- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 75e7e4: Fix 500 error when attempting to update installed ...
by GitHub 15 Nov '15

15 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 75e7e4c2cf7a0cb18b8096c8119e4b0cb207e2a3 https://github.com/galaxyproject/galaxy/commit/75e7e4c2cf7a0cb18b8096c8119e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 7150983aab78e4ceb71f8ad2592369523899d768 https://github.com/galaxyproject/galaxy/commit/7150983aab78e4ceb71f8ad25923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. Compare: https://github.com/galaxyproject/galaxy/compare/64b084067c73...7150983aab78

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[galaxyproject/galaxy] 7c45bf: Fix 500 error when attempting to update installed ...
by GitHub 14 Nov '15

14 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c45bf13fad2d60fbee8be409c6879af2ebc25d1 https://github.com/galaxyproject/galaxy/commit/7c45bf13fad2d60fbee8be409c68… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 321b64d8dcc1917eb107e46124cdb945c5005511 https://github.com/galaxyproject/galaxy/commit/321b64d8dcc1917eb107e46124cd… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Ensure that invalid parameters don't break things. Commit: 87f35ea9752a37da76595db1fee481c391ee686b https://github.com/galaxyproject/galaxy/commit/87f35ea9752a37da76595db1fee4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Use preexisting library to parse query string. Commit: 3ba139fe1bf8a40df647282a9884eae543a656bc https://github.com/galaxyproject/galaxy/commit/3ba139fe1bf8a40df647282a9884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1082 from davebx/hg_middleware Fix 500 error when attempting to update installed repository. Compare: https://github.com/galaxyproject/galaxy/compare/f1abf1e9ab4d...3ba139fe1bf8

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[galaxyproject/usegalaxy-playbook] bfc167: Update SSL certs
by GitHub 14 Nov '15

14 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfc167bedf63a660d83427562f78960b6bd3963c https://github.com/galaxyproject/usegalaxy-playbook/commit/bfc167bedf63a660… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M common/secret_vars/ssl.yml M common_infrastructure.yml M files/ssl/athena.galaxyproject.org_cert.pem R files/ssl/montana.galaxyproject.org_cert.pem A files/ssl/radegast.galaxyproject.org_cert.pem R files/ssl/wildcard_cert.pem M templates/nginx/cloudlaunch.j2 Log Message: ----------- Update SSL certs Commit: 23c400852d03206eb49265dbb6ee0c2517a680c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/23c400852d03206e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) 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 M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/57ec60640226...…

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[galaxyproject/galaxy] ce418d: Resolve conflicting label CSS class.
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce418d33fe221b27da162717a208381aa8042ea8 https://github.com/galaxyproject/galaxy/commit/ce418d33fe221b27da162717a208… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Resolve conflicting label CSS class. Commit: f1abf1e9ab4dc4f1d3e6987c6bb68ab3b188083c https://github.com/galaxyproject/galaxy/commit/f1abf1e9ab4dc4f1d3e6987c6bb6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1086 from jgoecks/trackster-pos-label Resolve conflicting label CSS class for trackster. Compare: https://github.com/galaxyproject/galaxy/compare/2dcb92aa0e83...f1abf1e9ab4d

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[galaxyproject/galaxy] ffda4a: Allow dockerized toolshed tests.
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffda4aa2cd033e8953ef780fb553afbc77e4a7f4 https://github.com/galaxyproject/galaxy/commit/ffda4aa2cd033e8953ef780fb553… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Allow dockerized toolshed tests. Commit: 096adbf8d0776d4b1085705f2881c2d46ab06611 https://github.com/galaxyproject/galaxy/commit/096adbf8d0776d4b1085705f2881… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Collect apt installs in one place. Commit: 1766b896e30ed1b2bc5aa5341cf19d313628c4f4 https://github.com/galaxyproject/galaxy/commit/1766b896e30ed1b2bc5aa5341cf1… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M config/datatypes_conf.xml.sample M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh A scripts/api/library_upload_dir.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge -dev. Commit: 2dcb92aa0e83f9893595b68222fc62cf052a9220 https://github.com/galaxyproject/galaxy/commit/2dcb92aa0e83f9893595b68222fc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Merge pull request #942 from davebx/docker Enable dockerized toolshed tests. Compare: https://github.com/galaxyproject/galaxy/compare/625d49e2de07...2dcb92aa0e83

