| b3da771 | Nate Coraor | 12 August 2015, 21:14:14 UTC | Bump version to 15.07 (drop .dev) Merge branch 'release_15.05' into release_15.07 Conflicts: lib/galaxy/version.py | 12 August 2015, 21:14:14 UTC |
| f01300d | Nate Coraor | 12 August 2015, 21:12:44 UTC | Bump version to 15.05.1. Merge branch 'release_15.03' into release_15.05 Conflicts: lib/galaxy/version.py | 12 August 2015, 21:12:44 UTC |
| a6a85cb | Nate Coraor | 12 August 2015, 21:11:02 UTC | Bump version to 15.03.3 | 12 August 2015, 21:11:02 UTC |
| 8f7f80d | Nate Coraor | 12 August 2015, 21:03:04 UTC | Merge branch 'release_15.05' into release_15.07 | 12 August 2015, 21:03:04 UTC |
| 3e4513f | Nate Coraor | 12 August 2015, 21:01:10 UTC | Merge branch 'security-20150812-xss' into release_15.07 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py | 12 August 2015, 21:01:10 UTC |
| 3c2762b | Nate Coraor | 12 August 2015, 21:00:44 UTC | Merge branch 'security-20150812-shed' into release_15.07 | 12 August 2015, 21:00:44 UTC |
| d9426da | Nate Coraor | 12 August 2015, 21:00:28 UTC | Merge branch 'security-20150812-ldap' into release_15.07 | 12 August 2015, 21:00:28 UTC |
| 052b6a6 | Nate Coraor | 12 August 2015, 21:00:02 UTC | Merge branch 'security-20150812-shed' into release_15.05 | 12 August 2015, 21:00:02 UTC |
| e3e9213 | Nate Coraor | 12 August 2015, 20:59:44 UTC | Merge branch 'security-20150812-xss' into release_15.05 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py | 12 August 2015, 20:59:44 UTC |
| 2a1b2db | Nicola Soranzo | 05 June 2015, 14:48:23 UTC | Prevent login with valid username/email and empty password via LDAP auth when anonymous bind is allowed. Also decreased the log level of LDAP bind exception to warning. | 12 August 2015, 20:58:05 UTC |
| a454c93 | Nate Coraor | 12 August 2015, 20:52:52 UTC | Merge branch 'security-20150812-xss' into release_15.03 | 12 August 2015, 20:52:52 UTC |
| 25d8a54 | Nate Coraor | 12 August 2015, 20:52:44 UTC | Merge branch 'security-20150812-shed' into release_15.03 | 12 August 2015, 20:52:44 UTC |
| 8e7017a | Martin Cech | 12 August 2015, 20:51:10 UTC | Fix a vulnerability in the Tool Shed API that allowed unauthorized users to upload new repository versions. | 12 August 2015, 20:51:10 UTC |
| cbae8fa | Nate Coraor | 12 August 2015, 20:43:52 UTC | Fix an XSS reflection vulnerability on the workflow import form. | 12 August 2015, 20:43:52 UTC |
| 15b5a33 | Dannon Baker | 11 August 2015, 23:29:38 UTC | Merge pull request #590 from nsoranzo/release_15.05 [15.05] Fix wrong call to LDAPObject.result() by using search_ext_s(). | 11 August 2015, 23:29:38 UTC |
| d9d365b | Nicola Soranzo | 05 June 2015, 15:03:33 UTC | Fix wrong call to LDAPObject.result() by using search_ext_s(). result() second parameter is 'all', which should be 0 or 1. result() call was passing 60 as second parameter, which was probably intended to be a timeout (third parameter). By using search_ext_s(), the search() and result() calls are combined in one and the number of search results retrieved is limited to 1. Also, if the search return no results, this is now logged separately at warning level. | 11 August 2015, 19:21:25 UTC |
