- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b61ca4: Make history sharing tests more robust and informa...
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b61ca47c99da6661dee64d6612f8aa30daa464f8 https://github.com/galaxyproject/galaxy/commit/b61ca47c99da6661dee64d6612f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Make history sharing tests more robust and informative. - Be sure when sharing a history with a user we wait to actually see that user's e-mail address appear in the history's sharing list after submission. - Print something for the failed history sharing assertions (I'm pretty sure they are 403 errors because some aspect of the sharing or login didn't work - but might as well verify). Commit: a190903bd031ff78f286977cdb7eaca04884de4c https://github.com/galaxyproject/galaxy/commit/a190903bd031ff78f286977cdb7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Merge pull request #4588 from jmchilton/selenium_fixes_25 Make history sharing Selenium tests more robust and informative. Compare: https://github.com/galaxyproject/galaxy/compare/31f2168c3d7f...a190903bd031

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[galaxyproject/galaxy] a1e79b: add the first test
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1e79b13e1471f73a9ef192c0b7762ec6322fa93 https://github.com/galaxyproject/galaxy/commit/a1e79b13e1471f73a9ef192c0b77… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: A test/selenium_tests/test_saved_histories.py Log Message: ----------- add the first test Commit: 29622bba69422389f7bae7dfa2b6f7c9a6542acb https://github.com/galaxyproject/galaxy/commit/29622bba69422389f7bae7dfa2b6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add history rename test Commit: c57b993b456d226da3896633a576013b977eab1b https://github.com/galaxyproject/galaxy/commit/c57b993b456d226da3896633a576… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- quick fix Commit: 7824fdab6b0001570001b60bc76e3a77da402877 https://github.com/galaxyproject/galaxy/commit/7824fdab6b0001570001b60bc76e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add delete/undelete test Commit: bca6dfefb6946aa5497819a5d80c74f3d2a7210f https://github.com/galaxyproject/galaxy/commit/bca6dfefb6946aa5497819a5d80c… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add history switch test Commit: da42c16ae7014723012dccdc17c0d39a32ab5713 https://github.com/galaxyproject/galaxy/commit/da42c16ae7014723012dccdc17c0… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add history view test Commit: ff769da9287ddc7f6ad598799a9773d6a2d77c30 https://github.com/galaxyproject/galaxy/commit/ff769da9287ddc7f6ad598799a97… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add history publish test Commit: 29ed1bec66ddfb5b1a8559a0a6a8f34aeb928c14 https://github.com/galaxyproject/galaxy/commit/29ed1bec66ddfb5b1a8559a0a6a8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add multiple histories delete/undelete test Commit: 5dedd397718166723cdc0bb054565b69e7435d23 https://github.com/galaxyproject/galaxy/commit/5dedd397718166723cdc0bb05456… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add sort by name test Commit: e6ebc9e022dd184109374f7f30dec3505b9a2c6e https://github.com/galaxyproject/galaxy/commit/e6ebc9e022dd184109374f7f30de… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add standard search test Commit: 90f0dfc8bcf04309873e8cd8771840c2c7e9fa8d https://github.com/galaxyproject/galaxy/commit/90f0dfc8bcf04309873e8cd87718… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add advanced search test Commit: 316eb330bb21b4bd54c340b389217de9f91f0097 https://github.com/galaxyproject/galaxy/commit/316eb330bb21b4bd54c340b38921… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add permanently delete history test Commit: ca59aaeda017d605f05f6a22b8c6dc09a6f3be3c https://github.com/galaxyproject/galaxy/commit/ca59aaeda017d605f05f6a22b8c6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- add the tags test Commit: d78e60186b6138efe45c1b4107254e624d7424f2 https://github.com/galaxyproject/galaxy/commit/d78e60186b6138efe45c1b410725… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/utils/uploadbox.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/lmod_modules_mapping.yml.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako A doc/source/dev/finding_and_improving_slow_code.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/xml_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/utils/uploadbox.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/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/utils/uploadbox.js A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/api/test_histories.py M test/api/test_libraries.py M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml A test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_management.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_deps.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge branch 'dev' into saved_histories_tests Commit: 8533c717879f7505b8f293c1ba945f3db63addcb https://github.com/galaxyproject/galaxy/commit/8533c717879f7505b8f293c1ba94… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- use the wait_for_and_click_selector function Commit: e2730ca7143f71758d6cd18f129c566447423302 https://github.com/galaxyproject/galaxy/commit/e2730ca7143f71758d6cd18f129c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Reduce duplication, increase robustness in Selenium history tests. - set_tags() appeared in both published and saved history tests, refactored into navigates_galaxy with function name history_panel_add_tags - is_displayed() appeared in both published and saved history tests, refactored into has_driver as selector_is_displayed - Introduced history_panel_rename to reduce duplication across history panel tests and newer published and saved history tests. - Removed custom history click option helper in saved and published history tests and just used the variant in navigates_galaxy. - use wait_for_and_click a couple more places... Commit: dcbe30515f02c3a9f7332f2f3a043132c6cf1fe5 https://github.com/galaxyproject/galaxy/commit/dcbe30515f02c3a9f7332f2f3a04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- More robust rename for histories. I think the wait_for_and_click_selector method will prevent errors like this one https://jenkins.galaxyproject.org/job/selenium/249/testReport/selenium_test…. Commit: dcc18134e79bcae7fb055162ba9f8d5f74e66b65 https://github.com/galaxyproject/galaxy/commit/dcc18134e79bcae7fb055162ba9f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- generate random history names Commit: 51464551647635e5a1859b3d42ddf281a4f89ad8 https://github.com/galaxyproject/galaxy/commit/51464551647635e5a1859b3d42dd… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- generate random history names for the published history grid tests Commit: 31f2168c3d7f321927a20f21baaddcbfec496389 https://github.com/galaxyproject/galaxy/commit/31f2168c3d7f321927a20f21baad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4587 from anatskiy/saved_histories_tests Add Selenium tests for the Saved Histories Compare: https://github.com/galaxyproject/galaxy/compare/1359965a992f...31f2168c3d7f