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[galaxyproject/galaxy] d824cc: In interactive environments, the /import volume ca...
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: d824cca31fcebe97b8c7cfd1040eecbb9e5f03d3 https://github.com/galaxyproject/galaxy/commit/d824cca31fcebe97b8c7cfd1040e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- In interactive environments, the /import volume can now be made conditional. Also, fix a bug when using a proxy for the node proxy and cookie_path is / Commit: c4351413265796dacc15b8e3fc7382b8514f5b59 https://github.com/galaxyproject/galaxy/commit/c4351413265796dacc15b8e3fc73… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Built image tag differs from intended. Commit: 64b084067c73cea1de455e4816d73101c3752165 https://github.com/galaxyproject/galaxy/commit/64b084067c73cea1de455e4816d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1076 from natefoo/ie-conditional-import-volume [15.10] Fix a bug in IEs when proxying the proxy Compare: https://github.com/galaxyproject/galaxy/compare/a3034ab6d99d...64b084067c73

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[galaxyproject/usegalaxy-playbook] 2656d9: Test mutable configs
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2656d95c0c1fb47012ef82a6d1a60599c975a323 https://github.com/galaxyproject/usegalaxy-playbook/commit/2656d95c0c1fb470… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) 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: ----------- Test mutable configs Commit: 57ec60640226b51f7664812ab99de1d7a5d56324 https://github.com/galaxyproject/usegalaxy-playbook/commit/57ec60640226b51f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- IPython config changes for Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5ad413739ce4...…

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[galaxyproject/usegalaxy-playbook] 5ad413: Run kraken in multi partition
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ad413739ce404f9efe3e3163844f0a881fd8908 https://github.com/galaxyproject/usegalaxy-playbook/commit/5ad413739ce404f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Run kraken in multi partition

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[galaxyproject/galaxy] d6d8e5: upload.py: Remove unused function parameter
by GitHub 13 Nov '15

13 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6d8e5ef86bbfe460709c82590596252de2d5a71 https://github.com/galaxyproject/galaxy/commit/d6d8e5ef86bbfe460709c8259059… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- upload.py: Remove unused function parameter Commit: 625d49e2de074c240555efbff1319c6ddf9676a1 https://github.com/galaxyproject/galaxy/commit/625d49e2de074c240555efbff131… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #1078 from einon/einon upload.py: Remove unused function parameter Compare: https://github.com/galaxyproject/galaxy/compare/2214f887a668...625d49e2de07

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[galaxyproject/galaxy] 240da5: Update both lped pbed pbed lped converters to be i...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 240da5e720c069b08caf77828dc4e3e598b56089 https://github.com/galaxyproject/galaxy/commit/240da5e720c069b08caf77828dc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Update both lped pbed pbed lped converters to be in sync with their html. Thanks @nsoranzo. Commit: 2214f887a668a4eed1e3b94d880c57e2e57ef9a1 https://github.com/galaxyproject/galaxy/commit/2214f887a668a4eed1e3b94d880c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Merge pull request #1072 from dannon/fix_lped_report_output Update both lped pbed pbed lped converters to be in sync with their h… Compare: https://github.com/galaxyproject/galaxy/compare/3a70dc395a2a...2214f887a668

