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

[galaxyproject/infrastructure-playbook] 8aa890: New TACC JS instances
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8aa890745cf9ed67bc9364b74b7bd0bf3119f99e https://github.com/galaxyproject/infrastructure-playbook/commit/8aa890745cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- New TACC JS instances

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[galaxyproject/galaxy] ebb49d: Make client, somehow this got out of sync.
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Compare: https://github.com/galaxyproject/galaxy/compare/3737fc9487ad...5aefe1b193d8

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[galaxyproject/galaxy] e9df73: Improve error message for data source tools, execu...
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9df73c565ddb1f6a3858ca4fc1e9a422a2c727c https://github.com/galaxyproject/galaxy/commit/e9df73c565ddb1f6a3858ca4fc1e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Improve error message for data source tools, executed through the tool_runner controller Commit: e88e615d6e6b10973aff3ed937649aafbf3f259e https://github.com/galaxyproject/galaxy/commit/e88e615d6e6b10973aff3ed93764… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #2204 from guerler/fix_error_message_000 [16.04] Improve error message for data source tools, executed through the tool_runner controller Commit: be588228869a921bf26b2d390b775b04699aba39 https://github.com/galaxyproject/galaxy/commit/be588228869a921bf26b2d390b77… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/97110e265525...be588228869a

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[galaxyproject/galaxy] e9df73: Improve error message for data source tools, execu...
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e9df73c565ddb1f6a3858ca4fc1e9a422a2c727c https://github.com/galaxyproject/galaxy/commit/e9df73c565ddb1f6a3858ca4fc1e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Improve error message for data source tools, executed through the tool_runner controller Commit: e88e615d6e6b10973aff3ed937649aafbf3f259e https://github.com/galaxyproject/galaxy/commit/e88e615d6e6b10973aff3ed93764… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #2204 from guerler/fix_error_message_000 [16.04] Improve error message for data source tools, executed through the tool_runner controller Compare: https://github.com/galaxyproject/galaxy/compare/8749c82bef47...e88e615d6e6b

