 20:23:06 UTC | Fix bug in finding relocated tool_data_table_conf.xml | 25 September 2014, 20:23:06 UTC |
| ad25fd6 | John Chilton | 25 September 2014, 17:49:04 UTC | Grunting at the scripts. | 25 September 2014, 17:49:04 UTC |
| a7f59b2 | John Chilton | 25 September 2014, 17:49:04 UTC | Fix various BibTex styling problems. Need to get out of the BibTeX formatting game as quickly as possible this is a loosing battle, but until then plugging holes in the ship. | 25 September 2014, 17:49:04 UTC |
| 965d1a3 | John Chilton | 25 September 2014, 13:00:38 UTC | Fixes to tool_list.py for legacy configurations and modified tool confs. Now uses roughly the same order of precedence as Galaxy proper's config. | 25 September 2014, 13:00:38 UTC |
| 1314ff2 | Saket Choudhary | 25 September 2014, 06:10:51 UTC | Update tool_list to reflect recent change in use of envirnoment variables tool_list.py now makese use of GALAXY_TEST_TOOL_CONF and exits throwing an appropriate error | 25 September 2014, 06:10:51 UTC |
| 6f8fbf6 | John Chilton | 24 September 2014, 19:21:44 UTC | Rework version command to work with job wrappers that have not had 'prepare' executed. Traditionally all synchronous job wrappers have had 'prepare' called when they are queued up, but prepare isn't called on the more transient job wrappers that are created in response to Pulsar asnchronous status update messages. | 24 September 2014, 19:21:44 UTC |
| 1d63a01 | John Chilton | 24 September 2014, 19:21:44 UTC | Allow remotely executed tools to write version files to the temp directory. Like with discovered datasets - such use of this directory should be phased out in favor of the job's working directory of a job relative to it. | 24 September 2014, 19:21:44 UTC |
| 5bcbbdc | Carl Eberhard | 24 September 2014, 17:54:04 UTC | Fix to 83aaac5: copy changes into client/ | 24 September 2014, 17:54:04 UTC |
| 8ba9d93 | Jeremy Goecks | 24 September 2014, 17:26:55 UTC | Fix dataset loading in Scratchbook: if dataset is tabular, load dynamically without iframe; otherwise load into iframe. | 24 September 2014, 17:26:55 UTC |
| ffdd754 | Carl Eberhard | 24 September 2014, 16:14:13 UTC | Fix history/view to allow scolling when use_panels=True | 24 September 2014, 16:14:13 UTC |
| ce110b5 | Nate Coraor | 24 September 2014, 15:20:22 UTC | Merged in martenson/galaxy-merging/next-stable (pull request #504) [NEXT-STABLE] merge of JS changes from #stable | 24 September 2014, 15:20:22 UTC |
| f0c218b | Jeremy Goecks | 24 September 2014, 14:24:50 UTC | Better stderr and exit code handling for interal wig-to-bigwig converter. | 24 September 2014, 14:24:50 UTC |
| fd52217 | Carl Eberhard | 24 September 2014, 13:49:41 UTC | Fixes to current dataset indicator and focused icon buttons | 24 September 2014, 13:49:41 UTC |
| 455d416 | Nate Coraor | 23 September 2014, 19:00:18 UTC | Update tag latest_2014.08.11 for changeset 548ab24667d6 | 23 September 2014, 19:00:18 UTC |
| d95aa46 | John Chilton | 23 September 2014, 17:38:25 UTC | Improved configuration error messages. | 23 September 2014, 17:38:25 UTC |
| 8c7c1b6 | John Chilton | 23 September 2014, 17:38:25 UTC | Fix run_tests.sh --with_framework_test_tools for 9a05d1e. Now appends test tools to sample tools instead of to default tools Galaxy would other wise load (config/tool_conf.xml or tool_conf.xml if these exist instead of sample) - so this is different behavior but I am unsure if it is worse. --with_framework_test_tools was added for API tests and these should probably target the distribution and not random tools someone might have configured so perhaps this new behavior is superior. | 23 September 2014, 17:38:25 UTC |
| 9c433b8 | Martin Cech | 23 September 2014, 14:59:49 UTC | merge stable into next-stable | 23 September 2014, 14:59:49 UTC |
