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22 May 2024, 15:32:24 UTC
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Revision Author Date Message Commit Date
079c4b1 Dannon Baker 25 November 2014, 19:26:52 UTC Prevent XSS in unknown tool display, update to actually use show_error_message instead of replying with plain text. 25 November 2014, 19:26:52 UTC
1f51b4a Carl Eberhard 25 November 2014, 19:22:08 UTC Sanitize tag output in tagging_common and user.tags_used; protect against closing tags in bootstrapped JSON (http://benalpert.com/2012/08/03/preventing-xss-json.html); minor fixes 25 November 2014, 19:22:08 UTC
8b70c6e Aysam Guerler 25 November 2014, 19:04:43 UTC Fixes security issue 2.2 for regular grid values 25 November 2014, 19:04:43 UTC
3fd2c1b Nate Coraor 25 November 2014, 17:00:20 UTC Update tag latest_2014.10.06 for changeset adc4aa8b3d9a 25 November 2014, 17:00:20 UTC
acd8563 John Chilton 24 November 2014, 15:06:11 UTC Sanitize object names throughout templates. 24 November 2014, 15:06:11 UTC
8f07e36 Aysam Guerler 21 November 2014, 21:41:44 UTC JS-santization of filter options before displaying them FIX 2.2 21 November 2014, 21:41:44 UTC
23aae23 Aysam Guerler 08 December 2014, 17:50:09 UTC Security fixes for assigned templates 08 December 2014, 17:50:09 UTC
044ee1c Nate Coraor 20 November 2014, 19:00:30 UTC Update tag latest_2014.10.06 for changeset bb79e87274d7 20 November 2014, 19:00:30 UTC
360fadf Dannon Baker 20 November 2014, 14:16:46 UTC Merged in jmchilton/galaxy-central-fork-1/stable (pull request #566) [STABLE] Fix Pulsar's default HTTP transport for poster hacking up urllib. 20 November 2014, 14:16:46 UTC
69103ff Nate Coraor 19 November 2014, 20:00:25 UTC Update tag latest_2014.10.06 for changeset acc8d1e2bc88 19 November 2014, 20:00:25 UTC
8e7c600 John Chilton 19 November 2014, 15:20:36 UTC Bugfix: composite uploads broken by upload common assuming bunch's have a UUID field. Reported by tjkarlsson@uma.es here http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-using-pbed-file-format-td4666000.html. 19 November 2014, 15:20:36 UTC
6b00a45 John Chilton 18 November 2014, 16:39:01 UTC Fix Pulsar's default HTTP transport for poster hacking up urllib. Behavior of urllib changes with respect of content length of mmap content after poster is loaded - is automatically loaded by Pulsar client as of 9207ecb43d81853da7a58cd5634683dc87991c4f (added as part of October 2014 stable release). Enis has confirmed this fixes some problems in latest stable. 18 November 2014, 16:39:01 UTC
88293eb Nate Coraor 17 November 2014, 15:00:27 UTC Update tag latest_2014.10.06 for changeset 011c8b2118be 17 November 2014, 15:00:27 UTC
52e0a68 John Chilton 14 November 2014, 17:58:29 UTC Fix passing nested parameter replacements to the workflow run API. Thanks to Nicola for finding the problem https://bitbucket.org/galaxy/galaxy-central/commits/fa92c5497232444ade0e7044184fb8ccf419177c. 14 November 2014, 17:58:29 UTC
7fb9b7c Nate Coraor 14 November 2014, 14:00:21 UTC Update tag latest_2014.10.06 for changeset e6de07f8c01f 14 November 2014, 14:00:21 UTC
23d3606 Martin Cech 13 November 2014, 19:41:49 UTC open citation url in _blank (prevents browser's insecure content error messages while trying to open in the middle pane - https vs http) 13 November 2014, 19:41:49 UTC
6161293 Nate Coraor 10 November 2014, 20:00:25 UTC Update tag latest_2014.10.06 for changeset c9759aa6e40f 10 November 2014, 20:00:25 UTC
1677e15 John Chilton 10 November 2014, 15:07:56 UTC Bugfix renaming individual parts of pairs. From Carl: "Yeah - that looks fine for stable. A better fix is probably adding the pair index directly into the DOM and getting it there - I'll add that to the 'Iteration 2' card. I'll approve now if you want to do the request." 10 November 2014, 15:07:56 UTC
5b3d1a2 Nate Coraor 10 November 2014, 14:00:34 UTC Update tag latest_2014.10.06 for changeset a1dca14d5b1a 10 November 2014, 14:00:34 UTC
5321bbf Nate Coraor 07 November 2014, 20:41:27 UTC Memory limit detection. This code is from default and is a partial graft. It includes the code for detecting if a Slurm job was killed due to exceeding memory limits but does not include resubmit functionality. 07 November 2014, 20:41:27 UTC
ef48b26 Nate Coraor 04 November 2014, 19:00:15 UTC Update tag latest_2014.10.06 for changeset 9b8cb8d48a79 04 November 2014, 19:00:15 UTC
e77f7b2 Carl Eberhard 04 November 2014, 14:51:53 UTC Fix: regenerate dataset-model urls on fetch even when silent 04 November 2014, 14:51:53 UTC
529ef2c Nate Coraor 23 October 2014, 14:00:16 UTC Update tag latest_2014.10.06 for changeset 9bc08bc7f393 23 October 2014, 14:00:16 UTC
e5c2a5a Dannon Baker 23 October 2014, 02:50:21 UTC Merged in BjoernGruening/galaxy-central/stable (pull request #537) [STABLE] Hide the GALAXY env variable. 23 October 2014, 02:50:21 UTC
