- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy]
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/16.04 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] b713ff: Fix off by one error, causing only first line of f...
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b713fff00d7c1a6c50e72f69647a6b5cbe3629dd https://github.com/galaxyproject/galaxy/commit/b713fff00d7c1a6c50e72f69647a… Author: Eric Enns <eric.enns(a)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/997fa1577b19d9daa31768731e7c… Author: Eric Enns <eric.enns(a)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/157da746d8c5da8985d71fee578b… Author: Eric Enns <eric.enns(a)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/a68381777df3e6c8165f5b9bdc4d… Author: Eric Enns <eric.enns(a)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: 10ac6ee132642e19b8bf0bd60903a85336337571 https://github.com/galaxyproject/galaxy/commit/10ac6ee132642e19b8bf0bd60903… Author: Carl Eberhard <carlfeberhard(a)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: 1e36eba631b2d5bb697dac8b2a7aae375dbe1fe3 https://github.com/galaxyproject/galaxy/commit/1e36eba631b2d5bb697dac8b2a7a… Author: carlfeberhard <carlfeberhard(a)gmail.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 branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e1e0a3ba10a9...1e36eba631b2

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[galaxyproject/galaxy] b713ff: Fix off by one error, causing only first line of f...
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: b713fff00d7c1a6c50e72f69647a6b5cbe3629dd https://github.com/galaxyproject/galaxy/commit/b713fff00d7c1a6c50e72f69647a… Author: Eric Enns <eric.enns(a)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/997fa1577b19d9daa31768731e7c… Author: Eric Enns <eric.enns(a)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/157da746d8c5da8985d71fee578b… Author: Eric Enns <eric.enns(a)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/a68381777df3e6c8165f5b9bdc4d… Author: Eric Enns <eric.enns(a)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: 10ac6ee132642e19b8bf0bd60903a85336337571 https://github.com/galaxyproject/galaxy/commit/10ac6ee132642e19b8bf0bd60903… Author: Carl Eberhard <carlfeberhard(a)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 … Compare: https://github.com/galaxyproject/galaxy/compare/8a5042d15b5b...10ac6ee13264

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[galaxyproject/galaxy] aa7ead: Strip whitespaces when processing <url_template> c...
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa7ead6dccd2c80152664c31bbf9b27f2f463799 https://github.com/galaxyproject/galaxy/commit/aa7ead6dccd2c80152664c31bbf9… Author: Nicola Soranzo <nicola.soranzo(a)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/8c59d1c953c61b6d73d9bef5c4dd… Author: Björn Grüning <bjoern(a)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/dfce1a973012d430823a3dfad6ed… Author: Dannon Baker <dannon.baker(a)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/f9416573325139c6449d9a8959a1… Author: Dannon Baker <dannon.baker(a)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: 8a5042d15b5b94fb804a1b1488375939dd88c3d2 https://github.com/galaxyproject/galaxy/commit/8a5042d15b5b94fb804a1b148837… Author: Martin Cech <cech.marten(a)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: e1e0a3ba10a9572051fa352760fab03baf4004d2 https://github.com/galaxyproject/galaxy/commit/e1e0a3ba10a9572051fa352760fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d351121d126f...e1e0a3ba10a9

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[galaxyproject/galaxy] dfce1a: This is an extra hammer swing at #1531 / #1542, wh...
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: dfce1a973012d430823a3dfad6edad08a31df747 https://github.com/galaxyproject/galaxy/commit/dfce1a973012d430823a3dfad6ed… Author: Dannon Baker <dannon.baker(a)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/f9416573325139c6449d9a8959a1… Author: Dannon Baker <dannon.baker(a)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: 8a5042d15b5b94fb804a1b1488375939dd88c3d2 https://github.com/galaxyproject/galaxy/commit/8a5042d15b5b94fb804a1b148837… Author: Martin Cech <cech.marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/8c59d1c953c6...8a5042d15b5b