| fcd1cb9 | Martin Cech | 23 September 2014, 14:56:26 UTC | trying to merge stable->next stable, this should take care of changes due to build process affecting the stable commit | 23 September 2014, 14:56:26 UTC |
| c9d0309 | Nate Coraor | 23 September 2014, 14:40:39 UTC | Use common_startup.sh for buildbot instead of maintaining a duplicate copy of the samples list. | 23 September 2014, 14:40:39 UTC |
| 41bbe96 | Nate Coraor | 23 September 2014, 14:09:17 UTC | Functional test fix for config file moves. | 23 September 2014, 14:09:17 UTC |
| 7754e7b | John Chilton | 23 September 2014, 14:06:38 UTC | Merged in martenson/galaxy-stable-pr/stable (pull request #503) [STABLE] fix for select2 bug with minimal width | 23 September 2014, 14:06:38 UTC |
| 175d518 | Nate Coraor | 23 September 2014, 13:00:19 UTC | Update tag latest_2014.08.11 for changeset 9f15bf53a11b | 23 September 2014, 13:00:19 UTC |
| 824eb5b | John Chilton | 23 September 2014, 00:01:05 UTC | Continue flailing on environment variable configuraiton of Galaxy. Expand variables earlier right in app_factory so middleware, etc... pick up defaults/overrrides. In particular GALAXY_CONFIG_OVERRIDE_DEBUG should now work properly. GALAXY_CONFIG_DEBUG cannot be used because the sample config template overrides debug's default. Thanks to Bjoern for the bug report. | 23 September 2014, 00:01:05 UTC |
| 8d3c256 | John Chilton | 22 September 2014, 23:14:12 UTC | Fix ORM scripts for 42f677bab2e4880b62758614fcb2c7dc27013788. Updating common Python module used by ORM scripts (create_db.sh/migrate_db.sh/db_shell.py) to allow the same configuration via enviornment variables as well. Thanks to Bjoern for the bug report/feature request. | 22 September 2014, 23:14:12 UTC |
| 38d73bb | Martin Cech | 22 September 2014, 22:09:45 UTC | the removed select2 class overrule for edit hda attributes is needed afterall, I at least did rename it to specific to its usage so other select2 items can work normally | 22 September 2014, 22:09:45 UTC |
| 21bc48e | Martin Cech | 22 September 2014, 19:17:51 UTC | putting back the removed exception messages | 22 September 2014, 19:17:51 UTC |
| da5b326 | Martin Cech | 22 September 2014, 18:52:11 UTC | Fix of a bug involving mistaking ld with ldda and vice versa which (together with our incremental ID approach ) leads to an incorrect dataset being downloaded. | 22 September 2014, 18:52:11 UTC |
| 365d5e5 | Nate Coraor | 22 September 2014, 15:36:25 UTC | Merge last minute bug fixes from default. | 22 September 2014, 15:36:25 UTC |
| e56943d | Nate Coraor | 22 September 2014, 15:31:56 UTC | Always access UCSC Main via HTTPS. | 22 September 2014, 15:31:56 UTC |
| 4a17892 | John Chilton | 22 September 2014, 15:23:02 UTC | Always access EBI SRA via HTTPS. Thanks to Ilya for opening pull request to make it conditionally use HTTPS - https://bitbucket.org/galaxy/galaxy-central/pull-request/491/remove-http-from-ebi-url-which-is/diff - but this goes one step further and always uses HTTPS as suggested by Nate in the pull request comments. | 22 September 2014, 15:23:02 UTC |
| 5cd4f5a | Dannon Baker | 22 September 2014, 15:09:07 UTC | Merged in BjoernGruening/galaxy-central-5/BjoernGruening/add-install_dir-to-perl5lib-and-path-bef-1410949639333 (pull request #499) Add $INSTALL_DIR to PERL5LIB and PATH before starting to install libraries. A few packages need this in order to recognise previous installed packages. | 22 September 2014, 15:09:07 UTC |
| 10bbe6d | Nate Coraor | 22 September 2014, 14:51:08 UTC | Merge stable. | 22 September 2014, 14:51:08 UTC |
| 3085a4f | Nate Coraor | 22 September 2014, 14:49:37 UTC | Open next-stable branch for 2014.10 release. | 22 September 2014, 14:49:37 UTC |
| e358f31 | John Chilton | 22 September 2014, 14:24:39 UTC | Merged in jmchilton/galaxy-central-fork-1 (pull request #496) More consistent tool API for map/reduce operations. | 22 September 2014, 14:24:39 UTC |