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[galaxyproject/galaxy] c49e78: fix biomart url
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c49e7803fa1814abd04afb26b54965fb7af612ac https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b549… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- fix biomart url Commit: 7bed69ba17b4ce633c621ee34a7544115eb95970 https://github.com/galaxyproject/galaxy/commit/7bed69ba17b4ce633c621ee34a75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Specify Ensembl biomart server in descriptions. Commit: 1e7edf0bd7a003e0abc63c4f0a17fdfac535ade3 https://github.com/galaxyproject/galaxy/commit/1e7edf0bd7a003e0abc63c4f0a17… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- no parens Commit: 81cf234576bc1f52f93a11b193f6cc9c26130c28 https://github.com/galaxyproject/galaxy/commit/81cf234576bc1f52f93a11b193f6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Merge pull request #14 from dannon/fix_biomart Specify Ensembl biomart server in descriptions. Commit: cc4911019077c5c6e1b4ec293670020f34aed596 https://github.com/galaxyproject/galaxy/commit/cc4911019077c5c6e1b4ec293670… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Enhance to_json such that it can be safely called multiple times Commit: f5060628d2de4802be610fd6caf5c878afdb4312 https://github.com/galaxyproject/galaxy/commit/f5060628d2de4802be610fd6caf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Fix pages encoding. Using str on previously unicodify'd extended set values does not work. ``` In [2]: str("Blah blah blah, this breaks the page: ಠ_ಠ") Out[2]: 'Blah blah blah, this breaks the page: \xe0\xb2\xa0_\xe0\xb2\xa0' In [3]: str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) --------------------------------------------------------------------------- UnicodeEncodeError Traceback (most recent call last) <ipython-input-3-4a83f5e5f5c8> in <module>() ----> 1 str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) UnicodeEncodeError: 'ascii' codec can't encode character u'\u0ca0' in position 38: ordinal not in range(128) ``` Commit: 659a900693b72886fd27731a2568ce71657c4401 https://github.com/galaxyproject/galaxy/commit/659a900693b72886fd27731a2568… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Simplify expression, trust upstream pieces. Commit: e13738868519d8c7c6f7dec8cfd598f7929b8828 https://github.com/galaxyproject/galaxy/commit/e13738868519d8c7c6f7dec8cfd5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Apply parameter translation for data source tools Commit: 7c7d6edbfd94e5b3e187778b89ac1febb5690cb9 https://github.com/galaxyproject/galaxy/commit/7c7d6edbfd94e5b3e187778b89ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/validation.py Log Message: ----------- Swap validate_and_sanitize_basestring to use unicodify Commit: a9280649b201dc8c1ce6e1601c5baaae211acbd7 https://github.com/galaxyproject/galaxy/commit/a9280649b201dc8c1ce6e1601c5b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Sync job_script module with Pulsar to fix doctest. Following test fails without this change and is fixed by it. ``` nosetests --with-doctest lib/galaxy/jobs/runners/util/job_script ``` I'm not sure why Travis doesn't pick this up - I should figure that out. Commit: 0cde386a2cfec1c18f68f1dfd939843328f8046f https://github.com/galaxyproject/galaxy/commit/0cde386a2cfec1c18f68f1dfd939… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/util/validation.py Log Message: ----------- Remove more unnecessary unicode/text_type, since sanitize_html will always return unicode. Commit: eac0fb9b26c6c52ab695d58cef13c73d3d2566b4 https://github.com/galaxyproject/galaxy/commit/eac0fb9b26c6c52ab695d58cef13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #2201 from guerler/fix_parameters_000 [16.04] Translate data source tool parameters on parameter expansion Commit: 4ea53d99aaa20b15e1d09f7140dff14336360686 https://github.com/galaxyproject/galaxy/commit/4ea53d99aaa20b15e1d09f7140df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2196 from guerler/extend_to_json_000 [16.04] Extend to_json for dataset tool parameters Commit: e5290e1964fcfc49fb5f57a232e4bcc35c28a52a https://github.com/galaxyproject/galaxy/commit/e5290e1964fcfc49fb5f57a232e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Merge pull request #2149 from martenson/fix-biomart [16.04] fix/replace biomart data source Commit: adbc66873a13dc3c6cbcbf86181f935d09fed490 https://github.com/galaxyproject/galaxy/commit/adbc66873a13dc3c6cbcbf86181f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Merge pull request #2203 from jmchilton/doctest_fix [16.04] Sync job_script module with Pulsar to fix doctest. Commit: 8749c82bef4789d810313a3fd853202a1748c63a https://github.com/galaxyproject/galaxy/commit/8749c82bef4789d810313a3fd853… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py Log Message: ----------- Merge pull request #2197 from dannon/pages_parser_fix [16.04] Pages parser fix Commit: 97110e2655255bf752bb00ca7df046f9c9e016cb https://github.com/galaxyproject/galaxy/commit/97110e2655255bf752bb00ca7df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M tools/data_source/biomart.xml Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c79d057ca459...97110e265525

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[galaxyproject/galaxy] f50606: Fix pages encoding. Using str on previously unico...
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: f5060628d2de4802be610fd6caf5c878afdb4312 https://github.com/galaxyproject/galaxy/commit/f5060628d2de4802be610fd6caf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Fix pages encoding. Using str on previously unicodify'd extended set values does not work. ``` In [2]: str("Blah blah blah, this breaks the page: ಠ_ಠ") Out[2]: 'Blah blah blah, this breaks the page: \xe0\xb2\xa0_\xe0\xb2\xa0' In [3]: str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) --------------------------------------------------------------------------- UnicodeEncodeError Traceback (most recent call last) <ipython-input-3-4a83f5e5f5c8> in <module>() ----> 1 str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) UnicodeEncodeError: 'ascii' codec can't encode character u'\u0ca0' in position 38: ordinal not in range(128) ``` Commit: 659a900693b72886fd27731a2568ce71657c4401 https://github.com/galaxyproject/galaxy/commit/659a900693b72886fd27731a2568… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Simplify expression, trust upstream pieces. Commit: 7c7d6edbfd94e5b3e187778b89ac1febb5690cb9 https://github.com/galaxyproject/galaxy/commit/7c7d6edbfd94e5b3e187778b89ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/validation.py Log Message: ----------- Swap validate_and_sanitize_basestring to use unicodify Commit: 0cde386a2cfec1c18f68f1dfd939843328f8046f https://github.com/galaxyproject/galaxy/commit/0cde386a2cfec1c18f68f1dfd939… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/util/validation.py Log Message: ----------- Remove more unnecessary unicode/text_type, since sanitize_html will always return unicode. Commit: 8749c82bef4789d810313a3fd853202a1748c63a https://github.com/galaxyproject/galaxy/commit/8749c82bef4789d810313a3fd853… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py Log Message: ----------- Merge pull request #2197 from dannon/pages_parser_fix [16.04] Pages parser fix Compare: https://github.com/galaxyproject/galaxy/compare/adbc66873a13...8749c82bef47