| 5346343 | Dannon Baker | 10 August 2015, 15:05:52 UTC | Merge pull request #580 from martenson/show-ts-fields-when-editing [release_15.07] show field for entering remote/home url when managing repo | 10 August 2015, 15:05:52 UTC |
| 913eb7f | Martin Cech | 10 August 2015, 14:53:35 UTC | show field for entering remote/home url when managing repo fixes #579 | 10 August 2015, 14:53:35 UTC |
| 395e103 | Aysam Guerler | 07 August 2015, 13:50:19 UTC | Merge pull request #570 from ericenns/new-tool-form-batch-collection [15.05] Fix batch mode input in new tool form ui | 07 August 2015, 13:50:19 UTC |
| 73cbe35 | John Chilton | 07 August 2015, 13:45:25 UTC | Merge pull request #571 from dannon/csv_sam_sniff_fix [15.07] Csv sam sniff fix | 07 August 2015, 13:45:25 UTC |
| 19d9145 | Dannon Baker | 06 August 2015, 21:19:12 UTC | One more bump to be the last tabular type detected, since ConnectivityTable is more specific. | 06 August 2015, 21:19:12 UTC |
| 864e2b5 | Eric Enns | 06 August 2015, 19:29:51 UTC | Fix batch mode for collection, when collection maps to multiple inputs | 06 August 2015, 19:29:51 UTC |
| d270ccd | Dannon Baker | 06 August 2015, 18:58:06 UTC | Fix sniff order with respect to CSV interpreting SAM files as valid CSV prior to SAM sniffing. Test with 1.sam. | 06 August 2015, 18:58:06 UTC |
| ef3d3f6 | Nitesh Turaga | 06 August 2015, 16:21:20 UTC | Merge pull request #567 from dannon/datatypes_registry_lower Normalize datatypes_by_ext upon entry | 06 August 2015, 16:21:20 UTC |
| f776deb | Dannon Baker | 06 August 2015, 15:56:11 UTC | Normalize extensions to lower upon adding to the datatypes registry. Elsewhere in the codebase (tools/parameters/basic.py, for example) we expect all extensions to be normalized to lower for matching. This resolves a bug where RData and Roadmap datatypes would never get detected and would be silently default to matching datatypes.Text. | 06 August 2015, 15:56:11 UTC |
| 50de63d | John Chilton | 06 August 2015, 15:16:40 UTC | Merge pull request #566 from martenson/release_15.07 [release_15.07] TS index - fix overriding the name variable | 06 August 2015, 15:16:40 UTC |
| 4d697b7 | Martin Cech | 06 August 2015, 14:38:12 UTC | fix overriding the name variable | 06 August 2015, 14:38:12 UTC |
| 265d869 | Dannon Baker | 05 August 2015, 23:58:29 UTC | Merge pull request #563 from martenson/release_15.07 [release_15.07] Fixes for TS search API | 05 August 2015, 23:58:29 UTC |
| d583c37 | Martin Cech | 05 August 2015, 18:27:25 UTC | flake8 spotted by @nsoranzo | 05 August 2015, 18:27:25 UTC |
| 0ad5c8a | Martin Cech | 05 August 2015, 17:55:01 UTC | fix TS search index building script to properly visit subdirectories | 05 August 2015, 17:55:01 UTC |
| 0b486a7 | Martin Cech | 05 August 2015, 17:51:59 UTC | do not encode id when returning TS tool search results | 05 August 2015, 17:51:59 UTC |
| ba26507 | carlfeberhard | 04 August 2015, 20:39:31 UTC | Merge pull request #456 from jmchilton/fix_expect_outputs [15.05] Fix expect_num_outputs parsing on tool test elements. | 04 August 2015, 20:39:31 UTC |
| 44ae751 | Martin Cech | 04 August 2015, 20:30:19 UTC | Merge pull request #551 from dannon/cloudlauch_fix Password field for old cloudlaunch's secret key. | 04 August 2015, 20:30:19 UTC |