271f910 Nate Coraor 22 October 2014, 22:00:15 UTC Fix slurm job post-mortem for `clusters` functionality added to slurm-drmaa (and currently in use on usegalaxy.org). 22 October 2014, 22:00:15 UTC
be132e8 Björn Grüning 22 October 2014, 13:10:32 UTC Hide the GALAXY env variable. This enables us to set it externally and just call the script. Very useful in docker containers. 22 October 2014, 13:10:32 UTC
ed2fc2e Nate Coraor 21 October 2014, 13:00:16 UTC Update tag latest_2014.10.06 for changeset a7b2aabb27ff 21 October 2014, 13:00:16 UTC
cbd467d Nate Coraor 16 October 2014, 17:00:13 UTC Update tag latest_2014.10.06 for changeset e1404e285ccb 16 October 2014, 17:00:13 UTC
d475080 John Chilton 15 October 2014, 16:57:10 UTC Fix for datatypes consuming output extra files path for the change in d781366. That change forced $output.extra_files_path to be the same thing as $output.files_path. See rational in changeset. Some datatypes however consume this path when generated metadata - post d781366 these datatypes would be accessing the wrong directory. This fixes them. The suggested best practice I would put forward is $input.extra_files_path and $output.files_path. $output.extra_files_path redirects to $output.files_path for newer Galaxy versions (August 2014+) so that Galaxy configurations requiring this directory be in the jobs working directory work. Datatypes consuming dataset.extra_files_path for these outputs will be broken when used with $output.files_path for the August release of Galaxy - but if this changeset is back-ported to the October 2014 release then these types and tools will work going forward (without modification). It can be verified that the older releases are broken with the following existing test (fixed with this changeset). ./run_functional_tests.sh -framework -id composite_output 15 October 2014, 16:57:10 UTC
d108236 Dannon Baker 15 October 2014, 14:21:13 UTC Move handler startup to immediately following full creation and association of the JobManager. 15 October 2014, 14:21:13 UTC
ff58b3a Nate Coraor 14 October 2014, 13:00:24 UTC Update tag latest_2014.10.06 for changeset 1744b7d8e9ab 14 October 2014, 13:00:24 UTC
a2eb301 Nate Coraor 14 October 2014, 00:48:30 UTC Merge closed duplicate stable head with current stable. 14 October 2014, 00:48:30 UTC
8f7d597 Nate Coraor 13 October 2014, 19:00:25 UTC Update tag latest_2014.10.06 for changeset cb0c2ea402e4 13 October 2014, 19:00:25 UTC
6343c1e Daniel Blankenberg 13 October 2014, 17:54:05 UTC Close branch stable 13 October 2014, 17:54:05 UTC
20d9741 Nicola Soranzo 13 October 2014, 16:27:45 UTC Fix import bug for run_reports.sh . Remove unused imports. Import bug: File "/opt/galaxy-central/lib/galaxy/webapps/reports/buildapp.py", line 25, in <module> class ReportsWebApplication( galaxy.web.framework.webapp.WebApplication ): AttributeError: 'module' object has no attribute 'webapp' The bug was introduced by commit d57655849ac4 . 13 October 2014, 16:27:45 UTC
f275034 Dannon Baker 13 October 2014, 14:19:32 UTC Relocate job_lock from the queue to the JobManager itself. This fixes NoopQueue not having a job_lock errors seen in Admin->Jobs 13 October 2014, 14:19:32 UTC
b14164c Nate Coraor 13 October 2014, 14:00:19 UTC Update tag latest_2014.10.06 for changeset 7436bde1f785 13 October 2014, 14:00:19 UTC
0b2a0d6 Dannon Baker 10 October 2014, 18:40:07 UTC Merge. 10 October 2014, 18:40:07 UTC
7e9fb01 Dannon Baker 10 October 2014, 18:13:46 UTC Strip r3 instance types for now; hvm virtualization required, which causes launch failures. 10 October 2014, 18:13:46 UTC
0b68bbf Nate Coraor 10 October 2014, 14:00:19 UTC Update tag latest_2014.10.06 for changeset 0f70d302b85e 10 October 2014, 14:00:19 UTC
d345be4 Dave Bouvier 09 October 2014, 18:17:33 UTC More flexibility for tool data table configuration in the install and test framework. 09 October 2014, 18:17:33 UTC
be87169 Nate Coraor 10 October 2014, 13:00:38 UTC Update tag latest_2014.10.06 for changeset a4f8476d787e 10 October 2014, 13:00:38 UTC
3e7e8ab Martin Cech 10 October 2014, 00:36:54 UTC fix a bug with parsing params in data libraries API introduced recently with refactoring into managers 10 October 2014, 00:36:54 UTC
857375f Nate Coraor 09 October 2014, 13:00:13 UTC Update tag latest_2014.10.06 for changeset bde1c35ef8e5 09 October 2014, 13:00:13 UTC
7c9869f John Chilton 08 October 2014, 20:21:35 UTC Merged in martenson/galaxy-stable-pr/stable (pull request #520) [STABLE] missing import 08 October 2014, 20:21:35 UTC
ab7e47f Martin Cech 08 October 2014, 18:27:41 UTC missing import 08 October 2014, 18:27:41 UTC
f3ab229 Nate Coraor 06 October 2014, 19:31:09 UTC Added tag latest_2014.10.06 for changeset 2092948937ac 06 October 2014, 19:31:09 UTC
a84fb51 Nate Coraor 06 October 2014, 16:59:17 UTC Added tag release_2014.10.06 for changeset 2092948937ac 06 October 2014, 16:59:17 UTC
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
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