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[galaxyproject/galaxy] 30668f: Fix for reloading tools that have non-standard too...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30668fe5344192e7b17f05060062fa330c5496a0 https://github.com/galaxyproject/galaxy/commit/30668fe5344192e7b17f05060062… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/admin/reload_tool.mako Log Message: ----------- Fix for reloading tools that have non-standard tool_ids/versions. Commit: 3f898677f19d7600648802b1a428ce916dd35e11 https://github.com/galaxyproject/galaxy/commit/3f898677f19d7600648802b1a428… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- HTML escape tool name, id, version, on tool reload message. Commit: 045832bd8ecd4515d134cb5e05f64d2b7b4e933a https://github.com/galaxyproject/galaxy/commit/045832bd8ecd4515d134cb5e05f6… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Also escape tool name, id, version in message when removing tools. Commit: 3a70dc395a2afb73363440edaa624d6f053467d2 https://github.com/galaxyproject/galaxy/commit/3a70dc395a2afb73363440edaa62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M templates/admin/reload_tool.mako Log Message: ----------- Merge pull request #1050 from blankenberg/reload-tool-id-fix Fix for reloading tools that have non-standard tool_ids/versions. Compare: https://github.com/galaxyproject/galaxy/compare/926b1a2cdd3c...3a70dc395a2a

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[galaxyproject/galaxy] 67d0bc: Trivial: Replace unnecessary duplicated var check ...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67d0bcb5b3bba9c13bfa0c556a4460e1304b63a9 https://github.com/galaxyproject/galaxy/commit/67d0bcb5b3bba9c13bfa0c556a44… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Trivial: Replace unnecessary duplicated var check with 'else if' Commit: 926b1a2cdd3c772f214a2ae62945427d2c36402f https://github.com/galaxyproject/galaxy/commit/926b1a2cdd3c772f214a2ae62945… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Merge pull request #1073 from einon/einon Trivial: Replace unnecessary duplicated var check with 'else if' Compare: https://github.com/galaxyproject/galaxy/compare/1cf5af4c2023...926b1a2cdd3c

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[galaxyproject/galaxy] be3d9c: Fix one more hanging div.
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be3d9cbf70b1899f316ff7cf5aabdd0d191179ce https://github.com/galaxyproject/galaxy/commit/be3d9cbf70b1899f316ff7cf5aab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py Log Message: ----------- Fix one more hanging div. Commit: 1cf5af4c20231996e58756ace72e4a1ca96b227d https://github.com/galaxyproject/galaxy/commit/1cf5af4c20231996e58756ace72e… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py Log Message: ----------- Merge pull request #1070 from dannon/fix_lped_report_output Fix one more hanging div in lped to pbed converter. Compare: https://github.com/galaxyproject/galaxy/compare/22ed188c0344...1cf5af4c2023

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[galaxyproject/galaxy] 11b23b: Fix lped report output from converter
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11b23bf8392c8ecf7c48978003f0fc3082d07234 https://github.com/galaxyproject/galaxy/commit/11b23bf8392c8ecf7c48978003f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Fix lped report output from converter Commit: 22ed188c0344a41df5cf015486be34de197b88fc https://github.com/galaxyproject/galaxy/commit/22ed188c0344a41df5cf015486be… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Merge pull request #1069 from dannon/fix_lped_report_output Fix lped report output from converter Compare: https://github.com/galaxyproject/galaxy/compare/c1bf4caea985...22ed188c0344

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[galaxyproject/galaxy] 11926b: add @mr-c
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11926b3b9c3241d0b72ee4fcea127c18c5aaf9c6 https://github.com/galaxyproject/galaxy/commit/11926b3b9c3241d0b72ee4fcea12… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- add @mr-c Commit: c1bf4caea985d53bbcdf844561a34a588f541eec https://github.com/galaxyproject/galaxy/commit/c1bf4caea985d53bbcdf844561a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #1067 from martenson/add-biocrusoe add biocrusoe to contributors Compare: https://github.com/galaxyproject/galaxy/compare/43b8addcbcbe...c1bf4caea985

