Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73
https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Changed GenomeSpace token handling to use manual OpenID association only
Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c
https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
Log Message:
-----------
replace syntax that is too new
Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67
https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-genomespace.js
M static/style/blue/base.css
Log Message:
-----------
build client
Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08
https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-genomespace.js
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge pull request #5631 from martenson/genomespace
[17.09] Changed GenomeSpace token handling to use manual OpenID association only
Commit: 10f8c3bc82b3a87dfa4125aa6eca9eb9071d3609
https://github.com/galaxyproject/galaxy/commit/10f8c3bc82b3a87dfa4125aa6eca…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge branch 'release_17.09' into release_18.01
dropped all static content from merge except of styles
Commit: e5d0c1c0eeffe9406f58f08b112fad332655e229
https://github.com/galaxyproject/galaxy/commit/e5d0c1c0eeffe9406f58f08b112f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge branch 'merge-in-18.01' into dev
Commit: cf369e84e3a8f1989bfb82284a6703994fdbe971
https://github.com/galaxyproject/galaxy/commit/cf369e84e3a8f1989bfb82284a67…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
Log Message:
-----------
re-add erroneously removed line
Commit: 300fffe73ee07d42a59c22b869eb3666b47dc720
https://github.com/galaxyproject/galaxy/commit/300fffe73ee07d42a59c22b869eb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge pull request #5660 from martenson/merge-genomespace
Merge forward genomespace changes
Compare: https://github.com/galaxyproject/galaxy/compare/fffca430d216...300fffe73ee0
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73
https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Changed GenomeSpace token handling to use manual OpenID association only
Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c
https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
Log Message:
-----------
replace syntax that is too new
Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67
https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-genomespace.js
M static/style/blue/base.css
Log Message:
-----------
build client
Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08
https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-genomespace.js
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge pull request #5631 from martenson/genomespace
[17.09] Changed GenomeSpace token handling to use manual OpenID association only
Commit: 10f8c3bc82b3a87dfa4125aa6eca9eb9071d3609
https://github.com/galaxyproject/galaxy/commit/10f8c3bc82b3a87dfa4125aa6eca…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge branch 'release_17.09' into release_18.01
dropped all static content from merge except of styles
Commit: b655a499f82a73f82f89bc8f962d4f0f0097cabc
https://github.com/galaxyproject/galaxy/commit/b655a499f82a73f82f89bc8f962d…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
Log Message:
-----------
re-add erroneously removed line
Commit: b601bcc429b47617e684158a62166575c244fd61
https://github.com/galaxyproject/galaxy/commit/b601bcc429b47617e684158a6216…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge pull request #5659 from martenson/merge-in-17.09
[18.01] Merge with 17.09
Compare: https://github.com/galaxyproject/galaxy/compare/9e6f3f57a0b2...b601bcc429b4
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4adaad4f0ee5444c6ef099f90681845c81901b82
https://github.com/galaxyproject/galaxy/commit/4adaad4f0ee5444c6ef099f90681…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/util/sanitize_html.py
Log Message:
-----------
Fix sanitazion of MathML and SVG
Broken in commit 66944ba7de178cc45ffa7a4aa9253ec4512cb6fd .
Commit: bacc1bf90b68a182492d484e5ded9003b5b03819
https://github.com/galaxyproject/galaxy/commit/bacc1bf90b68a182492d484e5ded…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/util/sanitize_html.py
Log Message:
-----------
Remove unused code
Commit: 271feecefa37aa69726ec3e47f4d73f12bb847e6
https://github.com/galaxyproject/galaxy/commit/271feecefa37aa69726ec3e47f4d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Use HTMLParser instead of Python2-only sgmllib
Commit: 326a564eb95f34c359cea14c2078f35c0ba55259
https://github.com/galaxyproject/galaxy/commit/326a564eb95f34c359cea14c2078…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
R scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
Log Message:
-----------
Stop shipping old BeautifulSoup library
Commit: 6906d15d928ef9da375227c14be4ff905941e30c
https://github.com/galaxyproject/galaxy/commit/6906d15d928ef9da375227c14be4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/managers/workflows.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Use bleach library for HTML sanitizing
Commit: 71c1c52d22e7fdbef2dc7d7b4b7993cc7f2de69d
https://github.com/galaxyproject/galaxy/commit/71c1c52d22e7fdbef2dc7d7b4b79…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/webapps/galaxy/controllers/page.py
Log Message:
-----------
Update code from upstream feedparser. Simplify __init__()
Commit: cd8a44ff195729c7e772ad461d9fab4797bbe252
https://github.com/galaxyproject/galaxy/commit/cd8a44ff195729c7e772ad461d9f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/webapps/galaxy/controllers/page.py
Log Message:
-----------
Merge _BaseHTMLProcessor class in _PageContentProcessor
Derive from HTMLParser instead of SGMLParser.
