Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 4f9d5df34fb84e2547a280ab7536491a66e1da28
https://github.com/galaxyproject/galaxy/commit/4f9d5df34fb84e2547a280ab7536…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-22 (Fri, 22 Sep 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
Log Message:
-----------
WIP a bunch of GIE javascript that probabaly won't work
Commit: 04b03b28530455ff850f41215c2cfa15b597ef19
https://github.com/galaxyproject/galaxy/commit/04b03b28530455ff850f41215c2c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-22 (Fri, 22 Sep 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
Log Message:
-----------
Make the URL spinner actually work.
Commit: 7edeedd7fe123ad8740f830e4c7b5e8478552137
https://github.com/galaxyproject/galaxy/commit/7edeedd7fe123ad8740f830e4c7b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
Log Message:
-----------
Additional GIE spinning fixes for when the error condition is not a
timeout.
Commit: 180bfe718485bdfd05233402d4720f67f114d88f
https://github.com/galaxyproject/galaxy/commit/180bfe718485bdfd05233402d472…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
Log Message:
-----------
Treat timeouts and errors the same, except that timeouts step the
ajax timeout of the next request. Also fixes for toastr messages.
Commit: 40900d76a96bb76542653e2c2bf886c7d88e9552
https://github.com/galaxyproject/galaxy/commit/40900d76a96bb76542653e2c2bf8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-27 (Wed, 27 Sep 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
Re-enable keepalive, build client.
Commit: c235382ceefb09e28c987621164f9f40450f1ed1
https://github.com/galaxyproject/galaxy/commit/c235382ceefb09e28c987621164f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-27 (Wed, 27 Sep 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
Log Message:
-----------
No need for this keep_alive invocation after all; removes the commented out code.
Commit: 242755ee9f6a267e416a525bbf69ef513c35a2f4
https://github.com/galaxyproject/galaxy/commit/242755ee9f6a267e416a525bbf69…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-27 (Wed, 27 Sep 2017)
Changed paths:
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
Merge pull request #7 from dannon/gie_fixes
Re-enable keepalive, build client.
Commit: 8230d14fad3765585517e02a6b74126835f46fce
https://github.com/galaxyproject/galaxy/commit/8230d14fad3765585517e02a6b74…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-27 (Wed, 27 Sep 2017)
Changed paths:
M client/galaxy/scripts/galaxy.interactive_environments.js
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
Log Message:
-----------
Merge pull request #4680 from natefoo/gie-client
[17.09] Client side fixes for GIEs
Compare: https://github.com/galaxyproject/galaxy/compare/1c5c046a63d6...8230d14fad37
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a373bbbfe506b81fbfd260002124be4d02b8a853
https://github.com/galaxyproject/galaxy/commit/a373bbbfe506b81fbfd260002124…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Add client-side routes to connect visualization edit controller endpoint with front-end form builder
Commit: 3e4b0a247123107a2ffe2e0e1fb8ecd6c19e9ee9
https://github.com/galaxyproject/galaxy/commit/3e4b0a247123107a2ffe2e0e1fb8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Add client input element definition for visualization editing form
Commit: ed11e87f9b567307ad12820f55c51d0b23880241
https://github.com/galaxyproject/galaxy/commit/ed11e87f9b567307ad12820f55c5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Add help text to annotation field, remove redundant visualization label from inputs
Commit: 279ccd11cd830dbcd298ebc9ec45d4d872d9ab9c
https://github.com/galaxyproject/galaxy/commit/279ccd11cd830dbcd298ebc9ec45…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Add support to save changed attributes
Commit: 1547d1b91e930b438162364db4ae8b7ed6e23a69
https://github.com/galaxyproject/galaxy/commit/1547d1b91e930b438162364db4ae…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-shared.js
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M static/maps/mvc/grid/grid-shared.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-shared.js
Log Message:
-----------
Add message handling support
Commit: 78aa69d456c3bd47531651bc36760e7de98b53e8
https://github.com/galaxyproject/galaxy/commit/78aa69d456c3bd47531651bc3676…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Add error handler
Commit: 6dec4f79e6492cd9d33f76edd67522c6341fb572
https://github.com/galaxyproject/galaxy/commit/6dec4f79e6492cd9d33f76edd675…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Add text sanitization, remove comments
