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Revision Author Date Message Commit Date
565e8b9 Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Release 14.08..15.01 version. 22 April 2015, 18:36:36 UTC
1c8f141 Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers. 05 March 2015, 14:57:34 UTC
885829d Clone .gitignore 23 February 2015, 16:26:32 UTC
6304c81 Bugfix: Skip extra wrapping around template-style macros. 15 January 2015, 21:01:33 UTC
136239b Make DatasetListWrapper and DatasetCollectionWrapper subclasses of ToolParameterValueWrapper. 14 January 2015, 22:07:46 UTC
703cbb0 Fix a critical security vulnerability where unsanitized user-modifiable values could be included in a command line template. 13 January 2015, 15:27:43 UTC
7754e7b 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 Update tag latest_2014.08.11 for changeset 9f15bf53a11b 23 September 2014, 13:00:19 UTC
38d73bb 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 putting back the removed exception messages 22 September 2014, 19:17:51 UTC
da5b326 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
a53a7ad Update tag latest_2014.08.11 for changeset 9f495158c5ba 17 September 2014, 20:00:21 UTC
6cd91a9 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
450e00b Update tag latest_2014.08.11 for changeset 21f2a42a06d7 17 September 2014, 13:00:22 UTC
1030b02 Handle Pulsar job stop when setting metadata remotely. 05 September 2014, 15:41:05 UTC
690bb7e Update tag latest_2014.08.11 for changeset 2c0a15d8d6b4 16 September 2014, 13:00:31 UTC
4254815 Merged in dan/galaxy-central-prs/stable (pull request #494) [STABLE] Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck 15 September 2014, 19:17:02 UTC
374fb70 Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck 15 September 2014, 18:58:14 UTC
2a89492 Update tag latest_2014.08.11 for changeset e8453771b1db 04 September 2014, 14:00:23 UTC
647a04c Fix tool rerunning for data_collection parameters. Bug report from takadonet - https://gist.github.com/Takadonet/ba21ca26748a459615e3. My testing shows this fixes that bug and likewise he confirmed the fix works. 03 September 2014, 20:05:29 UTC
13373e3 Update tag latest_2014.08.11 for changeset 20f4fdf1735a 03 September 2014, 14:00:28 UTC
9978e26 Pack scripts. 02 September 2014, 15:21:08 UTC
24e914f Fix workflow editor bug related state updates for collections attached to multiple input data parameters. Detail bug report from Michael Crusoe here : https://trello.com/c/0mdGCx4P. This also fixes a test case added in 289e48b which was both attempting to assert something wrong and was incorrectly implemented. Augmenting the workflow editor test suite with some actually valid test cases that assert the correct behaviors. For a longer explaination - workflow input terminals have two related concepts 'canAccept' and 'attachable'. An output terminal is 'attachable' if in the abstract it could be attached to the input regardless of whether the input is already filled or not. 'canAccept' is more stateful in that an output terminal is 'canAccept'able if the input terminal is not filled ('_inputFilled') and it is 'attachable'. So - the problem was 'attachable' was not correctly defined for a multiple input data parameters. 'attachable' was asserting that any connected input terminal could not be 'attachable' by an collection output terminal - so on these asynchronous node state changes collections attached to multiple input data parameters were being wiped out. The more percise/correct distinction is that if a multiple input data parameter has single inputs connected to it - it cannot also have a collection connected to it (yet anyway). This fixes the mentioned bug. The problematic test case was conflating 'attachable' and 'canAccept'able - I have fixed the test case to verify the correct 'attachable' logic and added newer, higher level test cases to test the canAccept logic and the actual behavior the end user would observe (of the connector being destroy). 02 September 2014, 15:20:44 UTC
7a5fed6 Update tag latest_2014.08.11 for changeset ea12550fbc34 29 August 2014, 18:00:23 UTC