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[galaxyproject/galaxy] ad2045: Fix output to print values and not hash key
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ad20452340d052570c1b3203259d10e1ad94a236 https://github.com/galaxyproject/galaxy/commit/ad20452340d052570c1b3203259d… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Fix output to print values and not hash key Commit: ad4458a458d7ccb5238094ab3d1967072b5a0b76 https://github.com/galaxyproject/galaxy/commit/ad4458a458d7ccb5238094ab3d19… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Revert to previous changes if using rpy2 Commit: 0ec1b17794d53ae1a535b00f13d955c62f702a94 https://github.com/galaxyproject/galaxy/commit/0ec1b17794d53ae1a535b00f13d9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Update list comprehension to go through headings instead of summary so that we output in the order we want. Commit: 50c27ace2c6eb260b88aafac72997cfa06ca6c13 https://github.com/galaxyproject/galaxy/commit/50c27ace2c6eb260b88aafac7299… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #885 from ericenns/fix_gsummary_in_release_15.07 [15.07] Fix gsummary in release 15.07 Commit: 0911287df7a5d7e810d83bbcd1e4cb1f849314d7 https://github.com/galaxyproject/galaxy/commit/0911287df7a5d7e810d83bbcd1e4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: create regexp from filters for name creation Commit: dc9c2e4b7569726263fac8ab06cefb889c2b8af5 https://github.com/galaxyproject/galaxy/commit/dc9c2e4b7569726263fac8ab06ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. Commit: 7bcbf140936bfc9d25b8e6bed8a0bc14270b0cf2 https://github.com/galaxyproject/galaxy/commit/7bcbf140936bfc9d25b8e6bed8a0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #978 from dannon/graft_to_stable [15.10] Fix grid bulk operations Commit: 3b133d0d9206f6162494b3f5aa4c04581368480e https://github.com/galaxyproject/galaxy/commit/3b133d0d9206f6162494b3f5aa4c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #917 from carlfeberhard/release_15.10 [15.10] UI, list of pairs collection creator: create regexp from filters for … Commit: d20677bb640de726574ae7f3e8d86739a8702cb5 https://github.com/galaxyproject/galaxy/commit/d20677bb640de726574ae7f3e8d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix Remote User failures due to apache null headers. Commit: 3b8edf6aebfb10d1b52b57701eb4cb07558e9c9e https://github.com/galaxyproject/galaxy/commit/3b8edf6aebfb10d1b52b57701eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #1003 from dannon/remote_user_apache_fix [15.10] Fix Remote User failures due to apache null headers. Commit: fef1e548bba39c856f6086f0eb2300e6a50d8559 https://github.com/galaxyproject/galaxy/commit/fef1e548bba39c856f6086f0eb23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix job permission handling Catch unavailable history Fix test Commit: 57d6c9872c21f0bddfde04b170e8e8021d20ff71 https://github.com/galaxyproject/galaxy/commit/57d6c9872c21f0bddfde04b170e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Commit: 7e6df4f46fe0eed8328b57543b069911e4988d02 https://github.com/galaxyproject/galaxy/commit/7e6df4f46fe0eed8328b57543b06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #1043 from jmchilton/release_15.10-forward-port [15.10] Forward port 15.07 fix to 15.10. Commit: a8147327af2e8a90108d11d7fa93fe4d4893f6ab https://github.com/galaxyproject/galaxy/commit/a8147327af2e8a90108d11d7fa93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Derive permission from job outputs Remove history manager Use dataset manager Commit: 36797b3195c84b416710029d86cf7b7a24c1faf0 https://github.com/galaxyproject/galaxy/commit/36797b3195c84b416710029d86cf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Add changed static files. Commit: ad016460dc2799e95ff26fdd0a69bf605f78358b https://github.com/galaxyproject/galaxy/commit/ad016460dc2799e95ff26fdd0a69… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Fix import of history datasets into library. Commit: b88864586c760e0e644bdc32c5d2349b1613446c https://github.com/galaxyproject/galaxy/commit/b88864586c760e0e644bdc32c5d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix warning statement Commit: 5603a96aecb29c7065206d8797205f49f2ed32b6 https://github.com/galaxyproject/galaxy/commit/5603a96aecb29c7065206d879720… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Merge pull request #1054 from martenson/fix-datalib-hist-import [15.10] Fix datalib hist import Commit: b2723e7467c5fb9722a1c6cb009251b0deaf9bc4 https://github.com/galaxyproject/galaxy/commit/b2723e7467c5fb9722a1c6cb0092… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Disable invalid test case. Add validation criteria. Fix comments Fix comment Commit: 65807013957c3f845b0b8fd793b52b6d9f057505 https://github.com/galaxyproject/galaxy/commit/65807013957c3f845b0b8fd793b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Fix parsing of message configuration Fix default value Add root to Galaxy object Commit: e4c9f06d3bd319cc1addfdf3d6fd1f6e48e9e4f3 https://github.com/galaxyproject/galaxy/commit/e4c9f06d3bd319cc1addfdf3d6fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Attempt to fix timing out tests. Continuation of work started by @nsoranzo here 92a152d89c507168a6085cc34acfa13566b6eda9. In addition to increasing the max timeout it will now print the timeout in the assertion error so we can see if it is being overridden and attempt to adjust timeouts too small. Commit: c85b0d9b0b2d6853b216ebb691987632a3b6bdc6 https://github.com/galaxyproject/galaxy/commit/c85b0d9b0b2d6853b216ebb69198… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #1060 from guerler/fix_assert_000 [15.10] Fix warning statement Commit: 177f73fcdb53ab4e172f7cf7f7a9950d4c842cd3 https://github.com/galaxyproject/galaxy/commit/177f73fcdb53ab4e172f7cf7f7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix lower timeout caught by @nsoranzo. Commit: 4f72178a9568e35f99a5824d66ce4c6911e50d93 https://github.com/galaxyproject/galaxy/commit/4f72178a9568e35f99a5824d66ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #1038 from guerler/fix_imported_rerun_000 [15.10] Fix job rerun for imported histories Commit: 6953bdf704f3e140ffc47f849fc54dc3d4c37013 https://github.com/galaxyproject/galaxy/commit/6953bdf704f3e140ffc47f849fc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Merge pull request #1059 from guerler/fix_message_000 [15.10] Fix parsing of message configuration Commit: 559c89afde2bb8b2be28d52a9973b72aa6c03edf https://github.com/galaxyproject/galaxy/commit/559c89afde2bb8b2be28d52a9973… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Testing: update casperjs functional tests; change expected size string; remove nice_size from expected history api keys; remove test for rerun button on uploaded dataset; attempt to fix linux+python unicode error in hda api tests Commit: 3a78d9df740cac8bdf9f0a3a0c622fc85506aba0 https://github.com/galaxyproject/galaxy/commit/3a78d9df740cac8bdf9f0a3a0c62… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/helpers.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #1062 from jmchilton/test_fixes [15.10] Test timeout fixes? Commit: a3034ab6d99d5087a7dcc1de0360fe2ebafde40f https://github.com/galaxyproject/galaxy/commit/a3034ab6d99d5087a7dcc1de0360… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Merge pull request #1065 from jmchilton/test_fix_3 [15.10] Testing: update casperjs functional tests; change expected size strin… Compare: https://github.com/galaxyproject/galaxy/compare/dab1ce3f03c2...a3034ab6d99d