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[galaxyproject/galaxy] 8ac38b: Move controller consistent workflow api endpoint t...
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ac38bee15ee2a67908a09d8fc85951a79dc348f https://github.com/galaxyproject/galaxy/commit/8ac38bee15ee2a67908a09d8fc85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js Log Message: ----------- Move controller consistent workflow api endpoint to internal api route Commit: 18f1593ead16544c523d0de4b03d87b215e064b4 https://github.com/galaxyproject/galaxy/commit/18f1593ead16544c523d0de4b03d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rename 'internal_api' endpoint to 'api_internal' so that the base webapp transaction switching (and thus controller matching) works correctly. Commit: e77c3fd01a19ea01b748c22f5fe6174aad44c6aa https://github.com/galaxyproject/galaxy/commit/e77c3fd01a19ea01b748c22f5fe6… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #11 from dannon/internal_api Rename 'internal_api' endpoint to 'api_internal' so that the base web… Commit: 9e07774bb3b15dcc15c7c67d4710014f42790199 https://github.com/galaxyproject/galaxy/commit/9e07774bb3b15dcc15c7c67d4710… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix comment to indicate proper route Commit: d351121d126f84e4c3a5f0123fe1b96d333aef22 https://github.com/galaxyproject/galaxy/commit/d351121d126f84e4c3a5f0123fe1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js Log Message: ----------- Merge pull request #2622 from guerler/internal_api Reroute consistent workflow endpoint to internal api Compare: https://github.com/galaxyproject/galaxy/compare/e21a81fbf0c0...d351121d126f

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[galaxyproject/galaxy] aa6919: User API tests: add show
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa69199bd17c3bfa5602d06a9b118187c1b68e1c https://github.com/galaxyproject/galaxy/commit/aa69199bd17c3bfa5602d06a9b11… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M test/api/test_users.py Log Message: ----------- User API tests: add show Commit: 54e07906f51f58c1580b1bec64cdfc1c74ff8779 https://github.com/galaxyproject/galaxy/commit/54e07906f51f58c1580b1bec64cd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M test/api/test_users.py Log Message: ----------- User API tests: add update test Commit: 86a3531730dfffb81014302b2495c939ae4bd4ec https://github.com/galaxyproject/galaxy/commit/86a3531730dfffb81014302b2495… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M test/unit/managers/test_UserManager.py Log Message: ----------- API, users: add deserializer to user manager - Adds deserialization method for usernames (note: still needs trans) - Adds tests for deserializer in test_UserManager.py Commit: f724e84fda22fb73042ea344ec00be86b3a7c564 https://github.com/galaxyproject/galaxy/commit/f724e84fda22fb73042ea344ec00… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/managers/users.py M test/api/test_users.py M test/unit/managers/test_UserManager.py Log Message: ----------- API, users: use default to assign username Commit: ad95cad99004f390dcd7937ac334fa655b48ac36 https://github.com/galaxyproject/galaxy/commit/ad95cad99004f390dcd7937ac334… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_users.py Log Message: ----------- API, users: implement users update - users and admin can now update usernames via the API - adds api tests to update Commit: e918d00cef31dca422b7348884db0e2055353bc4 https://github.com/galaxyproject/galaxy/commit/e918d00cef31dca422b7348884db… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- API, users: use api_inherit_admin in update Commit: 7ef9b2325e03c4a63023af39afb5ff5e742edc3b https://github.com/galaxyproject/galaxy/commit/7ef9b2325e03c4a63023af39afb5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M test/api/test_users.py Log Message: ----------- API, users: remove log, change assertion style Commit: 09d10147f98793b97282aaec1c44efaff7c62585 https://github.com/galaxyproject/galaxy/commit/09d10147f98793b97282aaec1c44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M test/unit/managers/test_UserManager.py Log Message: ----------- Tests, user: py3 exception and relative import fix Commit: e21a81fbf0c08dcaab2935211213c7afec56df7f https://github.com/galaxyproject/galaxy/commit/e21a81fbf0c08dcaab2935211213… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_users.py M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #2595 from carlfeberhard/users.api-update Users API: add the update endpoint Compare: https://github.com/galaxyproject/galaxy/compare/47d154f979b2...e21a81fbf0c0

