Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 949dcfdbc34331de7f0aa321e67e1255a7627306
https://github.com/galaxyproject/galaxy/commit/949dcfdbc34331de7f0aa321e67e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/authnz/managers.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/managers/cloud.py
M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/util/readme_util.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M test/base/populators.py
M tools/data_source/upload.py
Log Message:
-----------
Do not log exceptions twice
`logging.exception()` already adds the the exception information after
the supplied message.
Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.
xref. https://github.com/galaxyproject/galaxy/issues/1715
Commit: 210cdc998a8f8929362d881bfaded32ac1e45aef
https://github.com/galaxyproject/galaxy/commit/210cdc998a8f8929362d881bfade…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/authnz/managers.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/managers/cloud.py
M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/util/readme_util.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M test/base/populators.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #6916 from nsoranzo/fix_exception_logging
Do not log exception info twice
Compare: https://github.com/galaxyproject/galaxy/compare/2dcd126e82fc...210cdc998a8f
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5dfb743ae160f873db670bff26d3ba19d85d4ce9
https://github.com/galaxyproject/galaxy/commit/5dfb743ae160f873db670bff26d3…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/tools/parameters/dynamic_options.py
Log Message:
-----------
Allow ``remove_value`` filter on data tables
The `RemoveValueFilter.filter_options()` method was expecting `options` to
be a list of lists, where each inner list contains exactly 3-elements
(name, value, selected), which is the format returned by the `data_meta`
filter. In fact, the only known use of the `remove_falue` filter is in the
tool `tools/maf/maf_to_interval.xml`, to filter dataset metadata.
This commit generalises the filter to look for a column of the dynamic
options named `value`, and use it during the filtering.
Fix https://github.com/galaxyproject/tools-iuc/issues/2151
Commit: 26680e0ca1ace0ad8c857ab712f60d2fc4bf8c1b
https://github.com/galaxyproject/galaxy/commit/26680e0ca1ace0ad8c857ab712f6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
A test/functional/tools/remove_value.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add test for remove_value form dynamic options
Unfortunately you can select an invalid value (in the API, not the UI)
and Galaxy will replace the invalid value with the first valid value.
Commit: 7c81daa073dea39785144b9228b53b2cd9f6fdbe
https://github.com/galaxyproject/galaxy/commit/7c81daa073dea39785144b9228b5…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/tools/parameters/dynamic_options.py
Log Message:
-----------
Fix assertion in ``RemoveValueFilter``
Commit: 19c98b27455862e7f50570bbc147a28667182e31
https://github.com/galaxyproject/galaxy/commit/19c98b27455862e7f50570bbc147…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M test/functional/tools/remove_value.xml
Log Message:
-----------
Fix tests and name tool more appropriately
Commit: 014b9d76f76c2eb959266bc271ad0539a1ab0f6d
https://github.com/galaxyproject/galaxy/commit/014b9d76f76c2eb959266bc271ad…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/tools/parameters/dynamic_options.py
A test/functional/tools/remove_value.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #6914 from nsoranzo/remove_value
Allow ``remove_value`` filter on data tables
Compare: https://github.com/galaxyproject/galaxy/compare/51ca8dc0f5d4...014b9d76f76c
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 794d1e03be57fdc0cde02bab79f8404c0eed7626
https://github.com/galaxyproject/galaxy/commit/794d1e03be57fdc0cde02bab79f8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-22 (Mon, 22 Oct 2018)
Changed paths:
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Fix messed up printing of shed_tool_conf.xml file
This drops xml_to_string from lib/tool_shed/util/xml_util.py
and uses xml_to_string form lib/galaxy/utils/__init__.py.
Also reduces plain string manipulation of xml structures.
Uses xml.dom.minidom to make xml pretty if necessary.
Commit: 8a39f27b3c8d20c5adf933f6a3782525b3925432
https://github.com/galaxyproject/galaxy/commit/8a39f27b3c8d20c5adf933f6a378…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Fix toolshed tests
Commit: a4655432604a758f2725c5badc120f4836ffcbda
https://github.com/galaxyproject/galaxy/commit/a4655432604a758f2725c5badc12…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Drop threading lock and global try/except
The Lock wasn't actually preventing anything, and I don't think
anything would need ot be protected here. mkdtemp should be thread-safe.
We also remove the try/except Statement. I think it'd be better to
expose any exceptions here instead of producing broken capsules and
logging an exception.
Commit: 57a4e50d8cfe038632bbe25ed6cbb69662491f2e
https://github.com/galaxyproject/galaxy/commit/57a4e50d8cfe038632bbe25ed6cb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Fix capsule export in docker testing
Found this by removing the blank try/except in the previous commit.
This only affects testing when python can't determine the correct
locale and falls back to ASCII.
Commit: 3f172cc9880e58396e7f71b7480bea9e7163dda4
https://github.com/galaxyproject/galaxy/commit/3f172cc9880e58396e7f71b7480b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
Log Message:
-----------
Fix job stopping from DRMAA jobs broken in
a1c58a708829d79859426ecb7c39b5c5f69ad735 and improve logging around it.