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[galaxyproject/galaxy] 81dc3a: Fix typo.
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81dc3a955bae39d90f16441dad5a67a708177844 https://github.com/galaxyproject/galaxy/commit/81dc3a955bae39d90f16441dad5a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Fix typo. Commit: 86220c7685ff831d3d5b39732706c679e77afd38 https://github.com/galaxyproject/galaxy/commit/86220c7685ff831d3d5b39732706… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Extend users API with delete action. Commit: f700e38241d302406dde9c0eef9449ae2f054c6d https://github.com/galaxyproject/galaxy/commit/f700e38241d302406dde9c0eef94… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix is_admin value in users API show method to show if the requested user is an admin, not the current user. Commit: d4e7c601a095c9138f5f5841b29d345c8b2d96a9 https://github.com/galaxyproject/galaxy/commit/d4e7c601a095c9138f5f5841b29d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add check for allow_user_deletion. Commit: 43b8addcbcbe69eb1d223a3689fdb81ef1510f6d https://github.com/galaxyproject/galaxy/commit/43b8addcbcbe69eb1d223a3689fd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #1063 from nsoranzo/api_delete_user Extend users API with delete action. Compare: https://github.com/galaxyproject/galaxy/compare/24a7ee6205ac...43b8addcbcbe

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[galaxyproject/galaxy] 559c89: Testing: update casperjs functional tests; change ...
by GitHub 12 Nov '15

12 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 559c89afde2bb8b2be28d52a9973b72aa6c03edf https://github.com/galaxyproject/galaxy/commit/559c89afde2bb8b2be28d52a9973… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Testing: update casperjs functional tests; change expected size string; remove nice_size from expected history api keys; remove test for rerun button on uploaded dataset; attempt to fix linux+python unicode error in hda api tests Commit: a3034ab6d99d5087a7dcc1de0360fe2ebafde40f https://github.com/galaxyproject/galaxy/commit/a3034ab6d99d5087a7dcc1de0360… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Merge pull request #1065 from jmchilton/test_fix_3 [15.10] Testing: update casperjs functional tests; change expected size strin… Compare: https://github.com/galaxyproject/galaxy/compare/3a78d9df740c...a3034ab6d99d

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[galaxyproject/galaxy] e4c9f0: Attempt to fix timing out tests.
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: e4c9f06d3bd319cc1addfdf3d6fd1f6e48e9e4f3 https://github.com/galaxyproject/galaxy/commit/e4c9f06d3bd319cc1addfdf3d6fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Attempt to fix timing out tests. Continuation of work started by @nsoranzo here 92a152d89c507168a6085cc34acfa13566b6eda9. In addition to increasing the max timeout it will now print the timeout in the assertion error so we can see if it is being overridden and attempt to adjust timeouts too small. Commit: 177f73fcdb53ab4e172f7cf7f7a9950d4c842cd3 https://github.com/galaxyproject/galaxy/commit/177f73fcdb53ab4e172f7cf7f7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix lower timeout caught by @nsoranzo. Commit: 3a78d9df740cac8bdf9f0a3a0c622fc85506aba0 https://github.com/galaxyproject/galaxy/commit/3a78d9df740cac8bdf9f0a3a0c62… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/helpers.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #1062 from jmchilton/test_fixes [15.10] Test timeout fixes? Compare: https://github.com/galaxyproject/galaxy/compare/6953bdf704f3...3a78d9df740c

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[galaxyproject/galaxy] b3d5f8: Improved unicode handling stdout/stderr/command_li...
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3d5f80621cc7a450158c472aa4bffa0570fbe6c https://github.com/galaxyproject/galaxy/commit/b3d5f80621cc7a450158c472aa4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/parameters/basic.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml Log Message: ----------- Improved unicode handling stdout/stderr/command_line. Commit: c790fcb84d005025b331b2a9106e7097860a7545 https://github.com/galaxyproject/galaxy/commit/c790fcb84d005025b331b2a9106e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py Log Message: ----------- Unify standard error and output trimming and unicoding. Should be more complete now (were paths for task and jobs where it wasn't be unicodified) and with less duplication. Moved logic into model layer where it probably belongs anyway. Commit: 6b521a3557bc61e37200cbd4c14dbc037cf9696d https://github.com/galaxyproject/galaxy/commit/6b521a3557bc61e37200cbd4c14d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Fix failing tests for output checker changes. Commit: 69dcf36678db48851cb6d820aec85f9fa37ccfbf https://github.com/galaxyproject/galaxy/commit/69dcf36678db48851cb6d820aec8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fixes for c790fcb84d005025b331b2a9106e7097860a7545. Thanks to @nsoranzo. Commit: df576f3d3602cad77ea6829717ea11606bce97c2 https://github.com/galaxyproject/galaxy/commit/df576f3d3602cad77ea6829717ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove more unneeded stuff from galaxy.jobs now. Thanks to @nsoranzo. Commit: d0751ef80c3074e9f67cde240d4b512e1bc9a445 https://github.com/galaxyproject/galaxy/commit/d0751ef80c3074e9f67cde240d4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restore lost call. Caught by @nsoranzo. Commit: 8aab57a09eb322c7f10025ee4518995323fbc637 https://github.com/galaxyproject/galaxy/commit/8aab57a09eb322c7f10025ee4518… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix nit picks unrelated to PR #1052... ... as pointed out by @nsoranzo and @blankenberg. Commit: 24a7ee6205ac4cb45f9249a6aa3f89241121c7ca https://github.com/galaxyproject/galaxy/commit/24a7ee6205ac4cb45f9249a6aa3f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Merge pull request #1052 from jmchilton/unicode_stream_3 Improved Encoding Handling for Jobs Compare: https://github.com/galaxyproject/galaxy/compare/75d64893489d...24a7ee6205ac