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[galaxyproject/galaxy] 1e8327: Improve error reporting in Selenium tests when ``w...
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e832733db6c6d3e7e191886d836f05708a84440 https://github.com/galaxyproject/galaxy/commit/1e832733db6c6d3e7e191886d836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails. Previously just a notification about waiting for ``a.loggedin-only`` failed would show up. This doesn't indicate if the login failed completely or the masthead just failed to update. I suspect the login failed completely, but just in case I've updated the error handling to actually ping the API and check and print a better error message with this information. New messages look like: ``` TimeoutException: Message: Failed waiting for masthead to update for login, but user API response indicates [test0ol61vs8fo] is logged in. This seems to be a bug in Galaxy. API response was [{u'username': u'test0ol61vs8fo', u'quota_percent': None, u'preferences': {}, u'total_disk_usage': 0.0, u'deleted': False, u'id': u'adb5f5c93f827949', u'nice_total_disk_usage': u'0 bytes', u'quota': None, u'email': u'test0ol61vs8fo(a)test.test', u'is_admin': False, u'tags_used': [], u'purged': False}].Timeout waiting on CSS selector [a.loggedin-only-x] to become visible. ``` and ``` TimeoutException: Message: Failed waiting for masthead to update for login, API indicates no user is logged in - there is a problem with this test. API response was [{u'quota_percent': None, u'nice_total_disk_usage': u'0 bytes', u'total_disk_usage': 0}]. Timeout waiting on CSS selector [a.loggedin-only] to become visible. ``` Commit: 1359965a992f3a5f3a33276e6d1e1ea6afca0bd8 https://github.com/galaxyproject/galaxy/commit/1359965a992f3a5f3a33276e6d1e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #4589 from jmchilton/selenium_fixes_26 Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails. Compare: https://github.com/galaxyproject/galaxy/compare/a21f05d9a8aa...1359965a992f