Commit: fffca430d21655ede9f0369fe078f3a1972910b1
https://github.com/galaxyproject/galaxy/commit/fffca430d21655ede9f0369fe078…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/managers/workflows.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/tool_shed/util/workflow_util.py
R scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
Log Message:
-----------
Merge pull request #5642 from nsoranzo/evict_sgmllib
Python3: evict sgmllib and BeautifulSoup
Compare: https://github.com/galaxyproject/galaxy/compare/6675959069b0...fffca430d216
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 58ed0308faa7fa94f1b36dc2e62b866ac6f49bdd
https://github.com/galaxyproject/galaxy/commit/58ed0308faa7fa94f1b36dc2e62b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Create fewer objects when instantiating tools.
Commit: 5e6c1c9f517ad7d6353db777e82c8e48f4769f06
https://github.com/galaxyproject/galaxy/commit/5e6c1c9f517ad7d6353db777e82c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M lib/galaxy/app.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/base/driver_util.py
M test/base/interactor.py
M test/base/testcase.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
Log Message:
-----------
New abstraction to obtain tool test data paths.
Can be shared between tests and TDTs. A step toward not requiring one to load the tool to test the tool (important for external testing of tools).
Commit: 210d5cbd7a52ecc3bbbef24c1bee4362fbcb9770
https://github.com/galaxyproject/galaxy/commit/210d5cbd7a52ecc3bbbef24c1bee…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M test/base/driver_util.py
M test/base/testcase.py
Log Message:
-----------
Eliminate shed tools dict no longer used.
Commit: 58ac3b6eff5f2158d5690d684a143716c4471ba4
https://github.com/galaxyproject/galaxy/commit/58ac3b6eff5f2158d5690d684a14…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
R test/base/tool_shed_util.py
M test/shed_functional/base/twilltestcase.py
Log Message:
-----------
Eliminate tool shed test helper no longer used.
Commit: 7e372c5dd217fdb4c19f4da6a49d86d65d205f76
https://github.com/galaxyproject/galaxy/commit/7e372c5dd217fdb4c19f4da6a49d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
M test/base/interactor.py
M test/base/testcase.py
Log Message:
-----------
Refactor more tool test verification code into galaxy-lib.
Should enable greater reuse from outside the test framework (e.g. standalone scripts and Planemo).
Commit: 70e76cae9f1f354540a3b97020323be1caba9817
https://github.com/galaxyproject/galaxy/commit/70e76cae9f1f354540a3b9702032…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M test/base/interactor.py
M test/base/testcase.py
Log Message:
-----------
Refactor polling code from testcase into more standalone interactor.
Working toward making interactor stand-alone and independent of the test framework.
Commit: 289937506bc97b7c8783975316e0a236a6ebf76b
https://github.com/galaxyproject/galaxy/commit/289937506bc97b7c8783975316e0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
A lib/galaxy/tools/verify/interactor.py
M test/base/api.py
M test/base/driver_util.py
M test/base/interactor.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
M test/functional/twilltestcase.py
Log Message:
-----------
Refactor much more tool testing code into galaxy-lib.
Commit: 508047f00ece58c98ba0f9bb093d2ae7506ade77
https://github.com/galaxyproject/galaxy/commit/508047f00ece58c98ba0f9bb093d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/test.py
M lib/galaxy/tools/verify/interactor.py
M test/functional/test_toolbox.py
Log Message:
-----------
Refactor ToolTestBuilder to not require an in-memory Tool object.
This gets us a lot closer to being able to construct a ToolTestBuilder from simple dictionaries generated from the API for instance or from any tool really.
Commit: c3af6c8feae90bc2d4b6328559fb79e3d7d35a5c
https://github.com/galaxyproject/galaxy/commit/c3af6c8feae90bc2d4b6328559fb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/api/test_tools.py
M test/base/driver_util.py
M test/base/testcase.py
M test/functional/test_toolbox.py
Log Message:
-----------
Serialize tool test descriptions through the API.
Use this is in tool testing. Prevents needing to load / have tools in memory to run tool tests - should allow external tool testing.
Commit: b1779e1a46564d976a7c024084c48c94df2db8e5
https://github.com/galaxyproject/galaxy/commit/b1779e1a46564d976a7c024084c4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/verify/interactor.py
A lib/galaxy/tools/verify/script.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/base/driver_util.py
M test/functional/test_toolbox.py
Log Message:
-----------
Refactor tool test outline construction to allow more reuse.
Commit: cd002615ee8a1f251eac9c0a5ae3cc12c45d2bde
https://github.com/galaxyproject/galaxy/commit/cd002615ee8a1f251eac9c0a5ae3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/verify/test_data.py
Log Message:
-----------
Setup a default GALAXY_TEST_FILE_DIR in case unset in the Galaxy itself.
Previously this was set in the test framework but that doesn't help running Galaxies.
Commit: 6f908a76c5db474725c2e45b51ad6ee9c27487cc
https://github.com/galaxyproject/galaxy/commit/6f908a76c5db474725c2e45b51ad…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M test/integration/test_data_manager_table_reload.py
A test/integration/uses_shed.py
Log Message:
-----------
Refactor data manager test to allow more integration tests with tool shed.
