Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77
https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Fix Registry.get_datatype_by_extension() to return None if ext is unknown
Without this fix, the Cheetah expression:
$dataset.is_of_type('unknown_ext')
in a tool command would be equivalent to:
$dataset.is_of_type('txt')
meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.
xref. https://github.com/galaxyproject/tools-iuc/issues/1373
Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233
https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge pull request #4230 from nsoranzo/release_16.07_backport_4224
[16.07] Backport #4224
Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c
https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge branch 'release_16.07' into release_16.10
Commit: bfb3ce6e79074c42803444701e814c65631ac0cd
https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Conflicts:
test/functional/tools/sample_datatypes_conf.xml
Compare: https://github.com/galaxyproject/galaxy/compare/96e1cf58f480...bfb3ce6e7907
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77
https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Fix Registry.get_datatype_by_extension() to return None if ext is unknown
Without this fix, the Cheetah expression:
$dataset.is_of_type('unknown_ext')
in a tool command would be equivalent to:
$dataset.is_of_type('txt')
meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.
xref. https://github.com/galaxyproject/tools-iuc/issues/1373
Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233
https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge pull request #4230 from nsoranzo/release_16.07_backport_4224
[16.07] Backport #4224
Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c
https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge branch 'release_16.07' into release_16.10
Compare: https://github.com/galaxyproject/galaxy/compare/490e565611b5...fada8d2a60e6
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77
https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-06-26 (Mon, 26 Jun 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Fix Registry.get_datatype_by_extension() to return None if ext is unknown
Without this fix, the Cheetah expression:
$dataset.is_of_type('unknown_ext')
in a tool command would be equivalent to:
$dataset.is_of_type('txt')
meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.
xref. https://github.com/galaxyproject/tools-iuc/issues/1373
Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233
https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge pull request #4230 from nsoranzo/release_16.07_backport_4224
[16.07] Backport #4224
Compare: https://github.com/galaxyproject/galaxy/compare/80ecc79a4cb8...5a39d47b0add
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6f98634dd51ac40848a2e16662782378f8022bfd
https://github.com/galaxyproject/galaxy/commit/6f98634dd51ac40848a2e1666278…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-06-27 (Tue, 27 Jun 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/log_tempfile.py
Log Message:
-----------
Fix import order and Python3 compatibility for 51 files
xref. https://github.com/galaxyproject/galaxy/issues/1715
Also remove unused `get_track_window()` method of some datatypes.
Commit: 20ef3eebcf2cf02fa79ca752f79e430b14802800
https://github.com/galaxyproject/galaxy/commit/20ef3eebcf2cf02fa79ca752f79e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/log_tempfile.py
Log Message:
-----------
Merge pull request #4236 from nsoranzo/python3
Fix import order and Python3 compatibility for 51 files
Compare: https://github.com/galaxyproject/galaxy/compare/79f3dc00a61d...20ef3eebcf2c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 58a2cde89fdc5e52c4b6b10842d47f1e1f24bfca
https://github.com/galaxyproject/galaxy/commit/58a2cde89fdc5e52c4b6b10842d4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-06-27 (Tue, 27 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
Log Message:
-----------
Refactor deactivate_or_uninstall_repository
Move code that deals with repository uninstallation into
InstalledRepositoryManager, so that this can be reused by the API.
Commit: b29f23500d0b8ccb0ef94521cbb42aaae430c755
https://github.com/galaxyproject/galaxy/commit/b29f23500d0b8ccb0ef94521cbb4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-06-27 (Tue, 27 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Simplify uninstall message creation
Commit: 67c66861c50f02475e497aa0c4feec7dfa16c2c2
https://github.com/galaxyproject/galaxy/commit/67c66861c50f02475e497aa0c4fe…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-06-27 (Tue, 27 Jun 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add `uninstall_repository` to ToolShedRepositoriesController
And connect routes. It is now possible to POST to
api/tool_shed_repositories to trigger a Repository installation and to
DELETE to api/tool_shed_repositories to uninstall a repository. In
addition one can also DELETE to
api/tool_shed_repositories/<repository_id>, which will uninstall the
repository with repository_id.
Commit: 3492f0e18fe389496623d9a09b57c40fd113b7c8
https://github.com/galaxyproject/galaxy/commit/3492f0e18fe389496623d9a09b57…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-02 (Sun, 02 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Fix the uninstall/deactivate message that is send to the mako template
Commit: 6a8f15bacb147e5189be983ad829a492d6dc0657
https://github.com/galaxyproject/galaxy/commit/6a8f15bacb147e5189be983ad829…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-04 (Tue, 04 Jul 2017)
Changed paths:
M lib/tool_shed/galaxy_install/installed_repository_manager.py
A test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Add basic unittest for InstalledRepositoryManager
that exercises the most basic functionality, which is the deactivate and
to uninstall repositories. Also moves shared `_init_dynamic_tool_conf`
method to BaseToolBoxTestCase
Commit: 79f3dc00a61d2f6425f16cfa018d973b31fb4973
https://github.com/galaxyproject/galaxy/commit/79f3dc00a61d2f6425f16cfa018d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-05 (Wed, 05 Jul 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
A test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #4248 from mvdbeek/uninstall_repository_api_endpoint
Add API repository uninstall endpoint
Compare: https://github.com/galaxyproject/galaxy/compare/86caee96e91a...79f3dc00a61d
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9af36bd13b90eea2f2883ab623a4a60ccf58a8b8
https://github.com/galaxyproject/galaxy/commit/9af36bd13b90eea2f2883ab623a4…
Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com>
Date: 2017-06-28 (Wed, 28 Jun 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
change 'register or login' to just 'login' if 'allow_user_creation=False'
Commit: 010beb8270bddbddcbf4712c6466cd9831cd2ae3
https://github.com/galaxyproject/galaxy/commit/010beb8270bddbddcbf4712c6466…
Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com>
Date: 2017-07-04 (Tue, 04 Jul 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
code optimization - reuse userTab variable
Commit: 7ce50a8ff72424ffb3403f6026ba4ada9bc32ba3
https://github.com/galaxyproject/galaxy/commit/7ce50a8ff72424ffb3403f6026ba…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-07-04 (Tue, 04 Jul 2017)
Changed paths:
M CONTRIBUTING.md
A SECURITY_POLICY.md
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M config/datatypes_conf.xml.sample
M doc/source/project/organization.rst
M lib/galaxy/app.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.ptkscmp
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-base.js
R templates/webapps/galaxy/history/shared_grid.mako
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into login_only
Compare: https://github.com/galaxyproject/galaxy/compare/ac59d1d6e042...7ce50a8ff724