[galaxy-commits] [galaxyproject/galaxy] 9cf21b: Copied readme from Bjoern's repo

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 9cf21b3469d20eee1c269f02274e83388c4fbbb3 https://github.com/galaxyproject/galaxy/commit/9cf21b3469d20eee1c269f02274e8... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2014-07-31 (Thu, 31 Jul 2014) Changed paths: A README.md Log Message: ----------- Copied readme from Bjoern's repo Commit: bbc50545072e365664d5176720f3aa9ca9137dc1 https://github.com/galaxyproject/galaxy/commit/bbc50545072e365664d5176720f3a... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-07-31 (Thu, 31 Jul 2014) Changed paths: A LICENSE A config/rstudio.xml Log Message: ----------- Added licence/config file Commit: 2fb9e013579566679109120561ede41c66e3d100 https://github.com/galaxyproject/galaxy/commit/2fb9e013579566679109120561ede... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2014-07-31 (Thu, 31 Jul 2014) Changed paths: A templates/rstudio.mako Log Message: ----------- Copied from bgruening/galaxy-ipython Commit: d3fa742a41c79b9d5900c4209931b237ccadefb4 https://github.com/galaxyproject/galaxy/commit/d3fa742a41c79b9d5900c4209931b... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-07-31 (Thu, 31 Jul 2014) Changed paths: A templates/default.Rproj Log Message: ----------- Added empty default Rproject file Commit: e902372eea5c249b5d7b91e381d5aba4ce5320fb https://github.com/galaxyproject/galaxy/commit/e902372eea5c249b5d7b91e381d5a... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-08-04 (Mon, 04 Aug 2014) Changed paths: A config/rstudio.conf M templates/rstudio.mako Log Message: ----------- Initial version stuck to port 7777 Commit: 1cf5ac9df755a91c905e26998438eb413f868c1e https://github.com/galaxyproject/galaxy/commit/1cf5ac9df755a91c905e26998438e... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-08-08 (Fri, 08 Aug 2014) Changed paths: M config/rstudio.conf R templates/default.Rproj M templates/rstudio.mako Log Message: ----------- More progress Autologin may not be possible but we'll certainly try for it. This has the container come up and copies every dataset into the R container. No magic R/Galaxy sugar yet. Commit: 715e33b10b46ed525a1d99737637b7ff01ae63de https://github.com/galaxyproject/galaxy/commit/715e33b10b46ed525a1d99737637b... Author: Björn Grüning <bjoern.gruening@gmail.com> Date: 2014-08-09 (Sat, 09 Aug 2014) Changed paths: M README.md Log Message: ----------- Update README.md Commit: ce453a76cbb7888d9d5c08c11dfa5bce24a9586a https://github.com/galaxyproject/galaxy/commit/ce453a76cbb7888d9d5c08c11dfa5... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M config/rstudio.conf Log Message: ----------- Removed quotes Commit: fa412be0ddc729264d5370de4f203c429520989a https://github.com/galaxyproject/galaxy/commit/fa412be0ddc729264d5370de4f203... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Template updates Commit: 3d9c8a043ccc883978e6979fce95586804553372 https://github.com/galaxyproject/galaxy/commit/3d9c8a043ccc883978e6979fce955... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: A static/js/ie.js A static/js/rstudio.js A templates/ie.mako M templates/rstudio.mako Log Message: ----------- Moved to IE framework Commit: 30a9022c2265ce1ab3263fb74925781c391f64c9 https://github.com/galaxyproject/galaxy/commit/30a9022c2265ce1ab3263fb749257... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M config/rstudio.conf A static/js/crypto/base64.js A static/js/crypto/jsbn.js A static/js/crypto/prng4.js A static/js/crypto/rng.js A static/js/crypto/rsa.js M templates/ie.mako M templates/rstudio.mako Log Message: ----------- More progress towards new framework Commit: a0a39b43504981f586d3e6bf8af75adc34f41f5d https://github.com/galaxyproject/galaxy/commit/a0a39b43504981f586d3e6bf8af75... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M static/js/rstudio.js M templates/ie.mako M templates/rstudio.mako Log Message: ----------- Mostly working, CORS issues Commit: 7511fc868df46e6ead7a8f59a9e54d974cb6d826 https://github.com/galaxyproject/galaxy/commit/7511fc868df46e6ead7a8f59a9e54... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M config/rstudio.conf A static/js/crypto/base64.js A static/js/crypto/jsbn.js A static/js/crypto/prng4.js A static/js/crypto/rng.js A static/js/crypto/rsa.js A static/js/ie.js A static/js/rstudio.js A templates/ie.mako M templates/rstudio.mako Log Message: ----------- Merge branch 'ie-framework' Commit: b438695abfb3017933b71cf5f124d264b01544ed https://github.com/galaxyproject/galaxy/commit/b438695abfb3017933b71cf5f124d... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Wait on pubkey to exist before launching Commit: 4e64ce445df2d2fe8111c3711778ceb96b1d302e https://github.com/galaxyproject/galaxy/commit/4e64ce445df2d2fe8111c3711778c... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/ie.js Log Message: ----------- Corrected AJAX request call Commit: 8b1eec92c5c0142a6c63e813b88d217ac59fe6c2 https://github.com/galaxyproject/galaxy/commit/8b1eec92c5c0142a6c63e813b88d2... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/ie.js M templates/rstudio.mako Log Message: ----------- Updated port for nginx proxy, added more error catching Commit: e186a9673ce992b5ead3d5e5ad3c26fc7854fca3 https://github.com/galaxyproject/galaxy/commit/e186a9673ce992b5ead3d5e5ad3c2... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/rstudio.js Log Message: ----------- Updated URLs Commit: bcee19e71cdaa3e8c98d0b6bbcbe402adc220b6c https://github.com/galaxyproject/galaxy/commit/bcee19e71cdaa3e8c98d0b6bbcbe4... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Moved docker container to subpath Commit: bdfaed779d901460a060d3b382c30603396b8e50 https://github.com/galaxyproject/galaxy/commit/bdfaed779d901460a060d3b382c30... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/crypto/base64.js M static/js/crypto/jsbn.js M static/js/crypto/prng4.js M static/js/crypto/rng.js M static/js/crypto/rsa.js Log Message: ----------- Extracted files from official rstudio github They were different than files pulled from Tom Wu's personal webpage. As such, took apart the following file: https://github.com/rstudio/rstudio/blob/44b1b2815b76013d5a2ba6e9a203ab52be7e... and extracted constituent parts. Commit: 8d2d7a76517b43e0296769a7278f430a941ae787 https://github.com/galaxyproject/galaxy/commit/8d2d7a76517b43e0296769a7278f4... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/ie.js Log Message: ----------- Prevent multiple requests from fufilling by timeing out Commit: 4aff5a4445be4d88a856fb8754a735ca62721dee https://github.com/galaxyproject/galaxy/commit/4aff5a4445be4d88a856fb8754a73... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/rstudio.js M templates/rstudio.mako Log Message: ----------- Move encryption to JS only in rstudio.js Much better than waiting on reading the file from OS. Commit: 1ffbc4004094c019c41150e3f5d59c0aee6dce64 https://github.com/galaxyproject/galaxy/commit/1ffbc4004094c019c41150e3f5d59... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-25 (Thu, 25 Sep 2014) Changed paths: M static/js/crypto/base64.js M static/js/crypto/jsbn.js M static/js/crypto/prng4.js M static/js/crypto/rng.js M static/js/crypto/rsa.js M static/js/ie.js M static/js/rstudio.js M templates/rstudio.mako Log Message: ----------- Merge pull request #1 from erasche/develop Develop Commit: f1bda976bfbb27f232a8d4fc77486200a46d6fb3 https://github.com/galaxyproject/galaxy/commit/f1bda976bfbb27f232a8d4fc77486... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: A static/js/crypto/rstudio.big.js A static/js/crypto/rstudio.min.js A static/js/crypto/rstudio/base64.js A static/js/crypto/rstudio/jsbn.js A static/js/crypto/rstudio/prng4.js A static/js/crypto/rstudio/rng.js A static/js/crypto/rstudio/rsa.js A static/js/crypto/wu/base64.js A static/js/crypto/wu/jsbn.js A static/js/crypto/wu/prng4.js A static/js/crypto/wu/rng.js A static/js/crypto/wu/rsa.js M static/js/ie.js M static/js/rstudio.js Log Message: ----------- Last ditch JS attempts Also threw in all of the wu/rstudio originals Commit: fdb4b4b99774eac0fcd383476202aee2fd973984 https://github.com/galaxyproject/galaxy/commit/fdb4b4b99774eac0fcd383476202a... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: M templates/ie.mako Log Message: ----------- Remove IE specific text Commit: 15996446743521a93b02871396b82f9640082858 https://github.com/galaxyproject/galaxy/commit/15996446743521a93b02871396b82... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: A static/js/crypto/rstudio.big.js A static/js/crypto/rstudio.min.js A static/js/crypto/rstudio/base64.js A static/js/crypto/rstudio/jsbn.js A static/js/crypto/rstudio/prng4.js A static/js/crypto/rstudio/rng.js A static/js/crypto/rstudio/rsa.js A static/js/crypto/wu/base64.js A static/js/crypto/wu/jsbn.js A static/js/crypto/wu/prng4.js A static/js/crypto/wu/rng.js A static/js/crypto/wu/rsa.js M static/js/ie.js M static/js/rstudio.js M templates/ie.mako Log Message: ----------- Merge pull request #2 from erasche/develop Develop Commit: bc8191543cea3219d995a1cd4c0c69cee6c7bf87 https://github.com/galaxyproject/galaxy/commit/bc8191543cea3219d995a1cd4c0c6... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: M README.md Log Message: ----------- Updated the readme Commit: 34caec7c8316f851090a09085be3c72bda6862e8 https://github.com/galaxyproject/galaxy/commit/34caec7c8316f851090a09085be3c... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: M README.md A static/images/start_rstudio.png Log Message: ----------- Fixed URLs Commit: 75885e2ed15796372781611b6924a0e85b49c268 https://github.com/galaxyproject/galaxy/commit/75885e2ed15796372781611b6924a... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Change to enable apache_urls usage Commit: 7feac47c3b3dd7840616083a11acbde886586bc1 https://github.com/galaxyproject/galaxy/commit/7feac47c3b3dd7840616083a11acb... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: A INSTALL.md Log Message: ----------- Added installation instructions Commit: 6143a87abcb14d3522c328794ba4e724bc907462 https://github.com/galaxyproject/galaxy/commit/6143a87abcb14d3522c328794ba4e... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-09-26 (Fri, 26 Sep 2014) Changed paths: A static/js/crypto/rstudio.big.js A static/js/crypto/rstudio.min.js A static/js/crypto/rstudio/base64.js A static/js/crypto/rstudio/jsbn.js A static/js/crypto/rstudio/prng4.js A static/js/crypto/rstudio/rng.js A static/js/crypto/rstudio/rsa.js A static/js/crypto/wu/base64.js A static/js/crypto/wu/jsbn.js A static/js/crypto/wu/prng4.js A static/js/crypto/wu/rng.js A static/js/crypto/wu/rsa.js M static/js/ie.js M static/js/rstudio.js M templates/ie.mako Log Message: ----------- Merge branch 'master' of github.com:erasche/galaxy-rstudio Commit: 10d2ddb55e4b4926fbcfa2c06568cf92e61a908f https://github.com/galaxyproject/galaxy/commit/10d2ddb55e4b4926fbcfa2c06568c... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-25 (Sat, 25 Oct 2014) Changed paths: M static/js/rstudio.js M templates/rstudio.mako Log Message: ----------- Fixed login issue Not sure I'm entirely fond of this solution, however it functions perfectly Commit: 6bd9b9bc2e192a66a5ff4939d3f9e41f70e91b8a https://github.com/galaxyproject/galaxy/commit/6bd9b9bc2e192a66a5ff4939d3f9e... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-25 (Sat, 25 Oct 2014) Changed paths: R config/rstudio.conf A config/rstudio.ini.sample R static/js/ie.js R templates/ie.mako M templates/rstudio.mako Log Message: ----------- Mostly translated to new framework Commit: c857bffed09622dd0c1709db70205850ec9344cc https://github.com/galaxyproject/galaxy/commit/c857bffed09622dd0c1709db70205... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-25 (Sat, 25 Oct 2014) Changed paths: R INSTALL.md R LICENSE R README.md Log Message: ----------- Removed docs to align with ipython Commit: f81eb61772ff87ee6a59cd82fbbe304143e3dff6 https://github.com/galaxyproject/galaxy/commit/f81eb61772ff87ee6a59cd82fbbe3... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-25 (Sat, 25 Oct 2014) Changed paths: R static/images/start_rstudio.png Log Message: ----------- Removed picture Commit: fdd5719451d1c4aa3d62161e968bb7137697f750 https://github.com/galaxyproject/galaxy/commit/fdd5719451d1c4aa3d62161e968bb... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-25 (Sat, 25 Oct 2014) Changed paths: M config/rstudio.ini.sample Log Message: ----------- Fixed image name Commit: 76c9226ae6b550af794eae3b0999f75ebd016c31 https://github.com/galaxyproject/galaxy/commit/76c9226ae6b550af794eae3b0999f... Author: John Chilton <jmchilton@gmail.com> Date: 2014-10-26 (Sun, 26 Oct 2014) Changed paths: M config/rstudio.xml M templates/rstudio.mako Log Message: ----------- More fixes for moving interactive_environments into Galaxy. Commit: 8f190d731cea5685c641d3335a48df0c0cde6d60 https://github.com/galaxyproject/galaxy/commit/8f190d731cea5685c641d3335a48d... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-26 (Sun, 26 Oct 2014) Changed paths: M config/rstudio.xml M templates/rstudio.mako Log Message: ----------- Merge pull request #3 from jmchilton/new-viz-framework More fixes for moving IE framework into Galaxy. Commit: bb1bd81f8124d2b673918cfb58f5ee3bbaa21862 https://github.com/galaxyproject/galaxy/commit/bb1bd81f8124d2b673918cfb58f5e... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-26 (Sun, 26 Oct 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Temporary removal of non-root IE fix RStudio does not (yet) support running as an unprivleged user. The patch we applied to handle that was applied globally, resulting in issues for IEs that are not yet patched for root issues Commit: d528d394d36c5dc9d85250a5e3d4b61edecea3c2 https://github.com/galaxyproject/galaxy/commit/d528d394d36c5dc9d85250a5e3d4b... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-26 (Sun, 26 Oct 2014) Changed paths: M static/js/rstudio.js M templates/rstudio.mako Log Message: ----------- Fixes for use within new <interactive_environment> Numerous fixes and bugs introduced here ;) - Does not work with @jmchilton's proxy - Messily handles re-writing of passwords, this is a bug in Galaxy-IE that needs to be patched by @erasche - Hacks out non-root container setting, as rstudio currently must run as root (PAM authentication) Commit: 432caa230d3553bb9029f04ba784192ded00d82b https://github.com/galaxyproject/galaxy/commit/432caa230d3553bb9029f04ba7841... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-10-26 (Sun, 26 Oct 2014) Changed paths: R INSTALL.md R LICENSE R README.md R config/rstudio.conf A config/rstudio.ini.sample M config/rstudio.xml R static/images/start_rstudio.png R static/js/ie.js M static/js/rstudio.js R templates/ie.mako M templates/rstudio.mako Log Message: ----------- Merge branch 'new-viz-framework' Commit: 778f97ba1575349596058038b5c20f0ca33f74ab https://github.com/galaxyproject/galaxy/commit/778f97ba1575349596058038b5c20... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-06 (Thu, 06 Nov 2014) Changed paths: M config/rstudio.xml Log Message: ----------- Updated doctype Commit: bc63d84182e0c73313f564d23aedb144e50ccab1 https://github.com/galaxyproject/galaxy/commit/bc63d84182e0c73313f564d23aedb... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-06 (Thu, 06 Nov 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Proxy seems to be working now? Commit: 549d321d2550008f250a03b299be127913073d41 https://github.com/galaxyproject/galaxy/commit/549d321d2550008f250a03b299be1... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-06 (Thu, 06 Nov 2014) Changed paths: M static/js/rstudio.js Log Message: ----------- Removed warning Commit: d1d4cb9f4f78da0f791a13268c74c2254fd45832 https://github.com/galaxyproject/galaxy/commit/d1d4cb9f4f78da0f791a13268c74c... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-06 (Thu, 06 Nov 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Body was inheriting CSS from galaxy and havinga margin Commit: caa7ebbada49703bbd8a6ac542d93a3c269ec811 https://github.com/galaxyproject/galaxy/commit/caa7ebbada49703bbd8a6ac542d93... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-06 (Thu, 06 Nov 2014) Changed paths: M config/rstudio.xml M static/js/rstudio.js M templates/rstudio.mako Log Message: ----------- Merge pull request #4 from erasche/new-viz-framework New viz framework Commit: 0e5da3fc2753f5562f69ff3e0af73b4ba47fc0f8 https://github.com/galaxyproject/galaxy/commit/0e5da3fc2753f5562f69ff3e0af73... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-06 (Thu, 06 Nov 2014) Changed paths: M config/rstudio.xml M templates/rstudio.mako Log Message: ----------- Automatically restore .RData files from history Commit: 703ed2d2bbb15514843a300aa65145e6aa1964fa https://github.com/galaxyproject/galaxy/commit/703ed2d2bbb15514843a300aa6514... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-16 (Sun, 16 Nov 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Pass CORS_ORIGIN to NB, make sure URLs are correct Commit: 77b5df720d5262bec6f171eed5add750466139fd https://github.com/galaxyproject/galaxy/commit/77b5df720d5262bec6f171eed5add... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2014-11-17 (Mon, 17 Nov 2014) Changed paths: M templates/rstudio.mako Log Message: ----------- Set to port 80 for nginx Commit: 32d9390d9dffd82c6a10c31a0f679d7d78b7c904 https://github.com/galaxyproject/galaxy/commit/32d9390d9dffd82c6a10c31a0f679... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-04-03 (Fri, 03 Apr 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add EDAM IDs to datatypes I made a best-guess attempt at most of these, EDAM doesn't include image datatypes, nor graph datatypes, nor colourspace fastq (among other things, these just came to mind). - https://trello.com/c/TRgSWfT1/ - http://bioportal.bioontology.org/ontologies/EDAM/?p=summary Commit: 5c8ad19ddba639ea4bc09b67aaa3dde9c0fd2bae https://github.com/galaxyproject/galaxy/commit/5c8ad19ddba639ea4bc09b67aaa3d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-14 (Tue, 14 Apr 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-library.js M static/style/blue/base.css M static/style/src/less/ui.less Log Message: ----------- New library data selector for tool form Commit: ebafd06fea8cde1160cce0bba780494257e05f0d https://github.com/galaxyproject/galaxy/commit/ebafd06fea8cde1160cce0bba7804... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-16 (Thu, 16 Apr 2015) Changed paths: M lib/galaxy/eggs/scramble.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/base/pluginframework.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/tool_shed/build_ts_whoosh_index.py R scripts/tool_shed/build_ts_whoosh_index.sh M static/welcome.html.sample M test/api/test_tools.py M test/base/twilltestcase.py R test/functional/test_history_functions.py A test/functional/tools/detect_errors_aggressive.xml A test/functional/tools/md5sum.xml M test/functional/tools/samples_tool_conf.xml A test/unit/datatypes/__init__.py A test/unit/datatypes/dataproviders/__init__.py R test/unit/datatypes/dataproviders/tempfilecache.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/managers/__init__.py A test/unit/managers/base.py R test/unit/managers/mock.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py R test/unit/managers/test_ModelManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py A test/unit/unittest_utils/__init__.py A test/unit/unittest_utils/galaxy_mock.py A test/unit/unittest_utils/tempfilecache.py A test/unit/unittest_utils/utility.py R test/unit/util/utility.py A test/unit/visualizations/__init__.py R test/unit/visualizations/registry/test_VisualizationsRegistry.py A test/unit/visualizations/test_VisualizationsRegistry.py A test/unit/web/__init__.py A test/unit/web/base/__init__.py R test/unit/web/base/mock.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter Commit: b1d3552be432d505ce0d862db0c294784e3f061e https://github.com/galaxyproject/galaxy/commit/b1d3552be432d505ce0d862db0c29... Author: John Chilton <jmchilton@gmail.com> Date: 2015-04-17 (Fri, 17 Apr 2015) Changed paths: M lib/galaxy/tools/parameters/wrapped.py M test/api/test_tools.py A test/functional/tools/library_data.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add a library_data input test case and small fix. Commit: 5ec0bf2962069cf35bc0260a394d63314a28012e https://github.com/galaxyproject/galaxy/commit/5ec0bf2962069cf35bc0260a394d6... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-04-17 (Fri, 17 Apr 2015) Changed paths: M lib/galaxy/tools/parameters/wrapped.py M test/api/test_tools.py A test/functional/tools/library_data.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2 from jmchilton/library_data Add a library_data input test case and small fix. Commit: 27424139a01d80df0ba85a795844d920dd75470e https://github.com/galaxyproject/galaxy/commit/27424139a01d80df0ba85a795844d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-19 (Sun, 19 Apr 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Add generic list value wrapper and use it for the library data tool parameter, move wrapper import into parameters Commit: 5dec24c21e519d03dfdcd0928fa8401ee7cfcb8e https://github.com/galaxyproject/galaxy/commit/5dec24c21e519d03dfdcd0928fa84... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-19 (Sun, 19 Apr 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M eggs.ini M lib/galaxy/tools/wrappers.py M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/history/history-panel-edit-current.js M templates/webapps/galaxy/root/index.mako A test/functional/tools/cheetah_casting.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter Commit: f026690d2710d32644f6724398857e83f93f8c65 https://github.com/galaxyproject/galaxy/commit/f026690d2710d32644f6724398857... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-19 (Sun, 19 Apr 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Add optional feature to list input element Commit: 8b478c1005c2468278149ce271e8a96bf698f421 https://github.com/galaxyproject/galaxy/commit/8b478c1005c2468278149ce271e8a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-19 (Sun, 19 Apr 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix import for DatasetFilenameWrapper Commit: 3832de63b869946b58dcb064621c595964c17dc5 https://github.com/galaxyproject/galaxy/commit/3832de63b869946b58dcb064621c5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Add multiple option to library dataset parameter Commit: 0496310ef832368f6ad743b86c8a08e7a6844fa7 https://github.com/galaxyproject/galaxy/commit/0496310ef832368f6ad743b86c8a0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge new list wrapper functionality into default input wrapper Commit: 138ae47036a45decc136cbe4946bb897b17d654a https://github.com/galaxyproject/galaxy/commit/138ae47036a45decc136cbe4946bb... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Move to_param_dict_string call back to previous location in parameter wrapper Commit: 04a8d50b8b75dccb94b1f44ad3a5b91dea048384 https://github.com/galaxyproject/galaxy/commit/04a8d50b8b75dccb94b1f44ad3a5b... Author: Olivia Doppelt <olivia.doppelt@pasteur.fr> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Added in some missing EDAM types Commit: 5876e5f80cc7f33c808822697eb2ae71d44a6307 https://github.com/galaxyproject/galaxy/commit/5876e5f80cc7f33c808822697eb2a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M lib/galaxy/tools/wrappers.py M test/api/test_tools.py M test/functional/tools/library_data.xml Log Message: ----------- Revise library data parameter tests Commit: e2175d66e95f9bb31b7566f2ec53b131654a80b4 https://github.com/galaxyproject/galaxy/commit/e2175d66e95f9bb31b7566f2ec53b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/functional/tools/library_data.xml Log Message: ----------- Switch default for library data parameter to multiple entries Commit: 203329be27863cbb8a8ae153f883524f83f604a7 https://github.com/galaxyproject/galaxy/commit/203329be27863cbb8a8ae153f8835... Author: yhoogstrate <y.hoogstrate@erasmusmc.nl> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- run tests from outer directories Allows run_tests.sh to be executed from directories outside the galaxy home directory without returning the error "python: can't open file './scripts/functional_tests.py': [Errno 2] No such file or directory" Commit: dd0e76574ee6729f7bbf13483fcf2112bd0e5df6 https://github.com/galaxyproject/galaxy/commit/dd0e76574ee6729f7bbf13483fcf2... Author: yhoogstrate <y.hoogstrate@erasmusmc.nl> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1 from yhoogstrate/yhoogstrate-patch-2 run tests from outer directories Commit: 3ef1b21488c5592989e1d6285e12153875b1ad34 https://github.com/galaxyproject/galaxy/commit/3ef1b21488c5592989e1d6285e121... Author: yhoogstrate <y.hoogstrate@erasmusmc.nl> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- Update run_tests.sh fixed and tested it with ./galaxy/run_tests.sh -installed Commit: 3f9f72e5ee82a0dbfc7fa304d00d4628129e247b https://github.com/galaxyproject/galaxy/commit/3f9f72e5ee82a0dbfc7fa304d00d4... Author: yhoogstrate <y.hoogstrate@erasmusmc.nl> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- Update run_tests.sh Commit: e44c8db9dea56b8d1a2f941ce572b0f14e999d4c https://github.com/galaxyproject/galaxy/commit/e44c8db9dea56b8d1a2f941ce572b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.07.dev Commit: 17e10683b829d2f397831f5cb27b454a8ea41d74 https://github.com/galaxyproject/galaxy/commit/17e10683b829d2f397831f5cb27b4... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M lib/galaxy/app.py A lib/galaxy/visualization/plugins/__init__.py A lib/galaxy/visualization/plugins/config_parser.py A lib/galaxy/visualization/plugins/plugin.py A lib/galaxy/visualization/plugins/registry.py A lib/galaxy/visualization/plugins/resource_parser.py A lib/galaxy/visualization/plugins/utils.py R lib/galaxy/visualization/registry.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Visualizations registry: refactor registry/pluginframework, and promote plugins to class Commit: 660b92074eaf6f80bd173e462f34afb50227c055 https://github.com/galaxyproject/galaxy/commit/660b92074eaf6f80bd173e462f34a... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add emboss datatypes Commit: ce74ed5dce5fbc1d219f9f156a44ca578c2e8e60 https://github.com/galaxyproject/galaxy/commit/ce74ed5dce5fbc1d219f9f156a44c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add emboss datatypes Commit: 898d33dad4a4007cad9384055263f5f99d5daa1e https://github.com/galaxyproject/galaxy/commit/898d33dad4a4007cad9384055263f... Author: roalva1 <roalva1@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- added the possibility of merging bams from a parallelized job Commit: cbba7f49271fddbd3eeaed657bfbacea53c9e10c https://github.com/galaxyproject/galaxy/commit/cbba7f49271fddbd3eeaed657bfba... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- Fix external set_meta under sqlalchemy 1.0.0. I have *no* idea how this actually worked before -- we shouldn't have been directly assigning ids when a mapping exists. Commit: b946e3a38fd50cb10f8ed307e19dbc3e571a5513 https://github.com/galaxyproject/galaxy/commit/b946e3a38fd50cb10f8ed307e19db... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- consistent spacing Commit: ef69881e5603062a2e037376d4fd45582a133852 https://github.com/galaxyproject/galaxy/commit/ef69881e5603062a2e037376d4fd4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: A scripts/runtime_stats.py Log Message: ----------- Added a command line script for collecting stats on job runtimes to help admins make decisions about how/where to run jobs. Commit: be9796f2eb76888743086c52f2c62552e5af9e27 https://github.com/galaxyproject/galaxy/commit/be9796f2eb76888743086c52f2c62... Author: John Chilton <jmchilton@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- Merge pull request #150 from dannon/fix_external_meta Fix external set_meta under sqlalchemy 1.0.0. Commit: fd5c41e902c16347aa4389b0dcd1caf42abbcbde https://github.com/galaxyproject/galaxy/commit/fd5c41e902c16347aa4389b0dcd1c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M scripts/runtime_stats.py Log Message: ----------- Pull runtime stats from metrics by default (job state history remains an option), a couple other minor improvements to the script. Commit: bdbc98c47c16faf0b39534da8b7ef5116aa7ec22 https://github.com/galaxyproject/galaxy/commit/bdbc98c47c16faf0b39534da8b7ef... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M scripts/runtime_stats.py Log Message: ----------- Fix the connection string when a database username is provided (reported by @afgane in #151). Commit: 261bf02dc207099430ae9191ab4077ab472c8e36 https://github.com/galaxyproject/galaxy/commit/261bf02dc207099430ae9191ab407... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge branch 'release_15.05' into dev Commit: acf9e1bbe989d1f4894006e47e6d3e4ad2ad124f https://github.com/galaxyproject/galaxy/commit/acf9e1bbe989d1f4894006e47e6d3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-23 (Thu, 23 Apr 2015) Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 73dd0b1a6ff47c8604a1db78306d08349e54bba9 https://github.com/galaxyproject/galaxy/commit/73dd0b1a6ff47c8604a1db78306d0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-23 (Thu, 23 Apr 2015) Changed paths: M scripts/runtime_stats.py Log Message: ----------- Add some additional documentation/usage in the doc string Commit: eb538e00bdfb6cd87c71a620653c91854642b01a https://github.com/galaxyproject/galaxy/commit/eb538e00bdfb6cd87c71a620653c9... Author: guerler <aysam.guerler@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-list.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-parameters.js.map A static/maps/mvc/ui/ui-list.js.map A static/maps/mvc/ui/ui-select-ftp.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-list.js A static/scripts/mvc/ui/ui-select-ftp.js Log Message: ----------- Add ftpfile tool parameter Commit: b8261db255759a4725fd30de280fae19ee1a375b https://github.com/galaxyproject/galaxy/commit/b8261db255759a4725fd30de280fa... Author: abretaud <anthony.bretaudeau@rennes.inra.fr> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- perf optimization: store tools' section in a dict instead of looping through the whole list of sections/tools for each tool Commit: 43cd2083f6e293f94a55f477176f65e581cf691a https://github.com/galaxyproject/galaxy/commit/43cd2083f6e293f94a55f477176f6... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M scripts/drmaa_external_runner.py Log Message: ----------- runners/drmaa: set 'workingDirectory' correctly this fixes an issue with when the Galaxy lib (and therefore working directory) is not shared with the compute nodes Commit: 4f09010d849d25ad6bfc54c10482b553f8ab943f https://github.com/galaxyproject/galaxy/commit/4f09010d849d25ad6bfc54c10482b... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- runners/drmaa: revert to galaxy credentials for anonymous sessions there are no user credentials for anonymous sessions, and the runner crashes on the log message this patch reverts to galaxy instance credentials for anonymous sessions Commit: bc7113ba5f8490a4f0fbe2167175341f0c27d2ba https://github.com/galaxyproject/galaxy/commit/bc7113ba5f8490a4f0fbe21671753... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- runners/drmaa: create the job description json file if not exists Commit: 954276340c777a5845e58e78fd93ac651b6c1811 https://github.com/galaxyproject/galaxy/commit/954276340c777a5845e58e78fd93a... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- runners/drmaa: support 'embed_metadata_in_job' parameter previously, the metadata was always computed in the job - which is a good default, but it doesn't work if the compute nodes can't see the Galaxy lib. this patch adds an option for the 'drmaa' runner so it can compute metadata externally, after the jobs are finished Commit: ad97c4e83acd8afb32e30c016b448ef7c7d1d204 https://github.com/galaxyproject/galaxy/commit/ad97c4e83acd8afb32e30c016b448... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- runners/drmaa: configurable permissive mode for guest users 'allow_guests' If enabled, anonymous and usernames that can't be mapped to the real users will be permitted to run as a Galaxy user. Commit: 98beb9365b6f930584098851fee5c813e6e2056f https://github.com/galaxyproject/galaxy/commit/98beb9365b6f930584098851fee5c... Author: Dave B <dave@bx.psu.edu> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M test/install_and_test_tool_shed_repositories/base/util.py Log Message: ----------- Fix base.util to get the changeset from git. Now that buildbot is using git instead of hg to clone the galaxy code, it should use git instead of hg to determine which revision was cloned. Commit: e1302cb54e6da591a4b42948286f2143e98dd967 https://github.com/galaxyproject/galaxy/commit/e1302cb54e6da591a4b42948286f2... Author: John Chilton <jmchilton@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M test/install_and_test_tool_shed_repositories/base/util.py Log Message: ----------- Merge pull request #161 from davebx/dev Fix base.util to get the changeset from git. Commit: 385b4e71d6467ee98fac97c968bb9d0446fb56b9 https://github.com/galaxyproject/galaxy/commit/385b4e71d6467ee98fac97c968bb9... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M config/plugins/visualizations/common/templates/visualization_base.mako M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Visualizations registry: split plugin classes: interactive environments, script entry, static file entry; correct default title in visualization_base.mako Commit: 2fe38db10b3a2008ce37b58f23f85b968b083b37 https://github.com/galaxyproject/galaxy/commit/2fe38db10b3a2008ce37b58f23f85... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M config/plugins/visualizations/common/templates/visualization_base.mako Log Message: ----------- Visualizations registry: *actually* correct the default title in visualization_base.mako Commit: c4053f1427774b6b0490570fde44a586e3f4dcff https://github.com/galaxyproject/galaxy/commit/c4053f1427774b6b0490570fde44a... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako Log Message: ----------- Visualizations registry: add script_entry_point.mako and late_javascripts to visualization_base.mako Commit: 5f5678ca892df822f727c3c0e1f66e08d469bd97 https://github.com/galaxyproject/galaxy/commit/5f5678ca892df822f727c3c0e1f66... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/resource_parser.py Log Message: ----------- Visualizations plugins: use managers to instantiate resources and avoid passing a controller. Commit: 8586f7bcac434cdbeab9b7f55753298bb1fdb5a5 https://github.com/galaxyproject/galaxy/commit/8586f7bcac434cdbeab9b7f557532... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M eggs.ini M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge branch 'release_15.05' into dev Commit: bfe1e40480a61029652ecb0b5391b7b71ca5640c https://github.com/galaxyproject/galaxy/commit/bfe1e40480a61029652ecb0b5391b... Author: anton <anton@nekrut.org> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Added default indexing for bcc files Commit: 928612ac04d3d84d26ed0c53c41405c3ff061b56 https://github.com/galaxyproject/galaxy/commit/928612ac04d3d84d26ed0c53c4140... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M eggs.ini Log Message: ----------- Bump nose to 1.3.6 -- this enables lots of nice new out-of-the-box plugins and other features. Commit: d14aba2408b763165869f8624540a880af9e9e17 https://github.com/galaxyproject/galaxy/commit/d14aba2408b763165869f8624540a... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-24 (Fri, 24 Apr 2015) Changed paths: M config/plugins/visualizations/common/templates/script_entry_point.mako M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Visualizations registry: test script entry point; minor cleanup Commit: e31e8d3d44afac4e69ab22bdff472789225a7285 https://github.com/galaxyproject/galaxy/commit/e31e8d3d44afac4e69ab22bdff472... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-26 (Sun, 26 Apr 2015) Changed paths: M config/galaxy.ini.sample M eggs.ini M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/install_manager.py M test/install_and_test_tool_shed_repositories/base/util.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 911acd7a6ed364f2124e8673a02849f7922a0325 https://github.com/galaxyproject/galaxy/commit/911acd7a6ed364f2124e8673a0284... Author: abretaud <anthony.bretaudeau@rennes.inra.fr> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- handle adding/removing tools from toolshed Commit: b86388447e9252434d7f8aa7110bcda1f623bf94 https://github.com/galaxyproject/galaxy/commit/b86388447e9252434d7f8aa7110bc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- Add toggle to run_tests for pdb. Commit: 275dbc911678a41a950ba3cddd7080dfde685a6d https://github.com/galaxyproject/galaxy/commit/275dbc911678a41a950ba3cddd708... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- Document -p|--pdb option for testing. Commit: a1719ab5c42d8f33cc4a2aa9a58cb55f28330e8d https://github.com/galaxyproject/galaxy/commit/a1719ab5c42d8f33cc4a2aa9a58cb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M run_tests.sh Log Message: ----------- Swap --pdb to --debug to keep it general for now, since I'd really rather it be ipdb. Commit: 435710f5053197aa12b5b1e96866ca57b5b24a20 https://github.com/galaxyproject/galaxy/commit/435710f5053197aa12b5b1e96866c... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M client/GruntFile.js Log Message: ----------- Client build: add grunt command 'grunt decompress' to copy decompressed scripts to static/scripts to make debugging easier Commit: 4693a948e11a5f2fef059b4fb1dabc6244bf9fee https://github.com/galaxyproject/galaxy/commit/4693a948e11a5f2fef059b4fb1dab... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M client/GruntFile.js Log Message: ----------- Merge pull request #173 from carlfeberhard/grunt.decompress Client build: add grunt command 'grunt decompress' to copy decompressed ... Commit: 1cf6e64abf90aff2706e311addf86c24cf5bbb01 https://github.com/galaxyproject/galaxy/commit/1cf6e64abf90aff2706e311addf86... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Visualization registry: update test so that mako caching occurs in the proper place Commit: 7861ef5f8ca13702371e5725986dbe03a121e995 https://github.com/galaxyproject/galaxy/commit/7861ef5f8ca13702371e5725986db... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M config/galaxy.ini.sample M eggs.ini M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 32775e969207bb37a3a463c8a20d5f0a57b0886a https://github.com/galaxyproject/galaxy/commit/32775e969207bb37a3a463c8a20d5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M client/GruntFile.js M test/install_and_test_tool_shed_repositories/base/util.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 374a1826f639e204eaa6e44369f1c1f9bc403626 https://github.com/galaxyproject/galaxy/commit/374a1826f639e204eaa6e44369f1c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/drmaa.py M scripts/drmaa_external_runner.py Log Message: ----------- Merge pull request #160 from vavrusa/drmaa-external-jobs Fixes for DRMAA when Galaxy instance isn't on a shared volume with compute nodes Commit: 21e10e7a085013c0e255dd9f5af21f2139959bb2 https://github.com/galaxyproject/galaxy/commit/21e10e7a085013c0e255dd9f5af21... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M client/GruntFile.js M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/tool_shed/galaxy_install/update_repository_manager.py M scripts/drmaa_external_runner.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 41343e4b41116e36648f00b09b82417d71bf714a https://github.com/galaxyproject/galaxy/commit/41343e4b41116e36648f00b09b824... Author: anton <anton@nekrut.org> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M lib/galaxy/datatypes/binary.py A test-data/bcf_index_metadata_test.bcf A test-data/bcf_index_metadata_test.txt A test/functional/tools/metadata_bcf.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Added test for bcf index creation. Commit: 6e71a90cdd3ffd3bc140f580eb824b5ccafa9655 https://github.com/galaxyproject/galaxy/commit/6e71a90cdd3ffd3bc140f580eb824... Author: John Chilton <jmchilton@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: A scripts/runtime_stats.py Log Message: ----------- Merge pull request #151 from natefoo/runtime_stats A command line script for collecting stats on job runtimes Commit: ed36e625bb1e3468cc6efc535a2af6c6c4a90be4 https://github.com/galaxyproject/galaxy/commit/ed36e625bb1e3468cc6efc535a2af... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/controllers/visualization.py A test/unit/visualizations/test_VisualizationPlugin.py Log Message: ----------- Visualizations registry: refactor the relationship between plugins, the visualization controller, rendering, and rendering saved visualizations, minor fixes; Extend testing; Scatterplot: fix baseUrl resolution when used in own window Commit: 485bdafa35c93ca831e52d88ddab2acc38905313 https://github.com/galaxyproject/galaxy/commit/485bdafa35c93ca831e52d88ddab2... Author: John Chilton <jmchilton@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #159 from abretaud/dev Significant speedup of tool panel/homepage loading Commit: d1b939136bd6a17582b0c7869f50f851288388e3 https://github.com/galaxyproject/galaxy/commit/d1b939136bd6a17582b0c7869f50f... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Adding dataset uuid information to job and workflow invocation calls. Adding output mapping data to workflow invocation steps. Commit: 21a4927d4badccc202d83b84506e8b0c2be5d89c https://github.com/galaxyproject/galaxy/commit/21a4927d4badccc202d83b84506e8... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Making changes based on PR comments Commit: dab23a747c44eac647c623e13cfef656c2909678 https://github.com/galaxyproject/galaxy/commit/dab23a747c44eac647c623e13cfef... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Visualizations Registry: fix broken test that was sending mock template py files to the actual template cache dir Commit: 1b2cabc4b0f97ecc2a168c158890bb708f87dd5e https://github.com/galaxyproject/galaxy/commit/1b2cabc4b0f97ecc2a168c158890b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/ui/ui-slider.js M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/local.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 11fe79fbc4ee726f8480eaeabdfd3f232dff4848 https://github.com/galaxyproject/galaxy/commit/11fe79fbc4ee726f8480eaeabdfd3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #181 from kellrott/workflow-instance-data Re-issue of PR #176 now targeting dev, without additional commits Commit: 91feaacbf4c7767a11ccb1942d8c850ed90e9567 https://github.com/galaxyproject/galaxy/commit/91feaacbf4c7767a11ccb1942d8c8... Author: Daniel Blankenberg <blankenberg@users.noreply.github.com> Date: 2015-04-28 (Tue, 28 Apr 2015) Changed paths: M lib/galaxy/datatypes/binary.py A test-data/bcf_index_metadata_test.bcf A test-data/bcf_index_metadata_test.txt A test/functional/tools/metadata_bcf.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #163 from nekrut/bcf_metadata [WIP] Added default indexing for bcf files Commit: e11e1864effa4aa3363df3fe9cf243082d6fe4f6 https://github.com/galaxyproject/galaxy/commit/e11e1864effa4aa3363df3fe9cf24... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary dependencies. Commit: 9fd6a8b9f8d09a8848d11430c061f0c8dd756d38 https://github.com/galaxyproject/galaxy/commit/9fd6a8b9f8d09a8848d11430c061f... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Remove biomart_test tool, http://test.biomart.org/ is down. Commit: b3596d5b17c8920ea33f12f0cc8acaded1769551 https://github.com/galaxyproject/galaxy/commit/b3596d5b17c8920ea33f12f0cc8ac... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M eggs.ini M run_tests.sh Log Message: ----------- Merge pull request #172 from dannon/testing_updates [WIP] Nose update with --debug option added to run_tests Commit: 6f13a4be45c5f33b55143f7ef113feed0b6b659b https://github.com/galaxyproject/galaxy/commit/6f13a4be45c5f33b55143f7ef113f... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- drop python-module Commit: e5aa966f1db4faeefbc52e1578c24f3e0c9e6978 https://github.com/galaxyproject/galaxy/commit/e5aa966f1db4faeefbc52e1578c24... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- stats/gsummary: RPy is deprecated, use RPy2/classic as an alternative Commit: af1f9db527cce0203392d18570a8b61146d41561 https://github.com/galaxyproject/galaxy/commit/af1f9db527cce0203392d18570a8b... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M test/unit/visualizations/test_VisualizationPlugin.py M test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Visualizations registry: a bit more shuffling between methods and between plugins and the visualization controller Commit: 41abb7d00025ccc79d955956df9984203c079f12 https://github.com/galaxyproject/galaxy/commit/41abb7d00025ccc79d955956df998... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/test_VisualizationPlugin.py Log Message: ----------- Visualization registry: expand plugin testing Commit: 7fd6cc37047f041b80e187f5498223b3c1147acd https://github.com/galaxyproject/galaxy/commit/7fd6cc37047f041b80e187f549822... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationPlugin.py R test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Visualization registry: move tests into directory matching lib/galaxy/visualization/plugins Commit: 43a6c0ba2143c08c39b0d83328741eb930d274e2 https://github.com/galaxyproject/galaxy/commit/43a6c0ba2143c08c39b0d83328741... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Visualizations registry: correctly use config (and not kwargs) to build plugin rendering resources Commit: c15573bfeed893889232da623fe1e484cd0c5740 https://github.com/galaxyproject/galaxy/commit/c15573bfeed893889232da623fe1e... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/resource_parser.py Log Message: ----------- Visualizations registry: remove 'show_deprecations until we get a better way to configure that, remove lambdas where builtins are available Commit: d848ff861c58e1e4e35d9ea1a9187b6058bf8dd0 https://github.com/galaxyproject/galaxy/commit/d848ff861c58e1e4e35d9ea1a9187... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Visualizations registry: remove class level debugging switch for config parser Commit: 1dde01220c750446c4406a1318b6413c74526b65 https://github.com/galaxyproject/galaxy/commit/1dde01220c750446c4406a1318b64... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Remove plain R dependency Commit: 8ce2c86aa7fec9bf44c938753eaa0eea9395f002 https://github.com/galaxyproject/galaxy/commit/8ce2c86aa7fec9bf44c938753eaa0... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-29 (Wed, 29 Apr 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/ui/ui-slider.js M eggs.ini M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/workflows.py M run_tests.sh A scripts/runtime_stats.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/ui/ui-slider.js A test-data/bcf_index_metadata_test.bcf A test-data/bcf_index_metadata_test.txt A test/functional/tools/metadata_bcf.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 83dbaa7c41b2d48a2c38801bf59c0d494358cd8d https://github.com/galaxyproject/galaxy/commit/83dbaa7c41b2d48a2c38801bf59c0... Author: roalva1 <roalva1@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- reolve suggestion from PR: added more safety way Commit: 72bbace9c4a2d4e68790196f351fda6ac66e05f2 https://github.com/galaxyproject/galaxy/commit/72bbace9c4a2d4e68790196f351fd... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- add debug option to the example inject command Commit: 618078c5c16218b6222eeb242b803c93bf15046b https://github.com/galaxyproject/galaxy/commit/618078c5c16218b6222eeb242b803... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Refactore the configuration handling and add a new get_conf_dict() function. Commit: 04b8a884bd1f94e60c6eae84f457639a15330158 https://github.com/galaxyproject/galaxy/commit/04b8a884bd1f94e60c6eae84f4576... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako Log Message: ----------- Pass all configuration variables to Docker using ENV, rather than a config file. Commit: 13cb46210268286622ebb7e06820f433ab9282ed https://github.com/galaxyproject/galaxy/commit/13cb46210268286622ebb7e06820f... Author: roalva1 <roalva1@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove building a string for the command line Commit: bc8bdadca87ba643116cd3a41a7b4b3d3d0e70c9 https://github.com/galaxyproject/galaxy/commit/bc8bdadca87ba643116cd3a41a7b4... Author: Marek Vavrusa <marek@vavrusa.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M tools/data_source/upload.xml Log Message: ----------- datatypes: extracted TabularData superclass from Tabular, CSV subclass Commit: 6b796503fdcfcf362913c8226b31cbdf5f9e3cf0 https://github.com/galaxyproject/galaxy/commit/6b796503fdcfcf362913c8226b31c... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- include more information in default welcome.html Commit: 71c51e9a830f7e9f3f1e56d7a83b756ff436de01 https://github.com/galaxyproject/galaxy/commit/71c51e9a830f7e9f3f1e56d7a83b7... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove write_conf_file() Commit: fa3842ad3d4c8f91f11618d87dabf84866e637ed https://github.com/galaxyproject/galaxy/commit/fa3842ad3d4c8f91f11618d87dabf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M lib/galaxy/app.py A lib/galaxy/visualization/plugins/__init__.py A lib/galaxy/visualization/plugins/config_parser.py A lib/galaxy/visualization/plugins/plugin.py A lib/galaxy/visualization/plugins/registry.py A lib/galaxy/visualization/plugins/resource_parser.py A lib/galaxy/visualization/plugins/utils.py R lib/galaxy/visualization/registry.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #186 from carlfeberhard/vis.registry Promote visualization plugins to a class Commit: 4386ffdf3062d428c3de517fcc90ddc881ced6cf https://github.com/galaxyproject/galaxy/commit/4386ffdf3062d428c3de517fcc90d... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- abandon our old CS habits Commit: be4f3a40c66f515a5c71c7a179a3d32e751732db https://github.com/galaxyproject/galaxy/commit/be4f3a40c66f515a5c71c7a179a3d... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- nicer wording Commit: 535302b2d99f8e5931bcc26edc414e6361d1f6f0 https://github.com/galaxyproject/galaxy/commit/535302b2d99f8e5931bcc26edc414... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-04-30 (Thu, 30 Apr 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #190 from martenson/more-welcoming include more information in default welcome.html Commit: eba280515a63d4d43311869de4f59797df907444 https://github.com/galaxyproject/galaxy/commit/eba280515a63d4d43311869de4f59... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M lib/galaxy/jobs/__init__.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 9780d771415681c175018d7e1665e3840428cedc https://github.com/galaxyproject/galaxy/commit/9780d771415681c175018d7e1665e... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Set default value for sig proxy @afgane reported a backwards compatibility issue whereby an out of date `.ini` file would trigger an error when Galaxy tried to access a new variable. cc @bgruening Commit: b896515654e7354f485849c7566bd037fcfe3c52 https://github.com/galaxyproject/galaxy/commit/b896515654e7354f485849c7566bd... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #197 from erasche/ie-backwards-compat Set default value for sig proxy Commit: e3608d281763500c9de6d5ef9659d143699c083c https://github.com/galaxyproject/galaxy/commit/e3608d281763500c9de6d5ef9659d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 04fa5af9c086d88bb3dd021436513e4d1edbc644 https://github.com/galaxyproject/galaxy/commit/04fa5af9c086d88bb3dd021436513... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Factor out is_uwsgi_process, apply to use_interactive so I don't have to keep changing my config (and hopefully to benefit others ;) ) Commit: 81cea6872a4b5dbf3fac84999e5b7ac5714da2c8 https://github.com/galaxyproject/galaxy/commit/81cea6872a4b5dbf3fac84999e5b7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Whitespace cleanup. Commit: 70ff72bf1dd968d6474705dfdf17d910f8f813b8 https://github.com/galaxyproject/galaxy/commit/70ff72bf1dd968d6474705dfdf17d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Import and whitespace cleanup. Commit: f91398ea775f0870f2eb5dd4cd9ff253fbc4fc62 https://github.com/galaxyproject/galaxy/commit/f91398ea775f0870f2eb5dd4cd9ff... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py R lib/galaxy/webapps/tool_shed/api/search.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- refactor search into index() method as Carl taught me Commit: 0cb45e922e04d92aabf3d71aced784ad51a855d8 https://github.com/galaxyproject/galaxy/commit/0cb45e922e04d92aabf3d71aced78... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 8c55d13ae98afbe652db55bd42ccf55674cb5c56 https://github.com/galaxyproject/galaxy/commit/8c55d13ae98afbe652db55bd42ccf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Update reports, tool_shed to also refuse to load use_interactive under uwsgi. Commit: dd1378e0400ab3e28451f1ce9b1a40f3025ac0fc https://github.com/galaxyproject/galaxy/commit/dd1378e0400ab3e28451f1ce9b1a4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Use refactored process_is_uwsgi in toolshed buildapp. Commit: 456abe93f191e7f44e68802e7cb3c16ae5a28983 https://github.com/galaxyproject/galaxy/commit/456abe93f191e7f44e68802e7cb3c... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M test/casperjs/modules/user.js M test/casperjs/registration-tests.js Log Message: ----------- Fix broken browser tests Commit: 944a07eac2b3b25e94eab137e5f36d011ba893fd https://github.com/galaxyproject/galaxy/commit/944a07eac2b3b25e94eab137e5f36... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M client/GruntFile.js A client/galaxy/style/less/autocomplete_tagging.less A client/galaxy/style/less/base.less A client/galaxy/style/less/bootstrap.less A client/galaxy/style/less/bootstrap/alerts.less A client/galaxy/style/less/bootstrap/badges.less A client/galaxy/style/less/bootstrap/bootstrap.less A client/galaxy/style/less/bootstrap/breadcrumbs.less A client/galaxy/style/less/bootstrap/button-groups.less A client/galaxy/style/less/bootstrap/buttons.less A client/galaxy/style/less/bootstrap/carousel.less A client/galaxy/style/less/bootstrap/close.less A client/galaxy/style/less/bootstrap/code.less A client/galaxy/style/less/bootstrap/component-animations.less A client/galaxy/style/less/bootstrap/dropdowns.less A client/galaxy/style/less/bootstrap/forms.less A client/galaxy/style/less/bootstrap/glyphicons.less A client/galaxy/style/less/bootstrap/grid.less A client/galaxy/style/less/bootstrap/input-groups.less A client/galaxy/style/less/bootstrap/jumbotron.less A client/galaxy/style/less/bootstrap/labels.less A client/galaxy/style/less/bootstrap/list-group.less A client/galaxy/style/less/bootstrap/media.less A client/galaxy/style/less/bootstrap/mixins.less A client/galaxy/style/less/bootstrap/modals.less A client/galaxy/style/less/bootstrap/navbar.less A client/galaxy/style/less/bootstrap/navs.less A client/galaxy/style/less/bootstrap/normalize.less A client/galaxy/style/less/bootstrap/pager.less A client/galaxy/style/less/bootstrap/pagination.less A client/galaxy/style/less/bootstrap/panels.less A client/galaxy/style/less/bootstrap/popovers.less A client/galaxy/style/less/bootstrap/print.less A client/galaxy/style/less/bootstrap/progress-bars.less A client/galaxy/style/less/bootstrap/responsive-utilities.less A client/galaxy/style/less/bootstrap/scaffolding.less A client/galaxy/style/less/bootstrap/tables.less A client/galaxy/style/less/bootstrap/theme.less A client/galaxy/style/less/bootstrap/thumbnails.less A client/galaxy/style/less/bootstrap/tooltip.less A client/galaxy/style/less/bootstrap/type.less A client/galaxy/style/less/bootstrap/utilities.less A client/galaxy/style/less/bootstrap/variables.less A client/galaxy/style/less/bootstrap/wells.less A client/galaxy/style/less/circster.less A client/galaxy/style/less/collections.less A client/galaxy/style/less/embed_item.less A client/galaxy/style/less/fontawesome/bordered-pulled.less A client/galaxy/style/less/fontawesome/core.less A client/galaxy/style/less/fontawesome/fixed-width.less A client/galaxy/style/less/fontawesome/font-awesome.less A client/galaxy/style/less/fontawesome/icons.less A client/galaxy/style/less/fontawesome/larger.less A client/galaxy/style/less/fontawesome/list.less A client/galaxy/style/less/fontawesome/mixins.less A client/galaxy/style/less/fontawesome/path.less A client/galaxy/style/less/fontawesome/rotated-flipped.less A client/galaxy/style/less/fontawesome/spinning.less A client/galaxy/style/less/fontawesome/stacked.less A client/galaxy/style/less/fontawesome/variables.less A client/galaxy/style/less/frame.less A client/galaxy/style/less/galaxy_bootstrap.less A client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/galaxy/style/less/galaxy_bootstrap/variables.less A client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/history.less A client/galaxy/style/less/iconic_stroke.less A client/galaxy/style/less/iphone.less A client/galaxy/style/less/job.less A client/galaxy/style/less/jstree.less A client/galaxy/style/less/library.less A client/galaxy/style/less/list-item.less A client/galaxy/style/less/masthead.less A client/galaxy/style/less/select2.less A client/galaxy/style/less/theme/blue.less A client/galaxy/style/less/toastr.less A client/galaxy/style/less/trackster.less A client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/dataset-choice.less A client/galaxy/style/less/ui/icon-btn.less A client/galaxy/style/less/ui/pagination.less A client/galaxy/style/less/ui/paired-collection-creator.less A client/galaxy/style/less/ui/peek-column-selector.less A client/galaxy/style/less/ui/search-input.less A client/galaxy/style/less/upload.less A client/galaxy/style/source_material/circle.py A client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/galaxy_spinner.fla M client/package.json M static/style/blue/base.css R static/style/src/less/autocomplete_tagging.less R static/style/src/less/base.less R static/style/src/less/bootstrap.less R static/style/src/less/bootstrap/alerts.less R static/style/src/less/bootstrap/badges.less R static/style/src/less/bootstrap/bootstrap.less R static/style/src/less/bootstrap/breadcrumbs.less R static/style/src/less/bootstrap/button-groups.less R static/style/src/less/bootstrap/buttons.less R static/style/src/less/bootstrap/carousel.less R static/style/src/less/bootstrap/close.less R static/style/src/less/bootstrap/code.less R static/style/src/less/bootstrap/component-animations.less R static/style/src/less/bootstrap/dropdowns.less R static/style/src/less/bootstrap/forms.less R static/style/src/less/bootstrap/glyphicons.less R static/style/src/less/bootstrap/grid.less R static/style/src/less/bootstrap/input-groups.less R static/style/src/less/bootstrap/jumbotron.less R static/style/src/less/bootstrap/labels.less R static/style/src/less/bootstrap/list-group.less R static/style/src/less/bootstrap/media.less R static/style/src/less/bootstrap/mixins.less R static/style/src/less/bootstrap/modals.less R static/style/src/less/bootstrap/navbar.less R static/style/src/less/bootstrap/navs.less R static/style/src/less/bootstrap/normalize.less R static/style/src/less/bootstrap/pager.less R static/style/src/less/bootstrap/pagination.less R static/style/src/less/bootstrap/panels.less R static/style/src/less/bootstrap/popovers.less R static/style/src/less/bootstrap/print.less R static/style/src/less/bootstrap/progress-bars.less R static/style/src/less/bootstrap/responsive-utilities.less R static/style/src/less/bootstrap/scaffolding.less R static/style/src/less/bootstrap/tables.less R static/style/src/less/bootstrap/theme.less R static/style/src/less/bootstrap/thumbnails.less R static/style/src/less/bootstrap/tooltip.less R static/style/src/less/bootstrap/type.less R static/style/src/less/bootstrap/utilities.less R static/style/src/less/bootstrap/variables.less R static/style/src/less/bootstrap/wells.less R static/style/src/less/circster.less R static/style/src/less/collections.less R static/style/src/less/embed_item.less R static/style/src/less/fontawesome/bordered-pulled.less R static/style/src/less/fontawesome/core.less R static/style/src/less/fontawesome/fixed-width.less R static/style/src/less/fontawesome/font-awesome.less R static/style/src/less/fontawesome/icons.less R static/style/src/less/fontawesome/larger.less R static/style/src/less/fontawesome/list.less R static/style/src/less/fontawesome/mixins.less R static/style/src/less/fontawesome/path.less R static/style/src/less/fontawesome/rotated-flipped.less R static/style/src/less/fontawesome/spinning.less R static/style/src/less/fontawesome/stacked.less R static/style/src/less/fontawesome/variables.less R static/style/src/less/frame.less R static/style/src/less/galaxy_bootstrap.less R static/style/src/less/galaxy_bootstrap/overrides.less R static/style/src/less/galaxy_bootstrap/variables.less R static/style/src/less/galaxy_variables.less R static/style/src/less/history.less R static/style/src/less/iconic_stroke.less R static/style/src/less/iphone.less R static/style/src/less/job.less R static/style/src/less/jstree.less R static/style/src/less/library.less R static/style/src/less/list-item.less R static/style/src/less/masthead.less R static/style/src/less/select2.less R static/style/src/less/theme/blue.less R static/style/src/less/toastr.less R static/style/src/less/trackster.less R static/style/src/less/ui.less R static/style/src/less/ui/dataset-choice.less R static/style/src/less/ui/icon-btn.less R static/style/src/less/ui/pagination.less R static/style/src/less/ui/paired-collection-creator.less R static/style/src/less/ui/peek-column-selector.less R static/style/src/less/ui/search-input.less R static/style/src/less/upload.less R static/style/src/source_material/circle.py R static/style/src/source_material/galaxy_icons.svg R static/style/src/source_material/galaxy_spinner.fla Log Message: ----------- Client build: move static/style/src to client/galaxy/style and merge node/grunt build scripts (you should now use 'grunt style' to re-build css) Commit: 347acccf442f020016ec6b05ffa03496c4c15fc1 https://github.com/galaxyproject/galaxy/commit/347acccf442f020016ec6b05ffa03... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Cache process_is_uwsgi value and only attempt the import once. Related refactoring. Commit: c4644a36d6062bd39bbb15e74797900823b1222e https://github.com/galaxyproject/galaxy/commit/c4644a36d6062bd39bbb15e747979... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M test/casperjs/modules/user.js M test/casperjs/registration-tests.js Log Message: ----------- Merge pull request #202 from carlfeberhard/fix.casper Fix broken browser tests Commit: 2d7483613488a91895ea5219bd6b4a6be829b64c https://github.com/galaxyproject/galaxy/commit/2d7483613488a91895ea5219bd6b4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Log Message: ----------- Merge branch 'release_15.05' into dev Commit: ba228c57751f8422c23e147719e118d7183f6a9d https://github.com/galaxyproject/galaxy/commit/ba228c57751f8422c23e147719e11... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #137 from yhoogstrate/dev run tests from outer directories Commit: 73ca5d4c431c2aef8348f8846c3ac4efc0c4f734 https://github.com/galaxyproject/galaxy/commit/73ca5d4c431c2aef8348f8846c3ac... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #200 from dannon/interactive_no_uwsgi Refuse to load interactive debugging middleware under uwsgi Commit: ae0c22f9d87d9347ad5205b97af80fe825e98e79 https://github.com/galaxyproject/galaxy/commit/ae0c22f9d87d9347ad5205b97af80... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #182 from bgruening/patch-1 Update gsummary dependencies. Commit: 28dc0fa6cbe97f96d00fd00a77d8370cd162d7bf https://github.com/galaxyproject/galaxy/commit/28dc0fa6cbe97f96d00fd00a77d83... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-01 (Fri, 01 May 2015) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Merge pull request #183 from nsoranzo/dev Remove biomart_test tool, http://test.biomart.org/ is down. Commit: 0a506dc561f9bf73a241db727723f1a24ff401f3 https://github.com/galaxyproject/galaxy/commit/0a506dc561f9bf73a241db727723f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-02 (Sat, 02 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Workflow editor adjustments Commit: 183cf7f77479fd54951772fcd828cbc46f473605 https://github.com/galaxyproject/galaxy/commit/183cf7f77479fd54951772fcd828c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-05-03 (Sun, 03 May 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- flake8 fixes Commit: ffb47107904b17abf98dfe81e739be0a69e742fb https://github.com/galaxyproject/galaxy/commit/ffb47107904b17abf98dfe81e739b... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: R client/galaxy/style/source_material/circle.py R client/galaxy/style/source_material/galaxy_icons.svg R client/galaxy/style/source_material/galaxy_spinner.fla Log Message: ----------- Client build, styles: remove source_material directory Commit: d1ffc98d54f692870cc7c2f8a8214d0287b1ead0 https://github.com/galaxyproject/galaxy/commit/d1ffc98d54f692870cc7c2f8a8214... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/favicon.ico M static/images/galaxyIcon_noText.png M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 30b43d810af2e59182ea6b715dfe44e45a68c437 https://github.com/galaxyproject/galaxy/commit/30b43d810af2e59182ea6b715dfe4... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M client/GruntFile.js A client/grunt-tasks/install-libs.js A client/grunt-tasks/scripts.js A client/grunt-tasks/style.js Log Message: ----------- Client build: break up grunt tasks into separate files for clarity Commit: 2c964227cbb8560130a92b7ae123d16861b6671a https://github.com/galaxyproject/galaxy/commit/2c964227cbb8560130a92b7ae123d... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M client/GruntFile.js M client/README.md A client/galaxy/style/blue_colors.ini R static/style/Gruntfile.js R static/style/Makefile R static/style/README R static/style/blue_colors.ini R static/style/package.json Log Message: ----------- Client build, styles: remove style build system from static/style Commit: d6801566afdc62e1b8adee7cb88341b4291857cf https://github.com/galaxyproject/galaxy/commit/d6801566afdc62e1b8adee7cb8834... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- Client build: add jsdoc to scripts.js Commit: 9e3237cfbf6e4c760afc78ed5b3b39dbad3fecf9 https://github.com/galaxyproject/galaxy/commit/9e3237cfbf6e4c760afc78ed5b3b3... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: A client/galaxy/style/source_material/circle.py A client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/galaxy_spinner.fla Log Message: ----------- Client build, styles: re-add source_material directory Commit: 32eb1ea0fc05b47d9d5700c3c067e0088b1b93dc https://github.com/galaxyproject/galaxy/commit/32eb1ea0fc05b47d9d5700c3c067e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Fix flat sections Commit: fa858eb2c2807344200c31fd9fdff2fcb9cc2297 https://github.com/galaxyproject/galaxy/commit/fa858eb2c2807344200c31fd9fdff... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/user/register.mako M test/api/test_workflows_from_yaml.py Log Message: ----------- Merge branch 'release_15.05' into dev Commit: b96c6c91243d84758aaab626c1ecff7c6ce7ee7c https://github.com/galaxyproject/galaxy/commit/b96c6c91243d84758aaab626c1ecf... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #149 from roalva1/merge-bam added the possibility of merging bams from a parallelized job Commit: 647765a574814c6dc7eea4881a1cf9904ced4b11 https://github.com/galaxyproject/galaxy/commit/647765a574814c6dc7eea4881a1cf... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M client/GruntFile.js M client/README.md A client/galaxy/style/blue_colors.ini A client/galaxy/style/less/autocomplete_tagging.less A client/galaxy/style/less/base.less A client/galaxy/style/less/bootstrap.less A client/galaxy/style/less/bootstrap/alerts.less A client/galaxy/style/less/bootstrap/badges.less A client/galaxy/style/less/bootstrap/bootstrap.less A client/galaxy/style/less/bootstrap/breadcrumbs.less A client/galaxy/style/less/bootstrap/button-groups.less A client/galaxy/style/less/bootstrap/buttons.less A client/galaxy/style/less/bootstrap/carousel.less A client/galaxy/style/less/bootstrap/close.less A client/galaxy/style/less/bootstrap/code.less A client/galaxy/style/less/bootstrap/component-animations.less A client/galaxy/style/less/bootstrap/dropdowns.less A client/galaxy/style/less/bootstrap/forms.less A client/galaxy/style/less/bootstrap/glyphicons.less A client/galaxy/style/less/bootstrap/grid.less A client/galaxy/style/less/bootstrap/input-groups.less A client/galaxy/style/less/bootstrap/jumbotron.less A client/galaxy/style/less/bootstrap/labels.less A client/galaxy/style/less/bootstrap/list-group.less A client/galaxy/style/less/bootstrap/media.less A client/galaxy/style/less/bootstrap/mixins.less A client/galaxy/style/less/bootstrap/modals.less A client/galaxy/style/less/bootstrap/navbar.less A client/galaxy/style/less/bootstrap/navs.less A client/galaxy/style/less/bootstrap/normalize.less A client/galaxy/style/less/bootstrap/pager.less A client/galaxy/style/less/bootstrap/pagination.less A client/galaxy/style/less/bootstrap/panels.less A client/galaxy/style/less/bootstrap/popovers.less A client/galaxy/style/less/bootstrap/print.less A client/galaxy/style/less/bootstrap/progress-bars.less A client/galaxy/style/less/bootstrap/responsive-utilities.less A client/galaxy/style/less/bootstrap/scaffolding.less A 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client/galaxy/style/less/fontawesome/rotated-flipped.less A client/galaxy/style/less/fontawesome/spinning.less A client/galaxy/style/less/fontawesome/stacked.less A client/galaxy/style/less/fontawesome/variables.less A client/galaxy/style/less/frame.less A client/galaxy/style/less/galaxy_bootstrap.less A client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/galaxy/style/less/galaxy_bootstrap/variables.less A client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/history.less A client/galaxy/style/less/iconic_stroke.less A client/galaxy/style/less/iphone.less A client/galaxy/style/less/job.less A client/galaxy/style/less/jstree.less A client/galaxy/style/less/library.less A client/galaxy/style/less/list-item.less A client/galaxy/style/less/masthead.less A client/galaxy/style/less/select2.less A client/galaxy/style/less/theme/blue.less A client/galaxy/style/less/toastr.less A client/galaxy/style/less/trackster.less A client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/dataset-choice.less A client/galaxy/style/less/ui/icon-btn.less A client/galaxy/style/less/ui/pagination.less A client/galaxy/style/less/ui/paired-collection-creator.less A client/galaxy/style/less/ui/peek-column-selector.less A client/galaxy/style/less/ui/search-input.less A client/galaxy/style/less/upload.less A client/galaxy/style/source_material/circle.py A client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/galaxy_spinner.fla A client/grunt-tasks/install-libs.js A client/grunt-tasks/scripts.js A client/grunt-tasks/style.js M client/package.json R static/style/Gruntfile.js R static/style/Makefile R static/style/README M static/style/blue/base.css R static/style/blue_colors.ini R static/style/package.json R static/style/src/less/autocomplete_tagging.less R static/style/src/less/base.less R static/style/src/less/bootstrap.less R static/style/src/less/bootstrap/alerts.less R static/style/src/less/bootstrap/badges.less R static/style/src/less/bootstrap/bootstrap.less R static/style/src/less/bootstrap/breadcrumbs.less R static/style/src/less/bootstrap/button-groups.less R static/style/src/less/bootstrap/buttons.less R static/style/src/less/bootstrap/carousel.less R static/style/src/less/bootstrap/close.less R static/style/src/less/bootstrap/code.less R static/style/src/less/bootstrap/component-animations.less R static/style/src/less/bootstrap/dropdowns.less R static/style/src/less/bootstrap/forms.less R static/style/src/less/bootstrap/glyphicons.less R static/style/src/less/bootstrap/grid.less R static/style/src/less/bootstrap/input-groups.less R static/style/src/less/bootstrap/jumbotron.less R static/style/src/less/bootstrap/labels.less R static/style/src/less/bootstrap/list-group.less R static/style/src/less/bootstrap/media.less R static/style/src/less/bootstrap/mixins.less R static/style/src/less/bootstrap/modals.less R static/style/src/less/bootstrap/navbar.less R static/style/src/less/bootstrap/navs.less R static/style/src/less/bootstrap/normalize.less R static/style/src/less/bootstrap/pager.less R static/style/src/less/bootstrap/pagination.less R static/style/src/less/bootstrap/panels.less R static/style/src/less/bootstrap/popovers.less R static/style/src/less/bootstrap/print.less R static/style/src/less/bootstrap/progress-bars.less R static/style/src/less/bootstrap/responsive-utilities.less R static/style/src/less/bootstrap/scaffolding.less R static/style/src/less/bootstrap/tables.less R static/style/src/less/bootstrap/theme.less R static/style/src/less/bootstrap/thumbnails.less R static/style/src/less/bootstrap/tooltip.less R static/style/src/less/bootstrap/type.less R static/style/src/less/bootstrap/utilities.less R static/style/src/less/bootstrap/variables.less R static/style/src/less/bootstrap/wells.less R static/style/src/less/circster.less R static/style/src/less/collections.less R static/style/src/less/embed_item.less R static/style/src/less/fontawesome/bordered-pulled.less R static/style/src/less/fontawesome/core.less R static/style/src/less/fontawesome/fixed-width.less R static/style/src/less/fontawesome/font-awesome.less R static/style/src/less/fontawesome/icons.less R static/style/src/less/fontawesome/larger.less R static/style/src/less/fontawesome/list.less R static/style/src/less/fontawesome/mixins.less R static/style/src/less/fontawesome/path.less R static/style/src/less/fontawesome/rotated-flipped.less R static/style/src/less/fontawesome/spinning.less R static/style/src/less/fontawesome/stacked.less R static/style/src/less/fontawesome/variables.less R static/style/src/less/frame.less R static/style/src/less/galaxy_bootstrap.less R static/style/src/less/galaxy_bootstrap/overrides.less R static/style/src/less/galaxy_bootstrap/variables.less R static/style/src/less/galaxy_variables.less R static/style/src/less/history.less R static/style/src/less/iconic_stroke.less R static/style/src/less/iphone.less R static/style/src/less/job.less R static/style/src/less/jstree.less R static/style/src/less/library.less R static/style/src/less/list-item.less R static/style/src/less/masthead.less R static/style/src/less/select2.less R static/style/src/less/theme/blue.less R static/style/src/less/toastr.less R static/style/src/less/trackster.less R static/style/src/less/ui.less R static/style/src/less/ui/dataset-choice.less R static/style/src/less/ui/icon-btn.less R static/style/src/less/ui/pagination.less R static/style/src/less/ui/paired-collection-creator.less R static/style/src/less/ui/peek-column-selector.less R static/style/src/less/ui/search-input.less R static/style/src/less/upload.less R static/style/src/source_material/circle.py R static/style/src/source_material/galaxy_icons.svg R static/style/src/source_material/galaxy_spinner.fla Log Message: ----------- Merge pull request #208 from carlfeberhard/style.move Style.move Commit: 801adcd6944a9690ee15ee146c09601603a5dd87 https://github.com/galaxyproject/galaxy/commit/801adcd6944a9690ee15ee146c096... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M static/maps/libs/jquery/jquery.js.map M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js Log Message: ----------- Client libs: minor version bumps to jQuery and Raven Commit: eeecf4103c78af2486618dd60f609af07b10db86 https://github.com/galaxyproject/galaxy/commit/eeecf4103c78af2486618dd60f609... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Include hmmer3 text format Commit: 7ef0d4e6eb48e4ee91a83a93753afa01597a6b6f https://github.com/galaxyproject/galaxy/commit/7ef0d4e6eb48e4ee91a83a93753af... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py Log Message: ----------- Move msa datatypes into separate file Commit: 92ff779f050e7e6f74c9da89784f8d4a7ad9c3e1 https://github.com/galaxyproject/galaxy/commit/92ff779f050e7e6f74c9da89784f8... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Imported stockholm from @bgruening Commit: c1840a46b55db4446f46b48a67c11db76a5a80f5 https://github.com/galaxyproject/galaxy/commit/c1840a46b55db4446f46b48a67c11... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Bump version of hmm format Commit: ec363b2b39dd7b98eb1afe0c97f741f2344cf445 https://github.com/galaxyproject/galaxy/commit/ec363b2b39dd7b98eb1afe0c97f74... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py Log Message: ----------- Add in hmmer2 datatypes Commit: 5037c4de031c72fac50be4ec3de63877dd5138f7 https://github.com/galaxyproject/galaxy/commit/5037c4de031c72fac50be4ec3de63... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/util/generic_util.py Log Message: ----------- Refactor count_special Commit: d1c1af3bff2fa8959c09cdd26523dcf9c0e839a7 https://github.com/galaxyproject/galaxy/commit/d1c1af3bff2fa8959c09cdd26523d... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Move ddatatypes upwards of images Commit: afd8344a8d0c2764b506cdc6b2b531c32a69504d https://github.com/galaxyproject/galaxy/commit/afd8344a8d0c2764b506cdc6b2b53... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M static/maps/mvc/history/history-content-model.js.map M static/scripts/mvc/history/history-content-model.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/paired-collection-creator.js Log Message: ----------- Testing, qunit: remove unfortunately silent error of missing global Galaxy when running via require and phantom by checking scope first, update list of pairs tests with recent option changes, remove debugging cruft Commit: 662c38e7b10e4ec23269523f4eccaded7b956612 https://github.com/galaxyproject/galaxy/commit/662c38e7b10e4ec23269523f4ecca... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M test/qunit/README.txt A test/qunit/tests/list-of-pairs-collection-creator.html A test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/paired-collection-creator.html R test/qunit/tests/paired-collection-creator.js Log Message: ----------- Testing, qunit: rename paired-collection-creator test to match actual mvc script, update README to include silent error warning Commit: d39898cc70b37cba10a369fca7c5fcbb38554225 https://github.com/galaxyproject/galaxy/commit/d39898cc70b37cba10a369fca7c5f... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-05 (Tue, 05 May 2015) Changed paths: M lib/galaxy/webapps/tool_shed/search/repo_search.py Log Message: ----------- remove the python 2.5 compatibility trycatch Commit: 21aea9cef74f99ae56c1e83dc20a1fdcff207e9e https://github.com/galaxyproject/galaxy/commit/21aea9cef74f99ae56c1e83dc20a1... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M static/maps/mvc/history/history-content-model.js.map M static/scripts/mvc/history/history-content-model.js M test/qunit/README.txt M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js A test/qunit/tests/list-of-pairs-collection-creator.html A test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js R test/qunit/tests/paired-collection-creator.html R test/qunit/tests/paired-collection-creator.js Log Message: ----------- Merge pull request #219 from carlfeberhard/testing Update qunit tests Commit: b18d215c4464b142c06081c7a7b27489dbf4ec19 https://github.com/galaxyproject/galaxy/commit/b18d215c4464b142c06081c7a7b27... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/require.js M client/grunt-tasks/install-libs.js M static/maps/libs/require.js.map M static/scripts/libs/require.js Log Message: ----------- Client libs: update requirejs to 2.1.17, correct bower installation for same Commit: 673aef16858d3370c95d138bf21912de8608e289 https://github.com/galaxyproject/galaxy/commit/673aef16858d3370c95d138bf2191... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M client/bower.json Log Message: ----------- Client libs: correct dependency location for requirejs from dev to standard Commit: 791785c1a52159e0d9ff44f5c252e6c3ea0325d4 https://github.com/galaxyproject/galaxy/commit/791785c1a52159e0d9ff44f5c252e... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py Log Message: ----------- Move stockholm as well Commit: 7d85ae222980c23e796eb857f94a5fc55842cfdb https://github.com/galaxyproject/galaxy/commit/7d85ae222980c23e796eb857f94a5... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge remote-tracking branch 'bgruening/ie-updates' into ie-updates2 Commit: b202c450d086590a9b5d741b8648f49e04fc06ee https://github.com/galaxyproject/galaxy/commit/b202c450d086590a9b5d741b8648f... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Unstage @bgruening's datatype conf changes Commit: b2b25f595b3c618de4482bce6fdb791b6511c3d4 https://github.com/galaxyproject/galaxy/commit/b2b25f595b3c618de4482bce6fdb7... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/notebook.ipynb Log Message: ----------- Update documentation on the get() function Commit: 04bc0b211167ee1c9f6f46c67a31851c69029da6 https://github.com/galaxyproject/galaxy/commit/04bc0b211167ee1c9f6f46c67a318... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Fix assertions in test_VisualizationsRegistry.py... ...that were implicitly assumed fixed Python hashing. Commit: d15b68f31674d1fe7c0cd5ab19501e3b1c24aa4c https://github.com/galaxyproject/galaxy/commit/d15b68f31674d1fe7c0cd5ab19501... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M run_tests.sh Log Message: ----------- Fix run_tests.sh exit code. Recently broken with merge or PR #137. Commit: 34781a4ead3a624ce2a8f50bffb8238c188f9c07 https://github.com/galaxyproject/galaxy/commit/34781a4ead3a624ce2a8f50bffb82... Author: carlfeberhard <carlfeberhard@users.noreply.github.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #223 from jmchilton/viz_test_fix Fix assertions in test_VisualizationsRegistry.py... Commit: 74527e2031406aa833eb3150aecd6687e281ab7f https://github.com/galaxyproject/galaxy/commit/74527e2031406aa833eb3150aecd6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_15.05' into dev Commit: c2f9ffe1f38afe2cdd01ca85451efee921008697 https://github.com/galaxyproject/galaxy/commit/c2f9ffe1f38afe2cdd01ca85451ef... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #225 from jmchilton/run_test_exit_code Fix run_tests.sh exit code. Commit: e0f351ae2a6fbc27114dfb1ef0f0047d38f5ee5d https://github.com/galaxyproject/galaxy/commit/e0f351ae2a6fbc27114dfb1ef0f00... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/grunt-tasks/install-libs.js M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js Log Message: ----------- Merge pull request #221 from carlfeberhard/client.update-libs Update client libs Commit: 8bf094ea369a40dd9bb9790150db2315e6771812 https://github.com/galaxyproject/galaxy/commit/8bf094ea369a40dd9bb9790150db2... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- RStudio non-standards-compliant hacks RStudio doesn't like lower case HTTP headers. It also doesn't like a charset specified in content type. Thus, those get modified appropriately and everything plays nicely Commit: c9623c16ae46c409fb0e1921a0ae2c679bf563e3 https://github.com/galaxyproject/galaxy/commit/c9623c16ae46c409fb0e1921a0ae2... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: A config/rstudio.ini.sample A config/rstudio.xml A static/js/crypto/base64.js A static/js/crypto/jsbn.js A static/js/crypto/prng4.js A static/js/crypto/rng.js A static/js/crypto/rsa.js A static/js/crypto/rstudio.big.js A static/js/crypto/rstudio.min.js A static/js/crypto/rstudio/base64.js A static/js/crypto/rstudio/jsbn.js A static/js/crypto/rstudio/prng4.js A static/js/crypto/rstudio/rng.js A static/js/crypto/rstudio/rsa.js A static/js/crypto/wu/base64.js A static/js/crypto/wu/jsbn.js A static/js/crypto/wu/prng4.js A static/js/crypto/wu/rng.js A static/js/crypto/wu/rsa.js A static/js/rstudio.js A templates/rstudio.mako Log Message: ----------- Merge remote-tracking branch 'rstudio/master' into rstudio Commit: 7e9df4714a8bf67ae8581cf162f0bd2ebb7b4e47 https://github.com/galaxyproject/galaxy/commit/7e9df4714a8bf67ae8581cf162f0b... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rsa.js A config/plugins/interactive_environments/rstudio/static/js/rstudio.js A config/plugins/interactive_environments/rstudio/templates/rstudio.mako R config/rstudio.ini.sample R config/rstudio.xml R static/js/crypto/base64.js R static/js/crypto/jsbn.js R static/js/crypto/prng4.js R static/js/crypto/rng.js R static/js/crypto/rsa.js R static/js/crypto/rstudio.big.js R static/js/crypto/rstudio.min.js R static/js/crypto/rstudio/base64.js R static/js/crypto/rstudio/jsbn.js R static/js/crypto/rstudio/prng4.js R static/js/crypto/rstudio/rng.js R static/js/crypto/rstudio/rsa.js R static/js/crypto/wu/base64.js R static/js/crypto/wu/jsbn.js R static/js/crypto/wu/prng4.js R static/js/crypto/wu/rng.js R static/js/crypto/wu/rsa.js R static/js/rstudio.js R templates/rstudio.mako Log Message: ----------- Migrated to correct location Commit: b0b43919be7254e013d3abdccfc325a458adc2f7 https://github.com/galaxyproject/galaxy/commit/b0b43919be7254e013d3abdccfc32... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Fix import problem with msa.py. Commit: 0aabdd40481669c2c6aa73f4f189c9770558dd97 https://github.com/galaxyproject/galaxy/commit/0aabdd40481669c2c6aa73f4f189c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/functional_tests.py M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.05' into dev Commit: 8984c68104fe9d5576e82a1a34027b527394828d https://github.com/galaxyproject/galaxy/commit/8984c68104fe9d5576e82a1a34027... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-05-06 (Wed, 06 May 2015) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Merge pull request #1 from jmchilton/msa_fix Fix import problem with msa.py. Commit: 08d76ee0cf5a14c2818a6b11a1f6639746bc5391 https://github.com/galaxyproject/galaxy/commit/08d76ee0cf5a14c2818a6b11a1f66... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Fix automated section expansion for post job actions Commit: ea40e6b47ec8c4ad31348f9081188bd10db4648c https://github.com/galaxyproject/galaxy/commit/ea40e6b47ec8c4ad31348f9081188... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix annotations Commit: 76821247c8178d2b06bc24ce6b41c7f801954ad0 https://github.com/galaxyproject/galaxy/commit/76821247c8178d2b06bc24ce6b41c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py Log Message: ----------- Merge pull request #218 from erasche/hmmer Hmmer & Stockholm Datatypes Commit: 3e80076e6ad19bc4b7bf8b42cb5a888c942fd56a https://github.com/galaxyproject/galaxy/commit/3e80076e6ad19bc4b7bf8b42cb5a8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/form/form-data.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Merge pull request #233 from guerler/workflow_1 Fix post action job and annotation parsing in new workflow editor Commit: 2c04d1a768dbd2e5587cddfcbd1a112bf56ef528 https://github.com/galaxyproject/galaxy/commit/2c04d1a768dbd2e5587cddfcbd1a1... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin to :dev Commit: 148acf0ddc284652c914679460efd27abf408000 https://github.com/galaxyproject/galaxy/commit/148acf0ddc284652c914679460efd... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add RData and RData.gz formats Commit: d28ea4555609c6bc758776b112749fb544d553d5 https://github.com/galaxyproject/galaxy/commit/d28ea4555609c6bc758776b112749... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M .gitignore M .travis.yml M client/galaxy/scripts/mvc/history/history-panel-annotated.js M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/common/templates/script_entry_point.mako M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/job_files.py M run_tests.sh M static/maps/mvc/history/history-panel-annotated.js.map M static/scripts/mvc/history/history-panel-annotated.js M templates/webapps/galaxy/history/display.mako M test/unit/managers/base.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py A tox.ini Log Message: ----------- Merge branch 'release_15.05' into dev Conflicts: config/plugins/visualizations/common/templates/script_entry_point.mako Commit: edf794233d93939ac9eb58b6d5c1a4715bc2b357 https://github.com/galaxyproject/galaxy/commit/edf794233d93939ac9eb58b6d5c1a... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M client/galaxy/scripts/libs/d3.js M client/grunt-tasks/install-libs.js M static/maps/libs/d3.js.map M static/scripts/libs/d3.js Log Message: ----------- Client libs: update d3 from 3.4.8 to 3.5.5 Commit: a940f19e15a77f78888c0bac2da19c90ea8806f5 https://github.com/galaxyproject/galaxy/commit/a940f19e15a77f78888c0bac2da19... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merged down datatypes Commit: 6b8d4bfbe1250976b8c751a301addeb1aba4cff4 https://github.com/galaxyproject/galaxy/commit/6b8d4bfbe1250976b8c751a301add... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M .gitignore M .travis.yml M client/galaxy/scripts/mvc/history/history-panel-annotated.js M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/common/templates/script_entry_point.mako M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/job_files.py M run_tests.sh M static/maps/mvc/history/history-panel-annotated.js.map M static/scripts/mvc/history/history-panel-annotated.js M templates/webapps/galaxy/history/display.mako M test/unit/managers/base.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py A tox.ini Log Message: ----------- Merge pull request #240 from martenson/dev merge 15.05 into dev Commit: 18eb24391baa8858fa687ef7d9f8ef830d3d9104 https://github.com/galaxyproject/galaxy/commit/18eb24391baa8858fa687ef7d9f8e... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py R lib/galaxy/webapps/tool_shed/api/search.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- refactor search into index() method as Carl taught me Commit: 15b70e5e697d5f38cdccccfd6d0754fec0c014fd https://github.com/galaxyproject/galaxy/commit/15b70e5e697d5f38cdccccfd6d075... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M lib/galaxy/webapps/tool_shed/search/repo_search.py Log Message: ----------- remove the python 2.5 compatibility trycatch Commit: 06572eb3f407f025907ab6687e29ee07dede8c02 https://github.com/galaxyproject/galaxy/commit/06572eb3f407f025907ab6687e29e... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Log Message: ----------- Merge branch 'ts-search-expansion' of https://github.com/martenson/galaxy into ts-search-expansion Commit: 83d7942081f972366b357fa22f0df7fdba2244f9 https://github.com/galaxyproject/galaxy/commit/83d7942081f972366b357fa22f0df... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_15.05' into dev Commit: 117a3415d3d6e940ecb62d26db2a8cba9647d649 https://github.com/galaxyproject/galaxy/commit/117a3415d3d6e940ecb62d26db2a8... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M client/galaxy/scripts/libs/d3.js M client/grunt-tasks/install-libs.js M static/maps/libs/d3.js.map M static/scripts/libs/d3.js Log Message: ----------- Merge pull request #241 from carlfeberhard/client.update-d3 Client libs: update d3 from 3.4.8 to 3.5.5 Commit: d62b1d3d89e9105913dc146bca371d6127affee9 https://github.com/galaxyproject/galaxy/commit/d62b1d3d89e9105913dc146bca371... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M .travis.yml M lib/galaxy/main.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_15.05' into dev Commit: 9ab92973be879bc0a3bd40b64b0d98977a08d406 https://github.com/galaxyproject/galaxy/commit/9ab92973be879bc0a3bd40b64b0d9... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove unused import Commit: 11b2fbcb3b743691341d3b65ee6be3d99eda9067 https://github.com/galaxyproject/galaxy/commit/11b2fbcb3b743691341d3b65ee6be... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd Log Message: ----------- Visualizations registry: switch to entry_point config definition for built-in visualizations Commit: e0c7e02e40ab2be396743c3dadad49f1bb647f0a https://github.com/galaxyproject/galaxy/commit/e0c7e02e40ab2be396743c3dadad4... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- do not require option that is actualy in the config Commit: 229f4c2cc7c66100d266b1e44a96ecad92c59118 https://github.com/galaxyproject/galaxy/commit/229f4c2cc7c66100d266b1e44a96e... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- fix exception imports Commit: d675a6a0b37a5c977a1f5606a383f1de92d5ee7b https://github.com/galaxyproject/galaxy/commit/d675a6a0b37a5c977a1f5606a383f... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M test/unit/visualizations/plugins/test_VisualizationPlugin.py Log Message: ----------- Testing: use unittest2 to allow 2.7 assertions Commit: 10927bf721feb71d96aa97cd283d6a55da6ee6ff https://github.com/galaxyproject/galaxy/commit/10927bf721feb71d96aa97cd283d6... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-07 (Thu, 07 May 2015) Changed paths: M test/unit/visualizations/plugins/test_VisualizationPlugin.py Log Message: ----------- Merge pull request #246 from carlfeberhard/testing.fix-26 Testing: use unittest2 to allow 2.7 assertions Commit: 028d1b0252f88ce927dff0dc6eeed24d27065af1 https://github.com/galaxyproject/galaxy/commit/028d1b0252f88ce927dff0dc6eeed... Author: Renato Alves <alves.rjc@gmail.com> Date: 2015-05-08 (Fri, 08 May 2015) Changed paths: M .gitignore Log Message: ----------- Ignore sample files from toolshed installed tools Sample files already being tracked won't be affected. If an ignored file is to be added, add it with -f. Commit: a85eadfb741c8efde1cad3803c4915cee669aaaa https://github.com/galaxyproject/galaxy/commit/a85eadfb741c8efde1cad3803c491... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-08 (Fri, 08 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd Log Message: ----------- Merge pull request #243 from carlfeberhard/vis.remove-template Visualizations registry: switch to entry_point config definition for … Commit: f20c961afc3cf8759067c5ca161f665e46de1df7 https://github.com/galaxyproject/galaxy/commit/f20c961afc3cf8759067c5ca161f6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-08 (Fri, 08 May 2015) Changed paths: M .gitignore Log Message: ----------- Merge pull request #248 from Unode/patch-1 Ignore sample files from toolshed installed tools Commit: f7af19b82c36d75bc9f32bd0893594e50b43d98b https://github.com/galaxyproject/galaxy/commit/f7af19b82c36d75bc9f32bd089359... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-08 (Fri, 08 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #239 from erasche/rdata2 Add RData and RData.gz formats Commit: 201f2db1848964f4b3c5b5f1e172ffa03db55d32 https://github.com/galaxyproject/galaxy/commit/201f2db1848964f4b3c5b5f1e172f... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-08 (Fri, 08 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Pin to :dev Commit: bf9a2ab4eaf7c12b394fa1b22d767db1950a47cf https://github.com/galaxyproject/galaxy/commit/bf9a2ab4eaf7c12b394fa1b22d767... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-10 (Sun, 10 May 2015) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Add env test option for disabling truncation of test diffs. Commit: 213f21f89034cf4218eb50314a7587ad35b5b9f3 https://github.com/galaxyproject/galaxy/commit/213f21f89034cf4218eb50314a758... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-10 (Sun, 10 May 2015) Changed paths: M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Updates to take advantage of #229 infrastructure Commit: 67e7dcff17d6c3d79129371be95f0c8433a39092 https://github.com/galaxyproject/galaxy/commit/67e7dcff17d6c3d79129371be95f0... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-05-10 (Sun, 10 May 2015) Changed paths: M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #2 from erasche/rstudio2 Updates to take advantage of #229 infrastructure Commit: eb2034ac6e8a8a2b4984ddfdbe213d4e4e301aef https://github.com/galaxyproject/galaxy/commit/eb2034ac6e8a8a2b4984ddfdbe213... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-10 (Sun, 10 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge remote-tracking branch 'erasche/ie-updates2' into pr229 Conflicts: config/plugins/interactive_environments/ipython/config/ipython.ini.sample Commit: a1cfe3586ab9bdc0fe5bb3e3f1e4fced40c22b15 https://github.com/galaxyproject/galaxy/commit/a1cfe3586ab9bdc0fe5bb3e3f1e4f... Author: abretaud <abretaud@irisa.fr> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M .gitignore M .travis.yml M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/style/blue_colors.ini A client/galaxy/style/less/autocomplete_tagging.less A client/galaxy/style/less/base.less A client/galaxy/style/less/bootstrap.less A client/galaxy/style/less/bootstrap/alerts.less A client/galaxy/style/less/bootstrap/badges.less A client/galaxy/style/less/bootstrap/bootstrap.less A client/galaxy/style/less/bootstrap/breadcrumbs.less A client/galaxy/style/less/bootstrap/button-groups.less A client/galaxy/style/less/bootstrap/buttons.less A client/galaxy/style/less/bootstrap/carousel.less A client/galaxy/style/less/bootstrap/close.less A client/galaxy/style/less/bootstrap/code.less A client/galaxy/style/less/bootstrap/component-animations.less A client/galaxy/style/less/bootstrap/dropdowns.less A client/galaxy/style/less/bootstrap/forms.less A client/galaxy/style/less/bootstrap/glyphicons.less A client/galaxy/style/less/bootstrap/grid.less A client/galaxy/style/less/bootstrap/input-groups.less A client/galaxy/style/less/bootstrap/jumbotron.less A client/galaxy/style/less/bootstrap/labels.less A client/galaxy/style/less/bootstrap/list-group.less A client/galaxy/style/less/bootstrap/media.less A client/galaxy/style/less/bootstrap/mixins.less A client/galaxy/style/less/bootstrap/modals.less A client/galaxy/style/less/bootstrap/navbar.less A client/galaxy/style/less/bootstrap/navs.less A client/galaxy/style/less/bootstrap/normalize.less A client/galaxy/style/less/bootstrap/pager.less A client/galaxy/style/less/bootstrap/pagination.less A client/galaxy/style/less/bootstrap/panels.less A client/galaxy/style/less/bootstrap/popovers.less A client/galaxy/style/less/bootstrap/print.less A client/galaxy/style/less/bootstrap/progress-bars.less A client/galaxy/style/less/bootstrap/responsive-utilities.less A client/galaxy/style/less/bootstrap/scaffolding.less A client/galaxy/style/less/bootstrap/tables.less A client/galaxy/style/less/bootstrap/theme.less A client/galaxy/style/less/bootstrap/thumbnails.less A client/galaxy/style/less/bootstrap/tooltip.less A client/galaxy/style/less/bootstrap/type.less A client/galaxy/style/less/bootstrap/utilities.less A client/galaxy/style/less/bootstrap/variables.less A client/galaxy/style/less/bootstrap/wells.less A client/galaxy/style/less/circster.less A client/galaxy/style/less/collections.less A client/galaxy/style/less/embed_item.less A client/galaxy/style/less/fontawesome/bordered-pulled.less A client/galaxy/style/less/fontawesome/core.less A client/galaxy/style/less/fontawesome/fixed-width.less A client/galaxy/style/less/fontawesome/font-awesome.less A client/galaxy/style/less/fontawesome/icons.less A client/galaxy/style/less/fontawesome/larger.less A client/galaxy/style/less/fontawesome/list.less A client/galaxy/style/less/fontawesome/mixins.less A client/galaxy/style/less/fontawesome/path.less A client/galaxy/style/less/fontawesome/rotated-flipped.less A client/galaxy/style/less/fontawesome/spinning.less A client/galaxy/style/less/fontawesome/stacked.less A client/galaxy/style/less/fontawesome/variables.less A client/galaxy/style/less/frame.less A client/galaxy/style/less/galaxy_bootstrap.less A client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/galaxy/style/less/galaxy_bootstrap/variables.less A client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/history.less A client/galaxy/style/less/iconic_stroke.less A client/galaxy/style/less/iphone.less A client/galaxy/style/less/job.less A client/galaxy/style/less/jstree.less A client/galaxy/style/less/library.less A client/galaxy/style/less/list-item.less A client/galaxy/style/less/masthead.less A client/galaxy/style/less/select2.less A client/galaxy/style/less/theme/blue.less A client/galaxy/style/less/toastr.less A client/galaxy/style/less/trackster.less A client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/dataset-choice.less A client/galaxy/style/less/ui/icon-btn.less A client/galaxy/style/less/ui/pagination.less A client/galaxy/style/less/ui/paired-collection-creator.less A client/galaxy/style/less/ui/peek-column-selector.less A client/galaxy/style/less/ui/search-input.less A client/galaxy/style/less/upload.less A client/galaxy/style/source_material/circle.py A client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/galaxy_spinner.fla A client/grunt-tasks/install-libs.js A client/grunt-tasks/scripts.js A client/grunt-tasks/style.js M client/package.json M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/tool_conf.xml.sample M eggs.ini M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/main.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/visualization/plugins/__init__.py A lib/galaxy/visualization/plugins/config_parser.py A lib/galaxy/visualization/plugins/plugin.py A lib/galaxy/visualization/plugins/registry.py A lib/galaxy/visualization/plugins/resource_parser.py A lib/galaxy/visualization/plugins/utils.py R lib/galaxy/visualization/registry.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run_tests.sh M scripts/drmaa_external_runner.py M scripts/functional_tests.py A scripts/runtime_stats.py M static/favicon.ico M static/images/galaxyIcon_noText.png M static/maps/galaxy.masthead.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-panel-annotated.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/ui/ui-slider.js.map M static/scripts/galaxy.masthead.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-panel-annotated.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/ui/ui-slider.js R static/style/Gruntfile.js R static/style/Makefile R static/style/README M static/style/blue/base.css R static/style/blue_colors.ini R static/style/package.json R static/style/src/less/autocomplete_tagging.less R static/style/src/less/base.less R static/style/src/less/bootstrap.less R static/style/src/less/bootstrap/alerts.less R static/style/src/less/bootstrap/badges.less R static/style/src/less/bootstrap/bootstrap.less R static/style/src/less/bootstrap/breadcrumbs.less R static/style/src/less/bootstrap/button-groups.less R static/style/src/less/bootstrap/buttons.less R static/style/src/less/bootstrap/carousel.less R static/style/src/less/bootstrap/close.less R static/style/src/less/bootstrap/code.less R static/style/src/less/bootstrap/component-animations.less R static/style/src/less/bootstrap/dropdowns.less R static/style/src/less/bootstrap/forms.less R static/style/src/less/bootstrap/glyphicons.less R static/style/src/less/bootstrap/grid.less R static/style/src/less/bootstrap/input-groups.less R static/style/src/less/bootstrap/jumbotron.less R static/style/src/less/bootstrap/labels.less R static/style/src/less/bootstrap/list-group.less R static/style/src/less/bootstrap/media.less R static/style/src/less/bootstrap/mixins.less R static/style/src/less/bootstrap/modals.less R static/style/src/less/bootstrap/navbar.less R static/style/src/less/bootstrap/navs.less R static/style/src/less/bootstrap/normalize.less R static/style/src/less/bootstrap/pager.less R static/style/src/less/bootstrap/pagination.less R static/style/src/less/bootstrap/panels.less R static/style/src/less/bootstrap/popovers.less R static/style/src/less/bootstrap/print.less R static/style/src/less/bootstrap/progress-bars.less R static/style/src/less/bootstrap/responsive-utilities.less R static/style/src/less/bootstrap/scaffolding.less R static/style/src/less/bootstrap/tables.less R static/style/src/less/bootstrap/theme.less R static/style/src/less/bootstrap/thumbnails.less R static/style/src/less/bootstrap/tooltip.less R static/style/src/less/bootstrap/type.less R static/style/src/less/bootstrap/utilities.less R static/style/src/less/bootstrap/variables.less R static/style/src/less/bootstrap/wells.less R static/style/src/less/circster.less R static/style/src/less/collections.less R static/style/src/less/embed_item.less R static/style/src/less/fontawesome/bordered-pulled.less R static/style/src/less/fontawesome/core.less R static/style/src/less/fontawesome/fixed-width.less R static/style/src/less/fontawesome/font-awesome.less R static/style/src/less/fontawesome/icons.less R static/style/src/less/fontawesome/larger.less R static/style/src/less/fontawesome/list.less R static/style/src/less/fontawesome/mixins.less R static/style/src/less/fontawesome/path.less R static/style/src/less/fontawesome/rotated-flipped.less R static/style/src/less/fontawesome/spinning.less R static/style/src/less/fontawesome/stacked.less R static/style/src/less/fontawesome/variables.less R static/style/src/less/frame.less R static/style/src/less/galaxy_bootstrap.less R static/style/src/less/galaxy_bootstrap/overrides.less R static/style/src/less/galaxy_bootstrap/variables.less R static/style/src/less/galaxy_variables.less R static/style/src/less/history.less R static/style/src/less/iconic_stroke.less R static/style/src/less/iphone.less R static/style/src/less/job.less R static/style/src/less/jstree.less R static/style/src/less/library.less R static/style/src/less/list-item.less R static/style/src/less/masthead.less R static/style/src/less/select2.less R static/style/src/less/theme/blue.less R static/style/src/less/toastr.less R static/style/src/less/trackster.less R static/style/src/less/ui.less R static/style/src/less/ui/dataset-choice.less R static/style/src/less/ui/icon-btn.less R static/style/src/less/ui/pagination.less R static/style/src/less/ui/paired-collection-creator.less R static/style/src/less/ui/peek-column-selector.less R static/style/src/less/ui/search-input.less R static/style/src/less/upload.less R static/style/src/source_material/circle.py R static/style/src/source_material/galaxy_icons.svg R static/style/src/source_material/galaxy_spinner.fla M static/welcome.html.sample M templates/user/register.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/tool_shed/base_panels.mako A test-data/bcf_index_metadata_test.bcf A test-data/bcf_index_metadata_test.txt M test/api/test_workflows_from_yaml.py M test/casperjs/modules/user.js M test/casperjs/registration-tests.js A test/functional/tools/metadata_bcf.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/install_and_test_tool_shed_repositories/base/util.py M test/qunit/README.txt M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js A test/qunit/tests/list-of-pairs-collection-creator.html A test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js R test/qunit/tests/paired-collection-creator.html R test/qunit/tests/paired-collection-creator.js M test/unit/managers/base.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/stats/gsummary.xml A tox.ini Log Message: ----------- Merge pull request #1 from galaxyproject/dev Sync Commit: 01e09fefdced1d336a32e6763dd005107b34b613 https://github.com/galaxyproject/galaxy/commit/01e09fefdced1d336a32e6763dd00... Author: abretaud <anthony.bretaudeau@rennes.inra.fr> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- send signal to reload data table when adding an entry Commit: f3e81f148f4b13ef0e5846593c355d270f7baece https://github.com/galaxyproject/galaxy/commit/f3e81f148f4b13ef0e5846593c355... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Eliminate potential boilerplate code in new IE env stuff. Commit: d5372e892f3355bea41e5f77049206ec2d904f78 https://github.com/galaxyproject/galaxy/commit/d5372e892f3355bea41e5f7704920... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py Log Message: ----------- Merge pull request #250 from abretaud/reload_signal Send signal to reload data tables when adding an entry Commit: 7851c7eb32256595cccfe4595729727fc6371ec9 https://github.com/galaxyproject/galaxy/commit/7851c7eb32256595cccfe45957297... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M .gitignore M .travis.yml M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/grunt-tasks/install-libs.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/main.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/user.py M run_tests.sh M scripts/functional_tests.py M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/history/history-panel-annotated.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/history/history-panel-annotated.js M static/scripts/mvc/tools/tools-form-workflow.js M templates/webapps/galaxy/history/display.mako M templates/webapps/tool_shed/base_panels.mako M test/unit/managers/base.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py A tox.ini Log Message: ----------- Merge pull request #3 from jmchilton/pr229 Merge dev and add tighter env abstraction. Commit: 273bae44eca5786eb3a162f6932512252ed819e6 https://github.com/galaxyproject/galaxy/commit/273bae44eca5786eb3a162f693251... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Merge pull request #249 from jmchilton/no_slice Add env test option for disabling truncation of test diffs. Commit: 285eece97a4d45931eb6499e911e448791a78092 https://github.com/galaxyproject/galaxy/commit/285eece97a4d45931eb6499e911e4... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update RStudio to new IE infrastructure Commit: a9fb12a146e0b6384bc69ed230ec40a8c1a7a70b https://github.com/galaxyproject/galaxy/commit/a9fb12a146e0b6384bc69ed230ec4... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update RStudio to new IE infrastructure Commit: 13afcbd478d8e3c972b6489423ddbac219004210 https://github.com/galaxyproject/galaxy/commit/13afcbd478d8e3c972b6489423ddb... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove unused extra This moved to env_override in the run command builder Commit: 88456ca5d5ea1b5252ba825b2a38d72d92d6805a https://github.com/galaxyproject/galaxy/commit/88456ca5d5ea1b5252ba825b2a38d... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M .gitignore M .travis.yml M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/grunt-tasks/install-libs.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/main.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/user.py M run_tests.sh M scripts/functional_tests.py M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/history/history-panel-annotated.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/history/history-panel-annotated.js M static/scripts/mvc/tools/tools-form-workflow.js M templates/webapps/galaxy/history/display.mako M templates/webapps/tool_shed/base_panels.mako M test/unit/managers/base.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py A tox.ini Log Message: ----------- Merge branch 'ie-updates2' of github.com:erasche/galaxy into ie-updates2 Commit: a092aa2f590df8fd483557499b916a30100f3e27 https://github.com/galaxyproject/galaxy/commit/a092aa2f590df8fd483557499b916... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-12 (Tue, 12 May 2015) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py Log Message: ----------- Start providing usage information for the various cleanup scripts Commit: 4c20494011659da1c595aece91a6f58b4e3aa045 https://github.com/galaxyproject/galaxy/commit/4c20494011659da1c595aece91a6f... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-12 (Tue, 12 May 2015) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py Log Message: ----------- Make python scripts executable. Tweak remove_renamed_datasets_from_disk.py. Commit: 32e027d43180b524dc40f329ace2d721aff1974c https://github.com/galaxyproject/galaxy/commit/32e027d43180b524dc40f329ace2d... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M .gitignore M .travis.yml M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/ui/hoverhighlight.js A client/galaxy/style/blue_colors.ini A client/galaxy/style/less/autocomplete_tagging.less A client/galaxy/style/less/base.less A client/galaxy/style/less/bootstrap.less A client/galaxy/style/less/bootstrap/alerts.less A client/galaxy/style/less/bootstrap/badges.less A client/galaxy/style/less/bootstrap/bootstrap.less A client/galaxy/style/less/bootstrap/breadcrumbs.less A client/galaxy/style/less/bootstrap/button-groups.less A client/galaxy/style/less/bootstrap/buttons.less A client/galaxy/style/less/bootstrap/carousel.less A client/galaxy/style/less/bootstrap/close.less A client/galaxy/style/less/bootstrap/code.less A client/galaxy/style/less/bootstrap/component-animations.less A client/galaxy/style/less/bootstrap/dropdowns.less A client/galaxy/style/less/bootstrap/forms.less A client/galaxy/style/less/bootstrap/glyphicons.less A client/galaxy/style/less/bootstrap/grid.less A client/galaxy/style/less/bootstrap/input-groups.less A client/galaxy/style/less/bootstrap/jumbotron.less A client/galaxy/style/less/bootstrap/labels.less A client/galaxy/style/less/bootstrap/list-group.less A client/galaxy/style/less/bootstrap/media.less A client/galaxy/style/less/bootstrap/mixins.less A client/galaxy/style/less/bootstrap/modals.less A client/galaxy/style/less/bootstrap/navbar.less A client/galaxy/style/less/bootstrap/navs.less A client/galaxy/style/less/bootstrap/normalize.less A client/galaxy/style/less/bootstrap/pager.less A client/galaxy/style/less/bootstrap/pagination.less A client/galaxy/style/less/bootstrap/panels.less A client/galaxy/style/less/bootstrap/popovers.less A client/galaxy/style/less/bootstrap/print.less A client/galaxy/style/less/bootstrap/progress-bars.less A client/galaxy/style/less/bootstrap/responsive-utilities.less A 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client/galaxy/style/less/fontawesome/mixins.less A client/galaxy/style/less/fontawesome/path.less A client/galaxy/style/less/fontawesome/rotated-flipped.less A client/galaxy/style/less/fontawesome/spinning.less A client/galaxy/style/less/fontawesome/stacked.less A client/galaxy/style/less/fontawesome/variables.less A client/galaxy/style/less/frame.less A client/galaxy/style/less/galaxy_bootstrap.less A client/galaxy/style/less/galaxy_bootstrap/overrides.less A client/galaxy/style/less/galaxy_bootstrap/variables.less A client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/history.less A client/galaxy/style/less/iconic_stroke.less A client/galaxy/style/less/iphone.less A client/galaxy/style/less/job.less A client/galaxy/style/less/jstree.less A client/galaxy/style/less/library.less A client/galaxy/style/less/list-item.less A client/galaxy/style/less/masthead.less A client/galaxy/style/less/select2.less A client/galaxy/style/less/theme/blue.less A client/galaxy/style/less/toastr.less A client/galaxy/style/less/trackster.less A client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/dataset-choice.less A client/galaxy/style/less/ui/icon-btn.less A client/galaxy/style/less/ui/pagination.less A client/galaxy/style/less/ui/paired-collection-creator.less A client/galaxy/style/less/ui/peek-column-selector.less A client/galaxy/style/less/ui/search-input.less A client/galaxy/style/less/upload.less A client/galaxy/style/source_material/circle.py A client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/galaxy_spinner.fla A client/grunt-tasks/install-libs.js A client/grunt-tasks/scripts.js A client/grunt-tasks/style.js M client/package.json M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/tool_conf.xml.sample M config/tool_shed.ini.sample M eggs.ini M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/main.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py A lib/galaxy/visualization/plugins/__init__.py A lib/galaxy/visualization/plugins/config_parser.py A lib/galaxy/visualization/plugins/plugin.py A lib/galaxy/visualization/plugins/registry.py A lib/galaxy/visualization/plugins/resource_parser.py A lib/galaxy/visualization/plugins/utils.py R lib/galaxy/visualization/registry.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/api/search.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/tools/tool_validator.py M run_tests.sh M scripts/drmaa_external_runner.py M scripts/functional_tests.py A scripts/runtime_stats.py M scripts/tool_shed/build_ts_whoosh_index.py M static/favicon.ico M static/images/galaxyIcon_noText.png M static/maps/galaxy.masthead.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-panel-annotated.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/ui/ui-slider.js.map A static/maps/ui/hoverhighlight.js.map M static/scripts/galaxy.masthead.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M 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static/style/src/less/collections.less R static/style/src/less/embed_item.less R static/style/src/less/fontawesome/bordered-pulled.less R static/style/src/less/fontawesome/core.less R static/style/src/less/fontawesome/fixed-width.less R static/style/src/less/fontawesome/font-awesome.less R static/style/src/less/fontawesome/icons.less R static/style/src/less/fontawesome/larger.less R static/style/src/less/fontawesome/list.less R static/style/src/less/fontawesome/mixins.less R static/style/src/less/fontawesome/path.less R static/style/src/less/fontawesome/rotated-flipped.less R static/style/src/less/fontawesome/spinning.less R static/style/src/less/fontawesome/stacked.less R static/style/src/less/fontawesome/variables.less R static/style/src/less/frame.less R static/style/src/less/galaxy_bootstrap.less R static/style/src/less/galaxy_bootstrap/overrides.less R static/style/src/less/galaxy_bootstrap/variables.less R static/style/src/less/galaxy_variables.less R static/style/src/less/history.less R static/style/src/less/iconic_stroke.less R static/style/src/less/iphone.less R static/style/src/less/job.less R static/style/src/less/jstree.less R static/style/src/less/library.less R static/style/src/less/list-item.less R static/style/src/less/masthead.less R static/style/src/less/select2.less R static/style/src/less/theme/blue.less R static/style/src/less/toastr.less R static/style/src/less/trackster.less R static/style/src/less/ui.less R static/style/src/less/ui/dataset-choice.less R static/style/src/less/ui/icon-btn.less R static/style/src/less/ui/pagination.less R static/style/src/less/ui/paired-collection-creator.less R static/style/src/less/ui/peek-column-selector.less R static/style/src/less/ui/search-input.less R static/style/src/less/upload.less R static/style/src/source_material/circle.py R static/style/src/source_material/galaxy_icons.svg R static/style/src/source_material/galaxy_spinner.fla M static/welcome.html.sample M templates/user/register.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/base_panels.mako A test-data/bcf_index_metadata_test.bcf A test-data/bcf_index_metadata_test.txt M test/api/test_workflows_from_yaml.py M test/base/twilltestcase.py M test/casperjs/modules/user.js M test/casperjs/registration-tests.js A test/functional/tools/metadata_bcf.xml A test/functional/tools/output_auto_format.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/install_and_test_tool_shed_repositories/base/util.py M test/qunit/README.txt M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js A test/qunit/tests/list-of-pairs-collection-creator.html A test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js R test/qunit/tests/paired-collection-creator.html R test/qunit/tests/paired-collection-creator.js M test/unit/managers/base.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/stats/gsummary.xml A tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter Conflicts: static/maps/mvc/form/form-section.js.map static/scripts/mvc/form/form-section.js Commit: c06b8ece4ef33115c69bbd0bf752b65441d57b94 https://github.com/galaxyproject/galaxy/commit/c06b8ece4ef33115c69bbd0bf752b... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map A static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js A static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/style/blue/base.css M test/api/test_tools.py A test/functional/tools/library_data.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #132 from guerler/library_data_parameter Library data and FTP file parameter Commit: 687a8947e277e5ee460b42a5b8167e53069d9ccc https://github.com/galaxyproject/galaxy/commit/687a8947e277e5ee460b42a5b8167... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #229 from erasche/ie-updates2 IE Updates Commit: 0a5ec3e8d33f526e1934900e03cc019932123141 https://github.com/galaxyproject/galaxy/commit/0a5ec3e8d33f526e1934900e03cc0... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M .gitignore M .travis.yml M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/main.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/user.py M run_tests.sh M scripts/functional_tests.py M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-panel-annotated.js.map M static/maps/mvc/tools/tools-form-workflow.js.map A static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map A static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-panel-annotated.js M static/scripts/mvc/tools/tools-form-workflow.js A static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js A static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_tools.py M test/base/twilltestcase.py A test/functional/tools/library_data.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/base.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py A tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into rstudio Commit: 23459f318507255a2bb1d1fb647e1581bd2090e1 https://github.com/galaxyproject/galaxy/commit/23459f318507255a2bb1d1fb647e1... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Expose and cache raw IE password to simplify RStudio plugin. Commit: 55e523ea638e85323af993728da94e0c8cb64c03 https://github.com/galaxyproject/galaxy/commit/55e523ea638e85323af993728da94... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Introduce new IE launch abstraction. In addition to reducing duplication between IPython and RStudio - it also shields them from low-level details and creates an interface we could more reasonably generalize to something like qsubing the docker commands or using Docker Swarm. Commit: 624d540c04eb69ba0bf4f1879598277dfd69a7b2 https://github.com/galaxyproject/galaxy/commit/624d540c04eb69ba0bf4f18795982... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- IEs: Move temp dir handling into ie_request to simplify interface. Commit: 851186dc7f1bc8ee2876cb96ddd1315c76af8716 https://github.com/galaxyproject/galaxy/commit/851186dc7f1bc8ee2876cb96ddd13... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M lib/galaxy/managers/context.py Log Message: ----------- Have trans.user_ftp_dir return None instead of error if ftp_upload_dir unset. This is now called on each upload job eb538e00bdfb6cd87c71a620653c91854642b01a and if ftp_upload_dir is None and this was throwing the following exception - https://gist.github.com/jmchilton/fdfb808e13998fbe17bd. Commit: 0e2bf468709bb6ad9589aa5568a3040f359697b5 https://github.com/galaxyproject/galaxy/commit/0e2bf468709bb6ad9589aa5568a30... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M lib/galaxy/managers/context.py Log Message: ----------- Merge pull request #257 from jmchilton/upload_api_fix Have trans.user_ftp_dir return None instead of error if upload dir unset. Commit: 998d0e8a8c2d0def469ecf9280330fc78e450ee9 https://github.com/galaxyproject/galaxy/commit/998d0e8a8c2d0def469ecf9280330... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- IE: Move IPython-specific password hashing out of framework into plugin. See dicussion here - https://github.com/erasche/galaxy/commit/23459f318507255a2bb1d1fb647e1581bd2.... Commit: 656d9bef506cac653d66735ecfeff6437bb51422 https://github.com/galaxyproject/galaxy/commit/656d9bef506cac653d66735ecfeff... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M client/galaxy/scripts/utils/utils.js A doc/source/_static/style.css A doc/source/_templates/layout.html M doc/source/index.rst A doc/source/releases/13.01_announce.rst A doc/source/releases/13.02_announce.rst A doc/source/releases/13.04_announce.rst A doc/source/releases/13.06_announce.rst A doc/source/releases/13.08_announce.rst A doc/source/releases/13.11_announce.rst A doc/source/releases/14.02_announce.rst A doc/source/releases/14.04_announce.rst A doc/source/releases/14.06_announce.rst A doc/source/releases/14.08_announce.rst A doc/source/releases/14.10_announce.rst A doc/source/releases/15.01_announce.rst A doc/source/releases/15.03_announce.rst A doc/source/releases/15.05.rst A doc/source/releases/15.05_announce.rst A doc/source/releases/_header.rst A doc/source/releases/_thanks.rst A doc/source/releases/index.rst A doc/source/releases/older_releases.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/histories.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py A scripts/bootstrap_history.py M static/maps/utils/utils.js.map M static/scripts/utils/utils.js M templates/webapps/galaxy/workflow/run.mako M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_15.05' into dev Conflicts: lib/galaxy/version.py Commit: 411c674ac69e7207201b91128ed7e32be68d937b https://github.com/galaxyproject/galaxy/commit/411c674ac69e7207201b91128ed7e... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M .gitignore M .travis.yml M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/circster/config/circster.xml M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/metadata.py A lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/main.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/user.py M run_tests.sh M scripts/functional_tests.py M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/require.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-panel-annotated.js.map M static/maps/mvc/tools/tools-form-workflow.js.map A static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map A static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-panel-annotated.js M static/scripts/mvc/tools/tools-form-workflow.js A static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js A static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_tools.py M test/base/twilltestcase.py A test/functional/tools/library_data.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/base.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py A tox.ini Log Message: ----------- Merge pull request #4 from jmchilton/rstudio More IE Enhancements [WIP] Commit: 38bfe860057c76f638d365e9d23ebee05aaa1261 https://github.com/galaxyproject/galaxy/commit/38bfe860057c76f638d365e9d23eb... Author: Eric Rasche <esr@tamu.edu> Date: 2015-05-14 (Thu, 14 May 2015) Log Message: ----------- Pin to :dev CC @jmchilton @bgruening, pending the next Galaxy release, I've pinned both images to their :dev tags. This commit is really backing out a previous commit pinning to :15.05 which was the wrong thing to do as of #229 Commit: ed8112b422405482591a0b041f8414ff60bd943b https://github.com/galaxyproject/galaxy/commit/ed8112b422405482591a0b041f841... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix problems introduced in IE refactorings. Commit: 2a977039cc161d6f609b67cbe8d2e7aa62373d9e https://github.com/galaxyproject/galaxy/commit/2a977039cc161d6f609b67cbe8d2e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/templates/ipython.mako A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rsa.js A config/plugins/interactive_environments/rstudio/static/js/rstudio.js A config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #230 from erasche/rstudio RStudio IE Commit: f52bbbf50e53ca28db1a72dc1243e5d46cdef9b6 https://github.com/galaxyproject/galaxy/commit/f52bbbf50e53ca28db1a72dc1243e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/interval_as_bed.xml Log Message: ----------- Add display for Interval files at IGV via bedstrict. Commit: 3a998d0f2af3b7c85a55d87dc40a2c02142b9bd5 https://github.com/galaxyproject/galaxy/commit/3a998d0f2af3b7c85a55d87dc40a2... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M display_applications/igv/interval_as_bed.xml Log Message: ----------- Tweak display application id to match interval to bed. Commit: 218bf548b7ff1fc9defd13b0baaaa2674cfc6e0b https://github.com/galaxyproject/galaxy/commit/218bf548b7ff1fc9defd13b0baaaa... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/interval_as_bed.xml Log Message: ----------- Merge pull request #259 from blankenberg/igv-interval Add display for Interval files at IGV via bedstrict. Commit: 97c450293bd0fca71af9fec333e23429c43fa86e https://github.com/galaxyproject/galaxy/commit/97c450293bd0fca71af9fec333e23... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M display_applications/igv/bam.xml M display_applications/igv/gff.xml M display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml Log Message: ----------- IGV External displays cannot use a name with a comma in it, so replace commas with semicolons. Commit: 0630ae9ccfcca4ce9df7fbd2f606e1192ef535fa https://github.com/galaxyproject/galaxy/commit/0630ae9ccfcca4ce9df7fbd2f606e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M display_applications/igv/bam.xml M display_applications/igv/gff.xml M display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml Log Message: ----------- Merge pull request #261 from blankenberg/igv-no-commas IGV External displays cannot use a name with a comma in it, so replace commas with semicolons. Commit: 62772bc86e2504982f207a982542cbcc3faf0c65 https://github.com/galaxyproject/galaxy/commit/62772bc86e2504982f207a982542c... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix bug in history sharing. Commit: d658b7faf1d44b14f487e84eae8a867699ee1b6b https://github.com/galaxyproject/galaxy/commit/d658b7faf1d44b14f487e84eae8a8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #263 from bgruening/patch-2 Fix bug in history sharing Commit: 22d4a1d8c33b5207f4f1424b38c52fe25dc3b74b https://github.com/galaxyproject/galaxy/commit/22d4a1d8c33b5207f4f1424b38c52... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. Commit: 224d8f3fc45d9319f749ee24ad7c1ed4cae6c9e8 https://github.com/galaxyproject/galaxy/commit/224d8f3fc45d9319f749ee24ad7c1... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M tools/maf/maf_stats.xml Log Message: ----------- Remove numpy requirement, not used since commit 09ce7a9b1793b0400f7e6e8ee46a178a0543ad3a . Commit: 341a6cf7600df8d408853f154b510f1b5e8f26a5 https://github.com/galaxyproject/galaxy/commit/341a6cf7600df8d408853f154b510... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M tools/evolution/codingSnps.xml M tools/plotting/boxplot.xml Log Message: ----------- Use requirements of type="package" instead of deprecated "binary". Commit: 48023ed37428233fee04bc8d48d0469ed4225bba https://github.com/galaxyproject/galaxy/commit/48023ed37428233fee04bc8d48d04... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M config/plugins/visualizations/README.txt Log Message: ----------- Remove outdated sentence. Commit: a32ed94b50a18656453604cc469272e492c1cae7 https://github.com/galaxyproject/galaxy/commit/a32ed94b50a18656453604cc46927... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M config/plugins/visualizations/README.txt M tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #264 from nsoranzo/dev Mixed fixes. Commit: 308a8e37372abb6a25124d0782d3eef612f9bb43 https://github.com/galaxyproject/galaxy/commit/308a8e37372abb6a25124d0782d3e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M test/api/test_tools.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject-careful/release_15.05' into dev Conflicts: config/plugins/interactive_environments/ipython/config/ipython.ini.sample Commit: 906e9a08095529669381a751809848585ea6753a https://github.com/galaxyproject/galaxy/commit/906e9a08095529669381a75180984... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- Fix function names for dynamic tool test functions. When finding methods to invoke it seems nose uses the raw function name instead of the class's attribute name (I guess this terminology makes sense), but when reporting results it uses the latter. Synchronizing these names therefore allows calling specific tool test methods from the command-line. This change is required to implement galaxyproject/planemo#145. Commit: 6d62e6ef4fdc04863014cef0dd1ebc8a8cf09e9e https://github.com/galaxyproject/galaxy/commit/6d62e6ef4fdc04863014cef0dd1eb... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-16 (Sat, 16 May 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Revert EDAM approach. This reverts commits 04a8d50b8b75dccb94b1f44ad3a5b91dea048384 and 32d9390d9dffd82c6a10c31a0f679d7d78b7c904. Commit: 08e2c351d94bd002ee1fa51afc99bf4fa8c0cfd3 https://github.com/galaxyproject/galaxy/commit/08e2c351d94bd002ee1fa51afc99b... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-16 (Sat, 16 May 2015) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/xml.py A scripts/edam_mapping.py Log Message: ----------- Add edam formats to most Galaxy datatypes and a script for producing a mapping. See notes in scripts/edam_mapping.py for more information on mapping. This is based on mapping of terms done by Eric Rasche (@erasche) (in galaxyproject/galaxy#80) and by the team at Pasteur including @hmenager, @fmareuil, and @odoppelt (in https://docs.google.com/spreadsheets/d/1vptTpJvQfb5FOtRJOajjftUkL9aZ0eeVdhUP...). Current mapping at time of commit is https://gist.github.com/jmchilton/73cd540d7a08488843d7. Commit: 6c69602a336c8e01ee48f77caeeb2aabcad6c66b https://github.com/galaxyproject/galaxy/commit/6c69602a336c8e01ee48f77caeeb2... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-05-16 (Sat, 16 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/xml.py A scripts/edam_mapping.py Log Message: ----------- Merge pull request #5 from jmchilton/edam-jmchilton-3 Different approach to EDAM Mapping Commit: 7a53663c3491240b30d5e622a0f86e787e04bc7e https://github.com/galaxyproject/galaxy/commit/7a53663c3491240b30d5e622a0f86... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-17 (Sun, 17 May 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Parse history id through tool model building api Commit: 98d8c2cc2e227ad81145c7013d210607d18fbfa4 https://github.com/galaxyproject/galaxy/commit/98d8c2cc2e227ad81145c7013d210... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Allow config of shed tool conf used with ``run_tests.sh -installed``. Set with GALAXY_TEST_SHED_TOOL_CONF. This is required to implement galaxyproject/planemo#176. Commit: d5103412ab5df743b7fe6eb9fd0be10d5f685118 https://github.com/galaxyproject/galaxy/commit/d5103412ab5df743b7fe6eb9fd0be... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Replace current history by parsed history in sub functions Commit: 25d8aea20efffa1d1a49bdd0da2801c36cd2e7b0 https://github.com/galaxyproject/galaxy/commit/25d8aea20efffa1d1a49bdd0da280... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Provide proper validation messages for missing or unavailable histories Commit: 609739b7030f176a02fb916b226a05ca6e189c03 https://github.com/galaxyproject/galaxy/commit/609739b7030f176a02fb916b226a0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update error message Commit: ca9076f178edfd844ca2c3c0ee4bfdce0e6c5d51 https://github.com/galaxyproject/galaxy/commit/ca9076f178edfd844ca2c3c0ee4bf... Author: Daniel Blankenberg <blankenberg@users.noreply.github.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Merge pull request #267 from jmchilton/config_shed_test Allow config of shed tool conf used with ``run_tests.sh -installed``. Commit: 7c27b4456f77d73297322f81cd49bcadcf76b821 https://github.com/galaxyproject/galaxy/commit/7c27b4456f77d73297322f81cd49b... Author: Daniel Blankenberg <blankenberg@users.noreply.github.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #266 from jmchilton/fix_tool_test_function_name Fix function names for dynamic tool test functions. Commit: 4aab4214ec4d0edeb117702908b45e6e55376dc1 https://github.com/galaxyproject/galaxy/commit/4aab4214ec4d0edeb117702908b45... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: A doc/source/releases/15.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- include approx. dates for 15.07 release Commit: 21368266cefff1d6e4d08d4fba85e56340bf60b7 https://github.com/galaxyproject/galaxy/commit/21368266cefff1d6e4d08d4fba85e... Author: Eric Rasche <esr@tamu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py Log Message: ----------- Implement XMFA Datatype This is used with Mauve/ProgressiveMauve. Additionally a bug is fixed in the Stockholm datatype which would have prevented proper sequence count autodetection. Commit: 5853ecc2bee335d9de04864ca94165d8c8961637 https://github.com/galaxyproject/galaxy/commit/5853ecc2bee335d9de04864ca9416... Author: Eric Rasche <esr@tamu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M lib/galaxy/datatypes/util/generic_util.py Log Message: ----------- Switch to egrep for searching Commit: e54e3f2d0177a17eb6862281a65b84d6bd8dd6e5 https://github.com/galaxyproject/galaxy/commit/e54e3f2d0177a17eb6862281a65b8... Author: Eric Rasche <esr@tamu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Remove debugging Commit: da63f0bef9f8ac1d350a4c613e5d896e4906d279 https://github.com/galaxyproject/galaxy/commit/da63f0bef9f8ac1d350a4c613e5d8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-workflow.js Log Message: ----------- Add RuntimeValue handling for new workflow editor form Commit: b8289d20bbf4da782fa13869e8ee252649e053a5 https://github.com/galaxyproject/galaxy/commit/b8289d20bbf4da782fa13869e8ee2... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_15.05' into dev Commit: 6d20093f7b085bd304dac5b1432c438f5192877d https://github.com/galaxyproject/galaxy/commit/6d20093f7b085bd304dac5b1432c4... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/style/less/ui/dataset-choice.less M static/maps/mvc/dataset/dataset-choice.js.map M static/scripts/mvc/dataset/dataset-choice.js M static/style/blue/base.css Log Message: ----------- UI, Dataset chooser: fix underscore templating and right,left border Commit: b5615d28a4436aa274ad3de92c384e53c8b00afd https://github.com/galaxyproject/galaxy/commit/b5615d28a4436aa274ad3de92c384... 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lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/wrappers.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/controllers/history.py A scripts/bootstrap_history.py M scripts/functional_tests.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map A static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js A 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test/unit/managers/test_HistoryManager.py M tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge remote-tracking branch 'origin' into bitbucket.dataset-choice Commit: 06630c974a6130dcb9b32d0634158c25adb43c45 https://github.com/galaxyproject/galaxy/commit/06630c974a6130dcb9b32d0634158... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py M scripts/functional_tests.py M test/functional/test_toolbox.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 Commit: 0763cab37a818a9252a01a7aa387b1fecc07d17e https://github.com/galaxyproject/galaxy/commit/0763cab37a818a9252a01a7aa387b... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py Log Message: ----------- Update the remainder of the python cleanup scripts Commit: 0ff5a050d5f463ceb1bd11b6e35500add7f8d9c6 https://github.com/galaxyproject/galaxy/commit/0ff5a050d5f463ceb1bd11b6e3550... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M scripts/cleanup_datasets/populate_uuid.py Log Message: ----------- Indentation fix Commit: 18c708981d6d96b67b428e6ee689f4564cf911c5 https://github.com/galaxyproject/galaxy/commit/18c708981d6d96b67b428e6ee689f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/util/generic_util.py Log Message: ----------- Merge pull request #270 from erasche/xmfa Mauve XMFA datatype Commit: fc423a9bf4a72207e78fa74214c6429961ae3c48 https://github.com/galaxyproject/galaxy/commit/fc423a9bf4a72207e78fa74214c64... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #268 from guerler/api_build_history_id Accept history id in tool model building api Commit: ce7dd615b6ea19af8fa4c34421088ba961e970fc https://github.com/galaxyproject/galaxy/commit/ce7dd615b6ea19af8fa4c34421088... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/style/less/ui/dataset-choice.less M static/maps/mvc/dataset/dataset-choice.js.map M static/scripts/mvc/dataset/dataset-choice.js M static/style/blue/base.css Log Message: ----------- Merge pull request #272 from carlfeberhard/bitbucket.dataset-choice Fixes to dataset chooser Commit: ab2238e53313db46634c7cbd97a19c4f22dd5cfc https://github.com/galaxyproject/galaxy/commit/ab2238e53313db46634c7cbd97a19... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M static/maps/mvc/form/form-data.js.map M static/scripts/mvc/form/form-data.js Log Message: ----------- Merge branch 'tool_form_000' into workflow_form_000 Conflicts: static/maps/mvc/form/form-data.js.map static/scripts/mvc/form/form-data.js Commit: 4fcd23c0f39f5e62b79c244e4d699963c6ef4cab https://github.com/galaxyproject/galaxy/commit/4fcd23c0f39f5e62b79c244e4d699... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-view.js Log Message: ----------- Extend checksum to account for collapsed input tool parameters Commit: 5691d345fa6df7af1235714efe6c8bcde82aeaab https://github.com/galaxyproject/galaxy/commit/5691d345fa6df7af1235714efe6c8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/style/less/ui/dataset-choice.less M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M static/maps/mvc/dataset/dataset-choice.js.map M static/scripts/mvc/dataset/dataset-choice.js M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 Conflicts: lib/galaxy/tools/__init__.py Commit: ea1b1e778a2ab62d75d6f3245e27f0163a01cb81 https://github.com/galaxyproject/galaxy/commit/ea1b1e778a2ab62d75d6f3245e27f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Explicitly specify runtime value in check state Commit: 45b7a625ae0f6d311ec8e4b3b83e6ca1bcf97806 https://github.com/galaxyproject/galaxy/commit/45b7a625ae0f6d311ec8e4b3b83e6... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js Log Message: ----------- Explicitly identify runtime value in handling process Commit: 77966eb5f13a57c0619cdeab3ae7480f71f78061 https://github.com/galaxyproject/galaxy/commit/77966eb5f13a57c0619cdeab3ae74... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-19 (Tue, 19 May 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix parsing of unvalidated values Commit: 0742b43cc7a03940285771aad2ab3719df803d02 https://github.com/galaxyproject/galaxy/commit/0742b43cc7a03940285771aad2ab3... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Change set at runtime icons Commit: 70fab5c31910e557e6151ff28f7c5d117d25e792 https://github.com/galaxyproject/galaxy/commit/70fab5c31910e557e6151ff28f7c5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Enable new workflow editor form by default Commit: 3217a209272fdfa18148675fc80bb1532ec2cb6b https://github.com/galaxyproject/galaxy/commit/3217a209272fdfa18148675fc80bb... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M static/maps/mvc/ui/ui-slider.js.map M static/scripts/mvc/ui/ui-slider.js Log Message: ----------- Update integer fields while editing Commit: 09b900d87371b84a788fa9af7ca0627db5b0b280 https://github.com/galaxyproject/galaxy/commit/09b900d87371b84a788fa9af7ca06... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix typos in comment. Commit: feae4e08a42f6cdc20df48003dce0e2492e1070d https://github.com/galaxyproject/galaxy/commit/feae4e08a42f6cdc20df48003dce0... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M static/welcome.html.sample Log Message: ----------- Add <title> to make page XHTML conformant. Commit: 4bf447702f771de390bc995d18c2e464e749ac68 https://github.com/galaxyproject/galaxy/commit/4bf447702f771de390bc995d18c2e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M templates/webapps/galaxy/dataset/errors.mako Log Message: ----------- Substitute "Galaxy Team" with "local Galaxy administrators" in dataset error report form. Commit: 2d03d7d530e8a4969203c2c02a81aa30eee1ce94 https://github.com/galaxyproject/galaxy/commit/2d03d7d530e8a4969203c2c02a81a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M templates/user/register.mako Log Message: ----------- Do not try to send subscription email if mailing_join_addr is empty. Prevent "subscribing to the mailing list has failed." error. Commit: 6b2f01a5cad91697683210ee82fa06277595fb73 https://github.com/galaxyproject/galaxy/commit/6b2f01a5cad91697683210ee82fa0... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Explain how to remove the mailing list subscription option from the user registration form. Commit: 00eb96923f7edb6947eb3e5b1ec3dd4783887e49 https://github.com/galaxyproject/galaxy/commit/00eb96923f7edb6947eb3e5b1ec3d... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M scripts/cleanup_datasets/populate_uuid.py Log Message: ----------- Add a missing period in populate_uuid.py Commit: e1c4a512740ae26b267ff4bade92132825c9a14e https://github.com/galaxyproject/galaxy/commit/e1c4a512740ae26b267ff4bade921... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix edam format on BAM. Commit: 4228d32d35cf7f1a1aa81085b43b160d6bdf9ba2 https://github.com/galaxyproject/galaxy/commit/4228d32d35cf7f1a1aa81085b43b1... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add edam_format(s) to input and output descriptions in the API. Commit: 27a1dc4f5e99160cabf8c244d353dcedcec1bb6f https://github.com/galaxyproject/galaxy/commit/27a1dc4f5e99160cabf8c244d353d... Author: Daniel Blankenberg <blankenberg@users.noreply.github.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/managers/workflows.py M static/welcome.html.sample M templates/user/register.mako M templates/webapps/galaxy/dataset/errors.mako Log Message: ----------- Merge pull request #277 from nsoranzo/dev Mixed fixes, again. Commit: 7f12d33b678fb0c0e92e2190a6b19ba957e8c0db https://github.com/galaxyproject/galaxy/commit/7f12d33b678fb0c0e92e2190a6b19... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add endpoint /api/datatypes/edam_formats... ... which maps Galaxy extensions to EDAM formats. Commit: 03906fde796584a65c3abf42dbb6e3a625cfcb8f https://github.com/galaxyproject/galaxy/commit/03906fde796584a65c3abf42dbb6e... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6 from jmchilton/edam_api Add EDAM Info to Tool's API. Commit: 2cc5ea12255b3f2e30b4b4fe4afd07f649b0931b https://github.com/galaxyproject/galaxy/commit/2cc5ea12255b3f2e30b4b4fe4afd0... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/grunt-tasks/style.js M static/style/blue/base.css Log Message: ----------- Client style: fix sprite paths by using hardcoded path in task Commit: 1a39b6aa791edf3d6f0cae7c14a26bf3200863df https://github.com/galaxyproject/galaxy/commit/1a39b6aa791edf3d6f0cae7c14a26... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M lib/galaxy/tools/test.py A test/functional/tools/boolean_conditional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.xml M tool-data/shared/gbrowse/gbrowse_build_sites.txt M tools/data_source/fly_modencode.xml M tools/data_source/worm_modencode.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.05' into dev Commit: 97783c6b2352c7ae43ec1e36b4c3b2f8e67da2da https://github.com/galaxyproject/galaxy/commit/97783c6b2352c7ae43ec1e36b4c3b... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/grunt-tasks/style.js M static/style/blue/base.css Log Message: ----------- Merge pull request #279 from carlfeberhard/fix.toggle-png Client style: fix sprite paths by using hardcoded path in task Commit: 2257bdc6651d9bd48b8b8658e695acc77edc64e8 https://github.com/galaxyproject/galaxy/commit/2257bdc6651d9bd48b8b8658e695a... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- UI, Tool form: remove select2 search.blur handler that re-focuses its search and prevents focusing on other elements Commit: d76af9bb7e9ef740897d438014d97870364beaef https://github.com/galaxyproject/galaxy/commit/d76af9bb7e9ef740897d438014d97... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #280 from carlfeberhard/fix.select2-search-focus UI, Tool form: remove select2 search.blur handler that re-focuses its… Commit: 44739c645758070f0366ce35f83a6bd8f1e6be40 https://github.com/galaxyproject/galaxy/commit/44739c645758070f0366ce35f83a6... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-20 (Wed, 20 May 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/grunt-tasks/style.js M config/galaxy.ini.sample M lib/galaxy/managers/workflows.py M lib/galaxy/tools/test.py M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M static/welcome.html.sample M templates/user/register.mako M templates/webapps/galaxy/dataset/errors.mako A test/functional/tools/boolean_conditional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.xml M tool-data/shared/gbrowse/gbrowse_build_sites.txt M tools/data_source/fly_modencode.xml M tools/data_source/worm_modencode.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 Commit: 5e97f5a1ae47a98226ca48714e90d23b839c8872 https://github.com/galaxyproject/galaxy/commit/5e97f5a1ae47a98226ca48714e90d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-05-21 (Thu, 21 May 2015) Changed paths: M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Allow external display applications optional access to files within a datasets extra_files_path by setting allow_extra_files_access="True" within the parameter. Commit: be35618652cbb153d9d102069a066e319df82a9f https://github.com/galaxyproject/galaxy/commit/be35618652cbb153d9d102069a066... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-22 (Fri, 22 May 2015) Changed paths: M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #284 from blankenberg/display-apps-dev Allow external display applications optional access to files within a dataset's extra_files_path... Commit: bb88dcb059a84c7475ac437cb8fa08080c12771f https://github.com/galaxyproject/galaxy/commit/bb88dcb059a84c7475ac437cb8fa0... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-22 (Fri, 22 May 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make the data manager JSON datatype's class more specific. Use Json base class instead of text - fixes data manager type for PR #80. Commit: 9f853aac45675e434b63e306e5e9dcb5edc2ef84 https://github.com/galaxyproject/galaxy/commit/9f853aac45675e434b63e306e5e9d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-05-22 (Fri, 22 May 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #285 from jmchilton/data_manager_type_more_specific Make the data manager JSON datatype's class more specific. Commit: 887ebcd4a0ca5dd36e42ecad3f7610ed9e45a94f https://github.com/galaxyproject/galaxy/commit/887ebcd4a0ca5dd36e42ecad3f761... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-22 (Fri, 22 May 2015) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sequence.py Log Message: ----------- More tweaks to edam mappings. Commit: 3946ff50bb205e5aabee9e0e8026ae0b9fa4de38 https://github.com/galaxyproject/galaxy/commit/3946ff50bb205e5aabee9e0e8026a... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-22 (Fri, 22 May 2015) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/xml.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py A scripts/edam_mapping.py Log Message: ----------- Merge pull request #80 from erasche/jbrowse-ie Add EDAM IDs to datatypes Commit: d01c108375f30692bbf7f527fc8572fa6ef2b8ec https://github.com/galaxyproject/galaxy/commit/d01c108375f30692bbf7f527fc857... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-24 (Sun, 24 May 2015) Changed paths: M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/utils/utils.js M static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/galaxy.workflows.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/galaxy.workflows.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/utils/utils.js M templates/webapps/galaxy/tool_form.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Reduce form mako to json generation, load form just once Commit: 229577b5c2b38619d070aa444ded5cd4494ed21d https://github.com/galaxyproject/galaxy/commit/229577b5c2b38619d070aa444ded5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-24 (Sun, 24 May 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/xml.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A scripts/edam_mapping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 Commit: 3536ff923cf736b2dbefab3e04b7fcd79b909d22 https://github.com/galaxyproject/galaxy/commit/3536ff923cf736b2dbefab3e04b7f... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Allow the condor job runner to respect the embed_metadata_in_job parameter Commit: 6cc83bf0b90157318d3321a2789c0e8b397d2415 https://github.com/galaxyproject/galaxy/commit/6cc83bf0b90157318d3321a2789c0... Author: dpryan79 <dpryan79@gmail.com> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Ensure that asbool is imported Commit: cc1f56a118011b841b2f08d74b0ab0a7a6e1ab93 https://github.com/galaxyproject/galaxy/commit/cc1f56a118011b841b2f08d74b0ab... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Fix load order of require and d3 Commit: 3c12d9073045cb80cf9e24b9337df0aada03db2f https://github.com/galaxyproject/galaxy/commit/3c12d9073045cb80cf9e24b9337df... Author: carlfeberhard <carlfeberhard@users.noreply.github.com> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Merge pull request #290 from guerler/charts_000 Fix load order of require and d3 Commit: e76e8229eed9e158db35e8be679dcca9206a39b9 https://github.com/galaxyproject/galaxy/commit/e76e8229eed9e158db35e8be679dc... Author: guerler <aysam.guerler@gmail.com> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Trackster: Fix load order of require and d3 Commit: 0b825676e7f7f5804e3b3ed64c0d31302ea75c2d https://github.com/galaxyproject/galaxy/commit/0b825676e7f7f5804e3b3ed64c0d3... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #291 from guerler/trackster_000 Trackster: Fix load order of require and d3 Commit: 91bf1d37db59bc69404e9831893bd97ae7d378f3 https://github.com/galaxyproject/galaxy/commit/91bf1d37db59bc69404e9831893bd... Author: Dave B <dave@bx.psu.edu> Date: 2015-05-27 (Wed, 27 May 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for handling of unix permissions in .zip files. Commit: 5949abb2ce46016a92fabf86d9715e657790cc9e https://github.com/galaxyproject/galaxy/commit/5949abb2ce46016a92fabf86d9715... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-28 (Thu, 28 May 2015) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #289 from dpryan79/condor_fixes Condor fixes Commit: aa857fcdbd6c8654143af22dc67c769199d4460a https://github.com/galaxyproject/galaxy/commit/aa857fcdbd6c8654143af22dc67c7... Author: Renato Alves <rjalves@igc.gulbenkian.pt> Date: 2015-05-28 (Thu, 28 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py Log Message: ----------- Remove bad HTML tags from login template Commit: 253493c3937c67fee8f825dde3c1c24b0e47f154 https://github.com/galaxyproject/galaxy/commit/253493c3937c67fee8f825dde3c1c... Author: Renato Alves <rjalves@igc.gulbenkian.pt> Date: 2015-05-29 (Fri, 29 May 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Allow passing advanced options to the LDAP connection Useful to configure the connection if ldap.conf and/or ldaprc cannot be used auth_conf.xml.sample includes an example to connect to LDAPS using self-signed certificates. Commit: 0a0890a040a2a751fa6748e46fe85cc21f83ffc4 https://github.com/galaxyproject/galaxy/commit/0a0890a040a2a751fa6748e46fe85... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-29 (Fri, 29 May 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py Log Message: ----------- Merge pull request #294 from Unode/html_validation Remove bad HTML tags from login template Commit: ef74d06904142641ac7b41760f87d2956474cf2b https://github.com/galaxyproject/galaxy/commit/ef74d06904142641ac7b41760f87d... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M CONTRIBUTING.md A doc/source/project/organization.rst Log Message: ----------- Implement policies for commmitters and pull requests. - State and clarfiy my (@jmchilton's) understanding of existing informal pull request policies. - Add a list of committers who should have "commit" access to the repository according to my understanding of the team meeting held on 5/28/2015. - Add language describing how the Galaxy project might manage commit access and project governance going forward in accordance with my understanding of the team meeting discussion. This fills in a lot of gaps left by informal policies and informal discussions and I am eager to see much discussion on each of these topics. Much of the language and structure is borrowed with heavy modification from the Django and Apache variants of these documents. Also - congrats to @nsoranzo, @erasche, and @bgruening who the team unanimously voted to grant commit access to. Commit: b59d1bdf71e184896b4e3fc016816139cead2f61 https://github.com/galaxyproject/galaxy/commit/b59d1bdf71e184896b4e3fc016816... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M CONTRIBUTING.md A doc/source/project/organization.rst Log Message: ----------- Merge branch 'organization' of https://github.com/jmchilton/galaxy into organization Commit: 73aa35b63c1599ad8314767fdf2a1d78b33c1f35 https://github.com/galaxyproject/galaxy/commit/73aa35b63c1599ad8314767fdf2a1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- A few minor tweaks to organization/contributing doc. Commit: de8c0b1fbbcda5ff926fb935e962bdadbfe5ee74 https://github.com/galaxyproject/galaxy/commit/de8c0b1fbbcda5ff926fb935e962b... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M CONTRIBUTING.md M config/datatypes_conf.xml.sample M config/plugins/visualizations/charts/templates/charts.mako M doc/source/project/organization.rst M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py A scripts/edam_mapping.py M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #8 from dannon/organization Organization Commit: e585ba62d86f6899c89a88ef81e0bd4a5418460f https://github.com/galaxyproject/galaxy/commit/e585ba62d86f6899c89a88ef81e0b... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- add missing dash Commit: ac938798233cffbb9f596cf5d49b6c855687f6cd https://github.com/galaxyproject/galaxy/commit/ac938798233cffbb9f596cf5d49b6... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- typo fix Commit: faf8f31dfaa1875933ad815a67a6c80f780ee6fa https://github.com/galaxyproject/galaxy/commit/faf8f31dfaa1875933ad815a67a6c... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-30 (Sat, 30 May 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- capitalize and sentencisize Commit: c572b56670373b57b1c5138a7792cda11fa04e71 https://github.com/galaxyproject/galaxy/commit/c572b56670373b57b1c5138a7792c... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2015-05-31 (Sun, 31 May 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Fix typo Commit: b4cf6dba76ed7587420fdf1df9b05bf59d94c75e https://github.com/galaxyproject/galaxy/commit/b4cf6dba76ed7587420fdf1df9b05... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-05-31 (Sun, 31 May 2015) Changed paths: M lib/galaxy/datatypes/checkers.py Log Message: ----------- gzip is imported twice Remove one redundant gzip import. Commit: 5974167407115fb5f4e3979d64ded50f9a46e2a3 https://github.com/galaxyproject/galaxy/commit/5974167407115fb5f4e3979d64ded... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-05-31 (Sun, 31 May 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py Log Message: ----------- export ENV vars from all repositories This will export ENV vars from all given repository dependencies and not only the last one. Only taking the last one seems arbitrary to me and it makes the tool_dependencies.xml files a bit easier to write. Commit: 686ac9913a89ebac8052d323a4343caf3303e27f https://github.com/galaxyproject/galaxy/commit/686ac9913a89ebac8052d323a4343... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-05-31 (Sun, 31 May 2015) Changed paths: M lib/galaxy/datatypes/checkers.py Log Message: ----------- Merge pull request #296 from bgruening/patch-2 gzip is imported twice Commit: 608c827559216227d262bcb9b0c509efcd4d2655 https://github.com/galaxyproject/galaxy/commit/608c827559216227d262bcb9b0c50... Author: John Chilton <jmchilton@gmail.com> Date: 2015-05-31 (Sun, 31 May 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #287 from Unode/custom_ldap_options Allow setting connection options for LDAP authentication Commit: 30872e72bb635da6542ef5a4ea3e2a46d4f12ac3 https://github.com/galaxyproject/galaxy/commit/30872e72bb635da6542ef5a4ea3e2... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M config/auth_conf.xml.sample Log Message: ----------- Improve auth_conf.xml.sample documentation. Commit: bf9f8cd28366c18f77301dbb63a4f13e10476556 https://github.com/galaxyproject/galaxy/commit/bf9f8cd28366c18f77301dbb63a4f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh Log Message: ----------- Exclude curly braces from API-key to fix toolshed bootstrapping. Commit: a86ee81c28e73e20c3575e0b398931289a3740aa https://github.com/galaxyproject/galaxy/commit/a86ee81c28e73e20c3575e0b39893... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- update and clarify descriptions, cleanup admin menu Commit: 6d08accfa426dd7a27a2e664f5af393c4621bce5 https://github.com/galaxyproject/galaxy/commit/6d08accfa426dd7a27a2e664f5af3... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- fix minor typos, add wiki link Commit: d4aa8bbd91904aa2a0c82fff5afe5af4cce3b01e https://github.com/galaxyproject/galaxy/commit/d4aa8bbd91904aa2a0c82fff5afe5... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- open links in _blank Commit: 8e68ea23b6151bcd3d4eeb4b2573df115538638a https://github.com/galaxyproject/galaxy/commit/8e68ea23b6151bcd3d4eeb4b2573d... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- fix minor typo Commit: dbe91aa31614351ac85d99acae390d2df2dc4609 https://github.com/galaxyproject/galaxy/commit/dbe91aa31614351ac85d99acae390... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- reorder; add links; show help only if option is present Commit: 0369161eea9ea8dc4b3fe5f4f836e058998e73a1 https://github.com/galaxyproject/galaxy/commit/0369161eea9ea8dc4b3fe5f4f836e... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_per_tool.mako Log Message: ----------- Added the ability to sort by id and job number on the jobs per tool page Commit: d07db2583b6ade81d5dc44db6eea55b71e945240 https://github.com/galaxyproject/galaxy/commit/d07db2583b6ade81d5dc44db6eea5... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Remove paragraph describing license from organization.rst. Per-request by @jxtx. Commit: 0fe60d49ba3cbf2dc54cb7b045a17f732268c811 https://github.com/galaxyproject/galaxy/commit/0fe60d49ba3cbf2dc54cb7b045a17... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Adjust CONTRIBUTING.md security language per suggestion of @martenson. Commit: 8c3fdaa8747f3d7b5b6bb358f09b8f4935e6460e https://github.com/galaxyproject/galaxy/commit/8c3fdaa8747f3d7b5b6bb358f09b8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M lib/galaxy/tools/test.py M lib/galaxy/web/base/controller.py M static/maps/mvc/form/form-data.js.map M static/scripts/mvc/form/form-data.js M test/api/test_histories.py Log Message: ----------- Merge 15.05 to dev Commit: c6a6eeda36d015ddc2693f1cc249db28ddebfa01 https://github.com/galaxyproject/galaxy/commit/c6a6eeda36d015ddc2693f1cc249d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update organization.rst Dan --> Daniel Commit: 3316b25432453e5da2ba8f8b35e42be9c215c86c https://github.com/galaxyproject/galaxy/commit/3316b25432453e5da2ba8f8b35e42... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small clarification to CONTRIBUTING.md recommended by @nsoranzo. https://github.com/galaxyproject/galaxy/pull/295#discussion_r31454497. Commit: 0dd99b13f9dbca0668aa77d810c8597da2a3fc35 https://github.com/galaxyproject/galaxy/commit/0dd99b13f9dbca0668aa77d810c85... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M templates/webapps/reports/jobs_per_tool.mako Log Message: ----------- Removed hyperlink underline for unsorted columns in jobs per tool in reports page Commit: 04862bdc9a41c44bbec021d03c94fece30942b91 https://github.com/galaxyproject/galaxy/commit/04862bdc9a41c44bbec021d03c94f... 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display_applications/igv/bam.xml M display_applications/igv/gff.xml A display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml A doc/source/_static/style.css A doc/source/_templates/layout.html M doc/source/index.rst A doc/source/releases/13.01_announce.rst A doc/source/releases/13.02_announce.rst A doc/source/releases/13.04_announce.rst A doc/source/releases/13.06_announce.rst A doc/source/releases/13.08_announce.rst A doc/source/releases/13.11_announce.rst A doc/source/releases/14.02_announce.rst A doc/source/releases/14.04_announce.rst A doc/source/releases/14.06_announce.rst A doc/source/releases/14.08_announce.rst A doc/source/releases/14.10_announce.rst A doc/source/releases/15.01_announce.rst A doc/source/releases/15.03_announce.rst A doc/source/releases/15.05.rst A doc/source/releases/15.05_announce.rst A doc/source/releases/_header.rst A doc/source/releases/_thanks.rst A doc/source/releases/index.rst A doc/source/releases/older_releases.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/context.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/wrappers.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py A scripts/bootstrap_history.py A scripts/edam_mapping.py M scripts/functional_tests.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/ui/ui-list.js.map M 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test/api/test_tools.py M test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/tools/boolean_conditional.xml A test/functional/tools/library_data.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.xml M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/unit/managers/test_HistoryManager.py M tool-data/shared/gbrowse/gbrowse_build_sites.txt M tools/data_source/bed_convert.xml M tools/data_source/fly_modencode.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/worm_modencode.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 60f43733ee9771081be3d031be26169259782ece https://github.com/galaxyproject/galaxy/commit/60f43733ee9771081be3d031be261... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-01 (Mon, 01 Jun 2015) Changed paths: M config/auth_conf.xml.sample Log Message: ----------- Merge pull request #299 from nsoranzo/dev Improve auth_conf.xml.sample documentation. Commit: e56b2a3433fe1ea74dd5e2400dd347c070a6e37e https://github.com/galaxyproject/galaxy/commit/e56b2a3433fe1ea74dd5e2400dd34... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py Log Message: ----------- Merge pull request #274 from dpryan79/dev Add usage information to python cleanup scripts Commit: 4268a7ee57964491b1e458458b6a257db6e206d0 https://github.com/galaxyproject/galaxy/commit/4268a7ee57964491b1e458458b6a2... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M test/unit/tool_shed_unit_tests/test_td_common_util.py Log Message: ----------- fix unit test Commit: 4eea86c8b77cc1c91d2274bd3fb97a4b4846d3bb https://github.com/galaxyproject/galaxy/commit/4eea86c8b77cc1c91d2274bd3fb97... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh Log Message: ----------- Merge pull request #301 from mvdbeek/bootstrapping-fix Exclude curly braces from API-key to fix toolshed bootstrapping. Commit: ac4740f91dfd305f88e313c1b3e7fca02b088d70 https://github.com/galaxyproject/galaxy/commit/ac4740f91dfd305f88e313c1b3e7f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-02 (Tue, 02 Jun 2015) Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 151151c06589a2fbe588428899291bd8a60af709 https://github.com/galaxyproject/galaxy/commit/151151c06589a2fbe588428899291... Author: Dave B <dave@bx.psu.edu> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Fix repeated error messages with identical text. Previously, one would see the same error message, e.g. with invalid tool dependencies, repeated approximately X * Y times, where X is approximately 6, and Y is the number of <action> tags in a tool dependency definition. This commit ameliorates that issue somewhat. Commit: 30dd12249bf815eb752a9d8a1d197510a5733148 https://github.com/galaxyproject/galaxy/commit/30dd12249bf815eb752a9d8a1d197... Author: Dave B <dave@bx.psu.edu> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Fix typo. Commit: e47ccbc56dd849b7a54aaf3c19b3b53062b1f108 https://github.com/galaxyproject/galaxy/commit/e47ccbc56dd849b7a54aaf3c19b3b... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Added whitespace to pass Travis CI Commit: 6ffd3c3c2d77396dd8ef66f83b7ce2dc6d6f6314 https://github.com/galaxyproject/galaxy/commit/6ffd3c3c2d77396dd8ef66f83b7ce... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Deleted tab to pass Travis CI Commit: db105dbefae212a4b050a8301372b220a8a62e4c https://github.com/galaxyproject/galaxy/commit/db105dbefae212a4b050a8301372b... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/index.mako Log Message: ----------- Added a Errors per tool page to the report webpage Commit: c69945ff9526f4146f2559165db825d9d24bd45d https://github.com/galaxyproject/galaxy/commit/c69945ff9526f4146f2559165db82... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/utils/utils.js M config/galaxy.ini.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/galaxy.workflows.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/galaxy.workflows.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/utils/utils.js M templates/webapps/galaxy/tool_form.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Merge new workflow editor. Commit: f0b4f1c81ede5b47e010cf30de3cf8918e22e38a https://github.com/galaxyproject/galaxy/commit/f0b4f1c81ede5b47e010cf30de3cf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-02 (Tue, 02 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/utils/utils.js M config/galaxy.ini.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/galaxy.workflows.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/galaxy.workflows.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/utils/utils.js M templates/webapps/galaxy/tool_form.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Merge branch 'guerler-workflow_form_000' into dev Commit: 884e824d72b5a41afadf043d17b56cfb66945c2a https://github.com/galaxyproject/galaxy/commit/884e824d72b5a41afadf043d17b56... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-03 (Wed, 03 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M tools/data_source/upload.xml M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'vavrusa/table-datatype' into dev. Conflicts: lib/galaxy/datatypes/tabular.py Commit: 508194f22365cc568064f897de25d4a73163d8c6 https://github.com/galaxyproject/galaxy/commit/508194f22365cc568064f897de25d... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-03 (Wed, 03 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix sample datatype definition for CSV. For me it seems like the viz plugins only detect the datatype if the plugin datatype (e.g. ``tabular.CSV``) is explicitly instantiated by some extension directly. In your sample config you have ``subclass="True"`` so ``tabular.CSV`` wasn't working. This is probably a bug with the datatype code - but nonetheless I think dropping subclass from the sample is an okay workaround - because it does seem to be a direct mapping. Commit: f65da5f2c7615810d1857ab8d844420ec51d6bf3 https://github.com/galaxyproject/galaxy/commit/f65da5f2c7615810d1857ab8d8444... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-03 (Wed, 03 Jun 2015) Changed paths: A doc/source/releases/15.07_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #269 from martenson/future-release-notes include approx. dates for 15.07 release Commit: b985851f8a8e546124606f925fee793838cea7d3 https://github.com/galaxyproject/galaxy/commit/b985851f8a8e546124606f925fee7... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-03 (Wed, 03 Jun 2015) Changed paths: M templates/webapps/reports/jobs_per_tool.mako Log Message: ----------- Fixed extra space in jobs per tool page, underlined both titles Commit: 43166664f24b077a71772997e94f6a6751822b47 https://github.com/galaxyproject/galaxy/commit/43166664f24b077a71772997e94f6... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-03 (Wed, 03 Jun 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M test/unit/tool_shed_unit_tests/test_td_common_util.py Log Message: ----------- Merge pull request #297 from bgruening/patch-3 export ENV vars from all dependend repositories Commit: eb08088bcb23e37b19576dc7c7a3ca0989d0b1e5 https://github.com/galaxyproject/galaxy/commit/eb08088bcb23e37b19576dc7c7a3c... Author: Daniel Bouchard <dbouchard@corefacility.ca> Date: 2015-06-03 (Wed, 03 Jun 2015) Changed paths: A templates/webapps/reports/jobs_errors_per_tool.mako Log Message: ----------- Add errors per job mako Commit: a00461eaf61bdeeea0c42b8098ae5e6cfbe79694 https://github.com/galaxyproject/galaxy/commit/a00461eaf61bdeeea0c42b8098ae5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow.js M config/galaxy.ini.sample R static/maps/galaxy.workflow_editor.canvas.js.map R static/maps/galaxy.workflows.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map A static/maps/mvc/workflow/workflow-manager.js.map A static/maps/mvc/workflow/workflow.js.map R static/scripts/galaxy.workflow_editor.canvas.js R static/scripts/galaxy.workflows.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js A static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Merge workflow_001 Commit: 14b7cd6821873e1351f51db1ef653dab5b60e374 https://github.com/galaxyproject/galaxy/commit/14b7cd6821873e1351f51db1ef653... Author: Marek Vavruša <marek@vavrusa.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M .gitignore M .travis.yml M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/utils/utils.js A client/galaxy/style/blue_colors.ini A client/galaxy/style/less/autocomplete_tagging.less A client/galaxy/style/less/base.less A client/galaxy/style/less/bootstrap.less A client/galaxy/style/less/bootstrap/alerts.less A client/galaxy/style/less/bootstrap/badges.less A client/galaxy/style/less/bootstrap/bootstrap.less A client/galaxy/style/less/bootstrap/breadcrumbs.less A client/galaxy/style/less/bootstrap/button-groups.less A 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client/grunt-tasks/install-libs.js A client/grunt-tasks/scripts.js A client/grunt-tasks/style.js M client/package.json M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rsa.js A config/plugins/interactive_environments/rstudio/static/js/rstudio.js A config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/README.txt M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/circster/config/circster.xml A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/tool_conf.xml.sample M display_applications/igv/bam.xml M display_applications/igv/gff.xml A display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml A doc/source/_static/style.css A doc/source/_templates/layout.html M doc/source/index.rst A doc/source/releases/13.01_announce.rst A doc/source/releases/13.02_announce.rst A doc/source/releases/13.04_announce.rst A doc/source/releases/13.06_announce.rst A doc/source/releases/13.08_announce.rst A doc/source/releases/13.11_announce.rst A doc/source/releases/14.02_announce.rst A doc/source/releases/14.04_announce.rst A doc/source/releases/14.06_announce.rst A doc/source/releases/14.08_announce.rst A doc/source/releases/14.10_announce.rst A doc/source/releases/15.01_announce.rst A doc/source/releases/15.03_announce.rst A 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A test/qunit/tests/list-of-pairs-collection-creator.html A test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js R test/qunit/tests/paired-collection-creator.html R test/qunit/tests/paired-collection-creator.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/utility.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tool-data/shared/gbrowse/gbrowse_build_sites.txt M tools/data_source/bed_convert.xml M tools/data_source/fly_modencode.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/worm_modencode.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge pull request #1 from jmchilton/table Updates for PR #191 (checked the 508194f) Commit: 0dfa1c96893408c94541f6d501b7c34ea24d3ddc https://github.com/galaxyproject/galaxy/commit/0dfa1c96893408c94541f6d501b7c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M tools/data_source/upload.xml M tools/stats/gsummary.py Log Message: ----------- Merge pull request #191 from vavrusa/table-datatype [WIP] CSV datatype Commit: 9c89d4387519629938799bb2a6a2fd88e7d718af https://github.com/galaxyproject/galaxy/commit/9c89d4387519629938799bb2a6a2f... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M templates/export_base.mako M templates/form.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/sharing_base.mako Log Message: ----------- fix shared mako templates that would not work with TS by also looking for 'app' within context when 'webapp' is not present and defaulting to 'galaxy' afterwards Commit: 6493f2713151b47bd2c1809ad9bb32a6a2ebee45 https://github.com/galaxyproject/galaxy/commit/6493f2713151b47bd2c1809ad9bb3... Author: Dave B <dave@bx.psu.edu> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Preserve unix permissions, if any, in .zip files. Commit: 10c3f41e68836076e58946d4452f83fc0b446aed https://github.com/galaxyproject/galaxy/commit/10c3f41e68836076e58946d4452f8... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M templates/export_base.mako M templates/form.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/sharing_base.mako Log Message: ----------- Merge pull request #307 from martenson/fix-mako-webapp fix shared mako templates that would not work properly with TS Commit: 0bfd30a1a9d585a228ad962645421139ccc303eb https://github.com/galaxyproject/galaxy/commit/0bfd30a1a9d585a228ad962645421... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move global add_node function to workflow class Commit: fb945e06f6ae98bbf48815eb0d94289b977cf5a0 https://github.com/galaxyproject/galaxy/commit/fb945e06f6ae98bbf48815eb0d942... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M static/maps/mvc/workflow/workflow-manager.js.map Log Message: ----------- Remove initial tabs from workflow module Commit: 5f5336eb07107b2f6666ef916242ec8e9404e1ca https://github.com/galaxyproject/galaxy/commit/5f5336eb07107b2f6666ef916242e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map Log Message: ----------- Remove initial tabs from second workflow module Commit: 613089e75f29597c96a06a21a686375eda04ab94 https://github.com/galaxyproject/galaxy/commit/613089e75f29597c96a06a21a6863... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map Log Message: ----------- Re-insert indentation Commit: 62de13d0756f25c6c91eba863e2b89ab84b7899f https://github.com/galaxyproject/galaxy/commit/62de13d0756f25c6c91eba863e2b8... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Replace global by local functions and remove unused function Commit: 8d95a37515077ff0177a22b6d50250b64dccb02e https://github.com/galaxyproject/galaxy/commit/8d95a37515077ff0177a22b6d5025... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Merge pull request #302 from martenson/update-admin-page update and clarify admin menu Commit: 410fa30bb5f3c80c9cd8f8c3bb939e769fce74da https://github.com/galaxyproject/galaxy/commit/410fa30bb5f3c80c9cd8f8c3bb939... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix json sniffer for large files. Based on bug report by Keith Suderman http://osdir.com/ml/general/2015-06/msg04992.html and fix idea from Keith and Peter Cock. Commit: cc10ff90f4e677f389015f439d254801b9d5d310 https://github.com/galaxyproject/galaxy/commit/cc10ff90f4e677f389015f439d254... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #309 from jmchilton/json_type_fix Fix json sniffer for large files. Commit: 4872c9a895b9062f2ea2fe03a68d0f3821f62615 https://github.com/galaxyproject/galaxy/commit/4872c9a895b9062f2ea2fe03a68d0... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflow_editor.canvas.js Log Message: ----------- Modify galaxy.workflow_editor.canvas.js verbage for output collections. Commit: 620accaaad7c7d3244bc600298de2fa9340cc193 https://github.com/galaxyproject/galaxy/commit/620accaaad7c7d3244bc600298de2... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/galaxy.workflow_editor.canvas.js.map M static/scripts/galaxy.workflow_editor.canvas.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Extend workflow editor to allow output collections in tools. Mostly test cases - because I guess I could have sworn it was going to be harder than this. Commit: 20e4c3d6e47cec6f38a28846323950e9b9ef6994 https://github.com/galaxyproject/galaxy/commit/20e4c3d6e47cec6f38a2884632395... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Refine procedures related to governance changes... ... based on comments made by @blankenberg. Commit: 430f52755a425ca033ccc27d82856aac4d91c267 https://github.com/galaxyproject/galaxy/commit/430f52755a425ca033ccc27d82856... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-04 (Thu, 04 Jun 2015) Changed paths: M .gitignore M .travis.yml M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M 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tools/stats/gsummary.py M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into table-flake8 Commit: 25eb5d758ab77bab951d55f4e81a4b50c6e43768 https://github.com/galaxyproject/galaxy/commit/25eb5d758ab77bab951d55f4e81a4... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M lib/galaxy/visualization/plugins/resource_parser.py Log Message: ----------- Fixed a typo error in visualization/plugins/resource_parser.py Commit: b37f70063397268f179f54c1a3782a125c183d6c https://github.com/galaxyproject/galaxy/commit/b37f70063397268f179f54c1a3782... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M lib/galaxy/visualization/plugins/resource_parser.py Log Message: ----------- Merge pull request #312 from remimarenco/typoFix_ResourceParser Fixed a typo error in visualization/plugins/resource_parser.py Commit: e30ce642e75db39accf76aff12be34c8f4c4c6eb https://github.com/galaxyproject/galaxy/commit/e30ce642e75db39accf76aff12be3... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- More PEP-8 fixes for tabular.py. Commit: 960a9f77e44332008c836e94aa81f9483ace6103 https://github.com/galaxyproject/galaxy/commit/960a9f77e44332008c836e94aa81f... 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static/style/src/less/trackster.less R static/style/src/less/ui.less R static/style/src/less/ui/dataset-choice.less R static/style/src/less/ui/icon-btn.less R static/style/src/less/ui/pagination.less R static/style/src/less/ui/paired-collection-creator.less R static/style/src/less/ui/peek-column-selector.less R static/style/src/less/ui/search-input.less R static/style/src/less/upload.less R static/style/src/source_material/circle.py R static/style/src/source_material/galaxy_icons.svg R static/style/src/source_material/galaxy_spinner.fla M static/welcome.html.sample M templates/export_base.mako M templates/form.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/sharing_base.mako M templates/user/register.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M 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tools/stats/gsummary.py M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge pull request #1 from jmchilton/table-flake8 Merge latest dev, resolve conflicts. Commit: 90fe4320b8d6fb7f7abb31315adddf902198a796 https://github.com/galaxyproject/galaxy/commit/90fe4320b8d6fb7f7abb31315addd... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Update language in CONTIRBUTING.md... .. clarifying that people must be added or removed from the committers list one at a time. Also improve the language in that section of the document. Commit: 226b05db8a79897e7837ab8e129cbd7374ed782c https://github.com/galaxyproject/galaxy/commit/226b05db8a79897e7837ab8e129cb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Update galaxy-lab to primary mailing list in CONTRIBUTING Commit: 0e584eb4e7f56e4eea0338be05b2e2214438f996 https://github.com/galaxyproject/galaxy/commit/0e584eb4e7f56e4eea0338be05b2e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M static/welcome.rst Log Message: ----------- Update galaxy-dev list to non-alias in welcome.rst Commit: 20cfa44e48fc18874a9a09deca93a3958ff7c392 https://github.com/galaxyproject/galaxy/commit/20cfa44e48fc18874a9a09deca93a... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #204 from bgruening/flake8_fixes flake8 fixes for the tabular datatypes Commit: 5f6f052d98c0962b8ba5948331c7e8d1cfc8a498 https://github.com/galaxyproject/galaxy/commit/5f6f052d98c0962b8ba5948331c7e... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-05 (Fri, 05 Jun 2015) Changed paths: M CONTRIBUTING.md M static/welcome.rst Log Message: ----------- Merge pull request #316 from dannon/update_list_aliases Update mailing lists to use lists.galaxyproject.org addresses Commit: 8f23930d857a2e5ab0fbb830e08f3e7392ac094c https://github.com/galaxyproject/galaxy/commit/8f23930d857a2e5ab0fbb830e08f3... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-06 (Sat, 06 Jun 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add new argument to inject volumes in docker_cmd() and launch() Commit: bc9f707c0ce2619021cdc3e3d4f67b59e4824b14 https://github.com/galaxyproject/galaxy/commit/bc9f707c0ce2619021cdc3e3d4f67... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-06 (Sat, 06 Jun 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add volume() function to the interactive environment. This will enable us to construct volumes from make files. Commit: d22f1fb96db82e3584e62f12df8acc9725576596 https://github.com/galaxyproject/galaxy/commit/d22f1fb96db82e3584e62f12df8ac... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-06 (Sat, 06 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-objects.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow-manager.js.map A static/maps/mvc/workflow/workflow-objects.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-objects.js M static/scripts/mvc/workflow/workflow.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Replace global js variables by shared object module Commit: 0b07c48c6f7de3c492d95df318ee1162bfb38984 https://github.com/galaxyproject/galaxy/commit/0b07c48c6f7de3c492d95df318ee1... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-07 (Sun, 07 Jun 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for generating metadata on toolshed tools, under certain conditions. One known condition is when a boolean parameter is declared, but has no value set. Commit: ceeb9efd5fd222ec4bc56a21bf3545af801ccdad https://github.com/galaxyproject/galaxy/commit/ceeb9efd5fd222ec4bc56a21bf354... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-07 (Sun, 07 Jun 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #318 from bgruening/ie_volumes_injection add new argument to inject volumes in docker_cmd() and launch() Commit: c636e2e239e5e7ddfe0c264fc3b44f7a8a3058ad https://github.com/galaxyproject/galaxy/commit/c636e2e239e5e7ddfe0c264fc3b44... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-07 (Sun, 07 Jun 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #319 from blankenberg/toolshed_metadata_generation_fix Fix for generating metadata on toolshed tools tests, under certain conditions. Commit: 0652e99f9e2582725b8d9de42ec78f7839bf3671 https://github.com/galaxyproject/galaxy/commit/0652e99f9e2582725b8d9de42ec78... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-07 (Sun, 07 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/style/less/base.less M static/maps/mvc/workflow/workflow-manager.js.map Log Message: ----------- Fix indent, no code change Commit: 6594a466977bdf321e54489df4165a2dfe9a2aa2 https://github.com/galaxyproject/galaxy/commit/6594a466977bdf321e54489df4165... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-07 (Sun, 07 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M static/maps/mvc/workflow/workflow-manager.js.map Log Message: ----------- Fix spacing Commit: e466bcbc44566b1b9bfea36125f9726841d74c9b https://github.com/galaxyproject/galaxy/commit/e466bcbc44566b1b9bfea36125f97... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-07 (Sun, 07 Jun 2015) Changed paths: M CONTRIBUTING.md M config/datatypes_conf.xml.sample M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/tool_shed/metadata/metadata_generator.py M static/welcome.rst M templates/export_base.mako M templates/form.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/sharing_base.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako M tools/data_source/upload.xml M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Commit: 4411455ee9d90ee20d60fa6d14b8fecfb7a322ec https://github.com/galaxyproject/galaxy/commit/4411455ee9d90ee20d60fa6d14b8f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M client/galaxy/style/less/base.less Log Message: ----------- Fix style import Commit: b0a16eb40702c1ebd9217aa2963d48a87c7bd017 https://github.com/galaxyproject/galaxy/commit/b0a16eb40702c1ebd9217aa2963d4... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/index.mako A templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako Log Message: ----------- Merge pull request #303 from Airistotal/dev Added sorting ability to jobs per tool page in reporting Commit: e909be8c5bd7d5dad25a71e6b6c7d70e9f063050 https://github.com/galaxyproject/galaxy/commit/e909be8c5bd7d5dad25a71e6b6c7d... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/galaxy.workflow_editor.canvas.js.map M static/scripts/galaxy.workflow_editor.canvas.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #311 from jmchilton/workflow_editor_collections Extend workflow editor to allow tool output collections. Commit: 2a328b3e300e9e57fd2f31072e49682a3467c29a https://github.com/galaxyproject/galaxy/commit/2a328b3e300e9e57fd2f31072e496... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #308 from davebx/zip_handling Preserve unix permissions, if any, when extracting .zip files. Commit: 732abcc0db331833de16fcf38edf7c2f71009474 https://github.com/galaxyproject/galaxy/commit/732abcc0db331833de16fcf38edf7... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tools/tools-template.js M lib/galaxy/auth/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/galaxy.interactive_environments.js.map M static/maps/mvc/tools/tools-template.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/mvc/tools/tools-template.js M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.05' into dev Commit: c18616d14a21791d89a31db24cfe9a3f094d89f4 https://github.com/galaxyproject/galaxy/commit/c18616d14a21791d89a31db24cfe9... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M static/maps/mvc/workflow/workflow-manager.js.map M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Import js changes from https://github.com/galaxyproject/galaxy/pull/311/files Commit: 4bceafcbf4d68c23c400425b80e99e89aed1b791 https://github.com/galaxyproject/galaxy/commit/4bceafcbf4d68c23c400425b80e99... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tools/tools-template.js M lib/galaxy/auth/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/galaxy.interactive_environments.js.map M static/maps/mvc/tools/tools-template.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/mvc/tools/tools-template.js M templates/webapps/reports/index.mako A templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_HDAManager.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Conflicts: client/galaxy/scripts/galaxy.workflow_editor.canvas.js static/maps/galaxy.workflow_editor.canvas.js.map static/scripts/galaxy.workflow_editor.canvas.js Commit: b904a5fddd335ed333c9381610f71a2758386c3c https://github.com/galaxyproject/galaxy/commit/b904a5fddd335ed333c9381610f71... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/webapps/galaxy/api/errors.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py A templates/admin/tool_errors.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Adding system to log tool loading/preperation exceptions so that they can be viewed in an admin dialog Commit: d66bc114c1828694dc17198b228b312c9a240e07 https://github.com/galaxyproject/galaxy/commit/d66bc114c1828694dc17198b228b3... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-06-08 (Mon, 08 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/errors.py Log Message: ----------- Adding @web.require_admin to /api/error/tools Commit: 19cac9ac9d00b66a4d7340b63b6d4f6628a1871f https://github.com/galaxyproject/galaxy/commit/19cac9ac9d00b66a4d7340b63b6d4... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M run_tests.sh Log Message: ----------- Mention -installed option in run_tests.sh help. Commit: 2b568307520a922d447cddfbe22d29e5dbccfc26 https://github.com/galaxyproject/galaxy/commit/2b568307520a922d447cddfbe22d2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #323 from jmchilton/installed Mention -installed option in run_tests.sh help. Commit: bde53311a7a1befd75c179ff98f68234353c2a8b https://github.com/galaxyproject/galaxy/commit/bde53311a7a1befd75c179ff98f68... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: R lib/galaxy/webapps/galaxy/api/errors.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Removing /api/errors for the moment (the admin control panel doesn't use the API, so its not needed) Commit: 745c77787955a75606a072e25fe54694bd9bdf01 https://github.com/galaxyproject/galaxy/commit/745c77787955a75606a072e25fe54... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/tools/__init__.py M templates/admin/tool_errors.mako Log Message: ----------- Clarifing naming to use 'Phase' Commit: 28bab5849c4c2afee3b82513e9d25042bb012531 https://github.com/galaxyproject/galaxy/commit/28bab5849c4c2afee3b82513e9d25... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Create a separate application entry point to be used by uWSGI without --ini-paste/PasteDeploy. Commit: 6cb8482588ac0f6ba8a1f5d3e6a257798ba11abb https://github.com/galaxyproject/galaxy/commit/6cb8482588ac0f6ba8a1f5d3e6a25... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #325 from natefoo/uwsgi_app_factory Create a separate application entry point to be used by uWSGI without --ini-paste/PasteDeploy Commit: 6c9f924bafe51f10e644f7721cd21e4b60f6cf2a https://github.com/galaxyproject/galaxy/commit/6c9f924bafe51f10e644f7721cd21... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: A lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- initial TS group API include information about members and their repos in TS groups API Commit: 7378e445c43722acbb41b662f529cf0b209b229b https://github.com/galaxyproject/galaxy/commit/7378e445c43722acbb41b662f529c... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/groups.py A lib/tool_shed/managers/__init__.py A lib/tool_shed/managers/groups.py A lib/tool_shed/managers/repositories.py Log Message: ----------- first take on TS group manager introduce TS manager classes Commit: cfe96201927cde1a12ac3f16e4753c4e5628786d https://github.com/galaxyproject/galaxy/commit/cfe96201927cde1a12ac3f16e4753... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: A client/galaxy/scripts/mvc/groups/group-detail-view.js A client/galaxy/scripts/mvc/groups/group-list-view.js A client/galaxy/scripts/mvc/groups/group-listrow-view.js A client/galaxy/scripts/mvc/groups/group-model.js A client/galaxy/scripts/toolshed.groups.js M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/controllers/groups.py A static/maps/mvc/groups/group-detail-view.js.map A static/maps/mvc/groups/group-groupdetail-view.js.map A static/maps/mvc/groups/group-grouprow-view.js.map A static/maps/mvc/groups/group-list-view.js.map A static/maps/mvc/groups/group-listrow-view.js.map A static/maps/mvc/groups/group-model.js.map A static/maps/mvc/groups/group.model.js.map A static/maps/toolshed.groups.js.map A static/scripts/mvc/groups/group-detail-view.js A static/scripts/mvc/groups/group-groupdetail-view.js A static/scripts/mvc/groups/group-grouprow-view.js A static/scripts/mvc/groups/group-list-view.js A static/scripts/mvc/groups/group-listrow-view.js A static/scripts/mvc/groups/group-model.js A static/scripts/mvc/groups/group.model.js A static/scripts/toolshed.groups.js M templates/grid_base.mako M templates/webapps/tool_shed/base_panels.mako A templates/webapps/tool_shed/group/index.mako Log Message: ----------- backbone base of TS groups fix backbone hash problem; some more formatting and API polishing refactor group API controller; better format group detail view more formating and refactoring add column to group detail update details, add some more info to API response Commit: 815539ca953a13c50f933c34e69455c477e0052c https://github.com/galaxyproject/galaxy/commit/815539ca953a13c50f933c34e6945... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py A templates/sorting_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_tool.mako Log Message: ----------- Reimplemented sorting to be much easier to apply to other pages. Added sorting for Errorrs per Tool page. Commit: 4ea5d72850227c81daa21836308de49d3ebe2cf7 https://github.com/galaxyproject/galaxy/commit/4ea5d72850227c81daa21836308de... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/groups.py M lib/tool_shed/managers/repositories.py Log Message: ----------- fix flake8 problems and s/category/group bug Commit: 3450363fdeba236596225f015f64c9432e2027c8 https://github.com/galaxyproject/galaxy/commit/3450363fdeba236596225f015f64c... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-template.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/utils/utils.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml A doc/source/releases/15.07_announce.rst M doc/source/releases/index.rst M lib/galaxy/auth/__init__.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M run_tests.sh M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/galaxy.workflows.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-template.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/galaxy.workflows.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/utils/utils.js M static/welcome.rst M templates/export_base.mako M templates/form.mako M templates/grid_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/sharing_base.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/tool_form.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_HDAManager.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M tools/data_source/upload.xml M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 6254df8048bdc5589da0b12709c71b314c9fbab6 https://github.com/galaxyproject/galaxy/commit/6254df8048bdc5589da0b12709c71... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-09 (Tue, 09 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/managers/groups.py Log Message: ----------- allow creation of groups through API and use manager for it Commit: 66fa7c2ad27dc526d585e384e32fef9d4b631ab9 https://github.com/galaxyproject/galaxy/commit/66fa7c2ad27dc526d585e384e32fe... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflows.js M static/maps/galaxy.workflows.js.map M static/scripts/galaxy.workflows.js Log Message: ----------- Fix generic forms for modules Commit: 6e57eaa93f3404273e94826fc1267348d6eef43e https://github.com/galaxyproject/galaxy/commit/6e57eaa93f3404273e94826fc1267... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/webapps/galaxy/controllers/admin.py A templates/admin/tool_errors.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Merge pull request #322 from kellrott/sdk-tools Adding Tool Error tracking Commit: 63dcb849aec2cf953ddd9bedaa74e79e189ab3d7 https://github.com/galaxyproject/galaxy/commit/63dcb849aec2cf953ddd9bedaa74e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.workflows.js M static/maps/galaxy.workflows.js.map M static/scripts/galaxy.workflows.js Log Message: ----------- Merge pull request #328 from guerler/fix_generic_forms_000 Fix generic forms for modules Commit: 22f098f3219978e196dbec92227527adcd4bb149 https://github.com/galaxyproject/galaxy/commit/22f098f3219978e196dbec9222752... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Minor debugging improvement for loading datatypes. Commit: 9c911669380177e91467e84c4b96a272bd53bc77 https://github.com/galaxyproject/galaxy/commit/9c911669380177e91467e84c4b96a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- 'standard' whitespace :/ Commit: 98002f4349ef166e71ea7ada76482c8035de38aa https://github.com/galaxyproject/galaxy/commit/98002f4349ef166e71ea7ada76482... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #329 from dannon/registry_debugging Registry debugging Commit: b4715119dd862d69ef377a371fd5a83fce78cc3f https://github.com/galaxyproject/galaxy/commit/b4715119dd862d69ef377a371fd5a... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/sorting_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako Log Message: ----------- Generalized sorting and applied changes to all Jobs pages in Reporting Commit: db1513d8af5ef3a9ead06453310afa68f5fa9e56 https://github.com/galaxyproject/galaxy/commit/db1513d8af5ef3a9ead06453310af... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Fixed whitespaces to pass Travis CI Commit: 769585ce2e52524a85edbf74e728ee9ab542e9d0 https://github.com/galaxyproject/galaxy/commit/769585ce2e52524a85edbf74e728e... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-10 (Wed, 10 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Fixed more whitespace to pass Travis CI Commit: 7bea3621b6afd533dbb59eb5272c16976a1c837e https://github.com/galaxyproject/galaxy/commit/7bea3621b6afd533dbb59eb5272c1... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M client/GruntFile.js M client/README.md M client/grunt-tasks/scripts.js A client/toolshed/scripts/test-file.js A static/toolshed/src Log Message: ----------- Client build, toolshed: allow passing an 'app' option to the client/GruntFile, use 'grunt --app=toolshed' to watch for changes in toolshed scripts, duplicate our (unusual) galaxy scripts directories for the toolshed app (test-file.js to be removed). Commit: 6cc2e6bb73ad95b41993aadedd083d2643eebb36 https://github.com/galaxyproject/galaxy/commit/6cc2e6bb73ad95b41993aadedd083... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M client/GruntFile.js Log Message: ----------- Client build, toolshed: fix default task param in GruntFile Commit: be729992d1a11e9c71a7e73ea946a4911c14582d https://github.com/galaxyproject/galaxy/commit/be729992d1a11e9c71a7e73ea946a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Fix metadata generation bug This will fix a crash in metadata generation, where `self.inputs` is initialised as `list()` but will be changed to a `dict()` in the try block. However, if we enter `except` this still is a list and will cause a crash later downstream. Commit: 21db5169e2e6f05960c330f79bf2978142542e81 https://github.com/galaxyproject/galaxy/commit/21db5169e2e6f05960c330f79bf29... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Initialise the proper datastructure from the beginning Commit: 7986513bee02c82664d41c859f929b966d4306fe https://github.com/galaxyproject/galaxy/commit/7986513bee02c82664d41c859f929... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Merge pull request #333 from bgruening/patch-3 Fix metadata generation bug Commit: d94df7436fb9085645c119a9e0b2b259817dff50 https://github.com/galaxyproject/galaxy/commit/d94df7436fb9085645c119a9e0b2b... Author: nitesh1989 <nitesh.turaga@gmail.com> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Added Illumina methylation datatype (IDAT) to binary.py Commit: d3246c3f5f642fe3491062e2041c8a629d41e0e6 https://github.com/galaxyproject/galaxy/commit/d3246c3f5f642fe3491062e2041c8... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M templates/sorting_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Added fix for ORDER BY NULL case and added sorting to the rest of the reports pages. Added a link for errors per tool to inspect the erring jobs. Commit: 2cc687a6ce08e9ccd97a0934a0ba32c281394f15 https://github.com/galaxyproject/galaxy/commit/2cc687a6ce08e9ccd97a0934a0ba3... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Added whitespace to pass Travis CI Commit: 9b89ad008900c02af609903e3259aa6400dcb81b https://github.com/galaxyproject/galaxy/commit/9b89ad008900c02af609903e3259a... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Replace != with is not Commit: c971658a400cefec5ccefb9ca7cac6260abc90c4 https://github.com/galaxyproject/galaxy/commit/c971658a400cefec5ccefb9ca7cac... Author: Kyle Ellrott <kellrott@gmail.com> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fixing string appending error Commit: 0bd90e04a30a4a6b3e7a8028d137c62dbbb6d8cd https://github.com/galaxyproject/galaxy/commit/0bd90e04a30a4a6b3e7a8028d137c... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-11 (Thu, 11 Jun 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #336 from kellrott/dev Fixing string appending error Commit: d1f6cc570f8301fbf9312140ea5aaa25a5a3e4b7 https://github.com/galaxyproject/galaxy/commit/d1f6cc570f8301fbf9312140ea5aa... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M client/GruntFile.js M client/README.md M client/grunt-tasks/scripts.js A client/toolshed/scripts/test-file.js A static/toolshed/src Log Message: ----------- Merge pull request #332 from carlfeberhard/grunt.toolshed Add app option to client/GruntFile and allow building toolshed scripts Commit: 6404a6b51e34b11229c2921f13c62ce003292047 https://github.com/galaxyproject/galaxy/commit/6404a6b51e34b11229c2921f13c62... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #335 from nitesh1989/minfi_test Added Illumina methylation datatype (IDAT) to binary.py Commit: 2bd0012333040c15ef7836434f2919cc0a674930 https://github.com/galaxyproject/galaxy/commit/2bd0012333040c15ef7836434f291... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Rename sorter method to defalut_sort_id Commit: 034c001e37661ae5fa52edc768e947b0d3edb67e https://github.com/galaxyproject/galaxy/commit/034c001e37661ae5fa52edc768e94... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Renamed default_sort_id method to sorter and changed parameter defaultSortID to default_sort_id Commit: ec3ed556a13bc42e2701e3620e721ad86e959413 https://github.com/galaxyproject/galaxy/commit/ec3ed556a13bc42e2701e3620e721... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Added named tuple to the sorter method Commit: f787bee2b1fdae45fb59fd37ddd132f1c2becfba https://github.com/galaxyproject/galaxy/commit/f787bee2b1fdae45fb59fd37ddd13... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Fixed whitespace to pass Travis CI Commit: 9a3e1f86dbbe9d4287d9c3dc4319354416585045 https://github.com/galaxyproject/galaxy/commit/9a3e1f86dbbe9d4287d9c3dc43193... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M config/tool_shed.ini.sample Log Message: ----------- refactor TS sample config to follow 80char/line rule Commit: 16444026e6f69654acf8a53fbb10797c1d52555c https://github.com/galaxyproject/galaxy/commit/16444026e6f69654acf8a53fbb107... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py Log Message: ----------- Updated users and workflows to use the new named tuple Commit: 353ee2f22af8f07a42a72fd1cbf10751dab02e5f https://github.com/galaxyproject/galaxy/commit/353ee2f22af8f07a42a72fd1cbf10... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- introduce a config option to hide results of install & test framework Commit: a91c81679c50e741836084be05002bc3a1d2fa98 https://github.com/galaxyproject/galaxy/commit/a91c81679c50e741836084be05002... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M client/galaxy/style/less/base.less Log Message: ----------- Fixed bug where the left panel didn't scroll when the screen was too smal Commit: a09dd64d611a4f9772c35d9f38d45b1aa85d907c https://github.com/galaxyproject/galaxy/commit/a09dd64d611a4f9772c35d9f38d45... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/reports/index.mako Log Message: ----------- Added new css class for panel scrolling and compiled Commit: a2c44b4c8b29171000db419f8f6fe6785eb568cc https://github.com/galaxyproject/galaxy/commit/a2c44b4c8b29171000db419f8f6fe... Author: Airistotal <daniel.bouchard@phac-aspc.gc.ca> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/reports/index.mako Log Message: ----------- Renamed new class and moved inline styling Commit: cd4209f6bc2668c370e2c5a511b1b244eec297d4 https://github.com/galaxyproject/galaxy/commit/cd4209f6bc2668c370e2c5a511b1b... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css M templates/webapps/reports/index.mako Log Message: ----------- Merge pull request #338 from Airistotal/report_left_scrolling Reports left panel bug fix Commit: 017e181063f419d61d5055b8fa2d19bb71453bf8 https://github.com/galaxyproject/galaxy/commit/017e181063f419d61d5055b8fa2d1... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Add a GreaterThanZeroValidator for numeric tool parameters. Commit: ea98d47bebcea1af2c3fb7694854eb6245feaf7e https://github.com/galaxyproject/galaxy/commit/ea98d47bebcea1af2c3fb7694854e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #306 from davebx/toolshed_error Fix repeated error messages with identical text. Commit: 8ba8066a8ee8820fc982de4192a95d104b0c14eb https://github.com/galaxyproject/galaxy/commit/8ba8066a8ee8820fc982de4192a95... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-12 (Fri, 12 Jun 2015) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Restore link to mercurial browsing of repositories. Commit: 07072bd5685d13243a2dea811525aa93635d48e5 https://github.com/galaxyproject/galaxy/commit/07072bd5685d13243a2dea811525a... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-13 (Sat, 13 Jun 2015) Changed paths: A client/galaxy/scripts/mvc/groups/group-detail-view.js A client/galaxy/scripts/mvc/groups/group-list-view.js A client/galaxy/scripts/mvc/groups/group-listrow-view.js A client/galaxy/scripts/mvc/groups/group-model.js A client/galaxy/scripts/toolshed.groups.js M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/controllers/groups.py A lib/tool_shed/managers/__init__.py A lib/tool_shed/managers/groups.py A lib/tool_shed/managers/repositories.py A static/maps/mvc/groups/group-detail-view.js.map A static/maps/mvc/groups/group-groupdetail-view.js.map A static/maps/mvc/groups/group-grouprow-view.js.map A static/maps/mvc/groups/group-list-view.js.map A static/maps/mvc/groups/group-listrow-view.js.map A static/maps/mvc/groups/group-model.js.map A static/maps/mvc/groups/group.model.js.map A static/maps/toolshed.groups.js.map A static/scripts/mvc/groups/group-detail-view.js A static/scripts/mvc/groups/group-groupdetail-view.js A static/scripts/mvc/groups/group-grouprow-view.js A static/scripts/mvc/groups/group-list-view.js A static/scripts/mvc/groups/group-listrow-view.js A static/scripts/mvc/groups/group-model.js A static/scripts/mvc/groups/group.model.js A static/scripts/toolshed.groups.js M templates/grid_base.mako M templates/webapps/tool_shed/base_panels.mako A templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge pull request #326 from martenson/ts-groups TS groups Commit: fc016d8e875be10ec6ddcb6f00ba234f6b106723 https://github.com/galaxyproject/galaxy/commit/fc016d8e875be10ec6ddcb6f00ba2... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-06-14 (Sun, 14 Jun 2015) Changed paths: M CONTRIBUTING.md A doc/source/project/organization.rst Log Message: ----------- Merge pull request #314 from jmchilton/organization_v2 [PROCEDURES] Implement policies for committers and pull requests. Commit: bdf173888569b147fee7c391a18fe81ef7634476 https://github.com/galaxyproject/galaxy/commit/bdf173888569b147fee7c391a18fe... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-14 (Sun, 14 Jun 2015) Changed paths: M .gitignore M .travis.yml M CONTRIBUTING.md M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/groups/group-detail-view.js A client/galaxy/scripts/mvc/groups/group-list-view.js A client/galaxy/scripts/mvc/groups/group-listrow-view.js A client/galaxy/scripts/mvc/groups/group-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-panel-annotated.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-template.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/toolshed.groups.js M client/galaxy/scripts/utils/utils.js A client/galaxy/style/blue_colors.ini A client/galaxy/style/less/autocomplete_tagging.less A client/galaxy/style/less/base.less A client/galaxy/style/less/bootstrap.less A client/galaxy/style/less/bootstrap/alerts.less A client/galaxy/style/less/bootstrap/badges.less A client/galaxy/style/less/bootstrap/bootstrap.less A client/galaxy/style/less/bootstrap/breadcrumbs.less A client/galaxy/style/less/bootstrap/button-groups.less A client/galaxy/style/less/bootstrap/buttons.less A client/galaxy/style/less/bootstrap/carousel.less A client/galaxy/style/less/bootstrap/close.less A client/galaxy/style/less/bootstrap/code.less A client/galaxy/style/less/bootstrap/component-animations.less A client/galaxy/style/less/bootstrap/dropdowns.less A client/galaxy/style/less/bootstrap/forms.less A client/galaxy/style/less/bootstrap/glyphicons.less A client/galaxy/style/less/bootstrap/grid.less A client/galaxy/style/less/bootstrap/input-groups.less A client/galaxy/style/less/bootstrap/jumbotron.less A 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config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js A 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config/plugins/visualizations/circster/config/circster.xml A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/tool_conf.xml.sample M display_applications/igv/bam.xml M display_applications/igv/gff.xml A display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml A doc/source/_static/style.css A doc/source/_templates/layout.html M doc/source/index.rst A doc/source/releases/13.01_announce.rst A doc/source/releases/13.02_announce.rst A doc/source/releases/13.04_announce.rst A doc/source/releases/13.06_announce.rst A doc/source/releases/13.08_announce.rst A doc/source/releases/13.11_announce.rst A doc/source/releases/14.02_announce.rst A doc/source/releases/14.04_announce.rst A doc/source/releases/14.06_announce.rst A doc/source/releases/14.08_announce.rst A doc/source/releases/14.10_announce.rst A doc/source/releases/15.01_announce.rst A doc/source/releases/15.03_announce.rst A doc/source/releases/15.05.rst A doc/source/releases/15.05_announce.rst A doc/source/releases/15.07_announce.rst A doc/source/releases/_header.rst A doc/source/releases/_thanks.rst A doc/source/releases/index.rst A doc/source/releases/older_releases.rst M eggs.ini M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M 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lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py A lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py A lib/tool_shed/managers/__init__.py A lib/tool_shed/managers/groups.py A lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M run_tests.sh A scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py A scripts/edam_mapping.py M scripts/functional_tests.py A scripts/runtime_stats.py M static/favicon.ico M static/images/galaxyIcon_noText.png M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.masthead.js.map M 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tools/data_source/bed_convert.xml M tools/data_source/fly_modencode.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.xml M tools/data_source/worm_modencode.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into HEAD Conflicts: config/datatypes_conf.xml.sample Commit: 723c10769f855a1f4fc91a9ce2591bf2ebb8525d https://github.com/galaxyproject/galaxy/commit/723c10769f855a1f4fc91a9ce2591... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-14 (Sun, 14 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #148 from bgruening/emboss_datatypes Add emboss datatypes [WIP] Commit: b47500618a733eed0960df5cfd223044371ec5e9 https://github.com/galaxyproject/galaxy/commit/b47500618a733eed0960df5cfd223... Author: Charles <charles0126@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Fixed extra_dir ('job_works') doesn't overwrite from objectstore xml. Commit: fd9f027a5c5cfcb69e35e084c3fa9d4a34a74211 https://github.com/galaxyproject/galaxy/commit/fd9f027a5c5cfcb69e35e084c3fa9... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: A client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-connector.js A client/galaxy/scripts/mvc/workflow/workflow-globals.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-node.js R client/galaxy/scripts/mvc/workflow/workflow-objects.js A client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/mvc/workflow/workflow-view-data.js A client/galaxy/scripts/mvc/workflow/workflow-view-node.js A client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow.js A static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-connector.js.map A static/maps/mvc/workflow/workflow-globals.js.map M static/maps/mvc/workflow/workflow-manager.js.map A static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-objects.js.map A static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/mvc/workflow/workflow-view-data.js.map A static/maps/mvc/workflow/workflow-view-node.js.map A static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow.js.map A static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-connector.js A static/scripts/mvc/workflow/workflow-globals.js M static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-objects.js A static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow-view-data.js A static/scripts/mvc/workflow/workflow-view-node.js A static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Further workflow front-end refactoring Commit: 614b35e3a9510f2e4703c0ab6a6b59856dfd4c79 https://github.com/galaxyproject/galaxy/commit/614b35e3a9510f2e4703c0ab6a6b5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M CONTRIBUTING.md M client/GruntFile.js M client/README.md A client/galaxy/scripts/mvc/groups/group-detail-view.js A client/galaxy/scripts/mvc/groups/group-list-view.js A client/galaxy/scripts/mvc/groups/group-listrow-view.js A client/galaxy/scripts/mvc/groups/group-model.js A client/galaxy/scripts/toolshed.groups.js M client/galaxy/style/less/base.less M client/grunt-tasks/scripts.js A client/toolshed/scripts/test-file.js M config/datatypes_conf.xml.sample A doc/source/project/organization.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/test.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py A lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py A lib/tool_shed/managers/__init__.py A lib/tool_shed/managers/groups.py A lib/tool_shed/managers/repositories.py M run_tests.sh A static/maps/galaxy.workflows.js.map A static/maps/mvc/groups/group-detail-view.js.map A static/maps/mvc/groups/group-groupdetail-view.js.map A static/maps/mvc/groups/group-grouprow-view.js.map A static/maps/mvc/groups/group-list-view.js.map A static/maps/mvc/groups/group-listrow-view.js.map A static/maps/mvc/groups/group-model.js.map A static/maps/mvc/groups/group.model.js.map A static/maps/toolshed.groups.js.map A static/scripts/galaxy.workflows.js A static/scripts/mvc/groups/group-detail-view.js A static/scripts/mvc/groups/group-groupdetail-view.js A static/scripts/mvc/groups/group-grouprow-view.js A static/scripts/mvc/groups/group-list-view.js A static/scripts/mvc/groups/group-listrow-view.js A static/scripts/mvc/groups/group-model.js A static/scripts/mvc/groups/group.model.js A static/scripts/toolshed.groups.js M static/style/blue/base.css A static/toolshed/src A templates/admin/tool_errors.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako A templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Conflicts: client/galaxy/scripts/galaxy.workflows.js static/maps/galaxy.workflows.js.map static/scripts/galaxy.workflows.js Commit: 6bf4a45e259d0aa2a023470f5d7d0e1c31a1ce5d https://github.com/galaxyproject/galaxy/commit/6bf4a45e259d0aa2a023470f5d7d0... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M static/maps/mvc/workflow/workflow-view-data.js.map M static/scripts/mvc/workflow/workflow-view-data.js Log Message: ----------- Remove unnecessary export of OutputCalloutView Commit: 91b00044dc4aaf71be66de9105ed7616a022b213 https://github.com/galaxyproject/galaxy/commit/91b00044dc4aaf71be66de9105ed7... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: A client/galaxy/scripts/mvc/workflow/workflow-view.js R client/galaxy/scripts/mvc/workflow/workflow.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Use proper convention for main workflow view name Commit: 521b287b134691ddb50efc936b4e483351dc7b12 https://github.com/galaxyproject/galaxy/commit/521b287b134691ddb50efc936b4e4... Author: Charles <charles0126@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M config/object_store_conf.xml.sample M lib/galaxy/objectstore/s3.py Log Message: ----------- Add extra_dir options for S3/Swift ObjectStore. Commit: 584f673f8dbd0c419265bb7b10ae3af1d1cdf058 https://github.com/galaxyproject/galaxy/commit/584f673f8dbd0c419265bb7b10ae3... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M .gitignore M .travis.yml M CONTRIBUTING.md M client/GruntFile.js M client/README.md M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/groups/group-detail-view.js A client/galaxy/scripts/mvc/groups/group-list-view.js A client/galaxy/scripts/mvc/groups/group-listrow-view.js A client/galaxy/scripts/mvc/groups/group-model.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-template.js A client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/toolshed.groups.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/dataset-choice.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js A client/toolshed/scripts/test-file.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M 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lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/controllers/jobs.py A lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/workflow/modules.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A lib/tool_shed/managers/__init__.py A lib/tool_shed/managers/groups.py A lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M run_tests.sh A scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M 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tools/data_source/fly_modencode.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.xml M tools/data_source/worm_modencode.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.py M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into ts-search-expansion Conflicts: lib/galaxy/webapps/tool_shed/buildapp.py Commit: 185e4fe6f2b9cbdef9a26d6c69a0350275e243cb https://github.com/galaxyproject/galaxy/commit/185e4fe6f2b9cbdef9a26d6c69a03... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py R lib/galaxy/webapps/tool_shed/api/search.