Commit: 1578f92e074298fd9304b79ce1dca298578f8b8b
https://github.com/galaxyproject/galaxy/commit/1578f92e074298fd9304b79ce1dc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Flush visualization with new attributes to database
Commit: 43bd4e6abd0a61d69ee91f5fe26b6d36b0d716bb
https://github.com/galaxyproject/galaxy/commit/43bd4e6abd0a61d69ee91f5fe26b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
R templates/webapps/galaxy/visualization/create.mako
Log Message:
-----------
Remove visualization edit mako
Commit: 88f135d0d3b283ba81f911bac410ff9ba7f149d8
https://github.com/galaxyproject/galaxy/commit/88f135d0d3b283ba81f911bac410…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Add support to change dbkey for visualizations after creation
Commit: 4ee1473bab78dbb02b3c4fb7c96fdb4a40c95089
https://github.com/galaxyproject/galaxy/commit/4ee1473bab78dbb02b3c4fb7c96f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Remove trackster specific create form, visualizations are created through the visualization icon in the history
Commit: 9ceb4ac2ec42296ea6af126f747fe6cd8abf5d06
https://github.com/galaxyproject/galaxy/commit/9ceb4ac2ec42296ea6af126f747f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-23 (Sat, 23 Sep 2017)
Changed paths:
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Revise help text, make visualization dbkey optional since many do not require it
Commit: daa973a5d9e47cb9cc92dd8b83823fe8be7f7f52
https://github.com/galaxyproject/galaxy/commit/daa973a5d9e47cb9cc92dd8b8382…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-24 (Sun, 24 Sep 2017)
Changed paths:
M lib/galaxy/visualization/genomes.py
Log Message:
-----------
Improve resilience of backend if genome build is missing
Fix
Commit: b482ac162b8e04a88afdca9bf56ca6a8a05ee2f0
https://github.com/galaxyproject/galaxy/commit/b482ac162b8e04a88afdca9bf56c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M CITATION
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/external_services/actions.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/citations.py
M lib/galaxy/model/metadata.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/properties.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webhooks/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M scripts/api/data_manager_example_execute.py
M scripts/api/display.py
M scripts/api/search.py
R scripts/binary_compatibility.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M scripts/data_libraries/build_lucene_index.py
M scripts/dump_tour.py
M scripts/edam_mapping.py
M scripts/fetch_eggs.py
M scripts/grt/export.py
M scripts/grt/upload.py
M scripts/manage_tool_dependencies.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/paster.py
M scripts/rst2html.py
M scripts/summarize_timings.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tools/maf/check_loc_file.py
M scripts/transfer.py
M templates/display_base.mako
M templates/display_common.mako
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/populators.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
M test/functional/twilltestcase.py
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_anon_history.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_custom_builds.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_options.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
A test/unit/__init__.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_HistoryManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Merge branch 'dev' into replace_visualization_edit_form
Commit: df14b8dd02edb01b122704b89c459a928e698039
https://github.com/galaxyproject/galaxy/commit/df14b8dd02edb01b122704b89c45…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M static/maps/mvc/grid/grid-shared.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/grid/grid-shared.js
R templates/webapps/galaxy/visualization/create.mako
Log Message:
-----------
Merge pull request #4682 from guerler/replace_visualization_edit_form
Remove visualization edit form mako
Compare: https://github.com/galaxyproject/galaxy/compare/0dd7f01008d2...df14b8dd02ed
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 67e9dbc37aa41a873546098cad81fe4a2557281e
https://github.com/galaxyproject/galaxy/commit/67e9dbc37aa41a873546098cad81…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Fix invalid requests imports introduced in #4604.
Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests.
Commit: 1a635b3480403cad19c398dd4fe3a4f5562c60db
https://github.com/galaxyproject/galaxy/commit/1a635b3480403cad19c398dd4fe3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #4699 from jmchilton/fix_import
Fix invalid requests imports introduced in #4604.
