September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 5db56b: Increase Greenfield concurrency for testing.
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5db56b223d0c5afaa32877ea38f7605b0deb8192 https://github.com/galaxyproject/usegalaxy-playbook/commit/5db56b223d0c5afa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Increase Greenfield concurrency for testing.

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[galaxyproject/galaxy] 134c98: Updates and fixes for dockerized Galaxy testing.
by GitHub 19 Sep '15

19 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 134c985f90a538eef623e6bc58c540228658d599 https://github.com/galaxyproject/galaxy/commit/134c985f90a538eef623e6bc58c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M run_tests.sh M test/docker/README.md M test/docker/base/Dockerfile Log Message: ----------- Updates and fixes for dockerized Galaxy testing. Commit: 1f1eed0e05600e7d89e36a0b152c87d609c85a3d https://github.com/galaxyproject/galaxy/commit/1f1eed0e05600e7d89e36a0b152c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M run_tests.sh M test/docker/README.md M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #759 from jmchilton/dockerize_test Updates and fixes for dockerized Galaxy testing. Compare: https://github.com/galaxyproject/galaxy/compare/2e55eb11e551...1f1eed0e0560

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[galaxyproject/galaxy] 45d5e2: Extend test_map_over_two_collections timeout.
by GitHub 19 Sep '15

19 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45d5e29c1dcc30e896ed3fc408b2005a35d11ba6 https://github.com/galaxyproject/galaxy/commit/45d5e29c1dcc30e896ed3fc408b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M test/api/test_tools.py Log Message: ----------- Extend test_map_over_two_collections timeout. May be the cause of intermittent test failure on jenkins (https://jenkins.galaxyproject.org/job/G-API/lastCompletedBuild/default/test…) Commit: 69f4ace0bcdaedc4f2077baeaffe605eb7538d79 https://github.com/galaxyproject/galaxy/commit/69f4ace0bcdaedc4f2077baeaffe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix failing workflow to_dict editor test. Generating form HTML as part of this request requires a history now (since https://github.com/galaxyproject/galaxy/commit/a00461eaf61bdeeea0c42b8098ae…) This is a less than ideal since it should definitely not require a history, but it is also less than idea to be shipping HTML via the API for non-web transactions. So rather than solving the former problem, this solves the latter and just doesn't attach form HTML for API requests. Fixes #734. Commit: 2e55eb11e5513cf76cb970e16ea2102bc557865a https://github.com/galaxyproject/galaxy/commit/2e55eb11e5513cf76cb970e16ea2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_tools.py Log Message: ----------- Merge pull request #758 from jmchilton/framework_tests API Test Fixes Compare: https://github.com/galaxyproject/galaxy/compare/c7d7736472d0...2e55eb11e551

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[galaxyproject/galaxy] 2b0267: Workaround for metadata_bam.xml failure.
by GitHub 19 Sep '15

19 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b02677e85e57792a2aab52333ccc3f24c65393e https://github.com/galaxyproject/galaxy/commit/2b02677e85e57792a2aab52333cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: A test-data/3.bam M test/functional/tools/metadata_bam.xml Log Message: ----------- Workaround for metadata_bam.xml failure. Commit: c6be0bc12c6300f839d4b9dace05f567c493637d https://github.com/galaxyproject/galaxy/commit/c6be0bc12c6300f839d4b9dace05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: R test/functional/tools/compare_bam_as_sam.xml Log Message: ----------- Remove compare_bam_as_sam.xml test. It never passed, it was originally used by me to test failing tests compared output of bams as sam files. Now that we want all these tests to pass we need to rethink how to test that aspect of the testing framework. Commit: c7d7736472d06b4b8df169f6017f7a4afe97d7b3 https://github.com/galaxyproject/galaxy/commit/c7d7736472d06b4b8df169f6017f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: A test-data/3.bam R test/functional/tools/compare_bam_as_sam.xml M test/functional/tools/metadata_bam.xml Log Message: ----------- Merge pull request #757 from jmchilton/framework_tests Fix failing framework tests. Compare: https://github.com/galaxyproject/galaxy/compare/31c2d33ede1b...c7d7736472d0

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[galaxyproject/galaxy] cb303a: Fix the fix I added to make the unit tests pass.
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb303a46ef71c1b13d7760d2c8b840afff973b9e https://github.com/galaxyproject/galaxy/commit/cb303a46ef71c1b13d7760d2c8b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Fix the fix I added to make the unit tests pass. Commit: 31c2d33ede1b97672ff0a05faa6928a8d05b1422 https://github.com/galaxyproject/galaxy/commit/31c2d33ede1b97672ff0a05faa69… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-19 (Sat, 19 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Merge pull request #756 from dannon/oops Fix lack of a return in hda manager Compare: https://github.com/galaxyproject/galaxy/compare/ce9fe44b939a...31c2d33ede1b

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[galaxyproject/infrastructure-playbook] be0739: add node to n2 via brew
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: be07399e8ddafd6ead81aa0ee5e172642b01b7b9 https://github.com/galaxyproject/infrastructure-playbook/commit/be07399e8dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/group_vars/jenkinsservers.yml Log Message: ----------- add node to n2 via brew

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[galaxyproject/infrastructure-playbook] 044fce: add npm to n2
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 044fce8b07239d2080f8812bef886c6a3369cf8a https://github.com/galaxyproject/infrastructure-playbook/commit/044fce8b072… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add npm to n2

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[galaxyproject/galaxy] 4064d0: add Oxli datatypes
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4064d0c5980644f29ac06b83f28e7064479f28db https://github.com/galaxyproject/galaxy/commit/4064d0c5980644f29ac06b83f28e… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add Oxli datatypes Commit: cecea3ebc6e9043df85989cd74899779a06c1e41 https://github.com/galaxyproject/galaxy/commit/cecea3ebc6e9043df85989cd7489… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits Log Message: ----------- added doctests + 1 fix + cleanup Made helper function a proper @staticmethod fixed error in sniffer (thank you doctests) Moved registration lines after their respective classes Added test data Commit: 383e9e01817483b819e770e22cf9d2d0beebbd5b https://github.com/galaxyproject/galaxy/commit/383e9e01817483b819e770e22cf9… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- OxliLabelSet->OxliGraphLabels even in the config Commit: 02df796c7236b51382f7b1f77d50cc1709c76356 https://github.com/galaxyproject/galaxy/commit/02df796c7236b51382f7b1f77d50… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- drop trailing whitespace Commit: ce9fe44b939a693a87b18ab4dfaa1dfff4a715f4 https://github.com/galaxyproject/galaxy/commit/ce9fe44b939a693a87b18ab4dfaa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits Log Message: ----------- Merge pull request #721 from dib-lab/add-oxli-datatypes add Oxli datatypes Compare: https://github.com/galaxyproject/galaxy/compare/304e569730c8...ce9fe44b939a

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[galaxyproject/infrastructure-playbook] ae9fab: add nodejs to n2
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ae9faba6bc9f6503852e30770eb5c85e65d01172 https://github.com/galaxyproject/infrastructure-playbook/commit/ae9faba6bc9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add nodejs to n2

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[galaxyproject/galaxy] 304e56: Revert "Fixed broken RData sniffer"
by GitHub 18 Sep '15

18 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 304e569730c84f54176b06a175a49b7bce225325 https://github.com/galaxyproject/galaxy/commit/304e569730c84f54176b06a175a4… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Revert "Fixed broken RData sniffer" This reverts commit b2e9c8a36f9b1ba394b0d27bdc8287880abe27cd.

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