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

[galaxyproject/galaxy] 90fca4: Expose all API keys to admins under REMOTE_USER
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90fca4f47d762744b88923ff7404157f7027d235 https://github.com/galaxyproject/galaxy/commit/90fca4f47d762744b88923ff7404… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a937e233acb14a9b15164e7602df85d5c77b2570 https://github.com/galaxyproject/galaxy/commit/a937e233acb14a9b15164e7602df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #872 from erasche/api-key-fix Expose API keys to admins under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/5b93a66fae52...a937e233acb1

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[galaxyproject/galaxy] 5b93a6: Added missing lib/main.js
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b93a66fae521726dffb9fb4712a07dfb14788ad https://github.com/galaxyproject/galaxy/commit/5b93a66fae521726dffb9fb4712a… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Added missing lib/main.js

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[galaxyproject/galaxy] 47b34e: Verbosity is superfluous.
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47b34e844f174406eb3092e20bb89ff73d072da7 https://github.com/galaxyproject/galaxy/commit/47b34e844f174406eb3092e20bb8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Verbosity is superfluous. Commit: add784a3e91104835bf769768ab09d47113deb5f https://github.com/galaxyproject/galaxy/commit/add784a3e91104835bf769768ab0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #867 from davebx/docker Verbosity is superfluous. Compare: https://github.com/galaxyproject/galaxy/compare/cd9c13ab495f...add784a3e911

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[galaxyproject/galaxy] 82811d: Bump version of sqlite3 in nodejs proxy
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82811dd9217824946723ab54638da80ae40f2b54 https://github.com/galaxyproject/galaxy/commit/82811dd9217824946723ab54638d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Bump version of sqlite3 in nodejs proxy @nitesh1989 and I tested this this morning and it let him install the nodejs proxy on OSX Commit: cd9c13ab495fa946724e5a67cd70d0d6342bafba https://github.com/galaxyproject/galaxy/commit/cd9c13ab495fa946724e5a67cd70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #866 from erasche/gie-nodejs-proxy-sqlite Bump version of sqlite3 in nodejs proxy Compare: https://github.com/galaxyproject/galaxy/compare/a5e75e8bbe6e...cd9c13ab495f

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[galaxyproject/galaxy] 22a565: Try harder to verify script integrity before runni...
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 22a565d1a25a5eda466d49b69df3c3ab436e8b82 https://github.com/galaxyproject/galaxy/commit/22a565d1a25a5eda466d49b69df3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Try harder to verify script integrity before running job scripts. These "Text file busy" errors are occasionally encountered in the wild in production settings and more commonly when running Galaxy in Docker containers. Simply sycning the file system has proven insufficient to prevent the problem and I do not want to add an arbitrary sleep. So this new strategy is used. - Inject special functionality into each job script that when executed with a certain environment variable set causes the script to exit with a specific return code. - Have Galaxy rerun this script in that configuration until it can succeed in executing the script. - In between each iteration sleep for a small amount of time and try to cause a file system sync. This entire is ... insane ... so I have added a configuration option to disable it entirely check_job_script_integrity=False. Commit: c53aeaef7737ff897dd2a754b16a9e077273e776 https://github.com/galaxyproject/galaxy/commit/c53aeaef7737ff897dd2a754b16a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Simplify shell expression thanks to suggestion by @nsoranzo. Commit: a5e75e8bbe6e465327c7ef783e7236ea2e467b53 https://github.com/galaxyproject/galaxy/commit/a5e75e8bbe6e465327c7ef783e72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #865 from jmchilton/script_integrity Try harder to verify script integrity before running job scripts. Compare: https://github.com/galaxyproject/galaxy/compare/495e3db97fdc...a5e75e8bbe6e

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[galaxyproject/galaxy] 1fa7c1: Populate env.sh files with X_ROOT_DIR.
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fa7c103865d12d76e7450ed4eb4404498d04d71 https://github.com/galaxyproject/galaxy/commit/1fa7c103865d12d76e7450ed4eb4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Populate env.sh files with X_ROOT_DIR. Where X is tool_dependency.name.upper() Commit: 495e3db97fdc16ed3b8df3f64ab2f6d698d1b421 https://github.com/galaxyproject/galaxy/commit/495e3db97fdc16ed3b8df3f64ab2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #564 from davebx/root_dir_env Populate env.sh files with X_ROOT_DIR. Compare: https://github.com/galaxyproject/galaxy/compare/c98ad3e32ddd...495e3db97fdc