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[galaxyproject/galaxy] a92806: Sync job_script module with Pulsar to fix doctest.
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: a9280649b201dc8c1ce6e1601c5baaae211acbd7 https://github.com/galaxyproject/galaxy/commit/a9280649b201dc8c1ce6e1601c5b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Sync job_script module with Pulsar to fix doctest. Following test fails without this change and is fixed by it. ``` nosetests --with-doctest lib/galaxy/jobs/runners/util/job_script ``` I'm not sure why Travis doesn't pick this up - I should figure that out. Commit: adbc66873a13dc3c6cbcbf86181f935d09fed490 https://github.com/galaxyproject/galaxy/commit/adbc66873a13dc3c6cbcbf86181f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Merge pull request #2203 from jmchilton/doctest_fix [16.04] Sync job_script module with Pulsar to fix doctest. Compare: https://github.com/galaxyproject/galaxy/compare/e5290e1964fc...adbc66873a13

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[galaxyproject/galaxy] 1aa8eb: Attempted fix for server error on repo preview.
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aa8eb980aac5503a6cf585241fe974899922557 https://github.com/galaxyproject/galaxy/commit/1aa8eb980aac5503a6cf585241fe… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Attempted fix for server error on repo preview. This should handle cases where the database record specifies a repository dependency, but the repository in question (and its downloadable changeset) has been updated since the dependency was created. Commit: ad929f231076706167cd88274bcf7c074e74fac4 https://github.com/galaxyproject/galaxy/commit/ad929f231076706167cd88274bcf… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml Log Message: ----------- Add test for server error with updated repository. Commit: 8c3f458bca948fc5efda027a4e09b8b5b8289276 https://github.com/galaxyproject/galaxy/commit/8c3f458bca948fc5efda027a4e09… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py Log Message: ----------- Correct docs and names. Commit: f4993b782679096f2576e749b146c76b45397314 https://github.com/galaxyproject/galaxy/commit/f4993b782679096f2576e749b146… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py Log Message: ----------- Fix one more travis error. Commit: 78e2eef2fcb4bcc51f26307ee351a3c5a679c300 https://github.com/galaxyproject/galaxy/commit/78e2eef2fcb4bcc51f26307ee351… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py Log Message: ----------- Fix another travis error that escaped my notice. Commit: d8b0add9c20bf6aee7c96d1c6106178cbf72cb3d https://github.com/galaxyproject/galaxy/commit/d8b0add9c20bf6aee7c96d1c6106… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M .ci/py3_sources.txt M .gitignore M Makefile R buildbot_setup.sh M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/tool_data_table_conf.xml.sample M contrib/galaxy.debian-init A contrib/galaxy_supervisor.conf A display_applications/biom/biom_simple.xml R install_and_test_tool_shed_repositories.sh M lib/galaxy/config.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/issue1818.tabular M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py R lib/tool_shed/scripts/api/add_repository_registry_entry.py R lib/tool_shed/scripts/api/common.py R lib/tool_shed/scripts/api/create_categories.py R lib/tool_shed/scripts/api/create_users.py R lib/tool_shed/scripts/api/export.py R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py R lib/tool_shed/scripts/api/import_capsule.py R lib/tool_shed/scripts/api/remove_repository_registry_entry.py R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_repositories_for_functional_tests.py R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py A scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/sharing_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/visualization/gie.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/view_changeset.mako M test/base/driver_util.py A test/base/integration_util.py M test/casperjs/casperjs_runner.py A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/tools/test_conda_resolution.py A tool-data/biom_simple_display.loc.sample Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_bugfixes Commit: afa353b6fd00eb0ecf1d4bac9d64751537cae12a https://github.com/galaxyproject/galaxy/commit/afa353b6fd00eb0ecf1d4bac9d64… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py Log Message: ----------- Return current changeset if it is latest. Commit: d35d6a707f3b265b10b859714deec793ecf31a53 https://github.com/galaxyproject/galaxy/commit/d35d6a707f3b265b10b859714dee… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Update documentation. Commit: 4c126af1b0137fad228f0254dab45b6bec8fb9da https://github.com/galaxyproject/galaxy/commit/4c126af1b0137fad228f0254dab4… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Ensure legacy behavior remains unaltered. Per to the logic change in shed_util_common.get_next_downloadable_changeset_revision, this commit modifies some conditionals to check whether it previously would have returned None. Commit: e1b167b312385df2a02fb5c7d4c4c464e3733bd7 https://github.com/galaxyproject/galaxy/commit/e1b167b312385df2a02fb5c7d4c4… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py Log Message: ----------- Remove extra else statement. Commit: 50757a13baf060601b681795403ba503a8897ede https://github.com/galaxyproject/galaxy/commit/50757a13baf060601b681795403b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Fix test 0550. Commit: c79d057ca459586f4a01d50158d36530d0cbb163 https://github.com/galaxyproject/galaxy/commit/c79d057ca459586f4a01d50158d3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml Log Message: ----------- Merge pull request #2079 from davebx/api_install_bugfixes Attempted fix for server error on repo preview. Compare: https://github.com/galaxyproject/galaxy/compare/9b5fdbf9a497...c79d057ca459

