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

[galaxyproject/galaxy] cd3f28: Unicodify has different semantics to str
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd3f28d8a731475158bb97b807cb451929307cd0 https://github.com/galaxyproject/galaxy/commit/cd3f28d8a731475158bb97b807cb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Unicodify has different semantics to str Originally my patch was written with str()'s behaviour in mind. If a value is None, it gets cast. I did not test my patch well enough following @nsoranzo's request to replace with unicodify(). In that case a raw None gets passed to cgi.escape() causing a bug Commit: 75a99eb112355047692a3a97274f552eab58e705 https://github.com/galaxyproject/galaxy/commit/75a99eb112355047692a3a97274f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #2336 from erasche/fix-for-the-nth-bloody-time Unicodify has different semantics to str, causing bug reporter bug Compare: https://github.com/galaxyproject/galaxy/compare/3ac9d2aa0aa2...75a99eb11235

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[galaxyproject/galaxy] 3005bb: Remove SLURM memory limit warning from stderr if t...
by GitHub 10 May '16

10 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 3005bba5e389c86fccabe129326a1f3a675c6911 https://github.com/galaxyproject/galaxy/commit/3005bba5e389c86fccabe129326a… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Remove SLURM memory limit warning from stderr if the job was successful Commit: 338d25403109244f0b228f9a0df23e02e1de7578 https://github.com/galaxyproject/galaxy/commit/338d25403109244f0b228f9a0df2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Use partial messages to match SLURM memory warnings Commit: ad0647d677cb1979b9841cf0c56ba26d7ec5ca34 https://github.com/galaxyproject/galaxy/commit/ad0647d677cb1979b9841cf0c56b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Change elif to if because drmaa_state can be changed inside the if Commit: 0f984d3bfda9efaa6869286b13ff6842a6df67fb https://github.com/galaxyproject/galaxy/commit/0f984d3bfda9efaa6869286b13ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Unicodify pretty datetimes which can contain non-ASCII chars Commit: 41e6f22f338a6323cb48a23454ca95e798385045 https://github.com/galaxyproject/galaxy/commit/41e6f22f338a6323cb48a23454ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit [16.01] Remove SLURM memory limit warning from stderr if the job was successful Commit: 79dd8c82f034de51531fb843796249e2b21d9d62 https://github.com/galaxyproject/galaxy/commit/79dd8c82f034de51531fb8437962… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars Commit: afe5e0446ea3a943eb69616fda84fc9870c3b584 https://github.com/galaxyproject/galaxy/commit/afe5e0446ea3a943eb69616fda84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' Compare: https://github.com/galaxyproject/galaxy/compare/e77d3f009a8e...afe5e0446ea3

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[galaxyproject/galaxy] 37c50d: Relax default value acceptance condition
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 37c50d076803e5afd59ebd36691a154360464a45 https://github.com/galaxyproject/galaxy/commit/37c50d076803e5afd59ebd36691a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax default value acceptance condition Commit: 8ee9ad293790e066b23f205e43559a60110b7d76 https://github.com/galaxyproject/galaxy/commit/8ee9ad293790e066b23f205e4355… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2316 from guerler/fix_accept_000 [16.04] Relax default value acceptance condition Commit: 443a9e281c238121147af6192e92af80fb1eea53 https://github.com/galaxyproject/galaxy/commit/443a9e281c238121147af6192e92… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- fix proxy name Commit: d0830e0c226b6f3ae061b9d9e93556b3d1bc6c7d https://github.com/galaxyproject/galaxy/commit/d0830e0c226b6f3ae061b9d9e935… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #2333 from bgruening/proxy_fix Fixes the proxy naming Commit: 3ac9d2aa0aa2210959d5977646ba44b82e07adcf https://github.com/galaxyproject/galaxy/commit/3ac9d2aa0aa2210959d5977646ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/74e6d8b5d8e7...3ac9d2aa0aa2

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[galaxyproject/usegalaxy-playbook] 85e298: Update Pulsar
by GitHub 10 May '16

10 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 85e2989a7ded70fd0040f6a409956f9c456e1e6a https://github.com/galaxyproject/usegalaxy-playbook/commit/85e2989a7ded70fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar Commit: 1f0b0280019224bd88e17dc2a7a0f51de02fa90e https://github.com/galaxyproject/usegalaxy-playbook/commit/1f0b0280019224bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a573617ae335...…

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[galaxyproject/galaxy] 443a9e: fix proxy name
by GitHub 10 May '16

