Branch: refs/heads/release_18.09
Home: https://github.com/galaxyproject/galaxy
Commit: ab660686c26241ec4959711603919b80442d32a0
https://github.com/galaxyproject/galaxy/commit/ab660686c26241ec495971160391…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M test/api/test_tools.py
A test/functional/tools/identifier_in_conditional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add test for single and multi-input identifiers
test_identifier_map_over_input_in_conditional fails at the
moment (same issue as in https://github.com/galaxyproject/galaxy/issues/6182)
Commit: 73f8f3129b07cbe96c10da161a547bf2008706e2
https://github.com/galaxyproject/galaxy/commit/73f8f3129b07cbe96c10da161a54…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M lib/galaxy/tools/parameters/wrapped.py
Log Message:
-----------
Partially fix missing element identifier
This makes sure that any toplevel `|__identifier__` is passed on
to nested inputs.
Commit: f8d9a9e33a994a97c537ef15f1993fbe5d5866ea
https://github.com/galaxyproject/galaxy/commit/f8d9a9e33a994a97c537ef15f199…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Attempt to recover wrapper datasets
Otherwise we create new wrappers that lack the element identifier.
Commit: e226edc5ade76dd0ec2e3d8db2e799567e8c11d7
https://github.com/galaxyproject/galaxy/commit/e226edc5ade76dd0ec2e3d8db2e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/util/__init__.py
M test/api/test_tools.py
A test/functional/tools/identifier_in_conditional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #6798 from mvdbeek/fix_element_identifier_for_non_multiple_true_mapover_in_conditionals
[18.09] Fix element identifier for non multiple true mapover in conditionals
Compare: https://github.com/galaxyproject/galaxy/compare/a47887639d50...e226edc5ade7
**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: 565f611389e434b6df57d39ad5c01ae037e46e76
https://github.com/galaxyproject/galaxy/commit/565f611389e434b6df57d39ad5c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Fix remaining selenium py3 erorrs
Commit: 2e7adfbee4835f1374dffe7ba49760cfc19fdb0e
https://github.com/galaxyproject/galaxy/commit/2e7adfbee4835f1374dffe7ba497…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M lib/galaxy/web/framework/helpers/__init__.py
Log Message:
-----------
Cast to bytestring in md5 function
Commit: a47887639d50b2e5da55d9121b8d8e55509a9cd3
https://github.com/galaxyproject/galaxy/commit/a47887639d50b2e5da55d9121b8d…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M lib/galaxy/web/framework/helpers/__init__.py
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Merge pull request #6803 from mvdbeek/finish_py3_selenium
[18.09] Fix remaining selenium py3 errors
Compare: https://github.com/galaxyproject/galaxy/compare/f0131eff8b0c...a47887639d50
**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: 0743c7ba04fa6e61e2c48386a49a61f41d1eb493
https://github.com/galaxyproject/galaxy/commit/0743c7ba04fa6e61e2c48386a49a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
All extracted datasets should be visible
Commit: bf0370c1929def91bc69e1ab252dc0e8bfc2a387
https://github.com/galaxyproject/galaxy/commit/bf0370c1929def91bc69e1ab252d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix __encode_invocation signature and passthrough to manager that I busted in merging 18.05 forward
Commit: da3b6a1566dc0bb2665b2781cdb3c76551d68613
https://github.com/galaxyproject/galaxy/commit/da3b6a1566dc0bb2665b2781cdb3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
encode_invocation defers to manager and doesn't require trans passing anymore
Commit: becb922dc1e8c2d48e03a2badcb940ab1661e247
https://github.com/galaxyproject/galaxy/commit/becb922dc1e8c2d48e03a2badcb9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/rules_dsl.py
A test/unit/test_utils.py
Log Message:
-----------
Strip all control characters from rules
Similar to 366701cfb23d8de31eac3c4312c6accca2e74ef1, which is valid on its own, but here we just apply it to all rules.
Commit: b44379c3d9da4b7916b3c5a4fdf5eff39ee2267d
https://github.com/galaxyproject/galaxy/commit/b44379c3d9da4b7916b3c5a4fdf5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #6780 from mvdbeek/visible_extracted_datasets
[18.09] All extracted datasets should be visible
Commit: f54cba043354aa8fac339052462f7302613ca24a
https://github.com/galaxyproject/galaxy/commit/f54cba043354aa8fac339052462f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Merge pull request #6782 from dannon/fix-bad-workflow-invocation-merge
[18.09] Fix __encode_invocation signature
Commit: 53b062f804c6d495b187656c84597f953210a2b0
https://github.com/galaxyproject/galaxy/commit/53b062f804c6d495b187656c8459…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M test/api/test_tools_upload.py
Log Message:
-----------
Add bam upload test
`test_upload_bam_file` fails on release_18.09 but passes on 18.05.