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[galaxyproject/usegalaxy-playbook] 0e4ce0: remove banner with corral downtime
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e4ce017868812284109e9243e77a7fc6cbd613f https://github.com/galaxyproject/usegalaxy-playbook/commit/0e4ce01786881228… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- remove banner with corral downtime

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[galaxyproject/usegalaxy-playbook] 02587a: update Main
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 02587a8f5366e34e3fea8b8bdb47949aceddcdcc https://github.com/galaxyproject/usegalaxy-playbook/commit/02587a8f5366e34e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- update Main

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[galaxyproject/galaxy] 658070: Fix parsing of message configuration
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 65807013957c3f845b0b8fd793b52b6d9f057505 https://github.com/galaxyproject/galaxy/commit/65807013957c3f845b0b8fd793b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Fix parsing of message configuration Fix default value Add root to Galaxy object Commit: 6953bdf704f3e140ffc47f849fc54dc3d4c37013 https://github.com/galaxyproject/galaxy/commit/6953bdf704f3e140ffc47f849fc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Merge pull request #1059 from guerler/fix_message_000 [15.10] Fix parsing of message configuration Compare: https://github.com/galaxyproject/galaxy/compare/4f72178a9568...6953bdf704f3

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[galaxyproject/galaxy] fef1e5: Fix job permission handling
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: fef1e548bba39c856f6086f0eb2300e6a50d8559 https://github.com/galaxyproject/galaxy/commit/fef1e548bba39c856f6086f0eb23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix job permission handling Catch unavailable history Fix test Commit: a8147327af2e8a90108d11d7fa93fe4d4893f6ab https://github.com/galaxyproject/galaxy/commit/a8147327af2e8a90108d11d7fa93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Derive permission from job outputs Remove history manager Use dataset manager Commit: b2723e7467c5fb9722a1c6cb009251b0deaf9bc4 https://github.com/galaxyproject/galaxy/commit/b2723e7467c5fb9722a1c6cb0092… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Disable invalid test case. Add validation criteria. Fix comments Fix comment Commit: 4f72178a9568e35f99a5824d66ce4c6911e50d93 https://github.com/galaxyproject/galaxy/commit/4f72178a9568e35f99a5824d66ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #1038 from guerler/fix_imported_rerun_000 [15.10] Fix job rerun for imported histories Compare: https://github.com/galaxyproject/galaxy/compare/c85b0d9b0b2d...4f72178a9568

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[galaxyproject/galaxy] b88864: Fix warning statement
by GitHub 11 Nov '15

11 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: b88864586c760e0e644bdc32c5d2349b1613446c https://github.com/galaxyproject/galaxy/commit/b88864586c760e0e644bdc32c5d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix warning statement Commit: c85b0d9b0b2d6853b216ebb691987632a3b6bdc6 https://github.com/galaxyproject/galaxy/commit/c85b0d9b0b2d6853b216ebb69198… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #1060 from guerler/fix_assert_000 [15.10] Fix warning statement Compare: https://github.com/galaxyproject/galaxy/compare/5603a96aecb2...c85b0d9b0b2d

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