d3a50e2 Merged in jmchilton/galaxy-central-fork-1/stable (pull request #479) [STABLE] More collection-y workflow fixes. 29 August 2014, 13:44:47 UTC
d7b218b Update tag latest_2014.08.11 for changeset 0047ee06fef0 29 August 2014, 13:00:25 UTC
b78d059 Pack scripts. 29 August 2014, 04:31:59 UTC
2641d8e Don't persist literal string '<DummyDataset...>' when updating tool state in workflow editor. Doesn't seem to actually break the workflows because Galaxy tries to assign the value to the parameter afterward - fails and assigns it to None anyway and then connects up everything - but it does cause the workflow editor to pop-up an annoying warning about this value change. 29 August 2014, 04:30:30 UTC
d80d1b1 Fix for at workflow editor glitch. 29 August 2014, 04:30:30 UTC
0aef022 Merged in dannon/galaxy-central-prmaker/stable (pull request #478) [STABLE] Remove option for the (long since deprecated in favor of Data Managers) data_admin interface from admin 29 August 2014, 04:27:45 UTC
facac09 Remove option for the (long since deprecated in favor of Data Managers) data_admin interface from admin 28 August 2014, 21:21:03 UTC
7f927e5 Update tag latest_2014.08.11 for changeset a6cfe95047eb 28 August 2014, 18:00:16 UTC
09f1589 Fix SQlite datatype sniffing for old sqlite3. Remove unused imports. Bug fixed: when uploading a gzipped FASTQ file through upload1 tool on a machine with SQLite 3.3.6, it was detected as 'sqlite' datatype and not decompressed. In fact, the sqlite3 command 'pragma schema_version' on any file returns without error on this SQLite version. 28 August 2014, 13:09:10 UTC
bfb4688 Update tag latest_2014.08.11 for changeset 109b170188e9 28 August 2014, 13:00:13 UTC
d26617f Fix using multiple list collections with different identifiers in workflows. Tools will pair off (or triplize, quadraplate, quintukify, etc...) based only on the index of the elements in the collection (so any N element list can be used in the same tool execution as any other N element list). Originally, I had decided to require the element identifiers to be the same in both collections (allows mixing a matching fewer collections in tools - but probably less likely to mismatch in a way the user did not intend). At any rate - I changed that decision and updated tool execution appropriately but not every aspect workflow collection 'pairing' - this fixes that and closes out this card https://trello.com/c/m5PiF1lR. In very partical terms tools would ideally be consuming collection pairs - but for those that are still consuming two separate files (i.e. all of them) one can use two lists of datasets with pairs at matching indices and feed them into these tools - for workflows this doesn't work without this patch unless the identifiers and the indices match on these collections. Thanks for Michael Crusoe and takadonet for the bug reports. 27 August 2014, 18:39:43 UTC
29d4052 Update tag latest_2014.08.11 for changeset 9a4b43021fd1 26 August 2014, 13:00:14 UTC
d0f6c6d Bugfix for 0750859: Don't generate duplicate workflow slugs for private workflows. See full conversation on https://bitbucket.org/galaxy/galaxy-central/commits/07508592cb65845474b9f3e0f781260c. Would like to better and allow slugs of deleted items to be reused - they cannot be for workflows for instance. Because the slugs are not really handled uniformly though - pages do not have this problem and deleted pages can have their slugs reused because this is included in a check in the web controller which directly assigns valid slugs at that point. Slugs for deleted histories cannot be re-used - but they couldn't be prior to this commit - so this isn't making things worse in that respect. 25 August 2014, 16:36:34 UTC
b2460e6 Update tag latest_2014.08.11 for changeset 7e22f3579852 22 August 2014, 13:00:42 UTC
8ba3b5c Fix for FASTQ datasets peek/display of sequence counts. 21 August 2014, 19:52:35 UTC
11db71a Update tag latest_2014.08.11 for changeset 6445c0fe7612 21 August 2014, 13:00:21 UTC
