galaxy-commits April 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] e78add: Hide hidden data parameters in workflow editor
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e78add7decfb1bb2f262b0a7d4df3d586cffeb8e https://github.com/galaxyproject/galaxy/commit/e78add7decfb1bb2f262b0a7d4df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Hide hidden data parameters in workflow editor Commit: c78887c4ae3840d807c22bf2ce6bb8b20c3cef94 https://github.com/galaxyproject/galaxy/commit/c78887c4ae3840d807c22bf2ce6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use elif, do not require hidden attribute Commit: 88db9e6a0f0b9fe61bdc66e4fa598af82101c11c https://github.com/galaxyproject/galaxy/commit/88db9e6a0f0b9fe61bdc66e4fa59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2120 from guerler/fix_hidden_001 Hide hidden data parameters in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/411e33194b8c...88db9e6a0f0b

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[galaxyproject/galaxy] 34900f: Fix grouping tool broken in 7347d75a4a36d42f8060e1...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 34900f87f5bc52bc84efe866371588004a049ebf https://github.com/galaxyproject/galaxy/commit/34900f87f5bc52bc84efe8663715… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Fix grouping tool broken in 7347d75a4a36d42f8060e11d708291d796b266a5 / fd85979a8651e0907bebce05cdfb59d77f0d0f64, and enhance performance when removing lines. Commit: 7f101b8da8d09121a302a6707610434e1e2d3cdf https://github.com/galaxyproject/galaxy/commit/7f101b8da8d09121a302a6707610… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #2166 from blankenberg/release_16.04 [16.04] Fix grouping tool and enhance performance when removing lines. Compare: https://github.com/galaxyproject/galaxy/compare/8b49814859dc...7f101b8da8d0

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[galaxyproject/galaxy] 44a337: Add conditional statsd requirement. Wheel is live...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 44a337ab6f8388a4cc1a69dc44e6e1314a2af2dc https://github.com/galaxyproject/galaxy/commit/44a337ab6f8388a4cc1a69dc44e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. Commit: 238b90a7f5e045435b45db3626953308ad8577b0 https://github.com/galaxyproject/galaxy/commit/238b90a7f5e045435b45db362695… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Support configurable statsd prefix (was formerly just 'galaxy', which remains the default) Commit: 411e33194b8cad409b6ad6213699e6260350d3ca https://github.com/galaxyproject/galaxy/commit/411e33194b8cad409b6ad6213699… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2171 from dannon/mostats Stats prefix configurability and conditional wheel req. Compare: https://github.com/galaxyproject/galaxy/compare/5a747bd127c4...411e33194b8c

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[galaxyproject/galaxy] 5b0f23: Tools with auto_format='true' are connectable with...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b0f23562d2f90fadd63798ce9949c12f48f3a34 https://github.com/galaxyproject/galaxy/commit/5b0f23562d2f90fadd63798ce994… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) 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 Log Message: ----------- Tools with auto_format='true' are connectable with other tools in workflow editor via GUI Commit: 5a747bd127c4c003e95f95c6b8a6320fb49e1bef https://github.com/galaxyproject/galaxy/commit/5a747bd127c4c003e95f95c6b8a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) 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 Log Message: ----------- Merge pull request #2144 from yhoogstrate/galaxy_workflow_autosniff Tools with auto_format='true' connectable in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/fbf894ef1441...5a747bd127c4

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[galaxyproject/galaxy] cde04a: markupsafe.escape() in Python2 does not work on st...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Compare: https://github.com/galaxyproject/galaxy/compare/68ce6ce49cc8...18c00899a30c

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[galaxyproject/galaxy] 541738: Re-use ``trans`` logic for calculating user_ftp_di...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54173807e56e8ae4bef4cc0511249d6b87380de2 https://github.com/galaxyproject/galaxy/commit/54173807e56e8ae4bef4cc051124… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Re-use ``trans`` logic for calculating user_ftp_dir. Commit: f95cbf8f38801f03ba1ea9c065bc1796253d6eaf https://github.com/galaxyproject/galaxy/commit/f95cbf8f38801f03ba1ea9c065bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/context.py Log Message: ----------- More documentation and flexibility for configuring FTP imports. - Add missing documentation for the ftp_upload_dir_identifier option. - Add ftp_upload_dir_template option to configure how to combine identifier and base directory to generate an ftp upload directory. Commit: 997b53f3ae7586d4a2e90f6cb03f00b844bb4d42 https://github.com/galaxyproject/galaxy/commit/997b53f3ae7586d4a2e90f6cb03f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M tools/data_source/upload.py Log Message: ----------- Implement option to prevent FTP uploads from being deleted on import. - Simply set `ftp_upload_purge` to `False` in galaxy.ini to enable this. - xref http://dev.list.galaxyproject.org/Data-removal-after-ftp-import-td4667111.h… - slight xref http://dev.list.galaxyproject.org/Uploading-files-to-galaxy-from-a-folder-t… Commit: 3ce6fca52c1fce1027566d5dbc50811be614ca28 https://github.com/galaxyproject/galaxy/commit/3ce6fca52c1fce1027566d5dbc50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- config doc fixes spotted by @nsoranzo Commit: fbf894ef144101dec25237435040c82f945c3525 https://github.com/galaxyproject/galaxy/commit/fbf894ef144101dec25237435040… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/remote_files.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #2168 from jmchilton/ftp_upload More documentation and flexibility for FTP imports. Compare: https://github.com/galaxyproject/galaxy/compare/4ffee71969e7...fbf894ef1441

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[galaxyproject/galaxy] e67506: Implement config.single_user = <email> option.
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e67506802de481c5b604513d947048abe67a7dc8 https://github.com/galaxyproject/galaxy/commit/e67506802de481c5b604513d9470… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement config.single_user = <email> option. Let Planemo and other such applications serve a full-fledged Galaxy instance without having to worry about logins, etc.... Commit: 2546030c66fb453f98035ddf176ffb2b103d8d8d https://github.com/galaxyproject/galaxy/commit/2546030c66fb453f98035ddf176f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Do not require use_remote_user to be explicitly set if single_user is set. Based on comments from @erasche - https://github.com/galaxyproject/galaxy/pull/2165#issuecomment-210048830. Commit: 4ffee71969e77be22f28eeac567572ba5b548d4d https://github.com/galaxyproject/galaxy/commit/4ffee71969e77be22f28eeac5675… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2165 from jmchilton/single_user Implement ``single_user = <email>`` config option. Compare: https://github.com/galaxyproject/galaxy/compare/1e040258193a...4ffee71969e7

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Commit: 8b49814859dc4dcc85d5a4b3b8945f3f7e3342f4 https://github.com/galaxyproject/galaxy/commit/8b49814859dc4dcc85d5a4b3b894… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 16.01 into 16.04 Commit: 1e040258193ae105b1bcc312a0dde832fd3c0716 https://github.com/galaxyproject/galaxy/commit/1e040258193ae105b1bcc312a0dd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e81448c62ab5...1e040258193a

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Commit: 8b49814859dc4dcc85d5a4b3b8945f3f7e3342f4 https://github.com/galaxyproject/galaxy/commit/8b49814859dc4dcc85d5a4b3b894… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 16.01 into 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/f013cf2021ec...8b49814859dc

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 14 Apr '16

14 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/c0d65092fbbd...68ce6ce49cc8

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