Commit: 57fe3a741a9c3ac9c09513e21d44984ba046322e
https://github.com/galaxyproject/galaxy/commit/57fe3a741a9c3ac9c09513e21d44…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/model/metadata.py
Log Message:
-----------
Fix metadata spontaneuosly reverting
Similar to https://github.com/galaxyproject/galaxy/pull/6631/files.
This fixes https://github.com/galaxyproject/galaxy/issues/6769
Commit: c5a325d01535d9b46e28165c531a119d5f51b2d6
https://github.com/galaxyproject/galaxy/commit/c5a325d01535d9b46e28165c531a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/galaxy/util/rules_dsl.py
A test/unit/test_utils.py
Log Message:
-----------
Merge pull request #6785 from mvdbeek/escape_all_rules
[18.09] Strip all control characters from rules
Commit: b0dff4444085668cc3359b73d9d4d13b6da74cf6
https://github.com/galaxyproject/galaxy/commit/b0dff4444085668cc3359b73d9d4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M lib/galaxy/model/__init__.py
M lib/galaxy/web/base/controller.py
Log Message:
-----------
allow making all datasets within history public, when sharing
this is a one-off operation so notable behavior is that
if you create a new dataset in the shared history, it still
won't be public when there are default permissions set on history
Commit: 70e325574cb82be62b1be8090e714ce44441686b
https://github.com/galaxyproject/galaxy/commit/70e325574cb82be62b1be8090e71…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M test/api/test_tools_upload.py
Log Message:
-----------
Use with statement for all file uploads
Commit: e4399021520440a8f58e33dbae161f031f8da9eb
https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-09-27 (Thu, 27 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M lib/galaxy/web/base/controller.py
Log Message:
-----------
show warning to user if some of the items within were not published
Commit: 5a98515df88b68483ad59bb7208a57f1a7f71664
https://github.com/galaxyproject/galaxy/commit/5a98515df88b68483ad59bb7208a…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/model/metadata.py
M test/api/test_tools_upload.py
Log Message:
-----------
Merge pull request #6789 from mvdbeek/fix_bam_upload
[18.09] Fix bam upload resulting in 'auto' datatype
Commit: 29a3b6bbfbde469e59f6a896dc8a4f76a8d3ea3d
https://github.com/galaxyproject/galaxy/commit/29a3b6bbfbde469e59f6a896dc8a…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M lib/galaxy/model/__init__.py
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Merge pull request #6793 from martenson/fix-sharing-by-link
[18.09] allow making all datasets within history public, when sharing
Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9
https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Drop unused peek method (this used unencoded ids)
Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48
https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge pull request #6796 from dannon/peek_drop
[16.01] Drop unused peek method
Commit: 482f1ea35971d6a0fe979e793119d207eca4b438
https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.01' into release_16.04
Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568
https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.04' into release_16.07
Commit: 809ae58c52ed912a3256600ccf21456fac853782
https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into release_16.10
Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694
https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into release_17.01
Commit: c4150d200214aed7a150c44cc780d825b2628e83
https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into release_17.05
Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63
https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.05' into release_17.09
Commit: ac46d21ece75c4fce57836758f566eda8c878166
https://github.com/galaxyproject/galaxy/commit/ac46d21ece75c4fce57836758f56…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.09' into release_18.01
Commit: 9bc37c03b6572072bffabc797ea44f7816890103
https://github.com/galaxyproject/galaxy/commit/9bc37c03b6572072bffabc797ea4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_18.01' into release_18.05
Commit: 1e7677c3b2d7a5063a7340255140c3c8aa42129a
https://github.com/galaxyproject/galaxy/commit/1e7677c3b2d7a5063a7340255140…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_18.05' into release_18.09
Commit: ad76a0d57f1740d512826ad0749244af361fade1
https://github.com/galaxyproject/galaxy/commit/ad76a0d57f1740d512826ad07492…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M lib/galaxy/model/__init__.py
M lib/galaxy/model/metadata.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/rules_dsl.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M test/api/test_tools_upload.py
A test/unit/test_utils.py
Log Message:
-----------
Merge branch 'release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/3cd71b4864d2...ad76a0d57f17
**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.