November 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f60a75: extraneous %s
by GitHub 20 Nov '17

20 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: f60a75c285830bff963bd31120f3420e9815dbe2 https://github.com/galaxyproject/galaxy/commit/f60a75c285830bff963bd31120f3… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- extraneous %s Commit: 59e9809585e2322382eaeb7b3e0270485b7e8db0 https://github.com/galaxyproject/galaxy/commit/59e9809585e2322382eaeb7b3e02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #5048 from erasche/fix-ufr-6206 Remove extraneous %s in condor logging Compare: https://github.com/galaxyproject/galaxy/compare/2a0c7114dfaf...59e9809585e2

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[galaxyproject/galaxy] e56814: add cooler fileformat to datatypes_conf.xml
by GitHub 19 Nov '17

19 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e568141170b8dd01f103b061f764ab8ded5329e2 https://github.com/galaxyproject/galaxy/commit/e568141170b8dd01f103b061f764… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add cooler fileformat to datatypes_conf.xml Commit: 32a7dfc20bb7619890ab9a7a38a82155c4ca88ea https://github.com/galaxyproject/galaxy/commit/32a7dfc20bb7619890ab9a7a38a8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add cooler file format binary class Commit: 1718f8dc8ea183a4eb1247138e49f5059183c821 https://github.com/galaxyproject/galaxy/commit/1718f8dc8ea183a4eb1247138e49… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: A lib/galaxy/datatypes/test/matrix.cool Log Message: ----------- add test file Commit: 3e2e1493256724a498f9d4ea3c8add2d3fc74224 https://github.com/galaxyproject/galaxy/commit/3e2e1493256724a498f9d4ea3c8a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-19 (Sun, 19 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/matrix.cool Log Message: ----------- Merge pull request #5023 from bgruening/cooler add cool datatype Compare: https://github.com/galaxyproject/galaxy/compare/db2c3a43e22b...3e2e14932567

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[galaxyproject/galaxy] 8a35b9: add API that allows admins to decode galaxy object...
by GitHub 19 Nov '17

19 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a35b940de75173d3be592e2c0ca2b7aaf17de4a https://github.com/galaxyproject/galaxy/commit/8a35b940de75173d3be592e2c0ca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_configuration.py Log Message: ----------- add API that allows admins to decode galaxy objects' ids Commit: db2c3a43e22b1a6c4f6380a600737cfeb95c6bc3 https://github.com/galaxyproject/galaxy/commit/db2c3a43e22b1a6c4f6380a60073… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-19 (Sun, 19 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_configuration.py Log Message: ----------- Merge pull request #5018 from martenson/api-for-admin-decode add API that allows admins to decode galaxy objects' ids Compare: https://github.com/galaxyproject/galaxy/compare/299ae5c9f5fa...db2c3a43e22b

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[galaxyproject/galaxy] f1348c: Fix workflow editor output attributes (var shadowi...
by GitHub 18 Nov '17

18 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f1348c15c7792af86c507c8b2d8f9121532cfcf5 https://github.com/galaxyproject/galaxy/commit/f1348c15c7792af86c507c8b2d8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix workflow editor output attributes (var shadowing was silently making *everything* the first output attribute...) Commit: ec7c060a905c66039065ebfc781a0daa617de757 https://github.com/galaxyproject/galaxy/commit/ec7c060a905c66039065ebfc781a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map Log Message: ----------- Formatting. Commit: 5bcd59944d6c5969930bba3c9f4d83b2a82c42c5 https://github.com/galaxyproject/galaxy/commit/5bcd59944d6c5969930bba3c9f4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Unpack options in functions in keeping with previous style here (dunno about this long term though) Commit: 299ae5c9f5fac0cb701eed3fb30e9ae3b4602bbb https://github.com/galaxyproject/galaxy/commit/299ae5c9f5fac0cb701eed3fb30e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-18 (Sat, 18 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #5021 from dannon/fix-workflow-editor-outputs Workflow editor outputs fixes Compare: https://github.com/galaxyproject/galaxy/compare/83e9e07bd596...299ae5c9f5fa

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[galaxyproject/galaxy] d5aa25: Add metric to the core plugin to collect $GALAXY_M...
by GitHub 17 Nov '17

17 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5aa2595aa9e3db85bf3c4663cfc2ccdd5a9948b https://github.com/galaxyproject/galaxy/commit/d5aa2595aa9e3db85bf3c4663cfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/core.py Log Message: ----------- Add metric to the core plugin to collect $GALAXY_MEMORY_MB Commit: 83e9e07bd596ff7c3fcfe3767034991aa851b0de https://github.com/galaxyproject/galaxy/commit/83e9e07bd596ff7c3fcfe3767034… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/core.py Log Message: ----------- Merge pull request #5016 from natefoo/memory-mb-metric Add metric to the core plugin to collect $GALAXY_MEMORY_MB Compare: https://github.com/galaxyproject/galaxy/compare/b5864ad4f74f...83e9e07bd596

