Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0743c7ba04fa6e61e2c48386a49a61f41d1eb493 https://github.com/galaxyproject/galaxy/commit/0743c7ba04fa6e61e2c48386a49a6... Author: mvdbeek m.vandenbeek@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/bf0370c1929def91bc69e1ab252dc... Author: Dannon Baker dannon.baker@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/da3b6a1566dc0bb2665b2781cdb3c... Author: Dannon Baker dannon.baker@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/becb922dc1e8c2d48e03a2badcb94... Author: mvdbeek m.vandenbeek@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/b44379c3d9da4b7916b3c5a4fdf5e... Author: John Chilton jmchilton@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/f54cba043354aa8fac339052462f7... Author: Martin Cech marten@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/53b062f804c6d495b187656c84597... Author: mvdbeek m.vandenbeek@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/57fe3a741a9c3ac9c09513e21d449... Author: mvdbeek m.vandenbeek@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/c5a325d01535d9b46e28165c531a1... Author: John Chilton jmchilton@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/b0dff4444085668cc3359b73d9d4d... Author: Martin Cech marten@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/70e325574cb82be62b1be8090e714... Author: mvdbeek m.vandenbeek@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/e4399021520440a8f58e33dbae161... Author: Martin Cech marten@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/5a98515df88b68483ad59bb7208a5... Author: Dannon dannon.baker@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/29a3b6bbfbde469e59f6a896dc8a4... Author: Dannon dannon.baker@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/814c7f926dfe8d2aa344b5b17c83d... Author: Dannon Baker dannon.baker@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/f3ba9e2b9e924cd94bc35e7bf5d5c... Author: John Chilton jmchilton@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/482f1ea35971d6a0fe979e793119d... Author: Dannon Baker dannon.baker@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/8a1616aaf8160a4a7a7446b0cad07... Author: Dannon Baker dannon.baker@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/809ae58c52ed912a3256600ccf214... Author: Dannon Baker dannon.baker@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/fa7f2a4f5c18ff6f3255a5230adc6... Author: Dannon Baker dannon.baker@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/c4150d200214aed7a150c44cc780d... Author: Dannon Baker dannon.baker@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/40cecf6ff42134256bb53fcc7cb96... Author: Dannon Baker dannon.baker@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/ac46d21ece75c4fce57836758f566... Author: Dannon Baker dannon.baker@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/9bc37c03b6572072bffabc797ea44... Author: Dannon Baker dannon.baker@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/1e7677c3b2d7a5063a7340255140c... Author: Dannon Baker dannon.baker@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/ad76a0d57f1740d512826ad074924... Author: Dannon Baker dannon.baker@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
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