2ecd1b9 Merged in dan/galaxy-central-prs/stable (pull request #470) Fix for resetting installed toolshed repository metadata inside of Galaxy. 20 August 2014, 15:03:06 UTC
f3a74b6 Fix for resetting installed toolshed repository metadata inside of Galaxy. 20 August 2014, 14:48:48 UTC
8052679 Updated tag latest_2014.08.11 for changeset 7748a83f3361 20 August 2014, 14:36:22 UTC
a8d23c2 Merged in dannon/galaxy-central-prmaker/stable (pull request #469) [STABLE] For _ensure_valid_session with use_remote_user set, when galaxy_session.user.email != remote_user_email invalidate the session UNLESS allowing user impersonation and the remote user is an admin. 19 August 2014, 15:26:23 UTC
3c82db9 For _ensure_valid_session with use_remote_user set, when galaxy_session.user.email != remote_user_email invalidate the session UNLESS allowing user impersonation and the remote user is an admin. 19 August 2014, 13:33:36 UTC
80de8c1 Trackster: fix display of overlapping reads by correctly resolving read length regardless of data loading/tile drawing order. Unfortunately, the easiest way to accomplish this required refactoring, hence the large commit. Pack scripts. 13 August 2014, 21:25:35 UTC
d805c44 Adding missing imports. 13 August 2014, 12:56:37 UTC
bc66998 Updated tag latest_2014.08.11 for changeset 7e4d21621ce1 12 August 2014, 13:58:36 UTC
44dcfb4 initiate_repository_installation was not updated in the recent code restructuring efforts 12 August 2014, 08:41:45 UTC
2a68a41 First argument to __install_repositories is the Tool Shed URL (tool_shed_url) 12 August 2014, 08:38:24 UTC
cc2877f install_repository_manager do not need trans.app anymore. 12 August 2014, 08:33:27 UTC
3b787c2 Added tag latest_2014.08.11 for changeset 52b5cc75a175 11 August 2014, 21:22:49 UTC
7b030ca Added tag release_2014.08.11 for changeset ca45b78adb41 11 August 2014, 20:47:34 UTC
e7ac637 Merge next-stable branch for release_2014.08.11 11 August 2014, 20:47:21 UTC
37d9c45 Updated tag latest_2014.06.02 for changeset 7a4d321c0e38 11 August 2014, 20:46:48 UTC
55b69c6 Close next-stable for upcoming release_2014.08.11 11 August 2014, 20:46:18 UTC
fde948f Trackster: fix location of gap line and read-pair connector line. 11 August 2014, 15:18:46 UTC
d5fe1b1 Increase reference sequence size to data provider to support reference-based compression of spliced reads. 11 August 2014, 15:05:07 UTC
163866b Trackster: refine label track position calculation. 09 August 2014, 19:38:33 UTC
03ade2b Pack scripts. 07 August 2014, 13:36:18 UTC
4d5f0de Relax BibTeX parsing and accept header to handle figshare DOIs. For instance 10.6084/m9.figshare.979190 reported by Michael Crusoe. JavaScript parser didn't like @data entries produced by figshare and when requesting the entry dx.doi.org returns a 403 response for type accept type text/bibliography, also allowing application/x-bibtex fixes this. Interestingly dx.doi.org throws 500 exceptions if application/x-bibtex is the only acceptable type or appears first for some other DOIs. 07 August 2014, 13:35:43 UTC
c05cf52 Bugfix: Deal with BibTeX fields in a case insensitive fashion. Would have thought the parser would have done this already - oh well. 07 August 2014, 13:35:43 UTC
709f16b Merge. 06 August 2014, 15:25:12 UTC
7250bdd Pack scripts. 06 August 2014, 15:20:14 UTC
2892c6f Fixup citation rendering for DOI resolution failures. 06 August 2014, 15:19:48 UTC
870f3c4 Trackster: stabilize tile boundary calculations so that tiles do not overlap or yield visual artifacts. 06 August 2014, 14:28:01 UTC
e8e12df Fix for conditionally using bucket_default in cloudlaunch. 06 August 2014, 14:16:22 UTC
947ac3d Pack scripts. 06 August 2014, 13:37:08 UTC
e5d1910 Fix-up citation related GUI. Was displaying warning message about history citations being potentially incomplete for tools - which if they have annotated citations we should assume they are complete. 06 August 2014, 13:36:30 UTC
d4923c9 Fix for writing entries to shed_tool_conf.xml so that sym linked files are handled correctly (thanks Bjoern), and making changes to this and data manager config files thread-safe. 05 August 2014, 14:09:20 UTC