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[galaxyproject/galaxy] abf169: Reduce handle inputs and remove update state from ...
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: abf16905d600a75dbc80c1b011c16bc05ad894f1 https://github.com/galaxyproject/galaxy/commit/abf16905d600a75dbc80c1b011c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M templates/base/base_panels.mako M templates/webapps/galaxy/tool_executed.mako Log Message: ----------- Reduce handle inputs and remove update state from tools Fix lint Strip default makos from tools, handle input returns a dictionary now Commit: 862a1d11939a9e2d2807decf991e5fd61be72ad0 https://github.com/galaxyproject/galaxy/commit/862a1d11939a9e2d2807decf991e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py A templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako Log Message: ----------- Move remaining mako code to root/tool_runner Fix async controller (deprecated?) Fix lint Fix lint Commit: 59885c3afdce3c9f08f6fb94f78df636a974161b https://github.com/galaxyproject/galaxy/commit/59885c3afdce3c9f08f6fb94f78d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Fix error message handling Use common exception handlers Fix error message Fix error message More fixes Commit: ee1136d5bf9d5e8e0a7cf0a58130216c5dc217ee https://github.com/galaxyproject/galaxy/commit/ee1136d5bf9d5e8e0a7cf0a58130… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M test/base/interactor.py M test/unit/tools/test_execution.py Log Message: ----------- Fix test cases Fix lint Fix lint Fix test messages Remove unnecessary variable Remove unused test helper functions Fix lint Fix error message in tests Fix spaces Commit: c98ad3e32ddda29e0ef175eeb7ecebdd25d4e758 https://github.com/galaxyproject/galaxy/commit/c98ad3e32ddda29e0ef175eeb7ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js M templates/base/base_panels.mako A templates/webapps/galaxy/root/tool_runner.mako R templates/webapps/galaxy/tool_executed.mako M test/base/interactor.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #829 from guerler/tool_execution_000 Reduce handle inputs and remove update state from tools Compare: https://github.com/galaxyproject/galaxy/compare/8b2b55c989bb...c98ad3e32ddd

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[galaxyproject/galaxy] f8268f: Tighten up GG sniffing.
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8268f576aebcc4b1bf22eb9b5fe5a1f68871db5 https://github.com/galaxyproject/galaxy/commit/f8268f576aebcc4b1bf22eb9b5fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/1.gg Log Message: ----------- Tighten up GG sniffing. Commit: 06da566d46b3cb74973796637fc12b93ab6f3bc1 https://github.com/galaxyproject/galaxy/commit/06da566d46b3cb74973796637fc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Allow simple gg files with only one data column. Commit: 8b2b55c989bbf6645f3c2220dcbcce4e890c38bc https://github.com/galaxyproject/galaxy/commit/8b2b55c989bbf6645f3c2220dcbc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/1.gg Log Message: ----------- Merge pull request #864 from dannon/gg_fix Tighten up GG sniffing Compare: https://github.com/galaxyproject/galaxy/compare/57a88a167dcc...8b2b55c989bb

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[galaxyproject/galaxy] 996497: Test if parameter value is present to avoid index ...
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99649713c3105adc1137541a0d307c642df4e66a https://github.com/galaxyproject/galaxy/commit/99649713c3105adc1137541a0d30… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Test if parameter value is present to avoid index error. Commit: 77b96a6ca63c4c344c3ba61d7a48948ddc894e4b https://github.com/galaxyproject/galaxy/commit/77b96a6ca63c4c344c3ba61d7a48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Change parameter value to None instead of leaving the parameter out entirely. Commit: 61a2b4ba10a36f987f21fd6775ccafb5829a6383 https://github.com/galaxyproject/galaxy/commit/61a2b4ba10a36f987f21fd6775cc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Revert "Change parameter value to None instead of leaving the parameter out entirely." This reverts commit 77b96a6ca63c4c344c3ba61d7a48948ddc894e4b. Commit: 57a88a167dccb09aa6d1c9d129f0f31e870901c7 https://github.com/galaxyproject/galaxy/commit/57a88a167dccb09aa6d1c9d129f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #863 from mvdbeek/fix_workflow_import Test if parameter present in value to avoid index error. Compare: https://github.com/galaxyproject/galaxy/compare/6dbdaa9bfa79...57a88a167dcc

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[galaxyproject/galaxy] d45d66: Avoid confusing error message and double evaluatio...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d45d6676b00a3ef6c14742066bd68f520dacbffa https://github.com/galaxyproject/galaxy/commit/d45d6676b00a3ef6c14742066bd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Avoid confusing error message and double evaluation of to_dict in parameter handling Commit: 6dbdaa9bfa7918e19874419dcca6d4b793b03fdc https://github.com/galaxyproject/galaxy/commit/6dbdaa9bfa7918e19874419dcca6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #815 from guerler/tool_parameters_000 Avoid confusing error message and double evaluation of to_dict in par… Compare: https://github.com/galaxyproject/galaxy/compare/2b966ca4fae9...6dbdaa9bfa79

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