| aa6fa90 | John Chilton | 22 September 2014, 02:02:09 UTC | Allow configuration of Galaxy via environment variables. Allow overriding config defaults (those not specified in the configuration file) with GALAXY_CONFIG_<config-name> and allow overriding actual configured values with GALAXY_CONFIG_OVERRIDE_<config-name>. Here config-name is the actual value in galaxy.ini but in upper case. | 22 September 2014, 02:02:09 UTC |
| c00e56c | John Chilton | 22 September 2014, 01:48:58 UTC | Allow loading dependency resolvers and job metrics from YAML instead of XML. Mostly for downstream Pulsar configuration improvements - but I don't see a reason not to allow this in Galaxy as well. Besides simply being more pleasant to write - having everything configurable by Python dictionary should enable easier automation and programatic configuration of these job running systems. | 22 September 2014, 01:48:58 UTC |
| cf326c2 | John Chilton | 22 September 2014, 01:48:58 UTC | Reduce code duplication between job metrics and dependency resolution plugins. Same code reused again downstream in workflow schedulers plugin framework. | 22 September 2014, 01:48:58 UTC |
| 9ac19b5 | Aysam Guerler | 19 September 2014, 17:11:06 UTC | Charts: Fix selection grid | 19 September 2014, 17:11:06 UTC |
| c18f13c | Aysam Guerler | 19 September 2014, 16:47:17 UTC | ToolForm/Ui: Improve and extend option fields, add dataset/collection selector | 19 September 2014, 16:47:17 UTC |
| 41647cf | Dave Bouvier | 19 September 2014, 14:11:21 UTC | Fix page title on tool shed categories page, as pointed out by Greg. | 19 September 2014, 14:11:21 UTC |
| 46e0faf | Aysam Guerler | 18 September 2014, 18:58:12 UTC | Merge | 18 September 2014, 18:58:12 UTC |
| b23b946 | Aysam Guerler | 18 September 2014, 18:57:46 UTC | Ui: Fix option fields | 18 September 2014, 18:57:46 UTC |
| 014d7f5 | Martin Cech | 18 September 2014, 18:49:20 UTC | Merge | 18 September 2014, 18:49:20 UTC |
| 0476814 | Martin Cech | 18 September 2014, 18:48:50 UTC | tweaks to UI for library import, also added ext types and genome selection | 18 September 2014, 18:48:50 UTC |
| ca5dd79 | Carl Eberhard | 18 September 2014, 18:44:51 UTC | Visualizations registry: do not warn when a plugin is set to 'disabled' - use info | 18 September 2014, 18:44:51 UTC |
| 59369ff | Aysam Guerler | 18 September 2014, 18:07:44 UTC | ToolForm: Fix subsection creation | 18 September 2014, 18:07:44 UTC |
| 06f743f | Martin Cech | 18 September 2014, 16:45:04 UTC | removed the fix setting min-width to all select2 containers, I believe it is unnecessary with width: 'resolve' and dropdownAutoWidth: true settings | 18 September 2014, 16:45:04 UTC |
| 9754576 | Carl Eberhard | 18 September 2014, 16:33:52 UTC | History panel, current: highlight focused/active/current item, set active item on 'display,edit,rerun,info/params,visualize,report-error', cache scroll position in sessionstorage and re-render at same, allow list-panel.scrollTo to be animated and given a speed | 18 September 2014, 16:33:52 UTC |
| 422ab12 | Carl Eberhard | 18 September 2014, 14:00:11 UTC | Client build: remove potentially confusing copy of pack_scripts.py from client/galaxy/scripts; remove unused packed | 18 September 2014, 14:00:11 UTC |
| 21b2679 | John Chilton | 18 September 2014, 13:50:52 UTC | Refactor logic for generating dictified runtime inputs for workflow steps into workflow module. Continuing the pattern - this is one less place where consumers of workflows modules need to explicitly dispatch on type and should make it easier and clear what needs to be defined when adding new workflow modules. This also reduces the cyclomatic complexity of the large _workflow_to_dict method. Previous commit provides test coverage verifying this doesn't modify the behavior of workflow extraction. | 18 September 2014, 13:50:52 UTC |