| efe59ea | Dannon Baker | 04 August 2015, 17:28:49 UTC | Password field for old cloudlaunch's secret key. | 04 August 2015, 17:28:49 UTC |
| f17c533 | Dannon Baker | 04 August 2015, 13:33:41 UTC | Merge pull request #547 from jmchilton/intermediate_delete_fix [15.07] Fixes for DeleteIntermediatesAction. | 04 August 2015, 13:33:41 UTC |
| 52fa00b | John Chilton | 03 August 2015, 15:06:58 UTC | Fixes for DeleteIntermediatesAction. Shouldn't assume the workflow invocation has completely been evaluated or that a job is available yet for invocation steps. | 04 August 2015, 08:30:15 UTC |
| 4d4c68c | Dannon Baker | 30 July 2015, 18:00:03 UTC | Swap track_jobs_in_database to be True by default. This removes the current multiprocess detection logic in favor of simplifying the configuration, and fixes a bug where uwsgi + 1 handler will not work. | 01 August 2015, 12:09:32 UTC |
| fc829aa | Aysam Guerler | 31 July 2015, 17:04:58 UTC | Merge pull request #534 from jmchilton/more_failure [15.07] Fix dbkey filtering of multiple input targets. | 31 July 2015, 17:04:58 UTC |
| b481e74 | John Chilton | 28 July 2015, 16:45:06 UTC | Allow dbkey filtering of multiple input targets. Fixes #388. Includes a test case. | 31 July 2015, 10:09:45 UTC |
| 607aca8 | John Chilton | 28 July 2015, 11:39:19 UTC | Add test tool demontrating filtering selections based on dbkey. | 31 July 2015, 10:09:45 UTC |
| e8f3553 | John Chilton | 28 July 2015, 11:38:04 UTC | Fix expect_failure="true" failure semantics to cover tool submission failure. Previously it just covered runtime job failure - there should probably be a way for the tool developer to specify which sort of failure is expected. | 31 July 2015, 10:09:44 UTC |
| 6fadb2b | Dannon Baker | 30 July 2015, 16:42:51 UTC | Merge pull request #531 from blankenberg/toolshed-install-compile-fallback [15.07] Fix for installing dependencies from source when download of precompiled binaries has failed. | 30 July 2015, 16:42:51 UTC |
| 7c4a9ab | Daniel Blankenberg | 30 July 2015, 15:53:08 UTC | Fix for installing dependencies from source when download of precompiled binaries has failed. | 30 July 2015, 15:53:08 UTC |
| 349378a | Dannon Baker | 24 July 2015, 21:23:44 UTC | Adjust comment for flake8 | 24 July 2015, 23:17:41 UTC |
| 80f4bd7 | jgoecks | 24 July 2015, 20:45:18 UTC | Fix BBI data provider underflow bug when computing standard deviation | 24 July 2015, 23:17:30 UTC |
| 1c04e14 | Dannon Baker | 24 July 2015, 19:28:05 UTC | Merge pull request #490 from carlfeberhard/release_15.07 [15.07] Histories: include owner annotations of hdas in published history dis… | 24 July 2015, 19:28:05 UTC |
| 784e07c | Dannon Baker | 24 July 2015, 14:23:26 UTC | Merge branch 'release_15.05' into release_15.07 | 24 July 2015, 14:23:26 UTC |
| 8f175ef | Eric Rasche | 24 July 2015, 14:20:16 UTC | Merge pull request #497 from dannon/release_15.05 SCRIPT_NAME can be empty or not in the environment at all. This reso… | 24 July 2015, 14:20:16 UTC |
| 5788066 | Dannon Baker | 24 July 2015, 14:04:47 UTC | SCRIPT_NAME can be empty or not in the environment at all. This resolves http://dev.list.galaxyproject.org/NGINX-uWSGI-with-require-login-needs-uwsgi-param-SCRIPT-NAME-td4666901.html. Thanks to @dctrud and @ericenns for the help tracking it down. | 24 July 2015, 14:04:47 UTC |