10 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 443a9e281c238121147af6192e92af80fb1eea53 https://github.com/galaxyproject/galaxy/commit/443a9e281c238121147af6192e92… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- fix proxy name Commit: d0830e0c226b6f3ae061b9d9e93556b3d1bc6c7d https://github.com/galaxyproject/galaxy/commit/d0830e0c226b6f3ae061b9d9e935… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #2333 from bgruening/proxy_fix Fixes the proxy naming Compare: https://github.com/galaxyproject/galaxy/compare/8ee9ad293790...d0830e0c226b

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[galaxyproject/galaxy] b5c198: Build: remove redundant webpack step in makefile
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5c198a7bcd758935cbec88966cfbbe09e4658eb https://github.com/galaxyproject/galaxy/commit/b5c198a7bcd758935cbec88966cf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M Makefile M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build: remove redundant webpack step in makefile Removes the webpack make target and the 'webpack' call from client target. The webpack production build step is already called from the `grunt` step. Commit: 74e6d8b5d8e7c43f063a0b07e2141212495f9e0c https://github.com/galaxyproject/galaxy/commit/74e6d8b5d8e7c43f063a0b07e214… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2327 from carlfeberhard/make.client Build: remove redundant webpack step in makefile Compare: https://github.com/galaxyproject/galaxy/compare/3422b46fb48b...74e6d8b5d8e7

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[galaxyproject/galaxy] 41426e: Visualizations: remove graphview
by GitHub 09 May '16

09 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41426e4a3d67af916e53002566d6361f203ff9f3 https://github.com/galaxyproject/galaxy/commit/41426e4a3d67af916e53002566d6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako Log Message: ----------- Visualizations: remove graphview Has been replaced with graphviz. Commit: 3422b46fb48bdf835697bdfd8f5fa4cba8ebe73a https://github.com/galaxyproject/galaxy/commit/3422b46fb48bdf835697bdfd8f5f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako Log Message: ----------- Merge pull request #2329 from carlfeberhard/remove.graphview Visualizations: remove graphview Compare: https://github.com/galaxyproject/galaxy/compare/95c28ff46721...3422b46fb48b

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[galaxyproject/infrastructure-playbook] 2f0cbf: Fixes for old tool versions running on Jetstream
by GitHub 09 May '16

09 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2f0cbfcedada677d177c62a4d67c9dc0ab4a7368 https://github.com/galaxyproject/infrastructure-playbook/commit/2f0cbfcedad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml Log Message: ----------- Fixes for old tool versions running on Jetstream

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[galaxyproject/galaxy] 37c50d: Relax default value acceptance condition
by GitHub 09 May '16

09 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 37c50d076803e5afd59ebd36691a154360464a45 https://github.com/galaxyproject/galaxy/commit/37c50d076803e5afd59ebd36691a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax default value acceptance condition Commit: 8ee9ad293790e066b23f205e43559a60110b7d76 https://github.com/galaxyproject/galaxy/commit/8ee9ad293790e066b23f205e4355… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2316 from guerler/fix_accept_000 [16.04] Relax default value acceptance condition Compare: https://github.com/galaxyproject/galaxy/compare/5710506229e1...8ee9ad293790

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[galaxyproject/galaxy] 0f984d: Unicodify pretty datetimes which can contain non-A...
by GitHub 09 May '16

09 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0f984d3bfda9efaa6869286b13ff6842a6df67fb https://github.com/galaxyproject/galaxy/commit/0f984d3bfda9efaa6869286b13ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Unicodify pretty datetimes which can contain non-ASCII chars Commit: 427804ff823e4b4277e768e1822bd1642c549a1f https://github.com/galaxyproject/galaxy/commit/427804ff823e4b4277e768e1822b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Do not sniff one-line files as CSV/TSV Commit: 5bb7c1d448156c1d20f52eaac3fcab4b1a79e0e5 https://github.com/galaxyproject/galaxy/commit/5bb7c1d448156c1d20f52eaac3fc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2317 from nsoranzo/release_16.04_tsv_fix [16.04] Do not sniff one-line files as CSV/TSV Commit: 79dd8c82f034de51531fb843796249e2b21d9d62 https://github.com/galaxyproject/galaxy/commit/79dd8c82f034de51531fb8437962… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars Commit: 5710506229e16a64a6fe35279fb49df5c73bc0ce https://github.com/galaxyproject/galaxy/commit/5710506229e16a64a6fe35279fb4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: templates/show_params.mako Commit: 95c28ff4672116477851db4d1206adfb480f2b16 https://github.com/galaxyproject/galaxy/commit/95c28ff4672116477851db4d1206… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/995509776ef0...95c28ff46721

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