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[galaxyproject/galaxy] c49e78: fix biomart url
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c49e7803fa1814abd04afb26b54965fb7af612ac https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b549… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- fix biomart url Commit: 7bed69ba17b4ce633c621ee34a7544115eb95970 https://github.com/galaxyproject/galaxy/commit/7bed69ba17b4ce633c621ee34a75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Specify Ensembl biomart server in descriptions. Commit: 1e7edf0bd7a003e0abc63c4f0a17fdfac535ade3 https://github.com/galaxyproject/galaxy/commit/1e7edf0bd7a003e0abc63c4f0a17… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- no parens Commit: 81cf234576bc1f52f93a11b193f6cc9c26130c28 https://github.com/galaxyproject/galaxy/commit/81cf234576bc1f52f93a11b193f6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Merge pull request #14 from dannon/fix_biomart Specify Ensembl biomart server in descriptions. Commit: e5290e1964fcfc49fb5f57a232e4bcc35c28a52a https://github.com/galaxyproject/galaxy/commit/e5290e1964fcfc49fb5f57a232e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Merge pull request #2149 from martenson/fix-biomart [16.04] fix/replace biomart data source Compare: https://github.com/galaxyproject/galaxy/compare/4ea53d99aaa2...e5290e1964fc

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[galaxyproject/galaxy] cc4911: Enhance to_json such that it can be safely called ...
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: cc4911019077c5c6e1b4ec293670020f34aed596 https://github.com/galaxyproject/galaxy/commit/cc4911019077c5c6e1b4ec293670… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Enhance to_json such that it can be safely called multiple times Commit: 4ea53d99aaa20b15e1d09f7140dff14336360686 https://github.com/galaxyproject/galaxy/commit/4ea53d99aaa20b15e1d09f7140df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2196 from guerler/extend_to_json_000 [16.04] Extend to_json for dataset tool parameters Compare: https://github.com/galaxyproject/galaxy/compare/eac0fb9b26c6...4ea53d99aaa2

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