| 33181f5 | Carl Eberhard | 22 July 2015, 18:23:49 UTC | Histories: include owner annotations of hdas in published history display (HistoryManager._get_history_data) | 22 July 2015, 18:23:49 UTC |
| 2f8580b | Dannon Baker | 22 July 2015, 17:44:56 UTC | Merge branch 'release_15.05' into release_15.07 | 22 July 2015, 17:44:56 UTC |
| 558a590 | Dannon Baker | 22 July 2015, 17:41:04 UTC | Merge pull request #475 from blankenberg/custom_builds_objectstore_15.05 [15.05] Fix for users creating Custom DBKeys when objectstore is being used. | 22 July 2015, 17:41:04 UTC |
| 488d42d | Dannon Baker | 22 July 2015, 16:37:26 UTC | Merge branch 'release_15.05' into release_15.07 | 22 July 2015, 16:37:26 UTC |
| bcd1f74 | Nitesh Turaga | 22 July 2015, 16:36:12 UTC | Merge pull request #483 from dannon/old_cloudlaunch_errormsg Catch and return error message during key verification in cloudlaunch. | 22 July 2015, 16:36:12 UTC |
| 6049a74 | Dannon Baker | 21 July 2015, 18:03:22 UTC | Catch and return error message during key verification in cloudlaunch. | 21 July 2015, 18:03:22 UTC |
| 08136a8 | John Chilton | 20 July 2015, 12:48:01 UTC | Merge pull request #477 from blankenberg/15.05_metadata_autodect_fix [15.05] Fix autodection of metadata, from edit dataset attributes. | 20 July 2015, 12:48:01 UTC |
| 807dd81 | Daniel Blankenberg | 17 July 2015, 20:31:56 UTC | Turn of sanitizer for in __SET_METADATA__ autodetect metadata tool. Fixes issue that appears as a result of PR #474, but also could occur under corner-cases with interestlying named temp filenames. Also, add quotes around configfile filename. | 17 July 2015, 20:31:56 UTC |
| b11f5a5 | Daniel Blankenberg | 17 July 2015, 15:29:55 UTC | Minor white-space change. | 17 July 2015, 15:29:55 UTC |
| 0afcfcb | Daniel Blankenberg | 17 July 2015, 15:26:30 UTC | Fix for users creating Custom DBKeys when objectstore is being used. | 17 July 2015, 15:26:30 UTC |
| 4d0a9a8 | Daniel Blankenberg | 17 July 2015, 14:54:52 UTC | Merge pull request #474 from jmchilton/metadata_quoting [15.05] Quote more paths when building metadata command lines. | 17 July 2015, 14:54:52 UTC |
| 341a2f1 | John Chilton | 17 July 2015, 09:33:17 UTC | Quote more paths when building metadata command lines. Tested and fixes linked library uploads with spaces in the file path. Probably fixes other more obsecure problems like if the temp directory had a space in it, etc.... | 17 July 2015, 09:38:49 UTC |
| b631215 | Nate Coraor | 16 July 2015, 14:53:29 UTC | Merge pull request #470 from carlfeberhard/fix.h5-datatype-in-upload [15.07] Datatypes: allow display_in_upload for h5 files | 16 July 2015, 14:53:29 UTC |
| b1be4c1 | Carl Eberhard | 16 July 2015, 14:35:12 UTC | Datatypes: allow display_in_upload for h5 files | 16 July 2015, 14:35:12 UTC |
| 8c37677 | Daniel Blankenberg | 15 July 2015, 18:49:22 UTC | Merge pull request #466 from natefoo/default-metadata-limit [15.05] Set a default limit for metadata key size | 15 July 2015, 18:49:22 UTC |
