Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4ea881caa21602c5562224fa268ff87788eee0dd https://github.com/galaxyproject/galaxy/commit/4ea881caa21602c5562224fa268ff... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix old bug in non-allowed_images.yml GIEs Commit: b713fff00d7c1a6c50e72f69647a6b5cbe3629dd https://github.com/galaxyproject/galaxy/commit/b713fff00d7c1a6c50e72f69647a6... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 997fa1577b19d9daa31768731e7cd5f4a19db1e6 https://github.com/galaxyproject/galaxy/commit/997fa1577b19d9daa31768731e7cd... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 157da746d8c5da8985d71fee578ba68dc104a11f https://github.com/galaxyproject/galaxy/commit/157da746d8c5da8985d71fee578ba... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: a68381777df3e6c8165f5b9bdc4d4abf9bee41db https://github.com/galaxyproject/galaxy/commit/a68381777df3e6c8165f5b9bdc4d4... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Commit: 1069a69ae08a4a2db609aebb03c4a8fa53162777 https://github.com/galaxyproject/galaxy/commit/1069a69ae08a4a2db609aebb03c4a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2550 from erasche/asdf [16.04] Fix old bug in non-allowed_images.yml GIEs Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix tag_autocomplete issue. When we swapped to tag manager the signature changed and some of these were missed. Commit: 1507bd37fe8cb872975e46a6e7be468e984db0d8 https://github.com/galaxyproject/galaxy/commit/1507bd37fe8cb872975e46a6e7be4... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- More defensive proxying Commit: f8e40bb5951cc38dce118cebcc09a5cc3ca96930 https://github.com/galaxyproject/galaxy/commit/f8e40bb5951cc38dce118cebcc09a... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2585 from erasche/backport-proxy-fix [16.04] Backport proxy fixes Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e080533... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: acdfd2423f3e8764375d0b7a23dad3c919db47fc https://github.com/galaxyproject/galaxy/commit/acdfd2423f3e8764375d0b7a23dad... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: 84d152082009418f2fd5dfe0e9001e8924a678fc https://github.com/galaxyproject/galaxy/commit/84d152082009418f2fd5dfe0e9001... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Absolute positioning for tabular dataset chunking, vs abstract chunk. Ships a minimum of one line regardless of size, and relies on client to know position. Commit: ca4b51b390d14077188b5226e4c83ed0991dcbb5 https://github.com/galaxyproject/galaxy/commit/ca4b51b390d14077188b5226e4c83... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Make client with new tabular display. Commit: a65faa961ca434901baaaeffe2e5926d4ac523c1 https://github.com/galaxyproject/galaxy/commit/a65faa961ca434901baaaeffe2e59... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix tabular chunked display offset=0 request, pass through ck_size to allow client specification of chunk size overriding the app defaults (neither of these are used by the js client currently though) Commit: d7cdf74bdf2690ab1d83cb262021251ae3e28d14 https://github.com/galaxyproject/galaxy/commit/d7cdf74bdf2690ab1d83cb2620212... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Handle the case when the last character of the initial read is a newline. Commit: b7718a0f9ae3a626ab88080e0798a451597984c8 https://github.com/galaxyproject/galaxy/commit/b7718a0f9ae3a626ab88080e0798a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Swap ck_size default from 0 to None to indicate unset. This does not change any behavior at all, but @nsoranzo requested the change to make usage more clear. Commit: 1d8f39d987217c09048e05e1d5443173eb02a9f2 https://github.com/galaxyproject/galaxy/commit/1d8f39d987217c09048e05e1d5443... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove old, unused arguments from some display_dataset methods, minor argument tweaks. Commit: 4da2119c2560c68cb716270933959eb8cf3d48ed https://github.com/galaxyproject/galaxy/commit/4da2119c2560c68cb716270933959... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Remove explicit 'chunk' parameter passthrough in datasets API Commit: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe16... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #2569 from dannon/workflow_tag_fixes [16.04] Fix tag_autocomplete issue in workflow editor. Commit: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes Commit: aa7ead6dccd2c80152664c31bbf9b27f2f463799 https://github.com/galaxyproject/galaxy/commit/aa7ead6dccd2c80152664c31bbf9b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip whitespaces when processing <url_template> content Otherwise download_binary action tries to save the file to an invalid filename. Reported by @remimarenco on IRC. Fix typo. Commit: 8c59d1c953c61b6d73d9bef5c4dda8a8056240b7 https://github.com/galaxyproject/galaxy/commit/8c59d1c953c61b6d73d9bef5c4dda... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #2618 from nsoranzo/release_16.04_fix_download_binary [16.04] Strip whitespaces when processing <url_template> content Commit: dfce1a973012d430823a3dfad6edad08a31df747 https://github.com/galaxyproject/galaxy/commit/dfce1a973012d430823a3dfad6eda... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- This is an extra hammer swing at #1531 / #1542, which @rmarenco encountered. He said this resolves it. Commit: f9416573325139c6449d9a8959a138d5681d00d8 https://github.com/galaxyproject/galaxy/commit/f9416573325139c6449d9a8959a13... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Extra debugging to hopefully shed light on the PJA Async issue with delete intermediates action and new(ish) workflow scheduling. Clarified a few vars. Commit: bc79e9cc4a0f5597d6243f946e034f88106141d1 https://github.com/galaxyproject/galaxy/commit/bc79e9cc4a0f5597d6243f946e034... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, history: replace copy dialog on grid refresh Fixes #2624 init_grid is called from update_grid to rebuild the grid. This patches that call to replace the copy links with the dialog. Note: - related to #1303 which was an effort to make a single code path for copying histories. - Uses monkey patching to keep from porting build artifacts. Commit: 8a5042d15b5b94fb804a1b1488375939dd88c3d2 https://github.com/galaxyproject/galaxy/commit/8a5042d15b5b94fb804a1b1488375... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #2626 from dannon/backport_hammerthrow [16.04] Backport workflow fix Commit: 10ac6ee132642e19b8bf0bd60903a85336337571 https://github.com/galaxyproject/galaxy/commit/10ac6ee132642e19b8bf0bd60903a... Author: Carl Eberhard <carlfeberhard@users.noreply.github.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Merge pull request #2556 from ericenns/fix-2461-dataset-peek [16.04] Fix off by one error, causing only first line of file to be rendered … Commit: 5f24afb1b3eebb7e30cee3958015b972b0bf2b1d https://github.com/galaxyproject/galaxy/commit/5f24afb1b3eebb7e30cee3958015b... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 09b9339569d688e89b6f6fb9abc32b8e2b465e28 https://github.com/galaxyproject/galaxy/commit/09b9339569d688e89b6f6fb9abc32... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 7e389c7d54da91298c4b5970314c7e5040902952 https://github.com/galaxyproject/galaxy/commit/7e389c7d54da91298c4b5970314c7... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: 85671bd466e8bfca0dc22c8fbdc6385a3e9dcf1e https://github.com/galaxyproject/galaxy/commit/85671bd466e8bfca0dc22c8fbdc63... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Commit: f4631d2e59af6596afbf571e5cb983e5ce734115 https://github.com/galaxyproject/galaxy/commit/f4631d2e59af6596afbf571e5cb98... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge pull request #2629 from carlfeberhard/fix.saved-copy [16.01] UI, history: replace copy dialog on grid refresh Commit: ac64c0162ef5f9c68529ee730326c985f4430280 https://github.com/galaxyproject/galaxy/commit/ac64c0162ef5f9c68529ee730326c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 95c64c0ba917bfbc5d04ff603ec3ca2a58f6c54f https://github.com/galaxyproject/galaxy/commit/95c64c0ba917bfbc5d04ff603ec3c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild as a part of merging from 16.01. Commit: a5b836e9eeead2eab752d79b0e15197b82cb0720 https://github.com/galaxyproject/galaxy/commit/a5b836e9eeead2eab752d79b0e151... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/dataset/data.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/dataset/data.js M templates/webapps/galaxy/history/grid.mako A test/unit/datatypes/test_data.py Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/0ba99fe24609...a5b836e9eeea