| 9638009 | John Chilton | 18 September 2014, 13:50:52 UTC | More complete testing of workflow import and export. Test some new aspects of step description inputs. | 18 September 2014, 13:50:52 UTC |
| 7475d1a | Dannon Baker | 18 September 2014, 01:18:53 UTC | Client build. | 18 September 2014, 01:18:53 UTC |
| c01d472 | Dannon Baker | 18 September 2014, 01:17:30 UTC | Strip trailing whitespace in LazyDataLoader | 18 September 2014, 01:17:30 UTC |
| 577c856 | Dannon Baker | 18 September 2014, 01:12:53 UTC | Fix formatting to prevent potential semicolon insertion. | 18 September 2014, 01:12:53 UTC |
| e46efa2 | Dannon Baker | 18 September 2014, 01:11:12 UTC | Scratch the TODO, just removing those text replacements. Not necessary anymore. | 18 September 2014, 01:11:12 UTC |
| ad76d7e | Dannon Baker | 18 September 2014, 01:03:46 UTC | Client build. | 18 September 2014, 01:03:46 UTC |
| 68b1ad2 | Dannon Baker | 18 September 2014, 01:00:39 UTC | Add TODO in LazyDataLoader (the only place we were mucking about with Infinity/NaN in the client | 18 September 2014, 01:00:39 UTC |
| 325911d | Dannon Baker | 18 September 2014, 00:51:30 UTC | Might never need it, but, differentiate between and handle +/- inf. | 18 September 2014, 00:51:30 UTC |
| ad96541 | Dannon Baker | 18 September 2014, 00:46:16 UTC | Add method for shipping encoded inf/nan in json (as __Infinity__ / __NaN__). We should only be shipping valid JSON now, but it still needs to be parsed and handled on API consumers, of course. | 18 September 2014, 00:46:16 UTC |
| 0001b2c | Dannon Baker | 18 September 2014, 00:41:50 UTC | Pack scripts. | 18 September 2014, 00:41:50 UTC |
| a255996 | Aysam Guerler | 17 September 2014, 22:35:14 UTC | ToolForm: Fix style | 17 September 2014, 22:35:14 UTC |
| 4f93c54 | Aysam Guerler | 17 September 2014, 22:17:52 UTC | ToolForm: Revision of repeat blocks, Ui: Fixes and improvements | 17 September 2014, 22:17:52 UTC |
| a645b53 | Dannon Baker | 17 September 2014, 21:05:33 UTC | Be more explicit and warn about the deprecation of to_json_string/from_json_string. | 17 September 2014, 21:05:33 UTC |
| 57fbda6 | Dannon Baker | 17 September 2014, 20:16:34 UTC | to_json_string is deprecated and should not be used anymore, replace with dumps in api/lda_datasets | 17 September 2014, 20:16:34 UTC |
| ac60560 | Dannon Baker | 17 September 2014, 20:14:45 UTC | More pep8, remove unused variables. The only complaints left are needed refactoring to reduce method complexity, and the assigned lambda should be a proper function. | 17 September 2014, 20:14:45 UTC |
| 0c1dbe3 | Dannon Baker | 17 September 2014, 20:05:17 UTC | Import and whitespace cleanup in lda_datasets. | 17 September 2014, 20:05:17 UTC |
| a53a7ad | Nate Coraor | 17 September 2014, 20:00:21 UTC | Update tag latest_2014.08.11 for changeset 9f495158c5ba | 17 September 2014, 20:00:21 UTC |
| a71d3a7 | Nate Coraor | 17 September 2014, 19:23:51 UTC | With the exception of shed_*.xml configs, which are still instantiated from their samples by common_startup.sh, reverse the stream polarity and prefer the config/ version of config files, since their existence suggests the administrator took an intentional action to create them. Note that none of this magical detection applies unless you leave the options in galaxy.ini that set the paths to these configs commented/unset. Credit to John for the suggestion. | 17 September 2014, 19:23:51 UTC |
| afb3e63 | John Chilton | 17 September 2014, 19:21:34 UTC | Merge latest stable. | 17 September 2014, 19:21:34 UTC |
| 6cd91a9 | John Chilton | 17 September 2014, 15:56:03 UTC | Fix saving tool state modifications in workflow editor when resource parameters are enabled. Resource parameter selection is only available at runtime in the tool form - not in the workflow editor. It is fairly important that this state not be associated with the workflow since that would cause odd-ness when exporting one workflows to other deployments or as these unversioned resource parameters evolve over time. This fix addresses a consequence of that form not appearing and goes a step further in preventing this state from being associated with worklfow steps. Thanks to Dan for the bug report. | 17 September 2014, 15:56:03 UTC |