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[galaxyproject/galaxy] 888ee7: Graph visualization: add parsers, change datatypes
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 888ee700d7e8cb99d5e6c9674271c9da3b40ee74 https://github.com/galaxyproject/galaxy/commit/888ee700d7e8cb99d5e6c9674271… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Graph visualization: add parsers, change datatypes - Removes Data.Text and all subclasses from the applicable datatypes - Adds all datatypes that can provide node-edge data to be applicable (xgmll and sif) - Adds txt and json extensions as applicable - Minor clean up - Can use shift key to select multiple nodes Commit: 47d154f979b29a25fc2d9904583f677216a3b65d https://github.com/galaxyproject/galaxy/commit/47d154f979b29a25fc2d9904583f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Merge pull request #2620 from carlfeberhard/graphviz Graph visualization: add parsers, change datatypes Compare: https://github.com/galaxyproject/galaxy/compare/4bf21e624ece...47d154f979b2

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[galaxyproject/galaxy] 09b421: UI, history: implement list:list
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09b42113c6b9fb1bcddbe66a86e299866431c9a4 https://github.com/galaxyproject/galaxy/commit/09b42113c6b9fb1bcddbe66a86e2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: implement list:list Commit: 3646d08d7ff2303be21e9c12050a55039dc1219a https://github.com/galaxyproject/galaxy/commit/3646d08d7ff2303be21e9c12050a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: more feedback on bad collection type Commit: 510fe47ae19c170001eac652c83316d3fd2b181b https://github.com/galaxyproject/galaxy/commit/510fe47ae19c170001eac652c833… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- (bundle scripts) Commit: 4bf21e624ecea88ce67a9a802f6bd08b137e9a79 https://github.com/galaxyproject/galaxy/commit/4bf21e624ecea88ce67a9a802f6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M static/maps/mvc/history/history-contents.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/history/history-contents.js M templates/ind_share_base.mako M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into HEAD Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js Compare: https://github.com/galaxyproject/galaxy/compare/3b19a061cf89...4bf21e624ece

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[galaxyproject/galaxy] 9d3b30: UI, history: stringify contents copy params
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d3b304879959f9cea76cd2dd242b2eea6c1c478 https://github.com/galaxyproject/galaxy/commit/9d3b304879959f9cea76cd2dd242… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.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/history/history-contents.js Log Message: ----------- UI, history: stringify contents copy params Commit: 96cca7ccadba60c7aac970e656bf0932070b9d00 https://github.com/galaxyproject/galaxy/commit/96cca7ccadba60c7aac970e656bf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Core, request body: handle hex vs. float better When parsing a non-json request body, params for a payload have been parsed individually using loads on a single value. This can cause a hex id in the (regex) form '\d+e\d+' to be parsed as a float. This commit: - adds a parse_non_hex_float function that refuses to parse scientific notation in the above form - and uses it *only* in the payload parsing method for non-json request bodies Commit: d157865857589ef73a164219dc4ed630a16520ca https://github.com/galaxyproject/galaxy/commit/d157865857589ef73a164219dc4e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tool/tool-form-composite.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/runners/kubernetes.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M static/maps/mvc/dataset/data.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.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 static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix.hex-vs-float Commit: 3b19a061cf896ea1eed9933bf6bda549be7d8a06 https://github.com/galaxyproject/galaxy/commit/3b19a061cf896ea1eed9933bf6bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M static/maps/mvc/history/history-contents.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/history/history-contents.js Log Message: ----------- Merge pull request #2597 from carlfeberhard/fix.hex-vs-float Fix hex vs float parsing in request body Compare: https://github.com/galaxyproject/galaxy/compare/389b2f4fbd2e...3b19a061cf89

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[galaxyproject/galaxy] c9291d: Merge pull request #6 from galaxyproject/dev
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9291d0c949cb1469f62f53a3b4b370fd1b2f20f https://github.com/galaxyproject/galaxy/commit/c9291d0c949cb1469f62f53a3b4b… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_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/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/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/molecules.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/util/gff_util.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.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/0009_request_table.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/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.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/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.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/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.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/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.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/0044_add_notify_column_to_request_table.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/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.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/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.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/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.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/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.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/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.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/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.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/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.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/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.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/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/wrappers.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/modules.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.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/common_startup.sh M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py M setup.cfg M static/maps/mvc/dataset/data.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.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 static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js M templates/admin/impersonate.mako M templates/user/change_password.mako M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py A test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.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/tools/test_toolbox.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 M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge pull request #6 from galaxyproject/dev keeps up to date with galaxy:dev Commit: 4230a107373921c766d5dd6f19f405f54fafe1ab https://github.com/galaxyproject/galaxy/commit/4230a107373921c766d5dd6f19f4… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Reinstates workingDir setup for container on k8s. This was removed by mistake previously. Commit: 389b2f4fbd2e0f689f0e11ffc08f01f193e6026a https://github.com/galaxyproject/galaxy/commit/389b2f4fbd2e0f689f0e11ffc08f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2616 from phnmnl/feature/missingWorkingDirK8sOption Kubernetes runner corrects working directory not passed to container Compare: https://github.com/galaxyproject/galaxy/compare/5b3a27c0b0e2...389b2f4fbd2e

