June 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4cf8d6: fix image generation for workflows with missing to...
by GitHub 11 Jun '16

11 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 4cf8d691e525142125af56b0627f804eb1bddd7c https://github.com/galaxyproject/galaxy/commit/4cf8d691e525142125af56b0627f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix image generation for workflows with missing tools currently this ends up with a server error Commit: fdf9520783ae55795a01e4092b1d6718c5fca5b4 https://github.com/galaxyproject/galaxy/commit/fdf9520783ae55795a01e4092b1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- drop unnecessary raise and fix capitalization incorporate comments of Bjoern and Nicola Commit: 5245e8a693fc3633762f29a468b84e3487083133 https://github.com/galaxyproject/galaxy/commit/5245e8a693fc3633762f29a468b8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #2488 from martenson/wrap-svg-for-missing-tools [16.04] fix image generation for workflows with missing tools Compare: https://github.com/galaxyproject/galaxy/compare/43694be8647e...5245e8a693fc

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[galaxyproject/galaxy] 78c866: Relax validation condition
by GitHub 11 Jun '16

11 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 78c866fd34181ecda09488b6d19d2e37f6c69d02 https://github.com/galaxyproject/galaxy/commit/78c866fd34181ecda09488b6d19d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax validation condition Commit: a44f30140990c93aa92b8cb5f0f87b819942b116 https://github.com/galaxyproject/galaxy/commit/a44f30140990c93aa92b8cb5f0f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-05 (Sun, 05 Jun 2016) Changed paths: M test/unit/tools/test_select_parameters.py Log Message: ----------- Revise contradicting test case, workflow injection through api attempts full validation without available datasets Commit: d9d51d362e8ef3197e01c0440289e60a50ad85e8 https://github.com/galaxyproject/galaxy/commit/d9d51d362e8ef3197e01c0440289… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add break to interrupt loop Commit: 43694be8647e3d1686b6c4fa80d0300bb9c96d42 https://github.com/galaxyproject/galaxy/commit/43694be8647e3d1686b6c4fa80d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge pull request #2456 from guerler/fix_building_mode [16.04] Relax validation condition for dynamic parameters Compare: https://github.com/galaxyproject/galaxy/compare/08fb160b38fb...43694be8647e

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[galaxyproject/galaxy] 7610f8: fix markup for button links on sharing template
by GitHub 10 Jun '16

10 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7610f82a421edb422b8ba8f7731a1ae23fb9ac41 https://github.com/galaxyproject/galaxy/commit/7610f82a421edb422b8ba8f7731a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- fix markup for button links on sharing template (ff would fail to generate images) turn of autocomplete Commit: 08fb160b38fbcd9bcdfd776bb75ae5c92ca002d1 https://github.com/galaxyproject/galaxy/commit/08fb160b38fbcd9bcdfd776bb75a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2481 from martenson/fix-html-sharing [16.04] fix markup for button links on sharing template Compare: https://github.com/galaxyproject/galaxy/compare/14844e48eb38...08fb160b38fb

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[galaxyproject/usegalaxy-playbook] fa2feb: Switch Main to pycurl for Jetstream and enable the...
by GitHub 10 Jun '16

10 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa2febbe77a13f9dc77fc13a791723da8f0ee575 https://github.com/galaxyproject/usegalaxy-playbook/commit/fa2febbe77a13f9d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Switch Main to pycurl for Jetstream and enable the transport timeout

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[galaxyproject/galaxy] 7c40c8: Fix for job handlers losing track of jobs when usi...
by GitHub 10 Jun '16

10 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c40c85034d918c50e8b22c1a3eb39746a6e043d https://github.com/galaxyproject/galaxy/commit/7c40c85034d918c50e8b22c1a3eb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 933f42619e2fb2fb518702397aa2f11ea2cfb8e0 https://github.com/galaxyproject/galaxy/commit/933f42619e2fb2fb518702397aa2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Log all failed job status checks Commit: dbbf1edef3d943e13db4e926840061a65742eaab https://github.com/galaxyproject/galaxy/commit/dbbf1edef3d943e13db4e9268400… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 [16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 14844e48eb3869dbb2ecdca29e6069904bac4f28 https://github.com/galaxyproject/galaxy/commit/14844e48eb3869dbb2ecdca29e60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/jobs/runners/drmaa.py Commit: 77bd1d996de95d60d4e5e97ae533af6302612146 https://github.com/galaxyproject/galaxy/commit/77bd1d996de95d60d4e5e97ae533… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8f647b763f13...77bd1d996de9

