galaxy-commits July 2016

galaxy-commits@lists.galaxyproject.org

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109 discussions

[galaxyproject/galaxy] 5f24af: Fix off by one error, causing only first line of f...
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5f24afb1b3eebb7e30cee3958015b972b0bf2b1d https://github.com/galaxyproject/galaxy/commit/5f24afb1b3eebb7e30cee3958015… Author: Eric Enns <eric.enns(a)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/09b9339569d688e89b6f6fb9abc3… Author: Eric Enns <eric.enns(a)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/7e389c7d54da91298c4b5970314c… Author: Eric Enns <eric.enns(a)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/85671bd466e8bfca0dc22c8fbdc6… Author: Eric Enns <eric.enns(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/67c4df712a0d...85671bd466e8

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[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]
by GitHub 19 Jul '16

19 Jul '16

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

1 0

[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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galaxy-commits July 2016