- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ddfbf2: Handle None v
by GitHub 21 Nov '17

21 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ddfbf2c3f0877a8e197735ab8dfbb06bf6352d93 https://github.com/galaxyproject/galaxy/commit/ddfbf2c3f0877a8e197735ab8dfb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Handle None v Commit: 070ab533bd465a3bca7aafd0d11e5edc0d30c976 https://github.com/galaxyproject/galaxy/commit/070ab533bd465a3bca7aafd0d11e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Address comments Commit: ce4584956b72b32cd037b3b8701ac7cca885dfd7 https://github.com/galaxyproject/galaxy/commit/ce4584956b72b32cd037b3b8701a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #5050 from erasche/fix-ufr-7036 Safely handle possible None value encountered in processing and execution of post-job action arguments Compare: https://github.com/galaxyproject/galaxy/compare/1d72b260fee9...ce4584956b72

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[galaxyproject/galaxy] 306be8: Document fastest way to iterate on client and clie...
by GitHub 21 Nov '17

21 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 306be82a13a853fec94dc8d2a03a5e5e8dc64918 https://github.com/galaxyproject/galaxy/commit/306be82a13a853fec94dc8d2a03a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M run_tests.sh Log Message: ----------- Document fastest way to iterate on client and client tests. As fast as I've been able to make it anyway. Commit: 1d72b260fee98605e53d3ea2ac1f9073d533bd02 https://github.com/galaxyproject/galaxy/commit/1d72b260fee98605e53d3ea2ac1f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5051 from jmchilton/fast_client_test_setup Document fastest way to iterate on client & client tests together. Compare: https://github.com/galaxyproject/galaxy/compare/e9ef110a81b1...1d72b260fee9

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[galaxyproject/galaxy] efd762: Cleanup SA objects between workflow invocation sch...
by GitHub 21 Nov '17

21 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: efd762e18cba17383d717f9bd76198b1476aa1ae https://github.com/galaxyproject/galaxy/commit/efd762e18cba17383d717f9bd761… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts. This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more. Commit: e9ef110a81b11d7fba752d62bc1d5f12206c745c https://github.com/galaxyproject/galaxy/commit/e9ef110a81b11d7fba752d62bc1d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #5045 from jmchilton/scheduler_memory Cleanup SA objects between workflow invocation scheduling attempts. Compare: https://github.com/galaxyproject/galaxy/compare/b2cc634e8a2e...e9ef110a81b1

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[galaxyproject/galaxy] a7c8ed: Bug fix - expose proper element_identifier in tool...
by GitHub 20 Nov '17

20 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a7c8edbaa448805e0211fc75e3888d8426e5fa38 https://github.com/galaxyproject/galaxy/commit/a7c8edbaa448805e0211fc75e388… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Bug fix - expose proper element_identifier in tool action template expansions. (#5049) xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3…

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[galaxyproject/galaxy] b2cc63: python3 fix (#5043)
by GitHub 20 Nov '17

20 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2cc634e8a2eea74adf96ee7a4ee6c29d37b00f3 https://github.com/galaxyproject/galaxy/commit/b2cc634e8a2eea74adf96ee7a4ee… Author: M Bernt <m.bernt(a)ufz.de> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M tools/stats/gsummary.py Log Message: ----------- python3 fix (#5043) strings can not be written to byte mode file handlers. writing resulted in: TypeError: a bytes-like object is required, not 'str' Alternative would be to make string byte.

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[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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[galaxyproject/usegalaxy-playbook] a71ffe: Fix datatypes config path.
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a71ffea273966efec7805f500beb3edc874d45d0 https://github.com/galaxyproject/usegalaxy-playbook/commit/a71ffea273966efe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix datatypes config path.

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[galaxyproject/infrastructure-playbook] c15b07: Set up additional mail forwards at TACC
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c15b07641f91039d0acd69b379fff5cb9a0e1ac3 https://github.com/galaxyproject/infrastructure-playbook/commit/c15b07641f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M taccenv/playbook.yml Log Message: ----------- Set up additional mail forwards at TACC

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[galaxyproject/infrastructure-playbook] 189259: Fix grafana slurp database target for Main move
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1892596434860fba38194bf5974640e6bb8164c5 https://github.com/galaxyproject/infrastructure-playbook/commit/18925964348… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Fix grafana slurp database target for Main move

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[galaxyproject/usegalaxy-playbook] c8e661: Fix Jetstream datatypes config path.
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c8e661e86541b0a9567359d85b5215c6afc59538 https://github.com/galaxyproject/usegalaxy-playbook/commit/c8e661e86541b0a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Fix Jetstream datatypes config path.