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[galaxyproject/galaxy] d1ce99: Fix smart_str for Python 3. Add doctests
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1ce991dd4acc2c50c18990b01571216f483907e https://github.com/galaxyproject/galaxy/commit/d1ce991dd4acc2c50c18990b0157… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix smart_str for Python 3. Add doctests Commit: 5b3a27c0b0e2c1e40e9f933dae139dfefd8be373 https://github.com/galaxyproject/galaxy/commit/5b3a27c0b0e2c1e40e9f933dae13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2608 from nsoranzo/smart_str Fix smart_str for Python 3. Add doctests Compare: https://github.com/galaxyproject/galaxy/compare/bb9907a81da4...5b3a27c0b0e2

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[galaxyproject/galaxy] 102bc2: Update to make the workflow share dropdown the sam...
by GitHub 18 Jul '16

18 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 102bc28011023ec22604c559a6c10ed98e535e3a https://github.com/galaxyproject/galaxy/commit/102bc28011023ec22604c559a6c1… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Update to make the workflow share dropdown the same width as the impersonate user dropdown. Commit: bb9907a81da44ea0f01190e1642796140dc59657 https://github.com/galaxyproject/galaxy/commit/bb9907a81da44ea0f01190e16427… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Merge pull request #2617 from sszakony/dev Update workflow share dropdown width Compare: https://github.com/galaxyproject/galaxy/compare/0480e5e5505e...bb9907a81da4

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[galaxyproject/galaxy] aa7ead: Strip whitespaces when processing <url_template> c...
by GitHub 15 Jul '16

15 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: aa7ead6dccd2c80152664c31bbf9b27f2f463799 https://github.com/galaxyproject/galaxy/commit/aa7ead6dccd2c80152664c31bbf9… Author: Nicola Soranzo <nicola.soranzo(a)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/8c59d1c953c61b6d73d9bef5c4dd… Author: Björn Grüning <bjoern(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/05c063b13a3f...8c59d1c953c6

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[galaxyproject/galaxy] f7cbef: Update gsummary.xml
by GitHub 15 Jul '16

15 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7cbefc1f3e1c4feb215cff26dbbf463b6d6e362 https://github.com/galaxyproject/galaxy/commit/f7cbefc1f3e1c4feb215cff26dbb… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary.xml rpy seems not available within the Conda packages. So I add rpy2 in the requirements. It works for me! I :heart: Conda Commit: e86206733243f42ec414faab3148e32f76e004cb https://github.com/galaxyproject/galaxy/commit/e86206733243f42ec414faab3148… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary.xml Commit: f951249c797f0e944133e8402b5602d83c600276 https://github.com/galaxyproject/galaxy/commit/f951249c797f0e944133e8402b56… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Update gsummary.xml Delete r and rpy deps Commit: 0480e5e5505e47709193b3e33d3068187ed0e6ac https://github.com/galaxyproject/galaxy/commit/0480e5e5505e47709193b3e33d30… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #2590 from lecorguille/patch-1 Update gsummary.xml Compare: https://github.com/galaxyproject/galaxy/compare/7bbe0a217123...0480e5e5505e

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[galaxyproject/galaxy] 03b59a: Committing format changes to the user impersonatio...
by GitHub 13 Jul '16