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[galaxyproject/galaxy] 900699: Retry failed clicks more aggressively for Selenium...
by GitHub 10 Sep '17

10 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 900699037da5db8528a51a2f0dd7bc287e346301 https://github.com/galaxyproject/galaxy/commit/900699037da5db8528a51a2f0dd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-09 (Sat, 09 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py Log Message: ----------- Retry failed clicks more aggressively for Selenium tests. Would have prevented from this (https://jenkins.galaxyproject.org/job/selenium/238/testReport/junit/seleniu…) failure in retrospect. Also refactor that common pattern into a helper and use throughout. Add missing @selenium_test decorator on that test also - it would have retried if this had been there and we would have a screenshot. Commit: b9cff7ad91f4e157fc2f65e28d00969a4434c09a https://github.com/galaxyproject/galaxy/commit/b9cff7ad91f4e157fc2f65e28d00… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-09 (Sat, 09 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Fix another issue with sorting by owner for published histories Selenium test. Locally this never happens, but remotely sometimes when sorting by owner the histories are sorted by owner but not in the same order as the test was asserting. I would assume this is likely a postgres vs. sqlite difference - perhaps the former doesn't sort the rows by the order they were created within equal sort classifications (i.e. same owner) but the latter does. I've fixed this - the test should not have been asserting such a strong condition I don't think. Commit: a21f05d9a8aa457c7b73398caf946b5428ee24a9 https://github.com/galaxyproject/galaxy/commit/a21f05d9a8aa457c7b73398caf94… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4586 from jmchilton/selenium_fixes_24 Fix another issue with sorting by owner for published histories Selenium test. Compare: https://github.com/galaxyproject/galaxy/compare/a2ef2cc4b95b...a21f05d9a8aa

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[galaxyproject/galaxy] 2259c7: Retry failed clicks more aggressively for Selenium...
by GitHub 10 Sep '17

10 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2259c7d41380f6a2aa23ea1bc13169d1d7a5fb54 https://github.com/galaxyproject/galaxy/commit/2259c7d41380f6a2aa23ea1bc131… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py Log Message: ----------- Retry failed clicks more aggressively for Selenium tests. Would have prevented from this (https://jenkins.galaxyproject.org/job/selenium/238/testReport/junit/seleniu…) failure in retrospect. Also refactor that common pattern into a helper and use throughout. Add missing @selenium_test decorator on that test also - it would have retried if this had been there and we would have a screenshot. Commit: a2ef2cc4b95b1a5fd6f5be9d6ceb6cd1c8ed0e7d https://github.com/galaxyproject/galaxy/commit/a2ef2cc4b95b1a5fd6f5be9d6ceb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-10 (Sun, 10 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py Log Message: ----------- Merge pull request #4582 from jmchilton/selenium_fixes_23 Retry failed clicks more aggressively for Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/28fd37be40f0...a2ef2cc4b95b

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[galaxyproject/galaxy] 46b799: Make submitting logins for Selenium tests a bit mo...
by GitHub 08 Sep '17

08 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46b799dfbb56a25df10b3e85368db372ce97f8be https://github.com/galaxyproject/galaxy/commit/46b799dfbb56a25df10b3e85368d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_login.py Log Message: ----------- Make submitting logins for Selenium tests a bit more robust. There are a few different transiently failing tests on Jenkins that seem to fail because the test thinks Galaxy is logged in but it is not. So now after we click the login button in Selenium - we will wait for to see the "Register or Login" button turn into the "User" button. This is a similar problem and fix to what was done in #4562 - which seemed to help. Commit: 28fd37be40f09ac7054043eed7ef5fdbc10333ef https://github.com/galaxyproject/galaxy/commit/28fd37be40f09ac7054043eed7ef… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_login.py Log Message: ----------- Merge pull request #4576 from jmchilton/selenium_fixes_21 Make submitting logins for Selenium tests a bit more robust. Compare: https://github.com/galaxyproject/galaxy/compare/508fdb9d2b47...28fd37be40f0