Commit: 36383785697bed5db7e99461c3483f19836a016b
https://github.com/galaxyproject/galaxy/commit/36383785697bed5db7e99461c348…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
Log Message:
-----------
Merge pull request #6912 from natefoo/fix-drmaa-job-stop
[18.09] Fix stopping DRMAA jobs
Commit: 328c410fdcad8a870816dea307499fef31c812e7
https://github.com/galaxyproject/galaxy/commit/328c410fdcad8a870816dea30749…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Merge pull request #6904 from mvdbeek/fix_weird_xml
[18.09] Fix pretty printing of shed_tool_conf.xml file
Commit: c862d55ec8fe99e950df7984127461eaedd6f438
https://github.com/galaxyproject/galaxy/commit/c862d55ec8fe99e950df79841274…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Use with statement when handling NamedTemporaryFile
Commit: 91a9dbaf5cf093ff72f39d9ea606bef59ecfc45a
https://github.com/galaxyproject/galaxy/commit/91a9dbaf5cf093ff72f39d9ea606…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Revert unncessary double logging of exception
Commit: 843474e5e375a2359979a8f9ae46fb0e58ac148b
https://github.com/galaxyproject/galaxy/commit/843474e5e375a2359979a8f9ae46…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Merge pull request #6915 from mvdbeek/6904_followup
[18.09] Small followup to #6904
Commit: 51ca8dc0f5d4cb9ba4221cba5d2067f467087caa
https://github.com/galaxyproject/galaxy/commit/51ca8dc0f5d4cb9ba4221cba5d20…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Merge branch 'release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/096fe9b7b9c3...51ca8dc0f5d4
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a38fc541d14712b4a81e9aaf42a8041efc17c803
https://github.com/galaxyproject/galaxy/commit/a38fc541d14712b4a81e9aaf42a8…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Simplify imports
Commit: cbf8a6658d8bf386c6133213883d0f833049d445
https://github.com/galaxyproject/galaxy/commit/cbf8a6658d8bf386c6133213883d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M doc/source/admin/special_topics/bug_reports.rst
Log Message:
-----------
Update Bug Reports docs to use YAML syntax
Commit: 096fe9b7b9c37e066abe1d31f4a1eeb360b95097
https://github.com/galaxyproject/galaxy/commit/096fe9b7b9c37e066abe1d31f4a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M doc/source/admin/special_topics/bug_reports.rst
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Merge pull request #6909 from nsoranzo/error_reports
Update Bug Reports docs to use YAML syntax
Compare: https://github.com/galaxyproject/galaxy/compare/ade72dd8b638...096fe9b7b9c3
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.09
Home: https://github.com/galaxyproject/galaxy
Commit: 794d1e03be57fdc0cde02bab79f8404c0eed7626
https://github.com/galaxyproject/galaxy/commit/794d1e03be57fdc0cde02bab79f8…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-22 (Mon, 22 Oct 2018)
Changed paths:
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Fix messed up printing of shed_tool_conf.xml file
This drops xml_to_string from lib/tool_shed/util/xml_util.py
and uses xml_to_string form lib/galaxy/utils/__init__.py.
Also reduces plain string manipulation of xml structures.
Uses xml.dom.minidom to make xml pretty if necessary.
Commit: 8a39f27b3c8d20c5adf933f6a3782525b3925432
https://github.com/galaxyproject/galaxy/commit/8a39f27b3c8d20c5adf933f6a378…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Fix toolshed tests
Commit: a4655432604a758f2725c5badc120f4836ffcbda
https://github.com/galaxyproject/galaxy/commit/a4655432604a758f2725c5badc12…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Drop threading lock and global try/except
The Lock wasn't actually preventing anything, and I don't think
anything would need ot be protected here. mkdtemp should be thread-safe.
We also remove the try/except Statement. I think it'd be better to
expose any exceptions here instead of producing broken capsules and
logging an exception.
Commit: 57a4e50d8cfe038632bbe25ed6cbb69662491f2e
https://github.com/galaxyproject/galaxy/commit/57a4e50d8cfe038632bbe25ed6cb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Fix capsule export in docker testing
Found this by removing the blank try/except in the previous commit.
This only affects testing when python can't determine the correct
locale and falls back to ASCII.
Commit: 328c410fdcad8a870816dea307499fef31c812e7
https://github.com/galaxyproject/galaxy/commit/328c410fdcad8a870816dea30749…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/xml_util.py
Log Message:
-----------
Merge pull request #6904 from mvdbeek/fix_weird_xml
[18.09] Fix pretty printing of shed_tool_conf.xml file
Compare: https://github.com/galaxyproject/galaxy/compare/36383785697b...328c410fdcad
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 77f742d7ffd95167b3c4905ef4bdcb4e678e8158
https://github.com/galaxyproject/galaxy/commit/77f742d7ffd95167b3c4905ef4bd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-10-22 (Mon, 22 Oct 2018)
Changed paths:
M config/plugins/visualizations/scatterplot/package.json
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.css
M config/plugins/visualizations/scatterplot/static/scatterplot.js
Log Message:
-----------
Adjust scatterplot interface style
Commit: 4e426ce25621736c6e6c7a7d91fcf1845f46db03
https://github.com/galaxyproject/galaxy/commit/4e426ce25621736c6e6c7a7d91fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-10-22 (Mon, 22 Oct 2018)
Changed paths:
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
Log Message:
-----------
Fix scatterplot saving feature
Commit: ade72dd8b638292392f057767ad41f9ed4330eb9
https://github.com/galaxyproject/galaxy/commit/ade72dd8b638292392f057767ad4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-23 (Tue, 23 Oct 2018)
Changed paths:
M config/plugins/visualizations/scatterplot/package.json
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.css
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
Log Message:
-----------
Merge pull request #6905 from guerler/viz_frame
Fixes for built-in Scatterplot plugin
Compare: https://github.com/galaxyproject/galaxy/compare/02c71e2429ba...ade72dd8b638
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.