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[galaxyproject/galaxy] 715760: fix few stray wiki links
by GitHub 16 Nov '17

16 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7157600f85993eb8570079d7c7d5b82d0e2af3f6 https://github.com/galaxyproject/galaxy/commit/7157600f85993eb8570079d7c7d5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M templates/user/register.mako M tools/data_source/microbial_import.xml Log Message: ----------- fix few stray wiki links Commit: 7745897e59114f750425cddd7d8d3c271bf6f802 https://github.com/galaxyproject/galaxy/commit/7745897e59114f750425cddd7d8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M templates/user/register.mako M tools/data_source/microbial_import.xml Log Message: ----------- Merge pull request #5020 from martenson/wiki-cleanup fix few stray wiki links Compare: https://github.com/galaxyproject/galaxy/compare/5c28618a27d0...7745897e5911

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[galaxyproject/usegalaxy-playbook] 1a57b5: Changelog for manual fixes for Jetstream and Bridg...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a57b5cc5a7846773ec795b0a9b668e0196118b5 https://github.com/galaxyproject/usegalaxy-playbook/commit/1a57b5cc5a784677… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M CHANGELOG.md Log Message: ----------- Changelog for manual fixes for Jetstream and Bridges Commit: 4622552c52d0cfd70afe5e072976b3f184fefd99 https://github.com/galaxyproject/usegalaxy-playbook/commit/4622552c52d0cfd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test and Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/889b5d5e53dc...…

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[galaxyproject/usegalaxy-playbook] 889b5d: Disable use of the xsede manager on Stampede becau...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 889b5d5e53dc6d613c98c1b975b5c031be3e82ae https://github.com/galaxyproject/usegalaxy-playbook/commit/889b5d5e53dc6d61… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Disable use of the xsede manager on Stampede because the stats collection script is asking for a sudo password.

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[galaxyproject/galaxy] d53903: parse_interpreter: log a warning only if interpret...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5390350b8cfbdb4910cf0e671dbffb66f27f9e4 https://github.com/galaxyproject/galaxy/commit/d5390350b8cfbdb4910cf0e671db… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- parse_interpreter: log a warning only if interpreter is set Also return None instead of False if there is no `<command>`. Fix typo in warning. Commit: 5c28618a27d054c60285dc05064c03c3bb19ad14 https://github.com/galaxyproject/galaxy/commit/5c28618a27d054c60285dc05064c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #5015 from nsoranzo/fix_parse_interpreter parse_interpreter: log a warning only if interpreter is set Compare: https://github.com/galaxyproject/galaxy/compare/38c620c62bd7...5c28618a27d0

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[galaxyproject/galaxy] 08eb98: enhance hdca creation endpoint to accept lddas
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08eb9859f25dff98edbf2fc4be95012219d389a5 https://github.com/galaxyproject/galaxy/commit/08eb9859f25dff98edbf2fc4be95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- enhance hdca creation endpoint to accept lddas by implementing automatic conversion of any such elements Commit: 5609bfc307cd9a6bdd86cd49128d3c4f8407613b https://github.com/galaxyproject/galaxy/commit/5609bfc307cd9a6bdd86cd49128d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/api/test_libraries.py M test/base/populators.py Log Message: ----------- More API library testing. Commit: 8a41921b49106276d1e8ed925464e734c07664d8 https://github.com/galaxyproject/galaxy/commit/8a41921b49106276d1e8ed925464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Respect permissions when creating HDAs/HDCAs from LDDAs. Commit: 25e53e13453d594c56cf6f48474d74c7a9a09368 https://github.com/galaxyproject/galaxy/commit/25e53e13453d594c56cf6f48474d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/api/test_history_contents.py Log Message: ----------- API tests for creating HDCAs from LDDA elements. Commit: 47737659747955390292723d57381c2d3ca92f63 https://github.com/galaxyproject/galaxy/commit/47737659747955390292723d5738… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .travis.yml M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M 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static/scripts/viz/trackster.js M static/style/blue/trackster.css R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/show_params.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R 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test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection Commit: 87987b4c949b881ba59c17caa5fd8559c89eef6a https://github.com/galaxyproject/galaxy/commit/87987b4c949b881ba59c17caa5fd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .travis.yml M README.rst M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M 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static/scripts/viz/trackster.js M static/style/blue/trackster.css R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/show_params.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R 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test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge pull request #25 from jmchilton/lib-to-colllection Merge with dev and add more tests. Commit: abe1b240c33c0a2031a56fc52b8bcd5ec34ae27d https://github.com/galaxyproject/galaxy/commit/abe1b240c33c0a2031a56fc52b8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M test/api/test_libraries.py Log Message: ----------- Fix broken library test I recently added. Commit: 38c620c62bd7f9cce5c3a792563d88ec5120e3e0 https://github.com/galaxyproject/galaxy/commit/38c620c62bd7f9cce5c3a792563d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/base/populators.py Log Message: ----------- Merge pull request #4998 from martenson/lib-to-colllection enhance hdca creation API endpoint to accept lddas Compare: https://github.com/galaxyproject/galaxy/compare/f44cbd5d8210...38c620c62bd7

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[galaxyproject/galaxy] ae48c9: Remove search templates (unused)
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae48c9a3c1a4b50da6dadc1bb236456a22ed8472 https://github.com/galaxyproject/galaxy/commit/ae48c9a3c1a4b50da6dadc1bb236… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R templates/search/index.mako Log Message: ----------- Remove search templates (unused) Commit: f44cbd5d821096a667d6237f842e139c5d60fbc3 https://github.com/galaxyproject/galaxy/commit/f44cbd5d821096a667d6237f842e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R templates/search/index.mako Log Message: ----------- Merge pull request #5014 from dannon/remove_search_templates Remove unused search template Compare: https://github.com/galaxyproject/galaxy/compare/7bede53beff3...f44cbd5d8210

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