Compare: https://github.com/galaxyproject/galaxy/compare/08ef78285af9...1a635b348040
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8c984c9b3e4d1c7fb323448e55a936ec5112c8c1
https://github.com/galaxyproject/galaxy/commit/8c984c9b3e4d1c7fb323448e55a9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
R scripts/binary_compatibility.py
Log Message:
-----------
Remove unused binary_compatibility.py script
Follow-up on commit 39d78c7226d8f0417577bdea94b15ac2c77c45a2 from
PR https://github.com/galaxyproject/galaxy/pull/2383
Commit: 9b1832abb11b79a244e0505b4afc059ba894d944
https://github.com/galaxyproject/galaxy/commit/9b1832abb11b79a244e0505b4afc…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M cron/build_chrom_db.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/visualization/plugins/plugin.py
M scripts/api/data_manager_example_execute.py
M scripts/api/display.py
M scripts/api/search.py
M scripts/dump_tour.py
M scripts/edam_mapping.py
M scripts/fetch_eggs.py
M scripts/grt/export.py
M scripts/grt/upload.py
M scripts/manage_tool_dependencies.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/paster.py
M scripts/rst2html.py
M scripts/summarize_timings.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tools/maf/check_loc_file.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflows.py
M test/base/populators.py
M test/functional/twilltestcase.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_anon_history.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_options.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
M test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
A test/unit/__init__.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_HistoryManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
Log Message:
-----------
Fix import order for cron/, scripts/ and test/
Commit: 08ef78285af9d9ca045ba9945e5517aa2809b77c
https://github.com/galaxyproject/galaxy/commit/08ef78285af9d9ca045ba9945e55…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-26 (Tue, 26 Sep 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M cron/build_chrom_db.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/visualization/plugins/plugin.py
M scripts/api/data_manager_example_execute.py
M scripts/api/display.py
M scripts/api/search.py
R scripts/binary_compatibility.py
M scripts/dump_tour.py
M scripts/edam_mapping.py
M scripts/fetch_eggs.py
M scripts/grt/export.py
M scripts/grt/upload.py
M scripts/manage_tool_dependencies.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/paster.py
M scripts/rst2html.py
M scripts/summarize_timings.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tools/maf/check_loc_file.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflows.py
M test/base/populators.py
M test/functional/twilltestcase.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_anon_history.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_options.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
M test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
A test/unit/__init__.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_HistoryManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
Log Message:
-----------
Merge pull request #4697 from nsoranzo/flake8-import-order
Fix import order for cron/, scripts/ and test/
Compare: https://github.com/galaxyproject/galaxy/compare/0c6dfd7a41a8...08ef78285af9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 32b85ecb591d01acbbbb9ed1bedd1a48804a0837
https://github.com/galaxyproject/galaxy/commit/32b85ecb591d01acbbbb9ed1bedd…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/containers/__init__.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/properties.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webhooks/__init__.py
M scripts/grt/export.py
M scripts/grt/upload.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/navigates_galaxy.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Only permit yaml.safe_loading of data
Event trusted data, belt + suspenders method.
Commit: df41d4f4087f9b133750a2c350ea207753f30f54
https://github.com/galaxyproject/galaxy/commit/df41d4f4087f9b133750a2c350ea…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/transfer_manager.py
Log Message:
-----------
Remove some shell=True and fix commands
Commit: cd6a1afaa9980d958ad324fa987a07e7608bf841
https://github.com/galaxyproject/galaxy/commit/cd6a1afaa9980d958ad324fa987a…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Replace some os.system calls with subprocess
Commit: 73337725bdd654904563dc54b04083a23e4a252d
https://github.com/galaxyproject/galaxy/commit/73337725bdd654904563dc54b040…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/objectstore/s3.py
Log Message:
-----------
Two more commands to list
Commit: c85db3fd68590d3d2f61b0b3f88026773d9563a0
https://github.com/galaxyproject/galaxy/commit/c85db3fd68590d3d2f61b0b3f880…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
Log Message:
-----------
Some more command refactoring
Commit: 670897ec5ca2284c7fad453c3d595defe3cca280
https://github.com/galaxyproject/galaxy/commit/670897ec5ca2284c7fad453c3d59…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/webapps/reports/controllers/system.py
Log Message:
-----------
One more os command
Commit: 9b8e76f9d9df0ae0ba6238d44a8f07b97fe34d6f
https://github.com/galaxyproject/galaxy/commit/9b8e76f9d9df0ae0ba6238d44a8f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/managers/citations.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/capsule/capsule_manager.py
M scripts/data_libraries/build_lucene_index.py
M scripts/edam_mapping.py
M scripts/microbes/harvest_bacteria.py
M scripts/tool_shed/api/export.py
M scripts/transfer.py
Log Message:
-----------
Convert urllib to requests
Which has built-in protection against urls like "file:///tmp/a"
Commit: db0400298651f6d4c9d909406c3fe632d057bbf7
https://github.com/galaxyproject/galaxy/commit/db0400298651f6d4c9d909406c3f…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M cron/parse_builds.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
Log Message:
-----------
remove unused imports
Commit: a68d6be3a1c6e6fd85c5ae94232467f193156d53
https://github.com/galaxyproject/galaxy/commit/a68d6be3a1c6e6fd85c5ae942324…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M test/functional/webhooks/phdcomics/helper/__init__.py
Log Message:
-----------
reorder imports
Commit: 93ffc4055b145811b86191dae8b865ea45b55fcb
https://github.com/galaxyproject/galaxy/commit/93ffc4055b145811b86191dae8b8…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/tools/deps/container_resolvers/mulled.py
Log Message:
-----------
replace check_output with python processing and shell=False
Commit: d79a2459a95dfda7856b9898d40d062f00456006
https://github.com/galaxyproject/galaxy/commit/d79a2459a95dfda7856b9898d40d…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/webapps/config_manage.py
Log Message:
-----------
These we will revert to their original yaml.load
It would be nice to fix them eventually, but we'll settle for an
incremental improvement.
