Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1922d50f903f0c6ad1440d9128a1a23d37cc529c
https://github.com/galaxyproject/galaxy/commit/1922d50f903f0c6ad1440d9128a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/base/populators.py
M test/selenium_tests/framework.py
Log Message:
-----------
Increase patience of Galaxy tests throughout.
This should help reduce various API and Selenium transient failures.
Commit: 2ad612349683dd4ab3bde476f9153e90415f0b53
https://github.com/galaxyproject/galaxy/commit/2ad612349683dd4ab3bde476f915…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/base/populators.py
M test/selenium_tests/framework.py
Log Message:
-----------
Merge pull request #3589 from jmchilton/test_timeout_increases
Increase patience of Galaxy tests throughout.
Compare: https://github.com/galaxyproject/galaxy/compare/ed52230952a1...2ad612349683
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e
https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Prevent make_html_table() datatype methods from raising Exceptions
This was preventing the browse of a data library which contained a
purged dataset of gg datatype.
Also fix import order and Python3 compatibility.
Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7
https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Remove edam_format for Genbank from config/datatypes_conf.xml.sample
This was preventing the loading of the datatype:
WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype.
Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 .
Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev.
Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e
https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes
[17.01] Two datatypes fixes
Commit: ed52230952a1411a39cff3bde7a7ed66e1344f6f
https://github.com/galaxyproject/galaxy/commit/ed52230952a1411a39cff3bde7a7…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
config/datatypes_conf.xml.sample
Compare: https://github.com/galaxyproject/galaxy/compare/6f5743d052fb...ed52230952a1
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e
https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Prevent make_html_table() datatype methods from raising Exceptions
This was preventing the browse of a data library which contained a
purged dataset of gg datatype.
Also fix import order and Python3 compatibility.
Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7
https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Remove edam_format for Genbank from config/datatypes_conf.xml.sample
This was preventing the loading of the datatype:
WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype.
Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 .
Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev.
Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e
https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-10 (Fri, 10 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes
[17.01] Two datatypes fixes
Compare: https://github.com/galaxyproject/galaxy/compare/884cff33fa04...087c75e76ff4
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 139bacb7d3e507ea56b8c8997e47408db87b5fa3
https://github.com/galaxyproject/galaxy/commit/139bacb7d3e507ea56b8c8997e47…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Remove broken tour step.
This causes the Selenium tests to fail under various conditions - but legimately so. The referenced target link disappears pretty quickly after the step in the previous click. When I run them in the web browser and this step is "disconnected" and in the center of the screen and as a result it isn't clear what links are being referred to.
Commit: be09b7c2ccf2ef861927795c16fb1306ef37ff1a
https://github.com/galaxyproject/galaxy/commit/be09b7c2ccf2ef861927795c16fb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M config/plugins/tours/core.history.yaml
Log Message:
-----------
Merge pull request #3582 from jmchilton/selenium_fixes
Remove broken tour step.
Compare: https://github.com/galaxyproject/galaxy/compare/ca847e2d588d...be09b7c2ccf2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3b78907fdbbf2f26ea89f4459901e59164a033b7
https://github.com/galaxyproject/galaxy/commit/3b78907fdbbf2f26ea89f4459901…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/managers/deletable.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M test/api/test_history_contents.py
M test/unit/managers/test_HDAManager.py
Log Message:
-----------
Set 'deleted' to True when purging a history dataset association
Fix https://github.com/galaxyproject/galaxy/issues/3548
Add API and unit test cases.
Add migration to fix misaligned databases.
Commit: b215ea1eed127e61421cccb8ff5ddb68963e28ae
https://github.com/galaxyproject/galaxy/commit/b215ea1eed127e61421cccb8ff5d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/webapps/galaxy/api/histories.py
M test/api/test_histories.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Sync API history purge with hda implementation
Add API and unit test cases.
Import order and Python3 fixes.
Commit: ed3062b41de47d77974bfae97bac21b2d9806432
https://github.com/galaxyproject/galaxy/commit/ed3062b41de47d77974bfae97bac…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-08 (Wed, 08 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/managers/deletable.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/webapps/galaxy/api/histories.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge pull request #3572 from nsoranzo/fix_3548
Set 'deleted' to True when purging a history dataset association
Compare: https://github.com/galaxyproject/galaxy/compare/3b3bfad8e0af...ed3062b41de4