| cf29f6c | Daniel Blankenberg | 15 July 2015, 18:48:34 UTC | Merge pull request #465 from carlfeberhard/release_15.07 [15.07] Histories, structure: fix job query to allow admin to view other hist… | 15 July 2015, 18:48:34 UTC |
| 212b083 | Nate Coraor | 15 July 2015, 18:28:40 UTC | Set the default metadata key limit to 5MB | 15 July 2015, 18:28:40 UTC |
| 2ca8f36 | Carl Eberhard | 15 July 2015, 18:15:24 UTC | Histories, structure: fix job query to allow admin to view other history structures | 15 July 2015, 18:15:24 UTC |
| 13a40b3 | Daniel Blankenberg | 15 July 2015, 14:25:46 UTC | Merge pull request #461 from carlfeberhard/release_15.05 [15.05] UI, Collections: use Galaxy.options.root for API URL | 15 July 2015, 14:25:46 UTC |
| 6e8bfc6 | Carl Eberhard | 15 July 2015, 14:13:22 UTC | UI, Collections: use Galaxy.options.root for API URL | 15 July 2015, 14:13:22 UTC |
| 39f6730 | Nate Coraor | 15 July 2015, 02:48:30 UTC | Merge branch 'release_15.05' into release_15.07 | 15 July 2015, 02:48:30 UTC |
| ddf4ce5 | John Chilton | 15 July 2015, 02:42:35 UTC | Merge pull request #459 from natefoo/dev Lint fixes for #458 | 15 July 2015, 02:42:35 UTC |
| 37cf1af | Nate Coraor | 15 July 2015, 02:15:08 UTC | lint fixes for #458 | 15 July 2015, 02:15:08 UTC |
| cb8f635 | Nate Coraor | 15 July 2015, 02:12:17 UTC | Merge pull request #458 from pvanheus/auth_pam AuthProvider for PAM (Pluggable Authentication Modules) | 15 July 2015, 02:12:17 UTC |
| b9c9f11 | Peter van Heusden | 14 July 2015, 22:33:31 UTC | * New PAM AuthProvider for interfacing with the Pluggable Authentication Module system (http://www.linux-pam.org/) * Helper script to allow authenticating against modules as root | 14 July 2015, 22:47:13 UTC |
| 4fe2bd4 | Nate Coraor | 14 July 2015, 18:48:29 UTC | Merge pull request #398 from abretaud/section Fix error when displaying job params for tools containing a section | 14 July 2015, 18:48:29 UTC |
| 23209d5 | John Chilton | 14 July 2015, 16:54:16 UTC | Merge pull request #441 from Christian-B/unlinked_dependencies Added unlinked dependency resolver | 14 July 2015, 16:54:16 UTC |
| 1419804 | John Chilton | 14 July 2015, 16:48:02 UTC | Merge pull request #444 from yhoogstrate/dev Fix md5sum/sha256 in toolshed action | 14 July 2015, 16:48:02 UTC |
| ac75e6f | Nate Coraor | 14 July 2015, 15:34:13 UTC | Merge pull request #455 from jmchilton/output_collection_filter Implement <filter> tag for output collections. | 14 July 2015, 15:34:13 UTC |
| e1d5313 | yhoogstrate | 14 July 2015, 11:06:45 UTC | Merge pull request #4 from erasche/docs-fix Update docs, re-instate backwards compatability | 14 July 2015, 11:06:45 UTC |
| 0cbf97a | John Chilton | 14 July 2015, 09:00:55 UTC | Fix expect_num_outputs parsing on tool test elements. Broken with abstracting XML parsing out into its own module. | 14 July 2015, 09:21:21 UTC |
| 163b0e3 | John Chilton | 14 July 2015, 09:15:46 UTC | Implement <filter> tag for output collections. Closes #445. | 14 July 2015, 09:18:24 UTC |
| ec36199 | Dannon Baker | 13 July 2015, 19:13:28 UTC | Merge pull request #453 from natefoo/group_round Remove superflous assignment left over from... | 13 July 2015, 19:13:28 UTC |
| 6eafa52 | Nate Coraor | 13 July 2015, 18:55:33 UTC | Remove superflous assignment left over from 647fcf1f6069a272b73791915e989a1bccac4318, thanks @nsoranzo. | 13 July 2015, 18:55:33 UTC |
