Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5c48402b0202e438d663c4dc151d835c7725a4f6
https://github.com/galaxyproject/galaxy/commit/5c48402b0202e438d663c4dc151d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-17 (Tue, 17 Jan 2017)
Changed paths:
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Various fixes for test image Docker user switching.
- Fix if testing as user with GID 109 (fixes #3425).
- Fix if testing as a user with any UID or GID that already exists in the container.
- More logging to indicate the "problems" being printed to standard output in these cases are not problems.
- Fix sqlite being readonly in the container for the test user.
Commit: d9f9a31c32b9d1a2121d5db6e2b8f81dbf12d7c8
https://github.com/galaxyproject/galaxy/commit/d9f9a31c32b9d1a2121d5db6e2b8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-01-22 (Sun, 22 Jan 2017)
Changed paths:
M test/docker/base/run_test_wrapper.sh
Log Message:
-----------
Merge pull request #3443 from jmchilton/test_docker_fix
Various fixes for test image Docker user switching.
Compare: https://github.com/galaxyproject/galaxy/compare/3945f3b885a2...d9f9a31c32b9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f8552c19dc55ddeeeb7441190891f52cdd9d9ef3
https://github.com/galaxyproject/galaxy/commit/f8552c19dc55ddeeeb7441190891…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-20 (Fri, 20 Jan 2017)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Document shared_inputs for parallelism tag in tool XSD.
Commit: 22f4696f7d54a90a31f253d05a7ed1314db4b943
https://github.com/galaxyproject/galaxy/commit/22f4696f7d54a90a31f253d05a7e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-20 (Fri, 20 Jan 2017)
Changed paths:
A test/functional/tools/explicit_conversion.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Implement tool testing and documenting explicit conversion tags.
Commit: 074e10ac00a7dde7c2fc5e76928392e073791b30
https://github.com/galaxyproject/galaxy/commit/074e10ac00a7dde7c2fc5e769283…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-20 (Fri, 20 Jan 2017)
Changed paths:
M doc/schema_template.md
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/explicit_conversion.xml
M test/functional/tools/implicit_conversion.xml
Log Message:
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Fix tool XSD to document <conversion> tag for data parameters.
Rebased with English fixes and small tool cleanups thanks to @nsoranzo.
Commit: dba4d95961a3ccadd4a0822f13f0f02730889a8a
https://github.com/galaxyproject/galaxy/commit/dba4d95961a3ccadd4a0822f13f0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-20 (Fri, 20 Jan 2017)
Changed paths:
M test/functional/tools/column_param.xml
M test/functional/tools/explicit_conversion.xml
M test/functional/tools/implicit_conversion.xml
Log Message:
-----------
Reduced usage of from_work_dir in test tools.
Per recommendation of @bgruening.
Commit: 3945f3b885a291c9b1a1ebf85a56137e2d1b22e2
https://github.com/galaxyproject/galaxy/commit/3945f3b885a291c9b1a1ebf85a56…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-20 (Fri, 20 Jan 2017)
Changed paths:
M doc/schema_template.md
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/column_param.xml
A test/functional/tools/explicit_conversion.xml
M test/functional/tools/implicit_conversion.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3457 from jmchilton/xsd_fixes_2
Tool Documentation and Testing Improvements
Compare: https://github.com/galaxyproject/galaxy/compare/d8f23b393527...3945f3b885a2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1af1583caa1b5c62c92573fe42693338ba457fcf
https://github.com/galaxyproject/galaxy/commit/1af1583caa1b5c62c92573fe4269…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-19 (Thu, 19 Jan 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Fix various transiently failing Selenium tests.
I'm pretty sure the problem is that I was waiting on conditions (e.g. datasets to become "ok") using the API and then assuming the state of the GUI elements was the same. Obviously though the GUI is polling the API and there is some lag there. This commit changes things to specifically wait on history panel GUI changes - obviously the better thing to wait on in a GUI test.
Commit: d8f23b393527e2ea5b495cc850eeec25fdc64a8b
https://github.com/galaxyproject/galaxy/commit/d8f23b393527e2ea5b495cc850ee…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-19 (Thu, 19 Jan 2017)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merge pull request #3450 from jmchilton/selenium_fixes_2
Fix various transiently failing Selenium tests.
Compare: https://github.com/galaxyproject/galaxy/compare/60b57397e7f8...d8f23b393527
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b00887b9d7e471c65155740db548effd75dc4703
https://github.com/galaxyproject/galaxy/commit/b00887b9d7e471c65155740db548…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-18 (Wed, 18 Jan 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Fixup circular dependency in #3427.
Unfortunately the "root" of the problem is that galaxy.tools.deps.requirements.ToolRequirement should be importable without importing galaxy.tools - but it cannot be currently just because of the way things are structured.
Commit: c4f5a2cfb8b7a34faf05367a5f4d8073ab229b98
https://github.com/galaxyproject/galaxy/commit/c4f5a2cfb8b7a34faf05367a5f4d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-19 (Thu, 19 Jan 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge pull request #3447 from jmchilton/ts_import_cycle
Fixup circular dependency in #3427.
Compare: https://github.com/galaxyproject/galaxy/compare/94150df087b2...c4f5a2cfb8b7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e0990e2ab58895e9667438aa3207f1a15e9ec3bf
https://github.com/galaxyproject/galaxy/commit/e0990e2ab58895e9667438aa3207…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message:
-----------
extend API version information
extend API version information #1907
https://github.com/galaxyproject/galaxy/issues/1907
output json file contents with version_major
```
{"extra": {"user_tag": "_fix_job_runner_issue", "commit-id": "abcde123"}, "version_major": "16.10"}
```
First check environment value GALAXY_VERSION_JSON_FILE.
if it's not set, try "galaxy root direcotory"/version.json.
if json file is not find, extra set empty.
Commit: c2d1a2a1897ba05e5067433fcecdfcd60c761009
https://github.com/galaxyproject/galaxy/commit/c2d1a2a1897ba05e5067433fcecd…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message:
-----------
fix lint
Commit: 0c0e58d5fb6c48418c36e547e976dde1dfd79942
https://github.com/galaxyproject/galaxy/commit/0c0e58d5fb6c48418c36e547e976…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message:
-----------
fix lint
Commit: 8c34293602ec99b7deb128f60e2086f89f25e64a
https://github.com/galaxyproject/galaxy/commit/8c34293602ec99b7deb128f60e20…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-16 (Mon, 16 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message:
-----------
More idiomatic Python for extended version information.
- Eliminate the use of a bare except.
- Use a ``with`` to ensure file handling is cleaned up.
Commit: 9646d264a1a9d9d9107c2311deb4e6f319bb417d
https://github.com/galaxyproject/galaxy/commit/9646d264a1a9d9d9107c2311deb4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-18 (Wed, 18 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message:
-----------
Merge pull request #3411 from manabuishii/extend_api_version
extend API version information
Compare: https://github.com/galaxyproject/galaxy/compare/29cdd6007fa3...9646d264a1a9