5ba4b60 Merged in jmchilton/galaxy-central-fork-1/next-stable (pull request #449) Fix tool shed's logic related to finding tool externally referenced files. 04 August 2014, 18:57:31 UTC
f158a4e Trackster: fix single-pixel gap bug in quantitative track display. 04 August 2014, 18:50:28 UTC
fe0c53c Fix new Tool.get_externally_referenced_paths to find imported macro files. Should fix this bug https://trello.com/c/TeguDYSq discovered by Bjoern... on stage at the GCC. 04 August 2014, 16:18:00 UTC
daaf2c8 Restructure tool external file logic in load_tool_from_tmp_config in ToolValidator... ... so internals of tool XML description are only utilized in the galaxy.tools module (and submodules). Add some unit tests for this new method for finding externally referenced files. 04 August 2014, 16:18:00 UTC
9fa3425 Python 2.6 compat fix for 591f036. 04 August 2014, 14:15:57 UTC
b97d5cc More progress toward guarenteed workflow import step order stability. Previous commit ensured that topsort is stable - but keys are reshuffled by position prior to being sent to topsort - in case their are "ties" when sorting by position ensure that import order is preserved before sorting on position. This is all very dry and seemingly persnickety - but at any rate - after this commit I am fairly confident that Galaxy will import newly saved workflows that have been exported in the same order they were exported in. This means that 64a25838085978c250a0486b516bb2c8e7c3b850 is more correct. 04 August 2014, 13:33:40 UTC
ac91ae8 Ensure topological sorting is 'stable' w.r.t to first element of tuple. This improves correctness of 64a25838085978c250a0486b516bb2c8e7c3b850. 04 August 2014, 13:33:40 UTC
7fdcf1b Test cases and test workflows to verify workflow import stability. 04 August 2014, 13:33:40 UTC
4dc2b30 Fix 2 bugs in the Tool Shed's tag_handler module discovered by Bjoern Gruning (thanks!) 04 August 2014, 13:03:01 UTC
244d861 Trackster: remove visual artifact resulting from overlapping tiles when zoomed in at the base level. Pack scripts. 03 August 2014, 19:57:04 UTC
56993d2 Fix for MAF stitching tools handling of the number of open temporary files. Fixes https://trello.com/c/UgqThlrh and https://trello.com/c/CQePdepc. 01 August 2014, 19:46:53 UTC
6066a36 Merge next-stable 31 July 2014, 18:27:54 UTC
70de9f4 Fix for displaying Category name when browsing toolshed repositories by categories. 31 July 2014, 15:03:27 UTC
3eaee39 Merge default sqlite datatype improvements into next-stable. Not quite a bug fix per se, but this more testing/robustness for code in next release so I think it belonds in next-stable (certainly not a new feature at any rate). 31 July 2014, 01:30:00 UTC
ba16d0c Fallback for sql whitelisting when sqlparse is not available 30 July 2014, 23:59:53 UTC
d2c4af3 Merged galaxy/galaxy-central into default 30 July 2014, 23:58:21 UTC
09e6ba9 Merge with 1621b66460e0533de4ee155bf23a5f0fabb43e40 30 July 2014, 18:13:07 UTC
07d489d Fix the tool shed URL for tools that have been installed from a tool shed using a proxy prefix. 30 July 2014, 18:12:40 UTC
2767997 Merge with next-stable. 30 July 2014, 17:36:31 UTC
4609720 Fix missing import. 30 July 2014, 17:36:07 UTC
4c4870b Apply 2014.07.30 security fix to next-stable 30 July 2014, 15:25:13 UTC
6948784 Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae 30 July 2014, 15:13:20 UTC
d44c852 Apply 2014.07.30 security fix to release_2014.06.02 30 July 2014, 15:12:05 UTC
48187dd Updated tag latest_2014.04.14 for changeset 9661b9d5d5b3 30 July 2014, 15:10:33 UTC
5ae1915 Apply 2014.07.30 security fix to release_2014.04.14 30 July 2014, 15:07:29 UTC
08279ce Added tag latest_2014.02.10 for changeset 2a756ca2cb18 30 July 2014, 15:04:48 UTC
93173c3 Apply 2014.07.30 security fix to release_2014.02.10 30 July 2014, 15:04:40 UTC
db6c0f0 Added tag latest_2013.11.04 for changeset 81fbe25bd02e 30 July 2014, 15:02:24 UTC
4589d46 Apply 2014.07.30 security fix to release_2013.11.04 30 July 2014, 15:02:23 UTC
11853f8 Added tag latest_2013.08.12 for changeset 9ed84cd208e0 30 July 2014, 14:57:58 UTC
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