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[galaxyproject/galaxy] a0643e: More HDCA copying tests, add option to copy HDAs i...
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0643e0385c171294d4f57ec2804794df2fcac23 https://github.com/galaxyproject/galaxy/commit/a0643e0385c171294d4f57ec2804… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py Log Message: ----------- More HDCA copying tests, add option to copy HDAs into new history. Commit: b5864ad4f74f6f5afe0568c5ed17d75610b9ed87 https://github.com/galaxyproject/galaxy/commit/b5864ad4f74f6f5afe0568c5ed17… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py Log Message: ----------- Merge pull request #5004 from jmchilton/collection_copy_api More HDCA copying tests, add option to copy HDAs into new history. Compare: https://github.com/galaxyproject/galaxy/compare/36dc1560e574...b5864ad4f74f

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[galaxyproject/galaxy] de1bd5: Fix workflow editor output attributes.
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: de1bd5f5d5af7b9e67180b115407fbc2ccb75a3e https://github.com/galaxyproject/galaxy/commit/de1bd5f5d5af7b9e67180b115407… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix workflow editor output attributes. Commit: 2a0c7114dfafb0c91e3bafb03ae6ff4370ce9ed8 https://github.com/galaxyproject/galaxy/commit/2a0c7114dfafb0c91e3bafb03ae6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #5022 from dannon/workflow_editor_fix_backport [17.09] Fix workflow editor output attributes. Compare: https://github.com/galaxyproject/galaxy/compare/5dc225441766...2a0c7114dfaf

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[galaxyproject/galaxy] 44447e: Use github instead of NCBI for problematic data ma...
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 44447ed08940782a4d022cd2dcddbdb2c2813ff4 https://github.com/galaxyproject/galaxy/commit/44447ed08940782a4d022cd2dcdd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/integration/test_data_manager_table_reload.py Log Message: ----------- Use github instead of NCBI for problematic data manager test FASTA. Seems to be failing many of the integration tool runs I've seen today. I've seen a couple different errors: ``` | File "/tmp/tmpVp6xM0/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 312, in download_from_ncbi | return get_stream_reader(urlopen(url), tmp_dir) | File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen | return opener.open(url, data, timeout) | File "/usr/lib/python2.7/urllib2.py", line 435, in open | response = meth(req, response) | File "/usr/lib/python2.7/urllib2.py", line 548, in http_response | 'http', request, response, code, msg, hdrs) | File "/usr/lib/python2.7/urllib2.py", line 473, in error | return self._call_chain(*args) | File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain | result = func(*args) | File "/usr/lib/python2.7/urllib2.py", line 556, in http_error_default | raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) ``` and ``` Timed out after 60.25 seconds waiting on state. -------------------- >> begin captured stdout << --------------------- Problem in history with id adb5f5c93f827949 - summary of datasets below. -------------------------------------- | 1 - Create DBKey and Reference Genome (HID - NAME) | Dataset State: | queued | Dataset Blurb: | queued | Dataset Info: | None | Peek: | None | Dataset Job Standard Output: | None | Dataset Job Standard Error: | None | -------------------------------------- ``` Commit: 36dc1560e574c42550f9450184ae9c44e86459dc https://github.com/galaxyproject/galaxy/commit/36dc1560e574c42550f9450184ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M test/integration/test_data_manager_table_reload.py Log Message: ----------- Merge pull request #5007 from jmchilton/problematic_data_manager Use github instead of NCBI for problematic data manager test FASTA. Compare: https://github.com/galaxyproject/galaxy/compare/a9685d3acd4c...36dc1560e574

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[galaxyproject/galaxy] d3b5fa: Test renaming multiple different outputs in workfl...
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3b5fac7516408c7d86e65b2899b7c6a8c9887e8 https://github.com/galaxyproject/galaxy/commit/d3b5fac7516408c7d86e65b2899b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M test/api/test_workflows.py M test/functional/tools/create_2.xml Log Message: ----------- Test renaming multiple different outputs in workflows. Attempting to exercise a bug reported by @lparsons. Commit: a9685d3acd4c0099f73e68079826fed40acd548f https://github.com/galaxyproject/galaxy/commit/a9685d3acd4c0099f73e68079826… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M test/api/test_workflows.py M test/functional/tools/create_2.xml Log Message: ----------- Merge pull request #5017 from jmchilton/test_renaming_multiple_workflows Test renaming multiple different outputs in workflows. Compare: https://github.com/galaxyproject/galaxy/compare/7745897e5911...a9685d3acd4c

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[galaxyproject/galaxy] 06e950: Allow get_history calls with create=False when eva...
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 06e9509d3868c885d41d94e455d7245f4af10156 https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Allow get_history calls with create=False when evaluation workflows. No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history. Commit: 5dc2254417667216dab982a4bc375a85d3b55316 https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4997 from jmchilton/allow_create_false_in_work_context [17.09] Allow get_history calls with create=False when evaluation workflows. Compare: https://github.com/galaxyproject/galaxy/compare/18467e9b2cec...5dc225441766

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