Commit: 662f29fda271454a9976fbf4fdad273300a89bfa
https://github.com/galaxyproject/galaxy/commit/662f29fda271454a9976fbf4fdad…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
A test/integration/test_shed_tool_tests.py
Log Message:
-----------
Integration test case for running tool tests against shed installed tools.
Commit: db6dafac07b92a06cac1da728f8fffb979d81d87
https://github.com/galaxyproject/galaxy/commit/db6dafac07b92a06cac1da728f8f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Revise repository directory calculation in tool class.
Based on conversations with @mvdbeek on https://github.com/galaxyproject/galaxy/pull/5545/files.
Commit: e7f7759cc22aac8ace05eaeab5b706634322a80b
https://github.com/galaxyproject/galaxy/commit/e7f7759cc22aac8ace05eaeab5b7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Better default configuration of Galaxy test data directory.
Commit: dc080b926ec3c0ecb967224ffa3b505e0128f783
https://github.com/galaxyproject/galaxy/commit/dc080b926ec3c0ecb967224ffa3b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/verify/script.py
Log Message:
-----------
Add structured output json example to galaxy.tools.verify.script.
Capture more information about the test.
Commit: 52b6bf2486b08aa8bbe621961baed42bd27c1ddd
https://github.com/galaxyproject/galaxy/commit/52b6bf2486b08aa8bbe621961bae…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/webapps/galaxy/api/tools.py
M test/api/test_tools.py
Log Message:
-----------
Stronger security around test data path resolution, now with tests.
Commit: bb7de2c0db60d6a69d84401279830fa87e8d9000
https://github.com/galaxyproject/galaxy/commit/bb7de2c0db60d6a69d8440127983…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/verify/interactor.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Improved tool test API.
Cleanup up internal representations used to bridge the tool parser and the tool testing modules to produce more sensible dictified representations when exported via the API. This is mostly replacing tuples (which get converted to JSON lists) to dicts but there are some other small cleanups.
Commit: 28ba0279d90dfae7603cdb06bed69235bf4f6f06
https://github.com/galaxyproject/galaxy/commit/28ba0279d90dfae7603cdb06bed6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Bug fix for exclude mercurial repo from test data search.
Thanks to :eagle::eyes:.
Commit: 227bf4ad045fcecc1aaab77a9b04f0ad0daa1e19
https://github.com/galaxyproject/galaxy/commit/227bf4ad045fcecc1aaab77a9b04…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/verify/interactor.py
M test/base/driver_util.py
Log Message:
-----------
Cleanup external tool testing based on @nsoranzo's comments.
Commit: f741ab142adc2411397fb6ef28710b850e02db78
https://github.com/galaxyproject/galaxy/commit/f741ab142adc2411397fb6ef2871…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M lib/galaxy/tools/verify/interactor.py
Log Message:
-----------
Switch default tool test dbkey to '?'.
This makes a lot more sense, since the target Galaxy may not be configured with this dbkey. Thanks to @mvdbeek for the catch (https://github.com/galaxyproject/galaxy/pull/5628#pullrequestreview-1014615…).
Restore the legacy behavior with "export GALAXY_TEST_DEFAULT_DBKEY=hg17".
Commit: 3afb4abad3a387997c0cb1c9398f8644219b0298
https://github.com/galaxyproject/galaxy/commit/3afb4abad3a387997c0cb1c9398f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-03-07 (Wed, 07 Mar 2018)
Changed paths:
M config/galaxy.yml.sample
M config/plugins/webhooks/demo/tour_generator/__init__.py
M doc/source/admin/galaxy_options.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/test.py
A lib/galaxy/tools/verify/interactor.py
A lib/galaxy/tools/verify/script.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M test/api/test_tools.py
M test/base/api.py
M test/base/driver_util.py
M test/base/interactor.py
M test/base/testcase.py
R test/base/tool_shed_util.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
M test/functional/twilltestcase.py
M test/integration/test_data_manager_table_reload.py
A test/integration/test_shed_tool_tests.py
A test/integration/uses_shed.py
M test/shed_functional/base/twilltestcase.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge pull request #5628 from jmchilton/external_tool_tests_better_api
Externally Executable Tool Tests 2 (with better API)
Compare: https://github.com/galaxyproject/galaxy/compare/7ceb24601822...3afb4abad3a3
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73
https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae…
Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Changed GenomeSpace token handling to use manual OpenID association only
Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c
https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
Log Message:
-----------
replace syntax that is too new
Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67
https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-genomespace.js
M static/style/blue/base.css
Log Message:
-----------
build client
Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08
https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/ui/ui-select-genomespace.js
M static/style/blue/base.css
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge pull request #5631 from martenson/genomespace
[17.09] Changed GenomeSpace token handling to use manual OpenID association only
Compare: https://github.com/galaxyproject/galaxy/compare/28724ab795ac...f8d44c2b6951