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[galaxyproject/galaxy] 7c40c8: Fix for job handlers losing track of jobs when usi...
by GitHub 10 Jun '16

10 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7c40c85034d918c50e8b22c1a3eb39746a6e043d https://github.com/galaxyproject/galaxy/commit/7c40c85034d918c50e8b22c1a3eb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 933f42619e2fb2fb518702397aa2f11ea2cfb8e0 https://github.com/galaxyproject/galaxy/commit/933f42619e2fb2fb518702397aa2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Log all failed job status checks Commit: dbbf1edef3d943e13db4e926840061a65742eaab https://github.com/galaxyproject/galaxy/commit/dbbf1edef3d943e13db4e9268400… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 [16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 14844e48eb3869dbb2ecdca29e6069904bac4f28 https://github.com/galaxyproject/galaxy/commit/14844e48eb3869dbb2ecdca29e60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/jobs/runners/drmaa.py Compare: https://github.com/galaxyproject/galaxy/compare/04863c833bb1...14844e48eb38

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[galaxyproject/usegalaxy-playbook] b24ec5: Add transport timeout options to RESTful Pulsar pl...
by GitHub 10 Jun '16

10 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b24ec58dfe7c5a5a29c6859c1e510d99cd2aeac6 https://github.com/galaxyproject/usegalaxy-playbook/commit/b24ec58dfe7c5a5a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add transport timeout options to RESTful Pulsar plugin

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[galaxyproject/galaxy] 7c40c8: Fix for job handlers losing track of jobs when usi...
by GitHub 10 Jun '16

10 Jun '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7c40c85034d918c50e8b22c1a3eb39746a6e043d https://github.com/galaxyproject/galaxy/commit/7c40c85034d918c50e8b22c1a3eb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 933f42619e2fb2fb518702397aa2f11ea2cfb8e0 https://github.com/galaxyproject/galaxy/commit/933f42619e2fb2fb518702397aa2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Log all failed job status checks Commit: dbbf1edef3d943e13db4e926840061a65742eaab https://github.com/galaxyproject/galaxy/commit/dbbf1edef3d943e13db4e9268400… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 [16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Compare: https://github.com/galaxyproject/galaxy/compare/47a651609600...dbbf1edef3d9

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[galaxyproject/galaxy] 9f7d92: Set a default for tool_dependencies_dir.
by GitHub 09 Jun '16

09 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f7d921d5d387f0704db66f9e190688122be9170 https://github.com/galaxyproject/galaxy/commit/9f7d921d5d387f0704db66f9e190… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Set a default for tool_dependencies_dir. This should make some obsecure errors less easy to encounter and makes it less work to get going with conda or the Tool Shed. With config sample fix from @martenson. Commit: 8f647b763f13b87bb69d2ec50f1c607cfa58a3b3 https://github.com/galaxyproject/galaxy/commit/8f647b763f13b87bb69d2ec50f1c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Merge pull request #2480 from jmchilton/tool_dependencies_default Set a default for tool_dependencies_dir. Compare: https://github.com/galaxyproject/galaxy/compare/4da1f6a5eaf1...8f647b763f13

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[galaxyproject/galaxy] b3edbc: Workaround for circular import situation.
by GitHub 09 Jun '16

09 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3edbcaec785c93171ac5b08805dec3ade92e4b7 https://github.com/galaxyproject/galaxy/commit/b3edbcaec785c93171ac5b08805d… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Workaround for circular import situation. Commit: 4c6389fb05a50b8b2d8f5f3fb2c9ea635a2bb6a6 https://github.com/galaxyproject/galaxy/commit/4c6389fb05a50b8b2d8f5f3fb2c9… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/util/__init__.py R lib/galaxy/util/directory_hash.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Move directory_hash_id into galaxy/util.py. Use util.directory_hash_id throughout. Commit: 89ba1ddef4706436aa5b2f30a37a8247755ea1a8 https://github.com/galaxyproject/galaxy/commit/89ba1ddef4706436aa5b2f30a37a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Remove now-unused import. Commit: 4da1f6a5eaf1228aa42b0ee7e8d1327a58706602 https://github.com/galaxyproject/galaxy/commit/4da1f6a5eaf1228aa42b0ee7e8d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/util/__init__.py R lib/galaxy/util/directory_hash.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Merge pull request #2477 from davebx/circular_workaround Workaround for circular import. Refactor. Compare: https://github.com/galaxyproject/galaxy/compare/b7108cfb8b62...4da1f6a5eaf1

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