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[galaxyproject/galaxy] f48b1e: initial version of HiCBrowser as Galaxy IE
by GitHub 08 Sep '17

08 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f48b1edad34a1d7a204543d77cc0a946061b035c https://github.com/galaxyproject/galaxy/commit/f48b1edad34a1d7a204543d77cc0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako Log Message: ----------- initial version of HiCBrowser as Galaxy IE Commit: c0dfdfcfba4559e5a75ee6397e4f7802f9f14d34 https://github.com/galaxyproject/galaxy/commit/c0dfdfcfba4559e5a75ee6397e4f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.sample.ini Log Message: ----------- force add config file Commit: cdb3a1d79cd6b7f4115b1d5feb55eab965b4ff42 https://github.com/galaxyproject/galaxy/commit/cdb3a1d79cd6b7f4115b1d5feb55… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml Log Message: ----------- Only show this on compressed-archives. Commit: 63657c71c96129b0262a3f8a5386a0499cb8de83 https://github.com/galaxyproject/galaxy/commit/63657c71c96129b0262a3f8a5386… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample R config/plugins/interactive_environments/hicbrowser/config/hicbrowser.sample.ini Log Message: ----------- rename sample file Commit: d80ecbd7a7efd4e7a6d612a83e43b7a91629f4cd https://github.com/galaxyproject/galaxy/commit/d80ecbd7a7efd4e7a6d612a83e43… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml Log Message: ----------- Merge branch 'hicbrowser' of https://github.com/bgruening/galaxy into hicbrowser Commit: 508fdb9d2b4766668e3d1b962216db7e4e7b3e48 https://github.com/galaxyproject/galaxy/commit/508fdb9d2b4766668e3d1b962216… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako Log Message: ----------- Merge pull request #3330 from bgruening/hicbrowser HiCBrowser as Galaxy IE Compare: https://github.com/galaxyproject/galaxy/compare/f623613a392c...508fdb9d2b47

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[galaxyproject/galaxy] 5e179d: Fix logic error in new published histories sort by...
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e179df2a852aa956ce3bd48d4c365d646c2d035 https://github.com/galaxyproject/galaxy/commit/5e179df2a852aa956ce3bd48d4c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Fix logic error in new published histories sort by owner test. I switched to randomly generated usernames without actually ensure the random usernames would be generated in the same lexiographic order - that wasn't super bright of me. That sort by owner test should pass as frequently as the other tests in that test case class now. Commit: f623613a392ca21b23b5278530f95257e8d2f365 https://github.com/galaxyproject/galaxy/commit/f623613a392ca21b23b5278530f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4577 from jmchilton/selenium_fixes_22 Fix logic error in new published histories sort by owner test. Compare: https://github.com/galaxyproject/galaxy/compare/a8df8729b867...f623613a392c

