galaxy-commits March 2016

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208 discussions

[galaxyproject/galaxy] 7186fb: Add page layout test cases
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7186fbba9259ff9381c9253632a0269a6359cd6b https://github.com/galaxyproject/galaxy/commit/7186fbba9259ff9381c9253632a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js Log Message: ----------- Add page layout test cases Commit: fb549c80d49c9c89bcb94634a0ee4cafc4a6f116 https://github.com/galaxyproject/galaxy/commit/fb549c80d49c9c89bcb94634a0ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js Log Message: ----------- Merge pull request #1991 from guerler/fix_panel_003 Add page layout test cases Compare: https://github.com/galaxyproject/galaxy/compare/033241c99f8b...fb549c80d49c

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[galaxyproject/usegalaxy-playbook] c3d761: Mutable configs from Test
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3d761d62cd9a544c7f17bd80c3dcadfd4bce856 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3d761d62cd9a544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Test

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[galaxyproject/usegalaxy-playbook] d7e78c: Update Jupyter image, admin users
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d7e78ce06b34857da60d6eaa1820d9ba5e75fbcd https://github.com/galaxyproject/usegalaxy-playbook/commit/d7e78ce06b34857d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Jupyter image, admin users

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[galaxyproject/galaxy] 62b5f2: Remove unnecessary encoding in remote_files. This...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/layout/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/layout/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries Commit: 033241c99f8bb80e4ecac2504a4bdc1f3a4dd657 https://github.com/galaxyproject/galaxy/commit/033241c99f8bb80e4ecac2504a4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge 16.01, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/c171fd168d69...033241c99f8b

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[galaxyproject/galaxy] 62b5f2: Remove unnecessary encoding in remote_files. This...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries Compare: https://github.com/galaxyproject/galaxy/compare/8e41fda58a6b...21e71a9b46b9

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[galaxyproject/galaxy] 946458: Fix booleans
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 946458b8928be8d9ea901d280c4ec5ce36926ea1 https://github.com/galaxyproject/galaxy/commit/946458b8928be8d9ea901d280c4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix booleans Commit: c171fd168d69bbc1e703f89ac94c4145d3d2a883 https://github.com/galaxyproject/galaxy/commit/c171fd168d69bbc1e703f89ac94c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1990 from guerler/fix_boolean_000 Fix booleans in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/d10ee6f6c427...c171fd168d69

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[galaxyproject/galaxy] 79d16f: Fix scratchbook
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/layout/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/layout/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Compare: https://github.com/galaxyproject/galaxy/compare/cf16b1d692d0...8e41fda58a6b

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[galaxyproject/galaxy] 133f77: Fix 'Resend verification' link in inactive user me...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 133f77413e9fb933ec1964d279408c1fb8846db4 https://github.com/galaxyproject/galaxy/commit/133f77413e9fb933ec1964d27940… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- Fix 'Resend verification' link in inactive user message box which would display as [Object object] Commit: fef166545c36df5c7ba73924c7b0ea4e1d44ec82 https://github.com/galaxyproject/galaxy/commit/fef166545c36df5c7ba73924c7b0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Layout: Fix optional panel rendering and associated inline css Commit: dd476fc42c57b5e17d8e1e342d7a597b986b6b3e https://github.com/galaxyproject/galaxy/commit/dd476fc42c57b5e17d8e1e342d7a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- Merge pull request #1978 from carlfeberhard/release_16.01 [16.01] Fixes to page.js Commit: 9eb1db82ca4bbae598d0070de8da78172ca90fa9 https://github.com/galaxyproject/galaxy/commit/9eb1db82ca4bbae598d0070de8da… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Do not convert spaces to tabs when importing datasets into a library. Reported (with fix provided) by Fabien Mareuil in http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-head… Commit: cf16b1d692d0e96f3d0aa4d2cf0f9f52c8dd7bb3 https://github.com/galaxyproject/galaxy/commit/cf16b1d692d0e96f3d0aa4d2cf0f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1985 from nsoranzo/release_16.01_lda_fixes [16.01] Do not convert spaces to tabs when importing datasets into a library. Commit: d10ee6f6c42744fdd4db2981093c1411bd1be6db https://github.com/galaxyproject/galaxy/commit/d10ee6f6c42744fdd4db2981093c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/2bbae2bb1d11...d10ee6f6c427

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[galaxyproject/galaxy] 9eb1db: Do not convert spaces to tabs when importing datas...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9eb1db82ca4bbae598d0070de8da78172ca90fa9 https://github.com/galaxyproject/galaxy/commit/9eb1db82ca4bbae598d0070de8da… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Do not convert spaces to tabs when importing datasets into a library. Reported (with fix provided) by Fabien Mareuil in http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-head… Commit: cf16b1d692d0e96f3d0aa4d2cf0f9f52c8dd7bb3 https://github.com/galaxyproject/galaxy/commit/cf16b1d692d0e96f3d0aa4d2cf0f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1985 from nsoranzo/release_16.01_lda_fixes [16.01] Do not convert spaces to tabs when importing datasets into a library. Compare: https://github.com/galaxyproject/galaxy/compare/dd476fc42c57...cf16b1d692d0

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[galaxyproject/galaxy] 55e8ef: Optimize adding datasets to large histories.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55e8ef6e1dfc2cb0721956a7801bc6e2e523ba02 https://github.com/galaxyproject/galaxy/commit/55e8ef6e1dfc2cb0721956a7801b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Optimize adding datasets to large histories. Commit: 2bbae2bb1d11c8f9e9e9d398df9b707657d28df0 https://github.com/galaxyproject/galaxy/commit/2bbae2bb1d11c8f9e9e9d398df9b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1983 from jmchilton/history_append_opt Optimize adding datasets to large histories. Compare: https://github.com/galaxyproject/galaxy/compare/be78aac509bc...2bbae2bb1d11

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galaxy-commits March 2016