| 4753dd3 | Carl Eberhard | 17 September 2014, 15:28:16 UTC | Client build system, pack_scripts: the build system will now call pack_scripts on all files in static/scripts when called via 'grunt' or 'grunt pack', and pack_scripts automatically only on those that have changed when using 'grunt watch'; add README.txt | 17 September 2014, 15:28:16 UTC |
| a06f439 | Daniel Blankenberg | 17 September 2014, 15:14:50 UTC | Turn off sanitation of __ARCHIVE_SOURCE__ and __DEST_DIR__ in History Import Tool. Secure command-line using base64 encoding. Fixes issue where you couldn't import from a URL that has common characters such as e.g. '~' in it. | 17 September 2014, 15:14:50 UTC |
| 845fb3f | Nate Coraor | 17 September 2014, 14:26:48 UTC | Provide feedback on job failures due to tools removed from the config now that new state jobs are not recovered when tracking in the databsae (3d92d6f). | 17 September 2014, 14:26:48 UTC |
| 2035a1e | Carl Eberhard | 17 September 2014, 14:10:13 UTC | Client build system, copy task: make much more efficient by calling 'copy' with just those files that have changed | 17 September 2014, 14:10:13 UTC |
| 450e00b | Nate Coraor | 17 September 2014, 13:00:22 UTC | Update tag latest_2014.08.11 for changeset 21f2a42a06d7 | 17 September 2014, 13:00:22 UTC |
| 6af1eb0 | Björn Grüning | 17 September 2014, 10:27:56 UTC | Add $INSTALL_DIR to PERL5LIB and PATH before starting to install libraries. A few packages need this in order to recognise previous installed packages. | 17 September 2014, 10:27:56 UTC |
| d294af4 | Nate Coraor | 17 September 2014, 05:33:17 UTC | Fix scripts that use galaxy.model.orm.scripts' get_config method to find either config/galaxy.ini or universe_wsgi.ini. For the tool_shed database it'll find either config/tool_shed.ini or tool_shed_wsgi.ini. Also re-fix the unit test. Database and tool migrations won't work if you use galaxy.ini.sample. Perhaps it should automatically try appending .sample? Or we should really be encouraging people to use the config file properly. | 17 September 2014, 05:33:17 UTC |
| ddca497 | Martin Cech | 17 September 2014, 04:07:52 UTC | Merge | 17 September 2014, 04:07:52 UTC |
| c9bd294 | Martin Cech | 17 September 2014, 04:06:28 UTC | with John's help - this includes changed wording in user messages & errors to be more formal / no smilies :( / | 17 September 2014, 04:06:28 UTC |
| d585fbb | John Chilton | 17 September 2014, 01:40:35 UTC | Merged in martenson/galaxy-central-marten (pull request #497) importing into library folders from Galaxy filesystem | 17 September 2014, 01:40:35 UTC |
| 6ff787d | John Chilton | 17 September 2014, 01:29:10 UTC | More tool functional tests for validation stuff. Test default sanitization in repeat. Basic test of simpler santizer and mapping. | 17 September 2014, 01:29:10 UTC |
| 16ce5c0 | Nate Coraor | 16 September 2014, 22:29:23 UTC | Fix typo in Pulsar client lib. | 16 September 2014, 22:29:23 UTC |
| 48bb7cc | Nate Coraor | 16 September 2014, 22:29:12 UTC | Fix another instance of the renaming that I broke. | 16 September 2014, 22:29:12 UTC |
| eafd9aa | Martin Cech | 16 September 2014, 22:03:05 UTC | Merge | 16 September 2014, 22:03:05 UTC |
| ad43c62 | Martin Cech | 16 September 2014, 22:02:12 UTC | jstree refactoring, removed from global space, documentation to library imports, general JS cleanup | 16 September 2014, 22:02:12 UTC |
| 6e0e5f8 | Nate Coraor | 16 September 2014, 21:51:40 UTC | Stop recovering jobs that don't need to be recovered - jobs in the 'NEW' state when tracking in the database. | 16 September 2014, 21:51:40 UTC |