13 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03b59aacc33837f8160ecd45869d7f4df67fc6c6 https://github.com/galaxyproject/galaxy/commit/03b59aacc33837f8160ecd45869d… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M templates/admin/impersonate.mako Log Message: ----------- Committing format changes to the user impersonation dropdown. Commit: 7bbe0a2171232d6c7f04c57d045a9cce19b29476 https://github.com/galaxyproject/galaxy/commit/7bbe0a2171232d6c7f04c57d045a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M templates/admin/impersonate.mako Log Message: ----------- Merge pull request #2612 from sszakony/dev Committing format changes to the user impersonation dropdown. Compare: https://github.com/galaxyproject/galaxy/compare/f3e9736ca3a5...7bbe0a217123

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[galaxyproject/usegalaxy-playbook] a5cccb: Update Test
by GitHub 11 Jul '16

11 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a5cccbe1c250a70d005754e2bb28c54cc714e650 https://github.com/galaxyproject/usegalaxy-playbook/commit/a5cccbe1c250a70d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] ca82e6: Deletes existing jobs with same ID when re-submitt...
by GitHub 11 Jul '16

11 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca82e6d746a685209b9585b3f69128a55198f801 https://github.com/galaxyproject/galaxy/commit/ca82e6d746a685209b9585b3f691… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Deletes existing jobs with same ID when re-submitting. Commit: 01fd25b9f4b79b4f2868efc51ad76e19fc132b5d https://github.com/galaxyproject/galaxy/commit/01fd25b9f4b79b4f2868efc51ad7… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Changes use of produce_unique_k8s_job_name to be able to use both job and job_wrappers. Commit: 409eb373cd9233f7925c64e9c5716859a2363ba1 https://github.com/galaxyproject/galaxy/commit/409eb373cd9233f7925c64e9c571… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fixes stop job method so that it correctly scales down the Kubernetes job. Commit: 65a937965a22c46922f9b731475561e38809e588 https://github.com/galaxyproject/galaxy/commit/65a937965a22c46922f9b7314755… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improves handling of Kubernetes logs Commit: e8bf2df21fe7fb7405ea283a41eae22e6d58509f https://github.com/galaxyproject/galaxy/commit/e8bf2df21fe7fb7405ea283a41ea… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Corrects usage of pods retrials parameters set in runner and container destinations. Commit: 89b5f3f47f14fa82065b83326332313ec8cca629 https://github.com/galaxyproject/galaxy/commit/89b5f3f47f14fa82065b83326332… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Uses exception instead of pykube.exceptions.HTTPError to manage missing pod's log exception. Commit: 9db3453e6559cb883af22793b741a84f3abd071c https://github.com/galaxyproject/galaxy/commit/9db3453e6559cb883af22793b741… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Overrides parent fail_job to save stdout/stderr of pods when Kubernetes job fails (otherwise lost). Commit: 5eb60b3448f2cdf8706aa2ab43e4d51dcfc0a0cb https://github.com/galaxyproject/galaxy/commit/5eb60b3448f2cdf8706aa2ab43e4… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds missing whitespace to line in Kubernetes runner. Commit: f3e9736ca3a592d9aed006ecfd072f67cebfa006 https://github.com/galaxyproject/galaxy/commit/f3e9736ca3a592d9aed006ecfd07… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2559 from phnmnl/feature/failingPodsNotDetected Kubernetes runner: improves handling of failed jobs Compare: https://github.com/galaxyproject/galaxy/compare/a74a23764cc1...f3e9736ca3a5

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[galaxyproject/galaxy] 4ea881: Fix old bug in non-allowed_images.yml GIEs
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ea881caa21602c5562224fa268ff87788eee0dd https://github.com/galaxyproject/galaxy/commit/4ea881caa21602c5562224fa268f… Author: Eric Rasche <rasche.eric(a)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: 1069a69ae08a4a2db609aebb03c4a8fa53162777 https://github.com/galaxyproject/galaxy/commit/1069a69ae08a4a2db609aebb03c4… Author: Björn Grüning <bjoern(a)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/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)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/1507bd37fe8cb872975e46a6e7be… Author: Eric Rasche <rasche.eric(a)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/f8e40bb5951cc38dce118cebcc09… Author: Martin Cech <cech.marten(a)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/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)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/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)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/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)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/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)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/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)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/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)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/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)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/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)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/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)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/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)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/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)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: a74a23764cc1aa0a481d0e2ea65ac26a8f151865 https://github.com/galaxyproject/galaxy/commit/a74a23764cc1aa0a481d0e2ea65a… Author: Dannon Baker <dannon.baker(a)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 lib/galaxy/webapps/galaxy/controllers/tag.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 branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/77f547ed89a9...a74a23764cc1