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #334 from martenson/ts-search-expansion TS search refactoring and bugfix Commit: 374795f631377053635a78bdb20a970f00dffbdb https://github.com/galaxyproject/galaxy/commit/374795f631377053635a78bdb20a9... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Only cleanup successful jobs when testing. As per the recommendation of Ryan G. at http://dev.list.galaxyproject.org/keep-job-output-and-scripts-on-failed-test.... I considered making this 'never' - since those files will get cleaned up at the end anyway. This would actually reduce our test coverage related to job cleanup logic - so I have decided this is a fine a middle ground. Commit: 4d04d0fd5c5f918a4319518c524ee4a856560c29 https://github.com/galaxyproject/galaxy/commit/4d04d0fd5c5f918a4319518c524ee... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Merge pull request #341 from jmchilton/cleanup_tests Only cleanup successful jobs when testing. Commit: 19dbf2f78060c88017354aab3043413f521cad9f https://github.com/galaxyproject/galaxy/commit/19dbf2f78060c88017354aab30434... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py Log Message: ----------- Allow specifying EDAM format for dynamic subclass datatypes. Use this to specify the EDAM format for genbank. Commit: 35ab5c177e336c03c3dd74ff91338730fb10bf31 https://github.com/galaxyproject/galaxy/commit/35ab5c177e336c03c3dd74ff91338... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #342 from jmchilton/edam_dynamic Allow specifying EDAM format for dynamic subclass datatypes. Commit: 5e77f3f34aa40259315de17ec3cddabc5f77f945 https://github.com/galaxyproject/galaxy/commit/5e77f3f34aa40259315de17ec3cdd... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- bind to correct config option Commit: f472a67e7936fea6865e3a2664466b79779dee55 https://github.com/galaxyproject/galaxy/commit/f472a67e7936fea6865e3a2664466... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #337 from martenson/ts-hide-test-results TS hide test results Commit: 36a74a96dbf9a57ddb7264bf4e6da0f71d13b23b https://github.com/galaxyproject/galaxy/commit/36a74a96dbf9a57ddb7264bf4e6da... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Initial restriction of metadata size to ~5MB in-memory size per element Commit: 9f2c57ba49d8796fd87d5b0708dc39e1c089d779 https://github.com/galaxyproject/galaxy/commit/9f2c57ba49d8796fd87d5b0708dc3... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M CONTRIBUTING.md A client/galaxy/scripts/mvc/groups/group-detail-view.js A client/galaxy/scripts/mvc/groups/group-list-view.js A client/galaxy/scripts/mvc/groups/group-listrow-view.js A client/galaxy/scripts/mvc/groups/group-model.js A client/galaxy/scripts/toolshed.groups.js M config/datatypes_conf.xml.sample M config/tool_shed.ini.sample A doc/source/project/organization.rst M lib/galaxy/datatypes/registry.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py R lib/galaxy/webapps/tool_shed/api/search.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py A lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py A lib/tool_shed/managers/__init__.py A lib/tool_shed/managers/groups.py A lib/tool_shed/managers/repositories.py M scripts/functional_tests.py M scripts/tool_shed/build_ts_whoosh_index.py A static/maps/mvc/groups/group-detail-view.js.map A static/maps/mvc/groups/group-groupdetail-view.js.map A static/maps/mvc/groups/group-grouprow-view.js.map A static/maps/mvc/groups/group-list-view.js.map A static/maps/mvc/groups/group-listrow-view.js.map A static/maps/mvc/groups/group-model.js.map A static/maps/mvc/groups/group.model.js.map A static/maps/toolshed.groups.js.map A static/scripts/mvc/groups/group-detail-view.js A static/scripts/mvc/groups/group-groupdetail-view.js A static/scripts/mvc/groups/group-grouprow-view.js A static/scripts/mvc/groups/group-list-view.js A static/scripts/mvc/groups/group-listrow-view.js A static/scripts/mvc/groups/group-model.js A static/scripts/mvc/groups/group.model.js A static/scripts/toolshed.groups.js M templates/grid_base.mako M templates/webapps/tool_shed/base_panels.mako A templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 2a7f1f741e466223cf3d1e7c414ede5ee7ac4c5a https://github.com/galaxyproject/galaxy/commit/2a7f1f741e466223cf3d1e7c414ed... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Enhance the InRangeValidator to enalbe the use of new strict_min and strict_max attributes which, if set to true, will exclude the range end points. For example, if strict_min is true, min < value, whereas if strict_min is false (the default), then min <= value. Combinations of strict_min and strict_max are allowed. Commit: 0b96cbd0e93c5de5230155134e702ee13e8d23b8 https://github.com/galaxyproject/galaxy/commit/0b96cbd0e93c5de5230155134e702... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: R client/galaxy/scripts/mvc/workflow/workflow-globals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/workflow/workflow-globals.js.map R static/scripts/mvc/workflow/workflow-globals.js Log Message: ----------- Remove unnecessary files Commit: 97212e9b322f34d9aa9b1892ec36015d7a6ccccf https://github.com/galaxyproject/galaxy/commit/97212e9b322f34d9aa9b1892ec360... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Remove globals from workflow-node module Commit: 286aaba51e32489321fe57d09c5b87bcea01da2c https://github.com/galaxyproject/galaxy/commit/286aaba51e32489321fe57d09c5b8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/custom_types.py Log Message: ----------- Make metadata limit configurable, off by default. Commit: 2a3ad8148b95dc964620e8c6f0caff43c2c1d561 https://github.com/galaxyproject/galaxy/commit/2a3ad8148b95dc964620e8c6f0caf... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Simplify the checks for setting strict_min and strict_max operators. Commit: ca832ced3277f4ab432c06e527f9b92d681efb54 https://github.com/galaxyproject/galaxy/commit/ca832ced3277f4ab432c06e527f9b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js Log Message: ----------- Add tool parameter argument to parameter help Commit: e8087f7b12d76aceeff38f0a2c70706e3ee676b7 https://github.com/galaxyproject/galaxy/commit/e8087f7b12d76aceeff38f0a2c707... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: R client/galaxy/scripts/mvc/groups/group-detail-view.js R client/galaxy/scripts/mvc/groups/group-list-view.js R client/galaxy/scripts/mvc/groups/group-listrow-view.js R client/galaxy/scripts/mvc/groups/group-model.js R client/galaxy/scripts/toolshed.groups.js A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/test-file.js A client/toolshed/scripts/toolshed.groups.js M lib/galaxy/webapps/tool_shed/controllers/groups.py R static/scripts/mvc/groups/group-detail-view.js R static/scripts/mvc/groups/group-groupdetail-view.js R static/scripts/mvc/groups/group-grouprow-view.js R static/scripts/mvc/groups/group-list-view.js R static/scripts/mvc/groups/group-listrow-view.js R static/scripts/mvc/groups/group-model.js R static/scripts/mvc/groups/group.model.js R static/scripts/toolshed.groups.js A static/toolshed/maps/mvc/groups/group-detail-view.js.map A static/toolshed/maps/mvc/groups/group-list-view.js.map A static/toolshed/maps/mvc/groups/group-listrow-view.js.map A static/toolshed/maps/mvc/groups/group-model.js.map A static/toolshed/maps/test-file.js.map A static/toolshed/maps/toolshed.groups.js.map A static/toolshed/scripts/mvc/groups/group-detail-view.js A static/toolshed/scripts/mvc/groups/group-list-view.js A static/toolshed/scripts/mvc/groups/group-listrow-view.js A static/toolshed/scripts/mvc/groups/group-model.js A static/toolshed/scripts/test-file.js A static/toolshed/scripts/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- refactor TS javascript files to be separated from Galaxy JS thanks to Carl for helping me with this Commit: 4de4aecea288815c0fd0634e2a54e5c08974c658 https://github.com/galaxyproject/galaxy/commit/4de4aecea288815c0fd0634e2a54e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M config/tool_shed.ini.sample M lib/galaxy/datatypes/registry.py M lib/galaxy/webapps/tool_shed/api/repositories.py R lib/galaxy/webapps/tool_shed/api/search.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M scripts/functional_tests.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Commit: d2da9d9a17ef7f0d1839c21233b078b76cb6afd7 https://github.com/galaxyproject/galaxy/commit/d2da9d9a17ef7f0d1839c21233b07... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Only add argument name if unavailable in help text Commit: 1ebc0854dc20aafacd60367ab87929ce3e05df99 https://github.com/galaxyproject/galaxy/commit/1ebc0854dc20aafacd60367ab8792... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #344 from davebx/bugfix_zip_td Fix for fix for handling of unix permissions in .zip files. Commit: 6eddbf524b023115568cfbda7c396c9f54c1b798 https://github.com/galaxyproject/galaxy/commit/6eddbf524b023115568cfbda7c396... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M client/toolshed/scripts/toolshed.groups.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/toolshed.groups.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- allow the js dependencies to use generalized path using requirejs paths to provide the relative prefix Commit: ea96c7142a98b53baa5d5e38b157eb8d516dcb80 https://github.com/galaxyproject/galaxy/commit/ea96c7142a98b53baa5d5e38b157e... Author: Charles <charles0126@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Added job_work option support for S3/Swift ObjectStore. Fixed the failure when removes job script and files. Commit: 3983de3785201d4efa252a916c97bddfe62692f9 https://github.com/galaxyproject/galaxy/commit/3983de3785201d4efa252a916c97b... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #346 from guerler/add_argument_000 Add tool parameter argument to parameter help Commit: 8e3bb7029c4e0aa2f21e08064f87a8ea9efad67f https://github.com/galaxyproject/galaxy/commit/8e3bb7029c4e0aa2f21e08064f87a... Author: James Taylor <james@jamestaylor.org> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: A CONTRIBUTORS.md M LICENSE.txt Log Message: ----------- Add list of contributors Commit: 14ae88251eb20d26759f4d7a9b51e2c439f8e76b https://github.com/galaxyproject/galaxy/commit/14ae88251eb20d26759f4d7a9b51e... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- update my contact Commit: aa2a7c9fb3e5a4830720b6f13f1fe705ff5c93e0 https://github.com/galaxyproject/galaxy/commit/aa2a7c9fb3e5a4830720b6f13f1fe... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Added @nsoranzo's simplified validation logic. Commit: 0c69c5b92f3461559133b57637006d9614752eec https://github.com/galaxyproject/galaxy/commit/0c69c5b92f3461559133b57637006... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Add parenthesis to argument name search Commit: db5c81acd78728dee37173aaf034024af2e5f302 https://github.com/galaxyproject/galaxy/commit/db5c81acd78728dee37173aaf0340... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Simplify strict_min strict_max logic. Commit: 5e2d61536ca03c7dc5fa254289f472c6c4dbfc5d https://github.com/galaxyproject/galaxy/commit/5e2d61536ca03c7dc5fa254289f47... Author: James Taylor <james@jamestaylor.org> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #3 from martenson/patch-1 Update contact info for Marten. Commit: 7742e6d23c5a859ed53b531bb5fc02236a7f2cb6 https://github.com/galaxyproject/galaxy/commit/7742e6d23c5a859ed53b531bb5fc0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Fix Guru's name in CONTRIBUTORS.md Apparently I messed it up during the hg->git conversion, I'll have to see if I can fix that. =( Commit: 3211f8cb97d8dc0e36749b3f03e18e07c0e256cf https://github.com/galaxyproject/galaxy/commit/3211f8cb97d8dc0e36749b3f03e18... Author: James Taylor <james@jamestaylor.org> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4 from natefoo/patch-1 Fix Guru's name in CONTRIBUTORS.md Commit: daef3100ee505d8c8f6a56d56cb5b2b053f82a37 https://github.com/galaxyproject/galaxy/commit/daef3100ee505d8c8f6a56d56cb5b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Add log indicating when metadata setting is being aborted Commit: 508b685c70f648f100dc3230d3105bd1ca95977d https://github.com/galaxyproject/galaxy/commit/508b685c70f648f100dc3230d3105... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/tool_shed/scripts/api/common.py M scripts/api/common.py Log Message: ----------- fix common API scripts so they dont fail when response has no url param Commit: 0ba756e0f2affb115b482914d7f24e86d9d0259a https://github.com/galaxyproject/galaxy/commit/0ba756e0f2affb115b482914d7f24... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-15 (Mon, 15 Jun 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A templates/sorting_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #330 from Airistotal/reports_sorting Reports sorting Commit: f5160f296da24e80f0fc9337e458347603358b85 https://github.com/galaxyproject/galaxy/commit/f5160f296da24e80f0fc9337e4583... Author: Charles <charles0126@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Fixed pylint errors. Commit: 3b9158acfea6362f636b28ba849a484746f551c2 https://github.com/galaxyproject/galaxy/commit/3b9158acfea6362f636b28ba849a4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update sample text. Commit: 78214ba16418d6dfd2c64de09f03efec578e0a8b https://github.com/galaxyproject/galaxy/commit/78214ba16418d6dfd2c64de09f03e... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- whitespace cleanups Commit: 8f6a3f5d49e194222978a3349160853c71d4996d https://github.com/galaxyproject/galaxy/commit/8f6a3f5d49e194222978a33491608... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Improve debug output. Commit: 0943142a08752a95a8895691be8d582604aebe37 https://github.com/galaxyproject/galaxy/commit/0943142a08752a95a8895691be8d5... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- add titles to explan TS mercurial browser links Commit: 1113eba71a7467fc1b702dc02e00104c64464856 https://github.com/galaxyproject/galaxy/commit/1113eba71a7467fc1b702dc02e001... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #355 from bgruening/js_debug Make debugging output nicer for IE's Commit: b0b313c61768e66bb84877c0dedbc2f2998bedfa https://github.com/galaxyproject/galaxy/commit/b0b313c61768e66bb84877c0dedbc... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/custom_types.py Log Message: ----------- Merge pull request #345 from dannon/metadata_limit Metadata size limiting Commit: caf38a28e80a6c80b7fa827ad4c4cdeaab16268e https://github.com/galaxyproject/galaxy/commit/caf38a28e80a6c80b7fa827ad4c4c... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1 from martenson/toolshed-hg-link add titles to explan TS mercurial browser links Commit: 3bd4f9cd1804739af0c51328d7fdd939dc1207fd https://github.com/galaxyproject/galaxy/commit/3bd4f9cd1804739af0c51328d7fdd... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Initialize config object from the beginning and make docker_host configurable. Commit: 77169a2078553bee1a94ef574fe2f89f9ee45d29 https://github.com/galaxyproject/galaxy/commit/77169a2078553bee1a94ef574fe2f... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- add docker_host as configurable option Commit: 06cc164f9b0f431a4a7e26ffa2dc0bc38ce6d92c https://github.com/galaxyproject/galaxy/commit/06cc164f9b0f431a4a7e26ffa2dc0... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #340 from blankenberg/toolshed-hg-link Restore link to mercurial browsing of repositories. Commit: 3c40f32fa2c6024716d3fcb0e6b5a66a7ef3dd3a https://github.com/galaxyproject/galaxy/commit/3c40f32fa2c6024716d3fcb0e6b5a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/brew_util.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/workflow_util.py M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/code_file.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py Log Message: ----------- PEP-8 and pylint fixes. Commit: 1c05e34895e8e93b045a66fb92569b0faba8f602 https://github.com/galaxyproject/galaxy/commit/1c05e34895e8e93b045a66fb92569... Author: Greg Von Kuster <greg@bx.psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #1 from nsoranzo/for_greg Simplify strict_min strict_max logic. Commit: a19147543cb81a9faf69166bf9c220713a82a5ac https://github.com/galaxyproject/galaxy/commit/a19147543cb81a9faf69166bf9c22... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/custom_types.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js A templates/sorting_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 55a1105915a6216fb999b71593d04df1ebfe9b93 https://github.com/galaxyproject/galaxy/commit/55a1105915a6216fb999b71593d04... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge branch 'dev' of https://github.com/gregvonkuster/galaxy into dev Commit: 373c98098c884f85ef24a795334d4e49c10d4f58 https://github.com/galaxyproject/galaxy/commit/373c98098c884f85ef24a795334d4... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Change strict_mXX to exclude_mXX for InRangeValidator enhancement. Commit: 188f90e8f17278f9ece7b825584e0479c60e7c97 https://github.com/galaxyproject/galaxy/commit/188f90e8f17278f9ece7b825584e0... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: R static/toolshed/scripts/test-file.js Log Message: ----------- remove the test file Commit: 042ec77100e71304e158e7ccc4f71b5728c6b2ae https://github.com/galaxyproject/galaxy/commit/042ec77100e71304e158e7ccc4f71... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: R client/galaxy/scripts/mvc/groups/group-detail-view.js R client/galaxy/scripts/mvc/groups/group-list-view.js R client/galaxy/scripts/mvc/groups/group-listrow-view.js R client/galaxy/scripts/mvc/groups/group-model.js R client/galaxy/scripts/toolshed.groups.js A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/test-file.js A client/toolshed/scripts/toolshed.groups.js M lib/galaxy/webapps/tool_shed/controllers/groups.py R static/scripts/mvc/groups/group-detail-view.js R static/scripts/mvc/groups/group-groupdetail-view.js R static/scripts/mvc/groups/group-grouprow-view.js R static/scripts/mvc/groups/group-list-view.js R static/scripts/mvc/groups/group-listrow-view.js R static/scripts/mvc/groups/group-model.js R static/scripts/mvc/groups/group.model.js R static/scripts/toolshed.groups.js A static/toolshed/maps/mvc/groups/group-detail-view.js.map A static/toolshed/maps/mvc/groups/group-list-view.js.map A static/toolshed/maps/mvc/groups/group-listrow-view.js.map A static/toolshed/maps/mvc/groups/group-model.js.map A static/toolshed/maps/test-file.js.map A static/toolshed/maps/toolshed.groups.js.map A static/toolshed/scripts/mvc/groups/group-detail-view.js A static/toolshed/scripts/mvc/groups/group-list-view.js A static/toolshed/scripts/mvc/groups/group-listrow-view.js A static/toolshed/scripts/mvc/groups/group-model.js A static/toolshed/scripts/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge pull request #347 from martenson/ts-refactor-static refactor TS javascript files to be separated from Galaxy JS Commit: 032dd3e3fd7ae9fb18259df4235eefdfbb86175c https://github.com/galaxyproject/galaxy/commit/032dd3e3fd7ae9fb18259df4235ee... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_15.05' into dev Commit: d011ddbcf6cf379fce4f4f59ab9517ad5be87c63 https://github.com/galaxyproject/galaxy/commit/d011ddbcf6cf379fce4f4f59ab951... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #339 from gregvonkuster/dev Add new exclude_min and exclude_max attributes to InRangeValidator for numeric tool parameters. Commit: 21f1f8f171b51626ebc8e23972949ff2db3bbbba https://github.com/galaxyproject/galaxy/commit/21f1f8f171b51626ebc8e23972949... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M lib/tool_shed/scripts/api/common.py M scripts/api/common.py Log Message: ----------- Merge pull request #352 from martenson/scripts-api-display-optional-url fix common API scripts so they dont fail when response has no url param Commit: fe625bc6cf1ef4e1a4dc859773cf55307990df7a https://github.com/galaxyproject/galaxy/commit/fe625bc6cf1ef4e1a4dc859773cf5... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Merge pull request #351 from guerler/add_argument_001 Add parenthesis to argument name search Commit: 4e7dad284a04dd1f4f83af64fa32e339ccf3bcfb https://github.com/galaxyproject/galaxy/commit/4e7dad284a04dd1f4f83af64fa32e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Tweak institutional support language in CONTRIBUTORS.md. Commit: e185abcbb4a4ed73a74fe7dd36140512c9cf5df8 https://github.com/galaxyproject/galaxy/commit/e185abcbb4a4ed73a74fe7dd36140... Author: James Taylor <james@jamestaylor.org> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #5 from jmchilton/contributors-institutions Tweak institutional support language in CONTRIBUTORS.md. Commit: a136db404cc3bdf8c3e1b3e304711b01a04c8240 https://github.com/galaxyproject/galaxy/commit/a136db404cc3bdf8c3e1b3e304711... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: A CONTRIBUTORS.md M LICENSE.txt Log Message: ----------- Merge pull request #349 from jxtx/contributors Add list of contributors Commit: 04120145c5397f385bf2c4672307005f1f55848d https://github.com/galaxyproject/galaxy/commit/04120145c5397f385bf2c46723070... Author: Eric Rasche <rasche.eric@yandex.ru> Date: 2015-06-16 (Tue, 16 Jun 2015) Changed paths: M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml M display_applications/igv/gff.xml M display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml Log Message: ----------- CDATA and linting Commit: 7b06d5a13458f2cd97007ad74e68a857d2f354ea https://github.com/galaxyproject/galaxy/commit/7b06d5a13458f2cd97007ad74e68a... Author: yhoogstrate <y.hoogstrate@erasmusmc.nl> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M .ci/flake8_wrapper.sh M .gitignore M .travis.yml M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.workflow_editor.canvas.js M client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M 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test/unit/unittest_utils/tempfilecache.py A test/unit/unittest_utils/utility.py R test/unit/util/utility.py A test/unit/visualizations/__init__.py A test/unit/visualizations/plugins/__init__.py A test/unit/visualizations/plugins/test_VisualizationPlugin.py A test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/visualizations/registry/test_VisualizationsRegistry.py A test/unit/web/__init__.py A test/unit/web/base/__init__.py R test/unit/web/base/mock.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tool-data/shared/gbrowse/gbrowse_build_sites.txt M tools/data_source/bed_convert.xml M tools/data_source/fly_modencode.xml M tools/data_source/genbank.xml M tools/data_source/import.xml M tools/data_source/microbial_import.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.xml M tools/data_source/worm_modencode.xml M tools/evolution/codingSnps.xml M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.xml M tools/filters/axt_to_lav_code.py M tools/filters/catWrapper.xml M tools/filters/changeCase.xml M tools/filters/condense_characters.xml M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py A tox.ini Log Message: ----------- Merge pull request #2 from galaxyproject/dev update Commit: 41e346adfe21d1d0bd023ded515e53522f192909 https://github.com/galaxyproject/galaxy/commit/41e346adfe21d1d0bd023ded515e5... Author: y.hoogstrate@erasmusmc.nl <y.hoogstrate@erasmusmc.nl> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Added support for DotBracket notation Commit: 4e5338d24e17f237f496b8b97e7032f63dac523e https://github.com/galaxyproject/galaxy/commit/4e5338d24e17f237f496b8b97e703... Author: y.hoogstrate@erasmusmc.nl <y.hoogstrate@erasmusmc.nl> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- updates to DotBracket Commit: f8b364b9f546dcda3660b12f3435720e290ebbcb https://github.com/galaxyproject/galaxy/commit/f8b364b9f546dcda3660b12f34357... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: A CONTRIBUTORS.md M LICENSE.txt M client/galaxy/scripts/mvc/form/form-input.js R client/galaxy/scripts/mvc/groups/group-detail-view.js R client/galaxy/scripts/mvc/groups/group-list-view.js R client/galaxy/scripts/mvc/groups/group-listrow-view.js R client/galaxy/scripts/mvc/groups/group-model.js R client/galaxy/scripts/toolshed.groups.js A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/test-file.js A client/toolshed/scripts/toolshed.groups.js M lib/galaxy/tools/parameters/validation.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/workflow/modules.py M lib/tool_shed/scripts/api/common.py M scripts/api/common.py M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js R static/scripts/mvc/groups/group-detail-view.js R static/scripts/mvc/groups/group-groupdetail-view.js R static/scripts/mvc/groups/group-grouprow-view.js R static/scripts/mvc/groups/group-list-view.js R static/scripts/mvc/groups/group-listrow-view.js R static/scripts/mvc/groups/group-model.js R static/scripts/mvc/groups/group.model.js R static/scripts/toolshed.groups.js A static/toolshed/maps/mvc/groups/group-detail-view.js.map A static/toolshed/maps/mvc/groups/group-list-view.js.map A static/toolshed/maps/mvc/groups/group-listrow-view.js.map A static/toolshed/maps/mvc/groups/group-model.js.map A static/toolshed/maps/test-file.js.map A static/toolshed/maps/toolshed.groups.js.map A static/toolshed/scripts/mvc/groups/group-detail-view.js A static/toolshed/scripts/mvc/groups/group-list-view.js A static/toolshed/scripts/mvc/groups/group-listrow-view.js A static/toolshed/scripts/mvc/groups/group-model.js A static/toolshed/scripts/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako M test/api/test_workflows.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into pep8 Conflicts: lib/galaxy/tools/parameters/validation.py Commit: ec6ad5b1edeed07635551b67d56d9db4ad330be1 https://github.com/galaxyproject/galaxy/commit/ec6ad5b1edeed07635551b67d56d9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M lib/galaxy/queues.py Log Message: ----------- Merge branch 'release_15.05' into dev Commit: 8385a20bd7c383d9167d6a541edfd6b7f7fbd004 https://github.com/galaxyproject/galaxy/commit/8385a20bd7c383d9167d6a541edfd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Log Message: ----------- Merge branch 'master' into dev Commit: 43b2b7929bd5940d14a59e4cb3cfe320a840f464 https://github.com/galaxyproject/galaxy/commit/43b2b7929bd5940d14a59e4cb3cfe... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- change docker_host to docker_hostname to be more explicit Commit: 691b3d6602312d148fbea523862d9bcc2bbfc4f6 https://github.com/galaxyproject/galaxy/commit/691b3d6602312d148fbea523862d9... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #356 from bgruening/add_configurable_host Add configurable Docker hostname Commit: 10fc5196335530699d7a9f414d2789d1adc79ff2 https://github.com/galaxyproject/galaxy/commit/10fc5196335530699d7a9f414d278... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Fix bug introduced in 3c40f32fa2c6024716d3fcb0e6b5a66a7ef3dd3a . Commit: 7830bc62e09bd5928b08f2cde93bae8815a6ba45 https://github.com/galaxyproject/galaxy/commit/7830bc62e09bd5928b08f2cde93ba... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- Another fix for 3c40f32fa2c6024716d3fcb0e6b5a66a7ef3dd3a . Commit: 1830adfb3086bc384b766809d47de9c59493db74 https://github.com/galaxyproject/galaxy/commit/1830adfb3086bc384b766809d47de... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M tools/evolution/codingSnps_filter.py Log Message: ----------- Fixes for @jmchilton and @dannon. Commit: 9d807b85999bfdaaac8ec3c274013b2a687445e7 https://github.com/galaxyproject/galaxy/commit/9d807b85999bfdaaac8ec3c274013... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M client/toolshed/scripts/mvc/groups/group-model.js M lib/galaxy/webapps/tool_shed/api/groups.py M lib/tool_shed/managers/groups.py M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js Log Message: ----------- add more fields; include category links; some minor bugfixes Commit: cc979583ce33904790adf41843e0e7633e7e7850 https://github.com/galaxyproject/galaxy/commit/cc979583ce33904790adf41843e0e... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: A CONTRIBUTORS.md M LICENSE.txt M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js R client/galaxy/scripts/mvc/groups/group-detail-view.js R client/galaxy/scripts/mvc/groups/group-list-view.js R client/galaxy/scripts/mvc/groups/group-listrow-view.js R client/galaxy/scripts/mvc/groups/group-model.js R client/galaxy/scripts/toolshed.groups.js A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/test-file.js A client/toolshed/scripts/toolshed.groups.js M config/galaxy.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/config.py M lib/galaxy/model/custom_types.py M lib/galaxy/queues.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/scripts/api/common.py M scripts/api/common.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js R static/scripts/mvc/groups/group-detail-view.js R static/scripts/mvc/groups/group-groupdetail-view.js R static/scripts/mvc/groups/group-grouprow-view.js R static/scripts/mvc/groups/group-list-view.js R static/scripts/mvc/groups/group-listrow-view.js R static/scripts/mvc/groups/group-model.js R static/scripts/mvc/groups/group.model.js R static/scripts/toolshed.groups.js A static/toolshed/maps/mvc/groups/group-detail-view.js.map A static/toolshed/maps/mvc/groups/group-list-view.js.map A static/toolshed/maps/mvc/groups/group-listrow-view.js.map A static/toolshed/maps/mvc/groups/group-model.js.map A static/toolshed/maps/test-file.js.map A static/toolshed/maps/toolshed.groups.js.map A static/toolshed/scripts/mvc/groups/group-detail-view.js A static/toolshed/scripts/mvc/groups/group-list-view.js A static/toolshed/scripts/mvc/groups/group-listrow-view.js A static/toolshed/scripts/mvc/groups/group-model.js A static/toolshed/scripts/toolshed.groups.js A templates/sorting_base.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_user_per_month.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/api/test_workflows.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Commit: 110b12e571c06d75fd5856f899e8cd51a9cdd075 https://github.com/galaxyproject/galaxy/commit/110b12e571c06d75fd5856f899e8c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-17 (Wed, 17 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.tools.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/utils.js M static/maps/galaxy.tools.js.map M static/maps/mvc/tools.js.map M static/maps/utils/config.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.tools.js M static/scripts/mvc/tools.js M static/scripts/utils/config.js M static/scripts/utils/utils.js Log Message: ----------- Modify a few references to underscore. This fixes these references when importing these modules through qunit. Commit: 41484c3fd5c4b95dfa184212a37783caa955d275 https://github.com/galaxyproject/galaxy/commit/41484c3fd5c4b95dfa184212a3778... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml M display_applications/igv/gff.xml M display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml Log Message: ----------- Merge pull request #364 from erasche/xml-cdata CDATA and linting on external display applications. Commit: 31514c03dea36e1936ed6ebbe6447fd31fdb9af1 https://github.com/galaxyproject/galaxy/commit/31514c03dea36e1936ed6ebbe6447... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/brew_util.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/workflow_util.py M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/code_file.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py Log Message: ----------- Merge pull request #350 from nsoranzo/pep8 PEP-8 and pylint fixes of lib/galaxy/tools/ . Commit: adce4d48e09433f24374dae4c36b688f90d7b92c https://github.com/galaxyproject/galaxy/commit/adce4d48e09433f24374dae4c36b6... Author: James Taylor <james@jamestaylor.org> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M README.rst Log Message: ----------- Shields for biostar, irc, travis in README. Commit: be182022efffaa7d68908d399f628f179ccaa0d9 https://github.com/galaxyproject/galaxy/commit/be182022efffaa7d68908d399f628... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #368 from jxtx/jxtx-shields-1 Shields for biostar, irc, travis in README. Commit: 3d9492639840374b3a201a5b2ead1162f4743382 https://github.com/galaxyproject/galaxy/commit/3d9492639840374b3a201a5b2ead1... Author: Eric Rasche <esr@tamu.edu> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M README.rst Log Message: ----------- Fix link Commit: 41b0d31867e3dcf5cc424197020a020def1df09f https://github.com/galaxyproject/galaxy/commit/41b0d31867e3dcf5cc424197020a0... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #369 from erasche/link-fix Fix link Commit: b58127ed4a05190de56ff74a468ea81751009cee https://github.com/galaxyproject/galaxy/commit/b58127ed4a05190de56ff74a468ea... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M lib/galaxy/tools/loader.py Log Message: ----------- Refactor tool loader toward more reusable token expansion. Refactoring tool macro expansion to evaluate tokens along with XML which will give Galaxy a chance to evaluate xml macro dependent tokens. This in turn will allow parameterized XML macros in the next commit. Commit: 1de2d73f38a5a97fc33f3c814ceecd490b299fe4 https://github.com/galaxyproject/galaxy/commit/1de2d73f38a5a97fc33f3c814ceec... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M lib/galaxy/tools/loader.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Allow parameterization of XML macros. This comes in two modes - simple lists of required attributes and per-attribute parameters that may specify defaults. The following toy example: ``` <tool> <expand macro="inputs" bar="hello" /> <macros> <xml name="inputs" dollar_tokens="bar"> <inputs type="the type is $BAR$" /> </xml> </macros> </tool> ``` will evalute to ``<tool><inputs type="the type is hello" /><tool>``. The XML macro definition tag can now take in two new fixed attributes dollar_tokens and at_tokens - which will be interpreted as a list of parameter names. Each parameter can be specified when expanding the macros as simple attributes specifying the value of the parameter. The "dollar" parameter with name bar would map to a token with name $BAR$. Likewise an "at" parameter with name foo would map to a token with name @FOO@. Both parameter types can be specified on a per-parameter basis to also specify default values. So the following example: ``` <tool> <expand macro="inputs" foo="hello" /> <expand macro="inputs" foo="world" /> <expand macro="inputs" /> <macros> <xml name="inputs" at_token_foo="the_default"> <inputs>@FOO@</inputs> </xml> </macros> </tool> ``` Would evalute to ``<tool><inputs>hello</inputs><inputs>world</inputs><inputs>the_default</inputs>``. Updated unit tests explain the above much more succinctly - though some like English and words for reasons that escape me. Commit: db883b79591b98d1caa9168eddc9e9cecfbc5b75 https://github.com/galaxyproject/galaxy/commit/db883b79591b98d1caa9168eddc9e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M lib/galaxy/tools/loader.py A lib/galaxy/util/xml_macros.py Log Message: ----------- Refactor XML macro handling code for use outside of tools. Commit: 97390558c9ba9319dab64b45e34f5511ce945921 https://github.com/galaxyproject/galaxy/commit/97390558c9ba9319dab64b45e34f5... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Enable XML macros for the job conf XML file. Should allow large de-deduplication of repeated XML definitions when defining job destinations. Given that the same object type (destination) encodes per-tool information (such as resource allocations), per-filesystem such path configurations for Docker or Pulsar), and per-cluster information (such as cluster/Docker/pulsar connection information) - non-trivial deployments will likely have a lot of duplicated XML in job_conf.xml. Macros work exactly the same way as with tools and should allow a great decrease in this XML. Commit: 711d4bb2c50b091e08015be15a5546344c5a80d9 https://github.com/galaxyproject/galaxy/commit/711d4bb2c50b091e08015be15a554... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Modify XML macro parameters to allow arbitrary wrap string. Previously there were two hard-coded toke types at_tokens an dollar_tokens. Now all tokens for the same macro must have the same wrap string and this string can be set arbitrarily with token_quote attribute. The defualt token_quote value is @. Commit: 4e82c8029326e88ce775286ea56f63b80ce6d5b7 https://github.com/galaxyproject/galaxy/commit/4e82c8029326e88ce775286ea56f6... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-18 (Thu, 18 Jun 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Fix for 38679a0d32. Reported by @golharam. Commit: 486899c02167c9875a02a6e0706f097af2c5cffa https://github.com/galaxyproject/galaxy/commit/486899c02167c9875a02a6e0706f0... Author: youri <y.hoogstrate@erasmusmc.nl> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- DotBracket datatype definition is in line with Datatype description at Galaxy wiki Commit: 4b959c42a2cc23ce3d08117447f7ee23056e4ff4 https://github.com/galaxyproject/galaxy/commit/4b959c42a2cc23ce3d08117447f7e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix bug in Text.split() method which may result in producing 1 extra chunk. Commit: 55bcbf445a99f0b1e711305c836a7fcd007099c8 https://github.com/galaxyproject/galaxy/commit/55bcbf445a99f0b1e711305c836a7... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/data.py Log Message: ----------- PEP-8 and pylint fixes. Commit: b2d6238682eb922052c16947308a66c1be9048bd https://github.com/galaxyproject/galaxy/commit/b2d6238682eb922052c16947308a6... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #373 from nsoranzo/pep8 Fix bug in Text.split() method plus PEP-8. Commit: 226d7ef0187c353c70fc7225da7b70f9358602e4 https://github.com/galaxyproject/galaxy/commit/226d7ef0187c353c70fc7225da7b7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Merge pull request #371 from jmchilton/test-data-cache-fix Fix for 38679a0d32. Commit: eb54b1d854a55063cc6f780a6f1594d9e213842d https://github.com/galaxyproject/galaxy/commit/eb54b1d854a55063cc6f780a6f159... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py A lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/search/tool_search.py M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- expose searching full TS toolset over a separate index the index is created by the same script (build_ts_whoosh_index.py) Commit: 1bb4e99e27774b04f1485128949c489838b088e1 https://github.com/galaxyproject/galaxy/commit/1bb4e99e27774b04f1485128949c4... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-19 (Fri, 19 Jun 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py Log Message: ----------- make field boosts for TS search configurable Commit: 72580ef744cc8dadc35ca261935e3fcc8da3a319 https://github.com/galaxyproject/galaxy/commit/72580ef744cc8dadc35ca261935e3... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-21 (Sun, 21 Jun 2015) Changed paths: M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M client/toolshed/scripts/mvc/groups/group-model.js M lib/galaxy/webapps/tool_shed/api/groups.py M lib/tool_shed/managers/groups.py M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js Log Message: ----------- Merge pull request #374 from martenson/ts-groups-polishing TS groups: add more fields; include category links; some minor bugfixes Commit: f8c005c925119b30a3c6280f3a595ffa72dc4fd5 https://github.com/galaxyproject/galaxy/commit/f8c005c925119b30a3c6280f3a595... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-06-21 (Sun, 21 Jun 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/api/repositories.py A lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/search/repo_search.py A lib/galaxy/webapps/tool_shed/search/tool_search.py M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #376 from martenson/ts-expose-tools-api TS expose search tools API Commit: cc1db3543e4866b974e4c59e715cdbba5d9a8365 https://github.com/galaxyproject/galaxy/commit/cc1db3543e4866b974e4c59e715cd... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M .ci/pep8_sources.txt M README.rst M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M client/toolshed/scripts/mvc/groups/group-model.js M config/tool_shed.ini.sample M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml M display_applications/igv/gff.xml M display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/brew_util.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py A lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/search/repo_search.py A lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/managers/groups.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/workflow_util.py M scripts/functional_tests.py M scripts/tool_shed/build_ts_whoosh_index.py M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/code_file.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Conflicts: templates/webapps/galaxy/workflow/editor_tool_form.mako Commit: cbaaf91ebd7eecf8f788046334029e1144e8574d https://github.com/galaxyproject/galaxy/commit/cbaaf91ebd7eecf8f788046334029... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M .ci/pep8_sources.txt Log Message: ----------- Add new xml_macros file to pep8 sources. Commit: 654ffe97ea86202d31ffa00b0651de779e930f1c https://github.com/galaxyproject/galaxy/commit/654ffe97ea86202d31ffa00b0651d... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M test/unit/tools/test_tool_loader.py Log Message: ----------- Update out-dated comment in test_tool_loader. Commit: 086601b679a112d7df6b2f4b1eb01c580f85b275 https://github.com/galaxyproject/galaxy/commit/086601b679a112d7df6b2f4b1eb01... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- make valid rst Commit: 10cf0b02da20f2adcd164f70e292f891c91cf037 https://github.com/galaxyproject/galaxy/commit/10cf0b02da20f2adcd164f70e292f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #381 from martenson/rst-release-validation make rst valid Commit: e1c80f614fdf17a730045ac87315b5cab575ca92 https://github.com/galaxyproject/galaxy/commit/e1c80f614fdf17a730045ac87315b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M README.rst Log Message: ----------- Add Read The Docs badge. Commit: f98d4b27a03d9f4fff070a7ccb1607c499f13f73 https://github.com/galaxyproject/galaxy/commit/f98d4b27a03d9f4fff070a7ccb160... Author: David Trudgian <david.trudgian@utsouthwestern.edu> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M cron/parse_builds.py Log Message: ----------- Use passed in URL for getbuilds Commit: a5a474fd40c33295d766a176f0276da2d8fb4b36 https://github.com/galaxyproject/galaxy/commit/a5a474fd40c33295d766a176f0276... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/util/xml_macros.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Add example and test case for job configuration expansion. First suggestion by @nsoranzo and second was easy once example was added to advanced config. Commit: eafa4ac38113a95d696836dd54c9ecaea2fac1ce https://github.com/galaxyproject/galaxy/commit/eafa4ac38113a95d696836dd54c9e... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #383 from nsoranzo/dev Add Read The Docs badge. Commit: 07a0ae07638aac89e8bd48c211d1b6fc6ca17d20 https://github.com/galaxyproject/galaxy/commit/07a0ae07638aac89e8bd48c211d1b... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.tools.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/utils.js M static/maps/galaxy.tools.js.map M static/maps/mvc/tools.js.map M static/maps/utils/config.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.tools.js M static/scripts/mvc/tools.js M static/scripts/utils/config.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #3 from jmchilton/workflow_form_002_tests2 Modify a few references to underscore. Commit: 60eb856941311bbbf9b22abd04824dfac7467a07 https://github.com/galaxyproject/galaxy/commit/60eb856941311bbbf9b22abd04824... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Update 15.07 timeline to post-GCC Commit: f90e2e12f63225e81f48be8236f6f5bc5dd9a60c https://github.com/galaxyproject/galaxy/commit/f90e2e12f63225e81f48be8236f6f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-22 (Mon, 22 Jun 2015) Changed paths: M .ci/pep8_sources.txt M test/unit/jobs/test_job_configuration.py Log Message: ----------- Fix stray print noticed by @nsoranzo. And add that file to pep8 sources. Commit: 30f2b6e25f5bf4fe69166c92b5782581b993d1ca https://github.com/galaxyproject/galaxy/commit/30f2b6e25f5bf4fe69166c92b5782... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: A proteomics.py Log Message: ----------- Removed all tools except one. We need one tool for now until toolshed supports pure datatype repos Commit: f40d06fbd811741f0f68f0cfb303c2c8a1efac27 https://github.com/galaxyproject/galaxy/commit/f40d06fbd811741f0f68f0cfb303c... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- Added protkgff Commit: 33b5871b78f32c961ba77fec154769859340eb59 https://github.com/galaxyproject/galaxy/commit/33b5871b78f32c961ba77fec15476... Author: Bjoern Gruening <devnull@localhost> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- add new filetypes from OpenMS; sync with Galaxy-P Project Commit: b12d430f3e6d724c08f937be54d08a43b78fd0be https://github.com/galaxyproject/galaxy/commit/b12d430f3e6d724c08f937be54d08... Author: Bjoern Gruening <devnull@localhost> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- add missing import Commit: 663915c8f4ad99536ceb296d85dad4da98437cd6 https://github.com/galaxyproject/galaxy/commit/663915c8f4ad99536ceb296d85dad... Author: BjoernGruening <devnull@localhost> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- remove xls datatype definition Commit: 51f838964e89047f37d89ed1de9abee00076347f https://github.com/galaxyproject/galaxy/commit/51f838964e89047f37d89ed1de9ab... Author: BjoernGruening <devnull@localhost> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- add composite datatype for the wiff format Commit: 34358590874a769d743dbf35c9a029fc3c9d6ad9 https://github.com/galaxyproject/galaxy/commit/34358590874a769d743dbf35c9a02... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- Remove proteomics gff and proteogenomics display site Commit: 0a78ae817dd73b1d9f9938a2f67f36a1d9234d99 https://github.com/galaxyproject/galaxy/commit/0a78ae817dd73b1d9f9938a2f67f3... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- Add XTandem datatype Commit: 534d52ebb6088804da599a1ce17dfc5bbb11803e https://github.com/galaxyproject/galaxy/commit/534d52ebb6088804da599a1ce17df... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- Add splib datatype Commit: db514daaef946ee3cb4f379da4df1c5dd8c3b056 https://github.com/galaxyproject/galaxy/commit/db514daaef946ee3cb4f379da4df1... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- Make splib a composite datatype to include indexes Commit: d56f2ec999b419a099cc9c211fd7192ef90f8923 https://github.com/galaxyproject/galaxy/commit/d56f2ec999b419a099cc9c211fd71... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- add sf3 datatype Commit: 421cdc54cdb578fd1b06ea9244c7ec3c73c20c98 https://github.com/galaxyproject/galaxy/commit/421cdc54cdb578fd1b06ea9244c7e... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M proteomics.py Log Message: ----------- Add splibnoindex type Commit: b16d224fceff2475efd3a9a9a00fdeddc84c1585 https://github.com/galaxyproject/galaxy/commit/b16d224fceff2475efd3a9a9a00fd... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py R proteomics.py Log Message: ----------- Add proteomics datatypes Commit: 734a429d3caaf987dacec9279c0f617ed323e3c0 https://github.com/galaxyproject/galaxy/commit/734a429d3caaf987dacec9279c0f6... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Proteomics Sniffers above GenericXML Commit: 218f00d7e82dbff45bed7433489a55d8f4c1d617 https://github.com/galaxyproject/galaxy/commit/218f00d7e82dbff45bed7433489a5... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Remove sniffing tests Commit: 610e93ef4e8a61e85a217be962f72200b7690505 https://github.com/galaxyproject/galaxy/commit/610e93ef4e8a61e85a217be962f72... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Manually add Bjoern's recent changes Commit: 82553d67de411cf7bf292db6355d6f3b3924ad3a https://github.com/galaxyproject/galaxy/commit/82553d67de411cf7bf292db6355d6... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Remove sniff tests again Commit: d1179ebd145d475aa6db3f00db34f09698a58e87 https://github.com/galaxyproject/galaxy/commit/d1179ebd145d475aa6db3f00db34f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M .ci/pep8_sources.txt M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/loader.py A lib/galaxy/util/xml_macros.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #362 from jmchilton/xml_macros_3 More, Better XML Macros Commit: d25bd388960f3ad698654b17611266098f1acf00 https://github.com/galaxyproject/galaxy/commit/d25bd388960f3ad698654b1761126... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- UI, History structure: fix/update serializer call to non-trans form Commit: 9a3217e10a19eab3ce556cc63f6f4082a5103f2e https://github.com/galaxyproject/galaxy/commit/9a3217e10a19eab3ce556cc63f6f4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Merge pull request #390 from carlfeberhard/dev UI, History structure: fix/update serializer call to non-trans form Commit: 952089e67b2693cd63f0f2b59f088a24d92e860f https://github.com/galaxyproject/galaxy/commit/952089e67b2693cd63f0f2b59f088... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Log Message: ----------- Merge branch 'master' into dev Commit: fcd5552bdde80af7c929fd8d8e672d4679d51e4e https://github.com/galaxyproject/galaxy/commit/fcd5552bdde80af7c929fd8d8e672... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #386 from dannon/update_release_timeline Update 15.07 timeline to post-GCC Commit: 3eb203437c71b98362e8fe3bf5912f88d950a797 https://github.com/galaxyproject/galaxy/commit/3eb203437c71b98362e8fe3bf5912... Author: Dave B. <dave@bx.psu.edu> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh Log Message: ----------- Fix getting admin key when bootstrapping toolshed. Commit: 3593d9c45ca416e7612e29ce5c8d3c1f89da4542 https://github.com/galaxyproject/galaxy/commit/3593d9c45ca416e7612e29ce5c8d3... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove trailing spaces Commit: 1e86a77589779fe717fc0b39593005d379d4838c https://github.com/galaxyproject/galaxy/commit/1e86a77589779fe717fc0b3959300... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add fixes suggested by John Chilton Commit: 0e6fe6f279c23845555c829fcd9859080af363af https://github.com/galaxyproject/galaxy/commit/0e6fe6f279c23845555c829fcd985... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Don't add proteomics.py to registry.py Commit: 990535a280a5a77b789a884d96feb81c55e7dabb https://github.com/galaxyproject/galaxy/commit/990535a280a5a77b789a884d96feb... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt Log Message: ----------- Include proteomics.py in pep8_sources Commit: aad8cb1902d28665164d0132bad7fecd1e8ecee8 https://github.com/galaxyproject/galaxy/commit/aad8cb1902d28665164d0132bad7f... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- pep8 fixes Commit: 98edbadf685adcb252d31e4de40c6e5e328e85e3 https://github.com/galaxyproject/galaxy/commit/98edbadf685adcb252d31e4de40c6... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Syntax fixes Commit: 8ac5eb98a5071042799a6491d756fab753084d75 https://github.com/galaxyproject/galaxy/commit/8ac5eb98a5071042799a6491d756f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M .ci/pep8_sources.txt M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py Log Message: ----------- PEP-8 fixes for entire test/unit/tools module. Add the module to .ci/pep8_sources.txt. Commit: 3784fece91d9ec6ab068ec4d02270b31cf98d7df https://github.com/galaxyproject/galaxy/commit/3784fece91d9ec6ab068ec4d02270... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-23 (Tue, 23 Jun 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A test/functional/tools/environment_variables.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Allow environment variable definitions in tool XML. An ``<environment_variables>`` top-level XML block can be used to define these. ``` <environment_variables> <environment_variable name="FOO">$bar</environment_variable> <environment_variable name="FOO2">$bar2</environment_variable </environment_variables> ``` The expressions are contained in the text of the block. Implementation Detials: In order to avoid odd shell expression stuff - the evaluated expressions are written to files and environment variables are read from these files at runtime. Testing: A demo tool ``test/functional/tools/environment_variables.xml`` with a test case that can be executed with the following expression. ``` ./run_tests.sh -framework -id environment_variables ``` Commit: 2299839981e44a71ab7518cff4a3f9edf785b6bd https://github.com/galaxyproject/galaxy/commit/2299839981e44a71ab7518cff4a3f... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #394 from jmchilton/tool_unit_test_pep PEP-8 fixes for entire test/unit/tools module. Commit: 56f9303fce902b50a033231d70f9a67c35dcbbe9 https://github.com/galaxyproject/galaxy/commit/56f9303fce902b50a033231d70f9a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M cron/parse_builds.py Log Message: ----------- PEP-8 fixes. Commit: 91307345129486b871651f5bcd0f4c7f2762dd63 https://github.com/galaxyproject/galaxy/commit/91307345129486b871651f5bcd0f4... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M cron/parse_builds.py Log Message: ----------- Simplify code. Commit: 717b2064f4a8cc8fef2efe8d4233009a17463f74 https://github.com/galaxyproject/galaxy/commit/717b2064f4a8cc8fef2efe8d42330... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M cron/parse_builds.py Log Message: ----------- Fix missing substitution from f98d4b27a03d9f4fff070a7ccb1607c499f13f73 . Commit: 78a69c09a36035329eef7b5ea5140bb6f2f3e1bc https://github.com/galaxyproject/galaxy/commit/78a69c09a36035329eef7b5ea5140... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Better file I/O handling for refactored code. Suggested by @nsoranzo (https://github.com/galaxyproject/galaxy/pull/395#discussion_r33136542). Commit: 7879327c34d7485dc9a4665aeab93250112c6925 https://github.com/galaxyproject/galaxy/commit/7879327c34d7485dc9a4665aeab93... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M test/functional/tools/environment_variables.xml Log Message: ----------- Add more interesting expression to environment_variables demo tool. Per suggestion by @nsoranzo (https://github.com/galaxyproject/galaxy/pull/395#issuecomment-114827531). Commit: f090fb80b05f95cc7184b2903da51bc725215525 https://github.com/galaxyproject/galaxy/commit/f090fb80b05f95cc7184b2903da51... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A test/functional/tools/environment_variables.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #395 from jmchilton/tool_env_vars Allow environment variable definitions in tool XML. Commit: 4e537c86e1d56d821bb2601b162517633fd7b0c0 https://github.com/galaxyproject/galaxy/commit/4e537c86e1d56d821bb2601b16251... Author: David Trudgian <dave@trudgian.net> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M cron/parse_builds.py Log Message: ----------- Merge pull request #1 from nsoranzo/for_dctrud Code cleanup. from @nsoranzo Commit: bfc0a22780216f849d7c4d25cc1dbec74ef305b4 https://github.com/galaxyproject/galaxy/commit/bfc0a22780216f849d7c4d25cc1db... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M cron/parse_builds.py Log Message: ----------- Merge pull request #384 from dctrud/parse_builds_fix Use passed in URL for getbuilds method of parse_builds.py Commit: 416785e16d7a7530ece52eea43a5e989e8c53258 https://github.com/galaxyproject/galaxy/commit/416785e16d7a7530ece52eea43a5e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M doc/source/lib/galaxy.webapps.galaxy.api.rst Log Message: ----------- Update rst docs for bab978a4f473d592abf0ecccbb41223d5a0daea5 . Commit: 1ae11cbe08afec79f8a0aaab0386af89a0174bfb https://github.com/galaxyproject/galaxy/commit/1ae11cbe08afec79f8a0aaab0386a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix default qunit test cases for the workflow editor Commit: 63fee8f7ce82fce4402320df2af7aa384e17d9c6 https://github.com/galaxyproject/galaxy/commit/63fee8f7ce82fce4402320df2af7a... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M client/galaxy/scripts/galaxy.tools.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/utils.js M static/maps/galaxy.tools.js.map M static/maps/mvc/tools.js.map M static/maps/utils/config.js.map M static/maps/utils/utils.js.map M static/scripts/galaxy.tools.js M static/scripts/mvc/tools.js M static/scripts/utils/config.js M static/scripts/utils/utils.js M test/qunit/test-common.js Log Message: ----------- Undo merged fixed, replace underscore path rewrite Commit: 53d13e9284ad9d2f21e7fcd647864d2f650ea9b8 https://github.com/galaxyproject/galaxy/commit/53d13e9284ad9d2f21e7fcd647864... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M README.rst M config/job_conf.xml.sample_advanced M cron/parse_builds.py M doc/source/releases/15.07_announce.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/util/xml_macros.py M templates/webapps/galaxy/history/display_structured.mako A test/functional/tools/environment_variables.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 Commit: e51cd719dc6fb4041cd01fb533ac7d0b32251c2b https://github.com/galaxyproject/galaxy/commit/e51cd719dc6fb4041cd01fb533ac7... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix remaining qunit test cases for the workflow editor Commit: 61024b832e422981a6ffcd4bb31422b28bafd758 https://github.com/galaxyproject/galaxy/commit/61024b832e422981a6ffcd4bb3142... Author: guerler <aysam.guerler@gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: A static/maps/mvc/workflow/workflow-view.js.map A static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add missing packed files Commit: fea0243eb2a7dc653ecd094661e675a984f53983 https://github.com/galaxyproject/galaxy/commit/fea0243eb2a7dc653ecd094661e67... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix MsP sniffer Commit: 031b4e01c0eabda4259babc218b0ddd76a224676 https://github.com/galaxyproject/galaxy/commit/031b4e01c0eabda4259babc218b0d... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Back out trailing space removal Commit: c2cf786e76f15ece24ac9b2972d30c3d48a4714f https://github.com/galaxyproject/galaxy/commit/c2cf786e76f15ece24ac9b2972d30... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove trailing spaces on line 46 Commit: 8d2a6f2287467d5081e86114433455006105424e https://github.com/galaxyproject/galaxy/commit/8d2a6f2287467d5081e8611443345... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix sphinx doc building of galaxy.webapps.galaxy.api.tools . Commit: bd868be6eb9aff76f5e0ebec801d2525d7e1b055 https://github.com/galaxyproject/galaxy/commit/bd868be6eb9aff76f5e0ebec801d2... Author: abretaud <anthony.bretaudeau@rennes.inra.fr> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M templates/show_params.mako Log Message: ----------- fix error when displaying job params for tools containing a section Commit: b29f7244405a6fcdb18bf9099a07ad18a8e64028 https://github.com/galaxyproject/galaxy/commit/b29f7244405a6fcdb18bf9099a07a... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Almost complete PEP-8 fixes for api/tools.py . Commit: 7556c9a2b269332c4fae4c2b8f7af6b8c3b9d9e8 https://github.com/galaxyproject/galaxy/commit/7556c9a2b269332c4fae4c2b8f7af... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/model/search.py Log Message: ----------- Fix sphinx doc building of galaxy.webapps.galaxy.api.search . Commit: d501396f702a68557c64777d26e654efc97cf541 https://github.com/galaxyproject/galaxy/commit/d501396f702a68557c64777d26e65... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/model/search.py Log Message: ----------- PEP-8 and pylint fixes for lib/galaxy/model/search.py . Commit: 615dfb715bdbc470c74fe6436fe55e2be62c4a3f https://github.com/galaxyproject/galaxy/commit/615dfb715bdbc470c74fe6436fe55... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Extended the basic flake8 checks to (almost) all lib/ . Commit: 2bb4d5f48b4751d7fccd9a590b9a23034e3da669 https://github.com/galaxyproject/galaxy/commit/2bb4d5f48b4751d7fccd9a590b9a2... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M doc/source/lib/galaxy.webapps.galaxy.api.rst M lib/galaxy/model/search.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #399 from nsoranzo/dev [GCC2015] Fixes for ReadTheDocs API documentation. Commit: 97b19e422cf101e8135440bdad7b71aac23fa1da https://github.com/galaxyproject/galaxy/commit/97b19e422cf101e8135440bdad7b7... Author: Dave B <dave@bx.psu.edu> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh Log Message: ----------- Manually cherry-pick ecf8973484248c37f8dc96670f14a5ecce1a0c18. Commit: 2ca436a5a485c7adfa3260438f16a274b4b44624 https://github.com/galaxyproject/galaxy/commit/2ca436a5a485c7adfa3260438f16a... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh Log Message: ----------- Merge pull request #392 from galaxyproject/fix_bootstrap Fix getting admin key when bootstrapping toolshed. Commit: cca245c62c57077f596dae035a73f7e2e6b03fa8 https://github.com/galaxyproject/galaxy/commit/cca245c62c57077f596dae035a73f... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Change RAW to ThermoRAW and add to sniffers Commit: a85d03ff0dde3856d101caaf45d7477bb8b9ba82 https://github.com/galaxyproject/galaxy/commit/a85d03ff0dde3856d101caaf45d74... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add back Binary.sniffable code because sniffing doesn't work properly without it Commit: 03e3541cb907a72e6d1340e19f5b4e03f977d755 https://github.com/galaxyproject/galaxy/commit/03e3541cb907a72e6d1340e19f5b4... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Allow workflows executed via the API to run when Tool steps have upgrade messages, by providing allow_tool_upgrades=True within the payload. Commit: c65185d8bcd806bd2376c27e4bc73f1e64ad75a1 https://github.com/galaxyproject/galaxy/commit/c65185d8bcd806bd2376c27e4bc73... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-connector.js A client/galaxy/scripts/mvc/workflow/workflow-manager.js A client/galaxy/scripts/mvc/workflow/workflow-node.js A client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/mvc/workflow/workflow-view-data.js A client/galaxy/scripts/mvc/workflow/workflow-view-node.js A client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js A client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample R static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map A static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-connector.js.map A static/maps/mvc/workflow/workflow-manager.js.map A static/maps/mvc/workflow/workflow-node.js.map A static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/mvc/workflow/workflow-view-data.js.map A static/maps/mvc/workflow/workflow-view-node.js.map A static/maps/mvc/workflow/workflow-view-terminals.js.map A static/maps/mvc/workflow/workflow-view.js.map A static/maps/mvc/workflow/workflow.js.map R static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js A static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-connector.js A static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-node.js A static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow-view-data.js A static/scripts/mvc/workflow/workflow-view-node.js A static/scripts/mvc/workflow/workflow-view-terminals.js A static/scripts/mvc/workflow/workflow-view.js A static/scripts/mvc/workflow/workflow.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #397 from guerler/workflow_form_002 Strip former workflow editor, move js-files to sub-directory in mvc Commit: 089cd474d0351e4ac71b4af25f11e706d83f14e6 https://github.com/galaxyproject/galaxy/commit/089cd474d0351e4ac71b4af25f11e... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-27 (Sat, 27 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Change raw to thermo.raw Commit: 484e2f72ca12f5d7cde633ed8fda18287b1308e4 https://github.com/galaxyproject/galaxy/commit/484e2f72ca12f5d7cde633ed8fda1... Author: Ira Cooke <iracooke@gmail.com> Date: 2015-06-27 (Sat, 27 Jun 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- pep8 fixes Commit: 3deaf2f103669d12a150c46cb6e0fb6853205c7c https://github.com/galaxyproject/galaxy/commit/3deaf2f103669d12a150c46cb6e0f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-27 (Sat, 27 Jun 2015) Changed paths: M .ci/pep8_sources.txt M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #389 from iracooke/dev Proteomics Datatypes Commit: 71b963b2d00b85cc367fae9d964dcf10373789bb https://github.com/galaxyproject/galaxy/commit/71b963b2d00b85cc367fae9d964dc... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M .ci/pep8_sources.txt M doc/source/conf.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Fix a few tracebacks when building docs with 'make -C doc/ html' . Commit: 11e8a6c30ad174e558466ddd67b5ba70475fbac7 https://github.com/galaxyproject/galaxy/commit/11e8a6c30ad174e558466ddd67b5b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py Log Message: ----------- PEP-8 and pylint fixes. Commit: 025930bfd1af074638c7ce7b2b5190a2ffe42463 https://github.com/galaxyproject/galaxy/commit/025930bfd1af074638c7ce7b2b519... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: A doc/source/api_doc.rst M doc/source/index.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst Log Message: ----------- Move the additional API doc out of autogenerated docs. Commit: f339cc16313ddaeac066e2f1189c0dd09983ed59 https://github.com/galaxyproject/galaxy/commit/f339cc16313ddaeac066e2f1189c0... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: R doc/source/lib/fpconst.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.jobs.deferred.rst A doc/source/lib/galaxy.jobs.metrics.collectl.rst A doc/source/lib/galaxy.jobs.metrics.instrumenters.rst A doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.cli_job.rst R doc/source/lib/galaxy.jobs.runners.cli_shell.rst A doc/source/lib/galaxy.jobs.runners.lwr_client.rst A 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doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst A doc/source/lib/tool_shed.galaxy_install.tools.rst A doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst A doc/source/lib/tool_shed.managers.rst A doc/source/lib/tool_shed.metadata.rst A doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst A doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst A doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/15.05.rst Log Message: ----------- Fix doc/source/ using sphinx-apidoc v1.1.3 . Commit: ee0ce040cebd043bbb76930ac55cf4f5e11dd40c https://github.com/galaxyproject/galaxy/commit/ee0ce040cebd043bbb76930ac55cf... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M doc/source/conf.py M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.lwr_client.rst M doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst M doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M 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doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/galaxy_utils.rst M doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/mimeparse.rst M doc/source/lib/pkg_resources.rst M doc/source/lib/psyco_full.rst M doc/source/lib/pulsar.client.rst M doc/source/lib/pulsar.client.staging.rst M doc/source/lib/pulsar.client.transport.rst M doc/source/lib/pulsar.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst Log Message: ----------- Update to sphinx-apidoc v1.3.1 . sphinx-apidoc -M -o doc/source/lib/ lib/ Commit: 9567073475f28e94a1901000eae5e7c2fcd94af4 https://github.com/galaxyproject/galaxy/commit/9567073475f28e94a1901000eae5e... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for setting environment variable paths for installed tool dependencies in cases where $ENV[SOMEVAR] is used. This approach takes the value of SOMEVAR from the env_var_dict where the original approach called subprocess.Popen() to echo the value. This echoing occurred in the InstallEnvironment.handle_complex_command() function, which produces stdout in such a way that the value of the environment variable being echo'ed will likely be truncated or munged due to the way stdout logging works. Commit: c53170f215e10fe14420e4f85a845c4fc1326410 https://github.com/galaxyproject/galaxy/commit/c53170f215e10fe14420e4f85a845... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py Log Message: ----------- Fix managers to pass context necessary down the chain when purging. This should fix at least one quota calc error. Fix another bug in hda manager regarding quota reduction -- quota usage must be calculated prior to actually purging, otherwise the disk usage is 0 and this does nothing. Slight refactoring in manager purge -- we don't need to pass the user via context since we can just grab it where applicable from the history. Fix purge when handling an anonymous user Commit: c2917a78f87527bee5f3d0a531a2660d20eb24e5 https://github.com/galaxyproject/galaxy/commit/c2917a78f87527bee5f3d0a531a26... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M doc/source/conf.py Log Message: ----------- Change html_theme to sphinx_rtd_theme to fix left sidebar. Commit: 878dda02223b7dfcb5cc8f4549b2a23d953bce99 https://github.com/galaxyproject/galaxy/commit/878dda02223b7dfcb5cc8f4549b2a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M .ci/pep8_sources.txt A doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/fpconst.rst M doc/source/lib/galaxy.actions.rst A doc/source/lib/galaxy.auth.providers.rst A doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.dataset_collections.rst A doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst A doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst A 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doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst A doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst R doc/source/lib/galaxy.webapps.community.controllers.rst R doc/source/lib/galaxy.webapps.community.framework.middleware.rst R doc/source/lib/galaxy.webapps.community.framework.rst R doc/source/lib/galaxy.webapps.community.model.migrate.rst R doc/source/lib/galaxy.webapps.community.model.rst R doc/source/lib/galaxy.webapps.community.rst R doc/source/lib/galaxy.webapps.community.security.rst R doc/source/lib/galaxy.webapps.community.util.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M 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doc/source/lib/pkg_resources.rst M doc/source/lib/psyco_full.rst A doc/source/lib/pulsar.client.rst A doc/source/lib/pulsar.client.staging.rst A doc/source/lib/pulsar.client.transport.rst A doc/source/lib/pulsar.rst A doc/source/lib/tool_shed.capsule.rst A doc/source/lib/tool_shed.dependencies.repository.rst A doc/source/lib/tool_shed.dependencies.rst A doc/source/lib/tool_shed.dependencies.tool.rst A doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst A doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst A doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst A doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst A doc/source/lib/tool_shed.galaxy_install.tools.rst A doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst A doc/source/lib/tool_shed.managers.rst A doc/source/lib/tool_shed.metadata.rst A doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst A doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst A doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/15.05.rst M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py Log Message: ----------- Merge pull request #405 from nsoranzo/dev Sync doc/source/lib with current lib/ Commit: 71c38c482f8af0b52927fbc1944478de3aab3282 https://github.com/galaxyproject/galaxy/commit/71c38c482f8af0b52927fbc194447... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py Log Message: ----------- Merge pull request #406 from dannon/manager_quota_calc_fix Quota calculation fixes for managers Commit: 2b1ce19e45ec66b6d16fcad31405d25ad536e002 https://github.com/galaxyproject/galaxy/commit/2b1ce19e45ec66b6d16fcad31405d... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Change allow_tool_upgrades to allow_tool_state_corrections. Commit: 663dc3da6eac5509fd3faa7a0894c4fc692ed963 https://github.com/galaxyproject/galaxy/commit/663dc3da6eac5509fd3faa7a0894c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Merge pull request #402 from blankenberg/workflow-run-with-upgrade Allow workflows executed via the API to optionally run with tool upgrades Commit: 01f2ac19cafc3b41a718e6510a42b8158cb59d98 https://github.com/galaxyproject/galaxy/commit/01f2ac19cafc3b41a718e6510a42b... Author: John Chilton <jmchilton@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #403 from gregvonkuster/dev Fix for setting environment variable paths for installed tool Commit: 1020d46c52b1fc0fa2effa2882f1fd64216d2c75 https://github.com/galaxyproject/galaxy/commit/1020d46c52b1fc0fa2effa2882f1f... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py Log Message: ----------- fix paging issue with whoosh due to missing str to int conversion Commit: 56d9ae77fd0137e0c348ac8630a555466cd8df48 https://github.com/galaxyproject/galaxy/commit/56d9ae77fd0137e0c348ac8630a55... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-06-29 (Mon, 29 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py Log Message: ----------- Merge pull request #407 from martenson/fix-ts-search-paging fix paging issue with whoosh due to missing str to int conversion Commit: a212f81e2548c78b60796fa9763ff49ff57db3f5 https://github.com/galaxyproject/galaxy/commit/a212f81e2548c78b60796fa9763ff... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-30 (Tue, 30 Jun 2015) Log Message: ----------- Merge branch 'master' into dev Commit: db88231d12ed74cdd99f36e09d621148eb2cf7e3 https://github.com/galaxyproject/galaxy/commit/db88231d12ed74cdd99f36e09d621... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-30 (Tue, 30 Jun 2015) Log Message: ----------- Merge branch 'master' into dev Commit: 1387ae1e3e96d48f7faa0cfcc42ad9d39bb3d12c https://github.com/galaxyproject/galaxy/commit/1387ae1e3e96d48f7faa0cfcc42ad... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M config/object_store_conf.xml.sample M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge pull request #354 from charz/fixed_object_store_path Fixed object store path ('job_work') Commit: 4d20a61a345252e636befde68170291a506bfe9e https://github.com/galaxyproject/galaxy/commit/4d20a61a345252e636befde681702... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Use web.url_for( '/', qualified=True ) instead of '/' to generate URL for toolshed repository downloads. Fixes repository downloads from toolsheds that are on a subfolder (e.g. http://example.com/toolshed). Commit: fcc706e8d0c888a2a6b6b91e1b9312feb8021a7c https://github.com/galaxyproject/galaxy/commit/fcc706e8d0c888a2a6b6b91e1b931... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako Log Message: ----------- Whitespace/other small fixes Commit: 5409bf3be304adc0bf376613ecf7003c0431826f https://github.com/galaxyproject/galaxy/commit/5409bf3be304adc0bf376613ecf70... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-06-30 (Tue, 30 Jun 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Switch to full template It looks a *lot* nicer Commit: 43d6643a0b4a76601cc503fd18bff09ef75f3918 https://github.com/galaxyproject/galaxy/commit/43d6643a0b4a76601cc503fd18bff... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-01 (Wed, 01 Jul 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #412 from erasche/gcc2015-ie-updates GCC2015 ie updates Commit: 4f8ef6539c9c88857ec5205a409bde8dc6224010 https://github.com/galaxyproject/galaxy/commit/4f8ef6539c9c88857ec5205a409bd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-01 (Wed, 01 Jul 2015) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- cluster-side filtering of metadata keys. Still done once the final dict is assembled, to allow for all three passes to work correctly with their dependent keys, etc. Commit: be37fc491dcbdb7c4af3f0c8ac99c0b866813e1f https://github.com/galaxyproject/galaxy/commit/be37fc491dcbdb7c4af3f0c8ac99c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-01 (Wed, 01 Jul 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- One flake8 spacing fix. Commit: e6a4d1a54b42f701000ff22a1a2aa244026c2a37 https://github.com/galaxyproject/galaxy/commit/e6a4d1a54b42f701000ff22a1a2aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-01 (Wed, 01 Jul 2015) Changed paths: M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Add same key-dropping functionality for explicit metadata reset. Commit: 1f94bafa4bf1ac3e57af1549b293480c7537aeaf https://github.com/galaxyproject/galaxy/commit/1f94bafa4bf1ac3e57af1549b2934... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-01 (Wed, 01 Jul 2015) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #416 from dannon/even_more_metadata_fixes cluster-side filtering of metadata keys. Still done once the final d… Commit: 79562cf8d2034b922fca461c08c9b0156bcc7ad4 https://github.com/galaxyproject/galaxy/commit/79562cf8d2034b922fca461c08c9b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-01 (Wed, 01 Jul 2015) Changed paths: M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewport.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'master' into dev Commit: 80d7d4f70fa7067985669f51f7aaef185268c2b7 https://github.com/galaxyproject/galaxy/commit/80d7d4f70fa7067985669f51f7aae... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-02 (Thu, 02 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Merge pull request #414 from mvdbeek/fix_toolshed_repository_download Use web.url_for( '/', qualified=True ) instead of '/' to generate Commit: 235f432c43099132c2e53fcabf55728ea708e642 https://github.com/galaxyproject/galaxy/commit/235f432c43099132c2e53fcabf557... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-02 (Thu, 02 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #366 from yhoogstrate/dev Datatype definition for Dot-Bracket notation (dbn) Commit: 2a8aaab4a359e0d80759f34326259b8a03f0de30 https://github.com/galaxyproject/galaxy/commit/2a8aaab4a359e0d80759f34326259... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py Log Message: ----------- allow setting of page_size in the ts search request also return current page and page_size in the response Commit: 55f6ce0c1f798e8515901ac308d8e04820928db5 https://github.com/galaxyproject/galaxy/commit/55f6ce0c1f798e8515901ac308d8e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py Log Message: ----------- Merge pull request #420 from martenson/ts-search-adjustments allow setting of page_size in the ts search request Commit: 152ebeee103d4c31268c2d20073e77049838214a https://github.com/galaxyproject/galaxy/commit/152ebeee103d4c31268c2d20073e7... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/actions/admin.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/coverage.py Log Message: ----------- pep8 lint fixes Commit: 4d184f5a178315f2009894ec0016fec8dbd437ad https://github.com/galaxyproject/galaxy/commit/4d184f5a178315f2009894ec0016f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/actions/admin.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/coverage.py Log Message: ----------- Merge pull request #421 from jmchilton/lint_2 Pep-8 lint fixes (1) Commit: a649cefbadab3f611802695975d25b3b9b7b5600 https://github.com/galaxyproject/galaxy/commit/a649cefbadab3f611802695975d25... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Fix for Async datasources where URL is different from the original tool action and where URL already contains query parameters. Commit: 2a24c80970810396143515369fca335478a483a7 https://github.com/galaxyproject/galaxy/commit/2a24c80970810396143515369fca3... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/external_services/__init__.py M lib/galaxy/external_services/actions.py Log Message: ----------- lint fixes Commit: 58091b4b5b5c209f01ebf81fcbc0e89f30bca8fa https://github.com/galaxyproject/galaxy/commit/58091b4b5b5c209f01ebf81fcbc0e... Author: Oleksandr Moskalenko <om@rc.ufl.edu> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Make the Group tool return integer values when 'round to nearest integer' is selected Commit: 2b79fd3c1cb72b173f1c5f60dd0c311950cc42f8 https://github.com/galaxyproject/galaxy/commit/2b79fd3c1cb72b173f1c5f60dd0c3... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Merge pull request #423 from blankenberg/async-datasource Fix for Async datasources Commit: b93b186163846ab0496cbae93f593dd876e52718 https://github.com/galaxyproject/galaxy/commit/b93b186163846ab0496cbae93f593... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Updated histories content create action to have the ability to import a library folder Commit: 52b0332f243d377fc1e32bbe4165386213972717 https://github.com/galaxyproject/galaxy/commit/52b0332f243d377fc1e32bbe41653... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Updated galaxy library beta ui to be able to select a library folder for import Commit: 0c7c7db1e193ed1bbadb2843f49bcb4d914253a8 https://github.com/galaxyproject/galaxy/commit/0c7c7db1e193ed1bbadb2843f49bc... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Added compiled js Commit: 22a811beaedbd958f26027a20665c2da6ac95fc0 https://github.com/galaxyproject/galaxy/commit/22a811beaedbd958f26027a20665c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-04 (Sat, 04 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/external_services/__init__.py M lib/galaxy/external_services/actions.py Log Message: ----------- Merge pull request #424 from nsoranzo/dev Hackathon lint fixes, round 2 Commit: 5deb35a106438f85c243d0da28d30daf3375f7a3 https://github.com/galaxyproject/galaxy/commit/5deb35a106438f85c243d0da28d30... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- Updated library folder row to toggle checkbox when row is clicked Commit: 61a909978b2147f5584b18a801b84cff6bff1db9 https://github.com/galaxyproject/galaxy/commit/61a909978b2147f5584b18a801b84... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Updated library view to show toolbar when folder or file present instead of only when file present Commit: 5a3b6564bc549b67c5cc2e84b74654989a77dbad https://github.com/galaxyproject/galaxy/commit/5a3b6564bc549b67c5cc2e84b7465... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- Icon now changes properly when folder row selected in beta library interface Commit: a098b495b7618ff7d69840f97fee38a489b29d6e https://github.com/galaxyproject/galaxy/commit/a098b495b7618ff7d69840f97fee3... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Removed unused created_hdas and added rval to __create_datasets_from_library_folder Commit: ab4dc39a67ddecbd75fdf7090a2d773149f4baf5 https://github.com/galaxyproject/galaxy/commit/ab4dc39a67ddecbd75fdf7090a2d7... Author: Jim Johnson <jj@umn.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite This is a SQLite schema for representing Peptide Spectral Matches from mzid and mzML datatypes. Commit: 33abc49473143e19f73bca15a734ab71d1b5e8cb https://github.com/galaxyproject/galaxy/commit/33abc49473143e19f73bca15a734a... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- Fixed bug where panel wouldn't show unless a folder was present Commit: a9178527590b8732cca3474a1e9a7f10f02eeb19 https://github.com/galaxyproject/galaxy/commit/a9178527590b8732cca3474a1e9a7... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map Log Message: ----------- Removed commented out line which wasn't needed Commit: bc36230af32f7c79a711db0a206348e4dc4d5d15 https://github.com/galaxyproject/galaxy/commit/bc36230af32f7c79a711db0a20634... Author: Jim Johnson <jj@umn.edu> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix lib/galaxy/datatypes/proteomics.py Commit: 34d60749a0d90cfb152e3b40c56f3bafa46d294b https://github.com/galaxyproject/galaxy/commit/34d60749a0d90cfb152e3b40c56f3... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fixed download in beta library view to work with folders Commit: 4440240b55ecdea9cc404fa743a55964fc5097e8 https://github.com/galaxyproject/galaxy/commit/4440240b55ecdea9cc404fa743a55... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M templates/display_base.mako M templates/tagging_common.mako Log Message: ----------- Tagging (mako-based): extract js set up code for tagging from display_base.mako and move to tagging_common (hackathon quick fix) Commit: b18cfa09b087cd03a5a7a2af30872e49b3167cc2 https://github.com/galaxyproject/galaxy/commit/b18cfa09b087cd03a5a7a2af30872... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M static/maps/mvc/collection/collection-model.js.map M static/scripts/mvc/collection/collection-model.js Log Message: ----------- UI, collections: fix DatasetCollectionElement and DatasetAssociation id collision in DCECollection by preserving Element id in idAttribute 'element_id' Commit: 8a74ce914976f4afe24b8de398b11bdfb48e1d9e https://github.com/galaxyproject/galaxy/commit/8a74ce914976f4afe24b8de398b11... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M templates/display_base.mako M templates/tagging_common.mako Log Message: ----------- Merge pull request #429 from carlfeberhard/workflow-tag-js Tagging (mako-based): extract js set up code for tagging from display… Commit: b76a65f2cddee967e7ce4332493f6e831b3507dd https://github.com/galaxyproject/galaxy/commit/b76a65f2cddee967e7ce4332493f6... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M run_tests.sh Log Message: ----------- Fix example api test command. The -api parameter takes an optional argument so it can be thought of as "-api [testpath]". So in the example -with_framework_test_tools needs to come first. Commit: 8787f94cbb3ee96e03e801a56515a40c0588f1da https://github.com/galaxyproject/galaxy/commit/8787f94cbb3ee96e03e801a56515a... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Replace lf_ids with folder_ids Commit: d8f410faa24bb12ebe1c57a323a388af32e642c1 https://github.com/galaxyproject/galaxy/commit/d8f410faa24bb12ebe1c57a323a38... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix test for empty array Commit: cb09eb2caac51a2a81db0ddc4cc77bda71946c08 https://github.com/galaxyproject/galaxy/commit/cb09eb2caac51a2a81db0ddc4cc77... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Removed blank space from line Commit: 41d9fe1e40dd95d00e7fe188d96e977b8fb7052d https://github.com/galaxyproject/galaxy/commit/41d9fe1e40dd95d00e7fe188d96e9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #432 from jmchilton/test_doc_fix Fix example api test command. Commit: f9eb6f44e2aa56a07088524b4ad1d0eade36ae2d https://github.com/galaxyproject/galaxy/commit/f9eb6f44e2aa56a07088524b4ad1d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #427 from jj-umn/dev Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite Commit: 52dae6d6f87b801fc70671efc24b5a6e1a9faa9b https://github.com/galaxyproject/galaxy/commit/52dae6d6f87b801fc70671efc24b5... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/util/streamball.py Log Message: ----------- Fixed StreamBall, which was using to a dict to store files, which meant that only the deepest file was copied and all above were not included Commit: eeb84cd6a35ff1c3771a636c02ed3a7308fd5501 https://github.com/galaxyproject/galaxy/commit/eeb84cd6a35ff1c3771a636c02ed3... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/xml.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/jobs/datasets.py Log Message: ----------- lint fixes Commit: a838f9a536d88bce00ec5ea4b9d266e96170e5d8 https://github.com/galaxyproject/galaxy/commit/a838f9a536d88bce00ec5ea4b9d26... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py Log Message: ----------- lint fixes Commit: 09775e058b282b7b01340e69487744f3a9107019 https://github.com/galaxyproject/galaxy/commit/09775e058b282b7b01340e6948774... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/sharable.py M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/quota/__init__.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/biostar.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/debugging.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/expressions.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/inflection.py M lib/galaxy/util/jstree.py M lib/galaxy/util/lrucache.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/specs.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/template.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/params.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/base/twilltestcase.py Log Message: ----------- sqlalchemy linting can be complicated Commit: 6a2ac39c5a2fef83a0a09ebdeb2c80eec07116df https://github.com/galaxyproject/galaxy/commit/6a2ac39c5a2fef83a0a09ebdeb2c8... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/web/form_builder.py M lib/galaxy_ext/metadata/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- pep8 fixes Commit: c691b9216031dce4a66251c83fbdf680cd5a411e https://github.com/galaxyproject/galaxy/commit/c691b9216031dce4a66251c83fbdf... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/__init__.py Log Message: ----------- small linting fixes Commit: 0a1ab6ca7114b962b157b5b3c2ade01558c15f8d https://github.com/galaxyproject/galaxy/commit/0a1ab6ca7114b962b157b5b3c2ade... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/external_services/result_handlers/__init__.py M lib/galaxy/external_services/result_handlers/basic.py Log Message: ----------- linting! Commit: ab0eace3cf920a8fd75bb949e8602d7a2a61eaf1 https://github.com/galaxyproject/galaxy/commit/ab0eace3cf920a8fd75bb949e8602... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/cigar.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/genomes.py Log Message: ----------- Linting lib/galaxy/visualization/ Commit: 0a1e8d025f5d276bacf98d0e24945acc849a300f https://github.com/galaxyproject/galaxy/commit/0a1e8d025f5d276bacf98d0e24945... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/sample_tracking/request_types.py Log Message: ----------- Lint various files in lib/galaxy/ . Commit: 8c7a906d170986e4009e4c79757ba9546c2f8756 https://github.com/galaxyproject/galaxy/commit/8c7a906d170986e4009e4c79757ba... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/log/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- lint fixes to lib/galaxy/utils Commit: 4931b5ef9161ffcba4efee6e124e22fcd65fca8d https://github.com/galaxyproject/galaxy/commit/4931b5ef9161ffcba4efee6e124e2... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/lwr.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Linting lib/galaxy/jobs Commit: 53f533324ed5225d76f4b788b728223447e9312a https://github.com/galaxyproject/galaxy/commit/53f533324ed5225d76f4b788b7282... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py Log Message: ----------- Linting lib/galaxy/web Commit: 6135cb5764597aa9459f3fed16fddd8701c4807f https://github.com/galaxyproject/galaxy/commit/6135cb5764597aa9459f3fed16fdd... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/error.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- linting lib/galaxy/webapps Commit: 6668c072aa71b09ceb3c11101fd3081e91387c58 https://github.com/galaxyproject/galaxy/commit/6668c072aa71b09ceb3c11101fd30... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py Log Message: ----------- linting lib/galaxy/webapps/reports Commit: 8c91adf989a61f53e8063bbe859bce39a3544f10 https://github.com/galaxyproject/galaxy/commit/8c91adf989a61f53e8063bbe859bc... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/security/__init__.py Log Message: ----------- linting lib/galaxy/webapps/tool_shed/ Commit: 98a8fe66bb80719f2c9ca061e92dadbd133657e5 https://github.com/galaxyproject/galaxy/commit/98a8fe66bb80719f2c9ca061e92da... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py Log Message: ----------- Linting model...not finished yet! Commit: 92f14db71be6ed6988d71bb71665fe4eb63e39ac https://github.com/galaxyproject/galaxy/commit/92f14db71be6ed6988d71bb71665f... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py Log Message: ----------- linting lib/galaxy/webapps/tool_shed/ Commit: 0ffbe2e30faa4cbead3248327b7c8c28e91df3b5 https://github.com/galaxyproject/galaxy/commit/0ffbe2e30faa4cbead3248327b7c8... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/eggs/__init__.py M lib/galaxy/eggs/dist.py M lib/galaxy/eggs/scramble.py M lib/galaxy/model/orm/__init__.py Log Message: ----------- Fixed some problems of the previous commit + added the PEP8 check on lib/galaxy/eggs Commit: 360d4a081037bb1d82d7fcec36ac054d39750ff0 https://github.com/galaxyproject/galaxy/commit/360d4a081037bb1d82d7fcec36ac0... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M .ci/pep8_sources.txt Log Message: ----------- Added the lib/galaxy/forms folder Commit: 66129e49054b375e183f848d28a1145d95d63eb2 https://github.com/galaxyproject/galaxy/commit/66129e49054b375e183f848d28a11... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/tool_shed/__init__.py Log Message: ----------- small linting fixes Commit: ce6b23607048993dc3a94e04c4bdc5c6f8d05cc2 https://github.com/galaxyproject/galaxy/commit/ce6b23607048993dc3a94e04c4bdc... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/api_keys.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py Log Message: ----------- linting lib/galaxy/managers/ Commit: 0781744ca940a1944c58960c0ddc3e4140f8ee19 https://github.com/galaxyproject/galaxy/commit/0781744ca940a1944c58960c0ddc3... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py Log Message: ----------- lint lib/galaxy/managers Commit: 15400330ac34d6c769ae0ca68edf617f708c95e1 https://github.com/galaxyproject/galaxy/commit/15400330ac34d6c769ae0ca68edf6... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/lwr.py M lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py Log Message: ----------- linting lib/galaxy/jobs/runners/ Commit: 93a3dbe17f64b6067a73642304359929dfde9d68 https://github.com/galaxyproject/galaxy/commit/93a3dbe17f64b6067a73642304359... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- lint lib/galaxy/jobs/ Commit: 9b22e55a7cc3fe6aa70a19a836bc9ee8b56307c1 https://github.com/galaxyproject/galaxy/commit/9b22e55a7cc3fe6aa70a19a836bc9... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- various linting fixes Commit: a46f62be55472907796329b2909fcd8a70fd67be https://github.com/galaxyproject/galaxy/commit/a46f62be55472907796329b2909fc... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- linting of /lib/galaxy/datatypes Commit: 9949e18211ff85a4b8984146d358c64637268021 https://github.com/galaxyproject/galaxy/commit/9949e18211ff85a4b8984146d358c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/api_keys.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py Log Message: ----------- revert spaces around brackets Commit: dc365017f711da66b8edfd9dc26c02641ad343d7 https://github.com/galaxyproject/galaxy/commit/dc365017f711da66b8edfd9dc26c0... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- fix merge errors Commit: ac14f3381c4dd7416fd96a6ebdbc710f7cf3295d https://github.com/galaxyproject/galaxy/commit/ac14f3381c4dd7416fd96a6ebdbc7... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/mapping.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py Log Message: ----------- various lint fixes all over the place Commit: fa7c5c531e07056cbf194b514ea9ccee5c214e18 https://github.com/galaxyproject/galaxy/commit/fa7c5c531e07056cbf194b514ea9c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- lint fixes for /lib/galaxy/ Commit: baef86b326fd151975dcbc4553859762b70c1489 https://github.com/galaxyproject/galaxy/commit/baef86b326fd151975dcbc4553859... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/util/hash_util.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- small lint fixes Commit: edb72703debb860f97f0cd8a852d20a8ac128b1b https://github.com/galaxyproject/galaxy/commit/edb72703debb860f97f0cd8a852d2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Minor spelling tweak; ill-legitimate Commit: f4be448b35598a166ef0978298ba2b107953b183 https://github.com/galaxyproject/galaxy/commit/f4be448b35598a166ef0978298ba2... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- fix indentation Commit: b6931c5196e843a26dbb78a8a4c704a4e1712b93 https://github.com/galaxyproject/galaxy/commit/b6931c5196e843a26dbb78a8a4c70... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/inflection.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/sanitize_html.py Log Message: ----------- indentation fixes Commit: cef03056926a73ec7dfd4ee569bfdc14b3538bd0 https://github.com/galaxyproject/galaxy/commit/cef03056926a73ec7dfd4ee569bfd... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- indentation fixes Commit: 5e99eab3ae75e4b89e0c6a89d940abdb4c4f3319 https://github.com/galaxyproject/galaxy/commit/5e99eab3ae75e4b89e0c6a89d940a... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py Log Message: ----------- indentation fixes Commit: 7bde0945965a3ca2fbd5aa60a0853f34270c33e4 https://github.com/galaxyproject/galaxy/commit/7bde0945965a3ca2fbd5aa60a0853... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/tasks.py Log Message: ----------- indentation fixes Commit: e712e29778a8af50fd9d5d02eb345bd5f558a8a4 https://github.com/galaxyproject/galaxy/commit/e712e29778a8af50fd9d5d02eb345... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- indentation fixes Commit: c294909077d5d6dd2aa0ba74c1404c2e473031c5 https://github.com/galaxyproject/galaxy/commit/c294909077d5d6dd2aa0ba74c1404... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/search.py Log Message: ----------- indentation fixes Commit: 224fde656b12d6e56a0040208e027ca9363edf76 https://github.com/galaxyproject/galaxy/commit/224fde656b12d6e56a0040208e027... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/eggs/__init__.py Log Message: ----------- indentation fixes Commit: 3fcb9a5f211044f73f686ab6b2b0eed9f2c04881 https://github.com/galaxyproject/galaxy/commit/3fcb9a5f211044f73f686ab6b2b0e... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- indentation fixes Commit: 2160a032721f4dc7eff1ff6a449166a1a22d4455 https://github.com/galaxyproject/galaxy/commit/2160a032721f4dc7eff1ff6a44916... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/search/repo_search.py Log Message: ----------- indentation fixes Commit: 8b9aa5d8df82a42e51c02b6070ff8570280b2879 https://github.com/galaxyproject/galaxy/commit/8b9aa5d8df82a42e51c02b6070ff8... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/visualizations.py Log Message: ----------- indentation fixes Commit: 979e31bf71c8565dab2b35ce1bfde59554193557 https://github.com/galaxyproject/galaxy/commit/979e31bf71c8565dab2b35ce1bfde... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- indentation fixes Commit: fca6854ac08ded7acfb714b2fb84add0eceb7f84 https://github.com/galaxyproject/galaxy/commit/fca6854ac08ded7acfb714b2fb84a... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M 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Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/workflows.py Log Message: ----------- Indentation and typo fixes. Commit: ad8175928d444c4af5d23dbc080310f1d40f0da6 https://github.com/galaxyproject/galaxy/commit/ad8175928d444c4af5d23dbc08031... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- lint fixes for /test/unit/ Commit: eced982622b8028fbef28207979110e3d1d13c94 https://github.com/galaxyproject/galaxy/commit/eced982622b8028fbef2820797911... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2015-07-05 (Sun, 05 Jul 2015) Changed paths: M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py Log Message: ----------- lint fixes for /test/api/ Commit: 64e82bbd7b1a6fcc66082d696c25a025732eb18c https://github.com/galaxyproject/galaxy/commit/64e82bbd7b1a6fcc66082d696c25a... Author: abretaud <anthony.bretaudeau@rennes.inra.fr> Date: 2015-07-06 (Mon, 06 Jul 2015) Changed paths: M templates/show_params.mako Log Message: ----------- fix indentation Commit: 5cd3e3a7e02eee03a24006b47dfb98aff609cb1c https://github.com/galaxyproject/galaxy/commit/5cd3e3a7e02eee03a24006b47dfb9... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-06 (Mon, 06 Jul 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py Log Message: ----------- Linted util Commit: dc597e3010638f050ad1942c635e1cd8944b94a2 https://github.com/galaxyproject/galaxy/commit/dc597e3010638f050ad1942c635e1... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-06 (Mon, 06 Jul 2015) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Job linting ended Commit: 880f8c509c69312bfb980b3a659b602f1dcacb2f https://github.com/galaxyproject/galaxy/commit/880f8c509c69312bfb980b3a659b6... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-06 (Mon, 06 Jul 2015) Changed paths: M lib/galaxy/util/dictobj.py Log Message: ----------- Fixed an indentation in dictobj Commit: 531fd6fb9108d263255b11f19b9788a8535a80e7 https://github.com/galaxyproject/galaxy/commit/531fd6fb9108d263255b11f19b978... Author: Remi Marenco <remi.marenco@gmail.com> Date: 2015-07-06 (Mon, 06 Jul 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Removed the ignore of the only displayed F821 flake8 sublime plugin error Commit: 0a359add084daf99ee67be51afd3a42a8f98a7f1 https://github.com/galaxyproject/galaxy/commit/0a359add084daf99ee67be51afd3a... Author: Peter Cock <p.j.a.cock@googlemail.com> Date: 2015-07-07 (Tue, 07 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fixed typo in docstring Commit: e5341ab0203672d649dd89179324d3c104f5a87c https://github.com/galaxyproject/galaxy/commit/e5341ab0203672d649dd89179324d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-07 (Tue, 07 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #438 from peterjc/patch-3 Fixed typo in docstring Commit: 534d7b8b50760727157bad963c54d960e3ad974f https://github.com/galaxyproject/galaxy/commit/534d7b8b50760727157bad963c54d... Author: youri <y.hoogstrate@erasmusmc.nl> Date: 2015-07-07 (Tue, 07 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Added datatype definition for ConnectivityTable (*.ct) - RNA 2D structure file format Commit: b734aee99cd0de7418d95f7bafec93a5b3a9ec89 https://github.com/galaxyproject/galaxy/commit/b734aee99cd0de7418d95f7bafec9... Author: David Trudgian <david.trudgian@utsouthwestern.edu> Date: 2015-07-07 (Tue, 07 Jul 2015) Changed paths: M client/galaxy/style/less/trackster.less M static/style/blue/trackster.css Log Message: ----------- Stop trackster location wrap in chrome Commit: 839908b3b9cd3db37e3b099535bbe94595180e8a https://github.com/galaxyproject/galaxy/commit/839908b3b9cd3db37e3b099535bbe... Author: = <christian.brenninkmeijer@manchester.ac.uk> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Added unlinked depenency resolver Commit: 91bffc0e98c04e0fad3b97476dafd84a357c7bca https://github.com/galaxyproject/galaxy/commit/91bffc0e98c04e0fad3b97476dafd... Author: = <christian.brenninkmeijer@manchester.ac.uk> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Added log error for config file not found Commit: 9b0ee0589a7f19907f706ca9cb19e9e21a3bf4e2 https://github.com/galaxyproject/galaxy/commit/9b0ee0589a7f19907f706ca9cb19e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Resolve sample merge conflict. Commit: 6f475e9a5c053e96eef6ddd9604b2af9d019ad3f https://github.com/galaxyproject/galaxy/commit/6f475e9a5c053e96eef6ddd9604b2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge branch 'yhoogstrate-dev' into dev Commit: 7758fe4b33fa2193e186d0a94f69fc05aec8758f https://github.com/galaxyproject/galaxy/commit/7758fe4b33fa2193e186d0a94f69f... Author: youri <y.hoogstrate@erasmusmc.nl> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for md5-check urls for download_by_url Commit: def341b5c320f34db1b120c0ea20e867a2e387fb https://github.com/galaxyproject/galaxy/commit/def341b5c320f34db1b120c0ea20e... 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Commit: 432beb5782081f86854fea6bd8844b118d2c6e69 https://github.com/galaxyproject/galaxy/commit/432beb5782081f86854fea6bd8844... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip a trailing space from the merge. Commit: 3f4cd5b9def0ae7eb5f1ecd8cb3c9e2915bdb314 https://github.com/galaxyproject/galaxy/commit/3f4cd5b9def0ae7eb5f1ecd8cb3c9... 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lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/managers/groups.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M scripts/functional_tests.py M scripts/tool_shed/build_ts_whoosh_index.py R static/maps/galaxy.workflow_editor.canvas.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map A static/maps/mvc/workflow/workflow-canvas.js.map A static/maps/mvc/workflow/workflow-connector.js.map A static/maps/mvc/workflow/workflow-manager.js.map A static/maps/mvc/workflow/workflow-node.js.map A static/maps/mvc/workflow/workflow-terminals.js.map A static/maps/mvc/workflow/workflow-view-data.js.map A static/maps/mvc/workflow/workflow-view-node.js.map A static/maps/mvc/workflow/workflow-view-terminals.js.map A static/maps/mvc/workflow/workflow-view.js.map A static/maps/mvc/workflow/workflow.js.map R static/scripts/galaxy.workflow_editor.canvas.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js A static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-connector.js A static/scripts/mvc/workflow/workflow-manager.js A static/scripts/mvc/workflow/workflow-node.js A static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow-view-data.js A static/scripts/mvc/workflow/workflow-view-node.js A static/scripts/mvc/workflow/workflow-view-terminals.js A static/scripts/mvc/workflow/workflow-view.js A static/scripts/mvc/workflow/workflow.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M templates/display_base.mako M templates/tagging_common.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/code_file.py A test/functional/tools/environment_variables.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M tools/data_source/upload.py M tools/evolution/codingSnps_filter.py Log Message: ----------- merged dev Commit: edd754d1ae998c7c6605d948d4adae742a66fe6a https://github.com/galaxyproject/galaxy/commit/edd754d1ae998c7c6605d948d4ada... Author: youri <y.hoogstrate@erasmusmc.nl> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for md5-check urls for download_by_url Commit: b369ce49b80dc5ef861a6934c7a66933fe8c809a https://github.com/galaxyproject/galaxy/commit/b369ce49b80dc5ef861a6934c7a66... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Update docs, re-instate backwards compatability Commit: d1e122d41d74341b8ff2d6f9f3b751671aef18fe https://github.com/galaxyproject/galaxy/commit/d1e122d41d74341b8ff2d6f9f3b75... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-07-08 (Wed, 08 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #4 from dannon/bgruening-lint2 Resolves the merge conflict, one minor whitespace fix. Commit: 75ab206ca57da42582c0ac04dc903eb68c4824ab https://github.com/galaxyproject/galaxy/commit/75ab206ca57da42582c0ac04dc903... Author: Jeremy Goecks <jgoecks@gwu.edu> Date: 2015-07-09 (Thu, 09 Jul 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Trackster fixes: (a) close data provider files after reading from them (but there are some data providers that currently lack close functions so those files will remain open); (b) fix running tools by correcting HDA manager function call; (c) remove use of underscore template because uglify does not handle it well. Commit: 5c60fa6d21fd320f63f5decc43062074baa4621f https://github.com/galaxyproject/galaxy/commit/5c60fa6d21fd320f63f5decc43062... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-09 (Thu, 09 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M static/maps/mvc/collection/collection-model.js.map M static/scripts/mvc/collection/collection-model.js Log Message: ----------- Merge pull request #431 from carlfeberhard/fix.dcecollection-ids UI, collections: fix DatasetCollectionElement and DatasetAssociation … Commit: 58e319d3688328e280df96709db17916d739e5d6 https://github.com/galaxyproject/galaxy/commit/58e319d3688328e280df96709db17... Author: = <christian.brenninkmeijer@manchester.ac.uk> Date: 2015-07-09 (Thu, 09 Jul 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- downgraded warning to debug as would happen on default Commit: cd0a122d4d910cd521cbad8010c0710ed73deb78 https://github.com/galaxyproject/galaxy/commit/cd0a122d4d910cd521cbad8010c07... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-11 (Sat, 11 Jul 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix https://github.com/bgruening/galaxy/commit/c691b9216031dce4a66251c83fbdf680c.... Commit: 4dc96cc932cf57692076776025a869879cb22205 https://github.com/galaxyproject/galaxy/commit/4dc96cc932cf57692076776025a86... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-11 (Sat, 11 Jul 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #5 from jmchilton/fix_datatypes_pep8 Fix problematic PEP-8 fix. Commit: 37f1976d38c21eb08fe38a348d6cbf435c5afd8e https://github.com/galaxyproject/galaxy/commit/37f1976d38c21eb08fe38a348d6cb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-11 (Sat, 11 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/__init__.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M 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lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/eggs/__init__.py M lib/galaxy/eggs/dist.py M lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/__init__.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M 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lib/galaxy/managers/libraries.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/quota/__init__.py M lib/galaxy/sample_tracking/data_transfer.py M lib/galaxy/sample_tracking/external_service_types.py M 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lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/params.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M 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M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/error.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M 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lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Revert "[WIP] Mega flake8 linting" Commit: df1b30ebd864ddea5e2566a00acbbf1964f0a777 https://github.com/galaxyproject/galaxy/commit/df1b30ebd864ddea5e2566a00acbb... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-11 (Sat, 11 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/__init__.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M 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lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/eggs/__init__.py M lib/galaxy/eggs/dist.py M lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/__init__.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M 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lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M 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lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/params.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M 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M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/error.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M 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lib/galaxy_ext/metadata/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #433 from bgruening/lint2 [WIP] Mega flake8 linting Commit: 25cb291b803275a10ff12f0254e45bcad03e011c https://github.com/galaxyproject/galaxy/commit/25cb291b803275a10ff12f0254e45... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-11 (Sat, 11 Jul 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/__init__.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M 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lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M 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lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/params.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M 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M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/error.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #449 from galaxyproject/revert-433-lint2 Revert "[WIP] Mega flake8 linting" Commit: e9aa6e843de62086a74536fec87bff4bf046f255 https://github.com/galaxyproject/galaxy/commit/e9aa6e843de62086a74536fec87bf... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/util/streamball.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #426 from ericenns/feature/library_folder_export_to_history Feature/library folder export to history Commit: 2a63b7b9b3f9d4218defa9250681a18d8423d540 https://github.com/galaxyproject/galaxy/commit/2a63b7b9b3f9d4218defa9250681a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Merge branch 'group' of https://github.com/moskalenko/galaxy into group_round Commit: 647fcf1f6069a272b73791915e989a1bccac4318 https://github.com/galaxyproject/galaxy/commit/647fcf1f6069a272b73791915e989... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Only make the Group tool's return value an integer if rounding is selected, as pointed out by @nsoranzo. Commit: d5b28bea6d2123715b8adac004c7f157af785db1 https://github.com/galaxyproject/galaxy/commit/d5b28bea6d2123715b8adac004c7f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #443 from Christian-B/config_file_not_found Added log error for config file not found Commit: f122c87ec46fc0526e1f8b423d3da6b3e7bcf122 https://github.com/galaxyproject/galaxy/commit/f122c87ec46fc0526e1f8b423d3da... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Merge pull request #452 from natefoo/group_round Fixed: Return integer values when 'round to nearest integer' is selected in Group tool Commit: 2bf2844b21895bece70dc43d650675385ccd0b7a https://github.com/galaxyproject/galaxy/commit/2bf2844b21895bece70dc43d65067... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M client/galaxy/style/less/trackster.less M static/style/blue/trackster.css Log Message: ----------- Merge pull request #440 from dctrud/trackster_nowrap Stop trackster location wrap in chrome Commit: 47928259244308764ead8659457d93af4c500c2f https://github.com/galaxyproject/galaxy/commit/47928259244308764ead8659457d9... Author: carlfeberhard <carlfeberhard@users.noreply.github.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #446 from jgoecks/trackster-close-files Trackster fixes: (a) close data provider files after reading from the… Commit: 72b7381fc288fe78026493433171e11d6f7fae76 https://github.com/galaxyproject/galaxy/commit/72b7381fc288fe78026493433171e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Improvements to @erasche's download hash changes suggested by @yhoogstrate. Commit: 37b231cb3d0ece73daa4ba45149ec14d04abc1d6 https://github.com/galaxyproject/galaxy/commit/37b231cb3d0ece73daa4ba45149ec... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- 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. Commit: 6eafa52f411ee53d47b445439abfe12a818165a8 https://github.com/galaxyproject/galaxy/commit/6eafa52f411ee53d47b445439abfe... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Remove superflous assignment left over from 647fcf1f6069a272b73791915e989a1bccac4318, thanks @nsoranzo. Commit: ec36199a27f0c169a8a86159d36ac1a04645f98f https://github.com/galaxyproject/galaxy/commit/ec36199a27f0c169a8a86159d36ac... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-13 (Mon, 13 Jul 2015) Changed paths: M tools/stats/grouping.py Log Message: ----------- Merge pull request #453 from natefoo/group_round Remove superflous assignment left over from... Commit: 163b0e37ca4dec3606e9c56fa9e77fa8d1f09425 https://github.com/galaxyproject/galaxy/commit/163b0e37ca4dec3606e9c56fa9e77... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/output_collection_filter.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement <filter> tag for output collections. Closes #445. Commit: 0cbf97ac9a30d6006b5a75ab602231af68a4c3d9 https://github.com/galaxyproject/galaxy/commit/0cbf97ac9a30d6006b5a75ab60223... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Fix expect_num_outputs parsing on tool test elements. Broken with abstracting XML parsing out into its own module. Commit: e1d53139a816f862fdd727e5023714eb1008e77a https://github.com/galaxyproject/galaxy/commit/e1d53139a816f862fdd727e502371... Author: yhoogstrate <y.hoogstrate@erasmusmc.nl> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #4 from erasche/docs-fix Update docs, re-instate backwards compatability Commit: ac75e6ff8dd9cf48baf3f4e18337b4b69fe76e37 https://github.com/galaxyproject/galaxy/commit/ac75e6ff8dd9cf48baf3f4e18337b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/output_collection_filter.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #455 from jmchilton/output_collection_filter Implement <filter> tag for output collections. Commit: 141980451cbff94938a9df0d1c1934d749a930b4 https://github.com/galaxyproject/galaxy/commit/141980451cbff94938a9df0d1c193... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #444 from yhoogstrate/dev Fix md5sum/sha256 in toolshed action Commit: 23209d549781c9d4f742ebd26e611fe5fb823b8f https://github.com/galaxyproject/galaxy/commit/23209d549781c9d4f742ebd26e611... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge pull request #441 from Christian-B/unlinked_dependencies Added unlinked dependency resolver Commit: 4fe2bd4798d597327e9a3ce5a78c47a7cd85530a https://github.com/galaxyproject/galaxy/commit/4fe2bd4798d597327e9a3ce5a78c4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #398 from abretaud/section Fix error when displaying job params for tools containing a section Commit: b9c9f11ce1a433b49fd07f58334a7a24e3008029 https://github.com/galaxyproject/galaxy/commit/b9c9f11ce1a433b49fd07f58334a7... Author: Peter van Heusden <pvh@sanbi.ac.za> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: A lib/galaxy/auth/providers/pam_auth.py A scripts/auth/pam_auth_helper.py Log Message: ----------- * 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 Commit: cb8f6354dea29ece311a0650bcc2b95740bd6658 https://github.com/galaxyproject/galaxy/commit/cb8f6354dea29ece311a0650bcc2b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: A lib/galaxy/auth/providers/pam_auth.py A scripts/auth/pam_auth_helper.py Log Message: ----------- Merge pull request #458 from pvanheus/auth_pam AuthProvider for PAM (Pluggable Authentication Modules) Commit: 37cf1af4dfba2b18d0ede692d4d0e559a70463f4 https://github.com/galaxyproject/galaxy/commit/37cf1af4dfba2b18d0ede692d4d0e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- lint fixes for #458 Commit: ddf4ce5680d1eb08b4d57bb35429a060aad2ee40 https://github.com/galaxyproject/galaxy/commit/ddf4ce5680d1eb08b4d57bb35429a... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- Merge pull request #459 from natefoo/dev Lint fixes for #458 Commit: 39f6730e5f50b54f372b8c1e17d86d8936b5899f https://github.com/galaxyproject/galaxy/commit/39f6730e5f50b54f372b8c1e17d86... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-14 (Tue, 14 Jul 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 2ca8f369fa452f52212eaddbca8119dfe3e66844 https://github.com/galaxyproject/galaxy/commit/2ca8f369fa452f52212eaddbca811... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Histories, structure: fix job query to allow admin to view other history structures Commit: cf29f6c4a77a084bcf4732ddf1c5cbe4e6a2aac8 https://github.com/galaxyproject/galaxy/commit/cf29f6c4a77a084bcf4732ddf1c5c... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-07-15 (Wed, 15 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #465 from carlfeberhard/release_15.07 [15.07] Histories, structure: fix job query to allow admin to view other hist… Commit: b1be4c1450fcf3bc0240774ad230619cccfb4e12 https://github.com/galaxyproject/galaxy/commit/b1be4c1450fcf3bc0240774ad2306... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Datatypes: allow display_in_upload for h5 files Commit: b631215692b07906d7dace6e31cb921425982dc2 https://github.com/galaxyproject/galaxy/commit/b631215692b07906d7dace6e31cb9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #470 from carlfeberhard/fix.h5-datatype-in-upload [15.07] Datatypes: allow display_in_upload for h5 files Commit: 488d42deb569da76c6a8d9b9877a202ba0018ecc https://github.com/galaxyproject/galaxy/commit/488d42deb569da76c6a8d9b9877a2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 2f8580b9316d30c00e5e6c0e106e084fb2e05a90 https://github.com/galaxyproject/galaxy/commit/2f8580b9316d30c00e5e6c0e106e0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 33181f5607f51892839d8985135bf42ae6dbb415 https://github.com/galaxyproject/galaxy/commit/33181f5607f51892839d8985135bf... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-22 (Wed, 22 Jul 2015) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- Histories: include owner annotations of hdas in published history display (HistoryManager._get_history_data) Commit: 784e07c61f58aa2f9ae27e44009b6b1625730b6a https://github.com/galaxyproject/galaxy/commit/784e07c61f58aa2f9ae27e44009b6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 1c04e1498b74a657d6b1ab6c826997c2f6753b72 https://github.com/galaxyproject/galaxy/commit/1c04e1498b74a657d6b1ab6c82699... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- Merge pull request #490 from carlfeberhard/release_15.07 [15.07] Histories: include owner annotations of hdas in published history dis… Commit: 80f4bd7f3f9a72b63de25c2bb9961894e3f6fc3a https://github.com/galaxyproject/galaxy/commit/80f4bd7f3f9a72b63de25c2bb9961... Author: jgoecks <jgoecks@gwu.edu> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Fix BBI data provider underflow bug when computing standard deviation Commit: 349378a543ec44b258cb3619edf27c0416b35c5d https://github.com/galaxyproject/galaxy/commit/349378a543ec44b258cb3619edf27... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Adjust comment for flake8 Commit: 7c4a9abb23120d38e6efed974a21a2eede540049 https://github.com/galaxyproject/galaxy/commit/7c4a9abb23120d38e6efed974a21a... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix for installing dependencies from source when download of precompiled binaries has failed. Commit: 6fadb2b50e3202b7dc58ff7c698eff44db596276 https://github.com/galaxyproject/galaxy/commit/6fadb2b50e3202b7dc58ff7c698ef... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- 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. Commit: e8f3553404d4b348f58b3d839d97e0e32461f33c https://github.com/galaxyproject/galaxy/commit/e8f3553404d4b348f58b3d839d97e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- 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. Commit: 607aca84e77694fb5dc5270ebe89a6fa144bbcd5 https://github.com/galaxyproject/galaxy/commit/607aca84e77694fb5dc5270ebe89a... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool demontrating filtering selections based on dbkey. Commit: b481e74419bd06c4cba7d585f1133295a264c511 https://github.com/galaxyproject/galaxy/commit/b481e74419bd06c4cba7d585f1133... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow dbkey filtering of multiple input targets. Fixes #388. Includes a test case. Commit: fc829aa1b906deb6e4c8edafc1c8628e271b7c75 https://github.com/galaxyproject/galaxy/commit/fc829aa1b906deb6e4c8edafc1c86... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-07-31 (Fri, 31 Jul 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #534 from jmchilton/more_failure [15.07] Fix dbkey filtering of multiple input targets. Commit: 4d4c68c365953c360f53a427e2b81e742481c793 https://github.com/galaxyproject/galaxy/commit/4d4c68c365953c360f53a427e2b81... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-01 (Sat, 01 Aug 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- 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. Commit: 52fa00b03ccf85121288ae840a14b2b0654a150c https://github.com/galaxyproject/galaxy/commit/52fa00b03ccf85121288ae840a14b... Author: John Chilton <jmchilton@gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Fixes for DeleteIntermediatesAction. Shouldn't assume the workflow invocation has completely been evaluated or that a job is available yet for invocation steps. Commit: f17c533bf0b6b843beb2fa3e091af9a2eb4cf5e1 https://github.com/galaxyproject/galaxy/commit/f17c533bf0b6b843beb2fa3e091af... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #547 from jmchilton/intermediate_delete_fix [15.07] Fixes for DeleteIntermediatesAction. Commit: efe59eabc5f209408406157716aa1984ca9fc0c9 https://github.com/galaxyproject/galaxy/commit/efe59eabc5f209408406157716aa1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Password field for old cloudlaunch's secret key. Commit: 44ae75185196eb596b1938667d195eed7b60df1c https://github.com/galaxyproject/galaxy/commit/44ae75185196eb596b1938667d195... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge pull request #551 from dannon/cloudlauch_fix Password field for old cloudlaunch's secret key. Commit: ba265074dee13f1dad9b5b728559f4f7bb6cfeb2 https://github.com/galaxyproject/galaxy/commit/ba265074dee13f1dad9b5b728559f... Author: carlfeberhard <carlfeberhard@users.noreply.github.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #456 from jmchilton/fix_expect_outputs [15.05] Fix expect_num_outputs parsing on tool test elements. Commit: 0b486a7a1ba811746e7b06c8918ef5796441e450 https://github.com/galaxyproject/galaxy/commit/0b486a7a1ba811746e7b06c8918ef... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/search/tool_search.py Log Message: ----------- do not encode id when returning TS tool search results Commit: 0ad5c8a1a82cc64c2c17133eb8dc3c70f4017994 https://github.com/galaxyproject/galaxy/commit/0ad5c8a1a82cc64c2c17133eb8dc3... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- fix TS search index building script to properly visit subdirectories Commit: d583c376a57cf2acb870a1b48ebdbb5db4ba2892 https://github.com/galaxyproject/galaxy/commit/d583c376a57cf2acb870a1b48ebdb... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- flake8 spotted by @nsoranzo Commit: 265d8697d8a348ccc452682b13ac0bad718b82ac https://github.com/galaxyproject/galaxy/commit/265d8697d8a348ccc452682b13ac0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/search/tool_search.py M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #563 from martenson/release_15.07 [release_15.07] Fixes for TS search API Commit: 4d697b7b5036f81d87a0f74a898432d37d446b96 https://github.com/galaxyproject/galaxy/commit/4d697b7b5036f81d87a0f74a89843... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- fix overriding the name variable Commit: 50de63d679ca93058a3fc851d33a63028cd3c724 https://github.com/galaxyproject/galaxy/commit/50de63d679ca93058a3fc851d33a6... Author: John Chilton <jmchilton@gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #566 from martenson/release_15.07 [release_15.07] TS index - fix overriding the name variable Commit: f776deb36263287234e26d9021754c0d78a78243 https://github.com/galaxyproject/galaxy/commit/f776deb36263287234e26d9021754... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- 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. Commit: ef3d3f649a00653e96e7f3133d0ff021cc2020c8 https://github.com/galaxyproject/galaxy/commit/ef3d3f649a00653e96e7f3133d0ff... Author: Nitesh Turaga <nitesh.turaga@gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #567 from dannon/datatypes_registry_lower Normalize datatypes_by_ext upon entry Commit: d270ccd078cb7c9853db466fc3f7190c6e0ab8f2 https://github.com/galaxyproject/galaxy/commit/d270ccd078cb7c9853db466fc3f71... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix sniff order with respect to CSV interpreting SAM files as valid CSV prior to SAM sniffing. Test with 1.sam. Commit: 864e2b5111e0d25ac4cf8430f24e3eaf5e1bbe4d https://github.com/galaxyproject/galaxy/commit/864e2b5111e0d25ac4cf8430f24e3... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Fix batch mode for collection, when collection maps to multiple inputs Commit: 19d91455947908a70a167c7f3a790d612f939986 https://github.com/galaxyproject/galaxy/commit/19d91455947908a70a167c7f3a790... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-06 (Thu, 06 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- One more bump to be the last tabular type detected, since ConnectivityTable is more specific. Commit: 73cbe3560e93746e0c8bc562bfca8ba1be0abb03 https://github.com/galaxyproject/galaxy/commit/73cbe3560e93746e0c8bc562bfca8... Author: John Chilton <jmchilton@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #571 from dannon/csv_sam_sniff_fix [15.07] Csv sam sniff fix Commit: 395e103ee5ffad466ab485c5a1877540a8342d79 https://github.com/galaxyproject/galaxy/commit/395e103ee5ffad466ab485c5a1877... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge pull request #570 from ericenns/new-tool-form-batch-collection [15.05] Fix batch mode input in new tool form ui Commit: 913eb7f767feac65403bb289e7087d5fc0da2162 https://github.com/galaxyproject/galaxy/commit/913eb7f767feac65403bb289e7087... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- show field for entering remote/home url when managing repo fixes #579 Commit: 53463434b0dabe3c82c14260ce60275cb49a39ce https://github.com/galaxyproject/galaxy/commit/53463434b0dabe3c82c14260ce602... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Merge pull request #580 from martenson/show-ts-fields-when-editing [release_15.07] show field for entering remote/home url when managing repo Commit: d9d365b36e827adf859759fd41113a74204ce376 https://github.com/galaxyproject/galaxy/commit/d9d365b36e827adf859759fd41113... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- 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. Commit: 15b5a336c4c09524bacdc445ad47ce8a0be60168 https://github.com/galaxyproject/galaxy/commit/15b5a336c4c09524bacdc445ad47c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #590 from nsoranzo/release_15.05 [15.05] Fix wrong call to LDAPObject.result() by using search_ext_s(). Commit: cbae8fab672e302094bb5adaa3921e9feae87224 https://github.com/galaxyproject/galaxy/commit/cbae8fab672e302094bb5adaa3921... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix an XSS reflection vulnerability on the workflow import form. Commit: 8e7017a6b125ce5a079cc15c5f26148071b0c366 https://github.com/galaxyproject/galaxy/commit/8e7017a6b125ce5a079cc15c5f261... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix a vulnerability in the Tool Shed API that allowed unauthorized users to upload new repository versions. Commit: 25d8a54aeb6c34ebf48d9c3bead4f6390848a6a3 https://github.com/galaxyproject/galaxy/commit/25d8a54aeb6c34ebf48d9c3bead4f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.03 Commit: a454c93fd342783902887ecb66f63a658ad30270 https://github.com/galaxyproject/galaxy/commit/a454c93fd342783902887ecb66f63... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.03 Commit: 2a1b2dbb5ae83b3c6b7d4360a674432698e216da https://github.com/galaxyproject/galaxy/commit/2a1b2dbb5ae83b3c6b7d4360a6744... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- 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. Commit: e3e9213e28e02ed7439f7458ad079a099064e1b6 https://github.com/galaxyproject/galaxy/commit/e3e9213e28e02ed7439f7458ad079... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.05 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py Commit: 052b6a6a38fb0bba859d8c591aa78960d8b211db https://github.com/galaxyproject/galaxy/commit/052b6a6a38fb0bba859d8c591aa78... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.05 Commit: d9426dab92ef70528b021adff48e5c67be3b6a94 https://github.com/galaxyproject/galaxy/commit/d9426dab92ef70528b021adff48e5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge branch 'security-20150812-ldap' into release_15.07 Commit: 3c2762b6c7e9532cfbc9bd74ab402f96c77ead58 https://github.com/galaxyproject/galaxy/commit/3c2762b6c7e9532cfbc9bd74ab402... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.07 Commit: 3e4513f195de4e4a8e225d29fe3a9011b0bbc148 https://github.com/galaxyproject/galaxy/commit/3e4513f195de4e4a8e225d29fe3a9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.07 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py Commit: 8f7f80d295cabc1ecc79e492d463b2f9cc894d08 https://github.com/galaxyproject/galaxy/commit/8f7f80d295cabc1ecc79e492d463b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: a3e511292afe6dcdbb3bf533ef6b6e2520c2c652 https://github.com/galaxyproject/galaxy/commit/a3e511292afe6dcdbb3bf533ef6b6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge branch 'release_15.05' Commit: a6a85cbc4ccbde1a39ebb9b84a47da6332a6a27c https://github.com/galaxyproject/galaxy/commit/a6a85cbc4ccbde1a39ebb9b84a47d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.03.3 Commit: f01300d7da5625ac264552258b29818598d4d535 https://github.com/galaxyproject/galaxy/commit/f01300d7da5625ac264552258b298... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.05.1. Merge branch 'release_15.03' into release_15.05 Conflicts: lib/galaxy/version.py Commit: b3da771a637ac9f7a4778fd115a09da01f432b1c https://github.com/galaxyproject/galaxy/commit/b3da771a637ac9f7a4778fd115a09... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.07 (drop .dev) Merge branch 'release_15.05' into release_15.07 Conflicts: lib/galaxy/version.py Commit: a8a1a150c6ec1a474753052b96b25aec8a22813e https://github.com/galaxyproject/galaxy/commit/a8a1a150c6ec1a474753052b96b25... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge branch 'release_15.05' Commit: 130004feb10f1fe3a26908401146b8e47c1202ff https://github.com/galaxyproject/galaxy/commit/130004feb10f1fe3a26908401146b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M .gitignore M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js M client/README.md M client/bower.json R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M 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client/toolshed/scripts/toolshed.groups.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A 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tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/7144ed8f7299...130004feb10f