Commit: b3261309843f8cfec1a5a589b4628e44e6bf76df
https://github.com/galaxyproject/galaxy/commit/b3261309843f8cfec1a5a589b462…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
import ordering
Commit: 8f4491bfffce5d13e2199df5d60e06e3672a08c1
https://github.com/galaxyproject/galaxy/commit/8f4491bfffce5d13e2199df5d60e…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Consume stderr
Commit: 0f7dd52988269dc4567bdbbd71be0fd273741efd
https://github.com/galaxyproject/galaxy/commit/0f7dd52988269dc4567bdbbd71be…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
Log Message:
-----------
Copy changes over
Commit: 75df58ae86ff1796f0bb0ea975fc1d0d518c155a
https://github.com/galaxyproject/galaxy/commit/75df58ae86ff1796f0bb0ea975fc…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M cron/parse_builds_3_sites.py
Log Message:
-----------
fix
Commit: fd92ac3eedd145635a74530ba62bb7fea7c540f4
https://github.com/galaxyproject/galaxy/commit/fd92ac3eedd145635a74530ba62b…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
revert this change
Commit: 27beb7030d99a511a428ad59211a3137a2761559
https://github.com/galaxyproject/galaxy/commit/27beb7030d99a511a428ad59211a…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
Log Message:
-----------
revert/sync
Commit: 1a57c06d6a81dc6f92eb4843c89a7333f874bc32
https://github.com/galaxyproject/galaxy/commit/1a57c06d6a81dc6f92eb4843c89a…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Fix import ordering
Thanks @nsoranzo, I appreciate all the comments here.
Commit: 290971ca7a28eb579dc2d40c9653b9e160253634
https://github.com/galaxyproject/galaxy/commit/290971ca7a28eb579dc2d40c9653…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M cron/build_chrom_db.py
M cron/parse_builds.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/transfer_manager.py
M scripts/data_libraries/build_lucene_index.py
M scripts/edam_mapping.py
M scripts/microbes/harvest_bacteria.py
M scripts/tool_shed/api/export.py
Log Message:
-----------
more review comments
Commit: 15c73233c52b29ed94066c06ebb1e10c935ae28d
https://github.com/galaxyproject/galaxy/commit/15c73233c52b29ed94066c06ebb1…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M scripts/edam_mapping.py
Log Message:
-----------
fix lint
Commit: 19d03edc7ff8384a5360d71365076a2594fb0b8b
https://github.com/galaxyproject/galaxy/commit/19d03edc7ff8384a5360d7136507…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
Log Message:
-----------
refactor missed call
Commit: 626a3dc2995f0d797232aa666f1bdf3e6a5d22dd
https://github.com/galaxyproject/galaxy/commit/626a3dc2995f0d797232aa666f1b…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
Log Message:
-----------
fix ordering
Commit: 41574d022249bae4df4b89bfb50c3a599ee5585e
https://github.com/galaxyproject/galaxy/commit/41574d022249bae4df4b89bfb50c…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/__init__.py
Log Message:
-----------
swap for subprocess.call per @nsoranzo suggestion
Commit: 0c6dfd7a41a8df8c000b133d8833eb9963ae183e
https://github.com/galaxyproject/galaxy/commit/0c6dfd7a41a8df8c000b133d8833…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-25 (Mon, 25 Sep 2017)
Changed paths:
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/citations.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/properties.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webhooks/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M scripts/data_libraries/build_lucene_index.py
M scripts/edam_mapping.py
M scripts/grt/export.py
M scripts/grt/upload.py
M scripts/microbes/harvest_bacteria.py
M scripts/tool_shed/api/export.py
M scripts/transfer.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/navigates_galaxy.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Merge pull request #4604 from erasche/hardening
Various bits of hardening
Compare: https://github.com/galaxyproject/galaxy/compare/9f2582e9fbed...0c6dfd7a41a8