| 37b231c | Nate Coraor | 13 July 2015, 18:43:05 UTC | Verify MD5 and SHA256 sums on other types of actions. For all types of actions other than download_by_url, these must be specified as attributes on the <action> tag, the old `#hash#` method in the URL is not supported. | 13 July 2015, 18:43:05 UTC |
| 72b7381 | Nate Coraor | 13 July 2015, 15:36:16 UTC | Improvements to @erasche's download hash changes suggested by @yhoogstrate. | 13 July 2015, 15:36:16 UTC |
| 4792825 | carlfeberhard | 13 July 2015, 15:36:02 UTC | Merge pull request #446 from jgoecks/trackster-close-files Trackster fixes: (a) close data provider files after reading from the… | 13 July 2015, 15:36:02 UTC |
| 2bf2844 | Dannon Baker | 13 July 2015, 15:17:01 UTC | Merge pull request #440 from dctrud/trackster_nowrap Stop trackster location wrap in chrome | 13 July 2015, 15:17:01 UTC |
| f122c87 | Dannon Baker | 13 July 2015, 15:15:22 UTC | Merge pull request #452 from natefoo/group_round Fixed: Return integer values when 'round to nearest integer' is selected in Group tool | 13 July 2015, 15:15:22 UTC |
| d5b28be | Nate Coraor | 13 July 2015, 15:13:59 UTC | Merge pull request #443 from Christian-B/config_file_not_found Added log error for config file not found | 13 July 2015, 15:13:59 UTC |
| 647fcf1 | Nate Coraor | 13 July 2015, 15:01:55 UTC | Only make the Group tool's return value an integer if rounding is selected, as pointed out by @nsoranzo. | 13 July 2015, 15:01:55 UTC |
| 2a63b7b | Nate Coraor | 13 July 2015, 15:01:07 UTC | Merge branch 'group' of https://github.com/moskalenko/galaxy into group_round | 13 July 2015, 15:01:07 UTC |
| 5b8fe57 | Nicola Soranzo | 13 July 2015, 14:38:31 UTC | Merge pull request #451 from carlfeberhard/fix.tools-api-hda-mgr [15.05] API, tools: fix use of trans in _rerun_tool hda manager | 13 July 2015, 14:38:31 UTC |
| e9aa6e8 | Martin Cech | 13 July 2015, 14:29:01 UTC | Merge pull request #426 from ericenns/feature/library_folder_export_to_history Feature/library folder export to history | 13 July 2015, 14:29:01 UTC |
| 7002f65 | Carl Eberhard | 13 July 2015, 14:27:33 UTC | API, tools: fix use of trans in _rerun_tool hda manager | 13 July 2015, 14:27:33 UTC |
| 25cb291 | John Chilton | 11 July 2015, 22:06:20 UTC | Merge pull request #449 from galaxyproject/revert-433-lint2 Revert "[WIP] Mega flake8 linting" | 11 July 2015, 22:06:20 UTC |
| df1b30e | John Chilton | 11 July 2015, 20:37:28 UTC | Merge pull request #433 from bgruening/lint2 [WIP] Mega flake8 linting | 11 July 2015, 20:37:28 UTC |
| 37f1976 | Dannon Baker | 11 July 2015, 17:17:38 UTC | Revert "[WIP] Mega flake8 linting" | 11 July 2015, 17:17:38 UTC |
| 4dc96cc | John Chilton | 11 July 2015, 13:20:19 UTC | Merge pull request #5 from jmchilton/fix_datatypes_pep8 Fix problematic PEP-8 fix. | 11 July 2015, 13:20:19 UTC |
| cd0a122 | John Chilton | 11 July 2015, 13:17:16 UTC | Fix https://github.com/bgruening/galaxy/commit/c691b9216031dce4a66251c83fbdf680cd5a411e#commitcomment-12038966. | 11 July 2015, 13:17:16 UTC |
| 58e319d | = | 09 July 2015, 13:04:17 UTC | downgraded warning to debug as would happen on default | 09 July 2015, 13:04:17 UTC |