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[galaxyproject/galaxy] 7c2c2c: Tabular dataset chunking fix which should prevent ...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)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/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)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/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)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/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)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/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)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/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)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/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)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/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)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/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)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: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/ab2e48bae739...05c063b13a3f

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[galaxyproject/galaxy] 61a113: When CONDA_ALREADY_INSTALLED is undefined there's ...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61a11341f9eb5f18ac33bd88e6acefc37a6f46af https://github.com/galaxyproject/galaxy/commit/61a11341f9eb5f18ac33bd88e6ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- When CONDA_ALREADY_INSTALLED is undefined there's an error due to the number of arguments in the boolean expression (we actually *do* always want a 1 or 0 there, never empty) Commit: 77f547ed89a90e31df6e388e311bef29d18f2e65 https://github.com/galaxyproject/galaxy/commit/77f547ed89a90e31df6e388e311b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2599 from dannon/fix_startup_condaskip When CONDA_ALREADY_INSTALLED is undefined there's an error due to the… Compare: https://github.com/galaxyproject/galaxy/compare/c0101e011fc3...77f547ed89a9

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[galaxyproject/galaxy] c3bf89: Fix tag_autocomplete issue. When we swapped to ta...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)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: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/f8e40bb5951c...ab2e48bae739

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[galaxyproject/galaxy] b53a92: Add Warning when Conda is installed because we ski...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b53a9275d54d8ed0373a11a4e95c500619a3d5b0 https://github.com/galaxyproject/galaxy/commit/b53a9275d54d8ed0373a11a4e95c… Author: remimarenco <remi.marenco(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add Warning when Conda is installed because we skip the virtualenv creation Fix the case where we could have conda not installed but not setting VirtualEnv still (and have this non relevant warning Commit: de702db55d8f1ca397b4ab926085e006cd39a490 https://github.com/galaxyproject/galaxy/commit/de702db55d8f1ca397b4ab926085… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- s/creation/activation. Thx @nsoranzo Commit: c0101e011fc3aacad1533d1bb80fdf4588c6bdb6 https://github.com/galaxyproject/galaxy/commit/c0101e011fc3aacad1533d1bb80f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2596 from remimarenco/conda_virtualenv_warning Add Warning when Conda is installed Compare: https://github.com/galaxyproject/galaxy/compare/83f1b07687a5...c0101e011fc3

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[galaxyproject/galaxy] 89b838: Add controller consistent workflow api endpoint
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89b83885a79c58e28b305450ca33e08343d421cb https://github.com/galaxyproject/galaxy/commit/89b83885a79c58e28b305450ca33… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Add controller consistent workflow api endpoint Commit: 83f1b07687a5397bec60d4d57a2e0c9bcb44deda https://github.com/galaxyproject/galaxy/commit/83f1b07687a5397bec60d4d57a2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Merge pull request #2077 from guerler/revise_workflow_run_004 Run workflow form revision Compare: https://github.com/galaxyproject/galaxy/compare/834c97a81da6...83f1b07687a5

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[galaxyproject/galaxy] a074af: Ignore W503 as PEP 8 has reversed its position on ...
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a074af5668bc37685649a245e48f2f6e60613591 https://github.com/galaxyproject/galaxy/commit/a074af5668bc37685649a245e48f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M setup.cfg Log Message: ----------- Ignore W503 as PEP 8 has reversed its position on this. Commit: 834c97a81da6cef6cfab0a14e86318fcc7cb38fe https://github.com/galaxyproject/galaxy/commit/834c97a81da6cef6cfab0a14e863… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M setup.cfg Log Message: ----------- Merge pull request #2594 from natefoo/ignore-w503 Ignore W503 (line break before binary operator) as PEP 8 has reversed its position on this. Compare: https://github.com/galaxyproject/galaxy/compare/05eebac85ded...834c97a81da6

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