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[galaxyproject/galaxy] 80c976: add biom2 datatype
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80c9763757a626355a70e360fd9aedffd8f8dac3 https://github.com/galaxyproject/galaxy/commit/80c9763757a626355a70e360fd9a… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add biom2 datatype Commit: 86902068268903292d1caf003a2274e0a5438f7d https://github.com/galaxyproject/galaxy/commit/86902068268903292d1caf003a22… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom Log Message: ----------- add test biom2 file Commit: b9fb935be594db1224c524bfd03c22b8b90f4bea https://github.com/galaxyproject/galaxy/commit/b9fb935be594db1224c524bfd03c… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- add edam format to biom1 datatype Commit: 8314867ecb57b58caceb4843c021f300dc39472e https://github.com/galaxyproject/galaxy/commit/8314867ecb57b58caceb4843c021… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fix sniffer order Commit: 6feb3e22d19c2cb162adc0b5d80655540305a805 https://github.com/galaxyproject/galaxy/commit/6feb3e22d19c2cb162adc0b5d806… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- order matters Commit: 07ef9b4f4b2a38259ae55f382ebee36e43743a9d https://github.com/galaxyproject/galaxy/commit/07ef9b4f4b2a38259ae55f382ebe… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- use h5py to parse hdf5 header Commit: ca1ebf97c02e7261fc36352206834de5ab74a0fd https://github.com/galaxyproject/galaxy/commit/ca1ebf97c02e7261fc3635220683… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- set metadata Commit: ac61072452cd345d45e87d3548e6564858589029 https://github.com/galaxyproject/galaxy/commit/ac61072452cd345d45e87d3548e6… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- add h5py requirement for extracting metadata from biom2/hdf5 datatypes Commit: 92e25158410238bfbc80a931fedb80a55b570e2d https://github.com/galaxyproject/galaxy/commit/92e25158410238bfbc80a931fedb… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix import order Commit: 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1 https://github.com/galaxyproject/galaxy/commit/4119caf9b7fbd1fc9c374403e7f7… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- remove unused variable Commit: 062c88a3cce66df350dc0da7aed14542fe6ad65b https://github.com/galaxyproject/galaxy/commit/062c88a3cce66df350dc0da7aed1… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml Log Message: ----------- add converters Commit: a3b316031c5aa1565d7255eab5aa92ff4a749f4d https://github.com/galaxyproject/galaxy/commit/a3b316031c5aa1565d7255eab5aa… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- simplify Commit: 995f2cee4a2914c157420467829ff647a2e8c7d6 https://github.com/galaxyproject/galaxy/commit/995f2cee4a2914c157420467829f… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- add guess_ext test Commit: 95aacc010e730ce24e2e10557bac8395c538d2af https://github.com/galaxyproject/galaxy/commit/95aacc010e730ce24e2e10557bac… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add metadata to peek Commit: 907e931fa8f62856fa846d2b9a9bc6392f26952a https://github.com/galaxyproject/galaxy/commit/907e931fa8f62856fa846d2b9a9b… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't cast to string Commit: 8f3c65c59efe623c325f54e2407c383688ffeedb https://github.com/galaxyproject/galaxy/commit/8f3c65c59efe623c325f54e2407c… Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- use version 2.7.1 of h5py Commit: d4cf4bff4f249c5e100fde8a31315c92acbe4fc8 https://github.com/galaxyproject/galaxy/commit/d4cf4bff4f249c5e100fde8a3131… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- PEP8 fix Commit: 2615094597ff6bdb0b03e496ea075c2a16f561b9 https://github.com/galaxyproject/galaxy/commit/2615094597ff6bdb0b03e496ea07… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Revert "remove unused variable" This reverts commit 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1. Commit: a8df8729b8670e23c4f77616cd775aed98463ca7 https://github.com/galaxyproject/galaxy/commit/a8df8729b8670e23c4f77616cd77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4519 from shiltemann/biom2_datatype add biom2 datatype Compare: https://github.com/galaxyproject/galaxy/compare/b3f0f36c89a0...a8df8729b867

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[galaxyproject/galaxy] 65b2fe: Fix delete option in history menu.
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 65b2fe8a4aa48ec0fefa36b4f30aeab1627ff33d https://github.com/galaxyproject/galaxy/commit/65b2fe8a4aa48ec0fefa36b4f30a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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/history/options-menu.js Log Message: ----------- Fix delete option in history menu. Commit: 31043698d0a8a20294c9964d93a0e726b0ff91ca https://github.com/galaxyproject/galaxy/commit/31043698d0a8a20294c9964d93a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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/history/options-menu.js Log Message: ----------- Fix purge option in history menu. Now delete&purge use modern models/handling. Commit: b3f0f36c89a09056e6a49e4e5c65779a676fc1c5 https://github.com/galaxyproject/galaxy/commit/b3f0f36c89a09056e6a49e4e5c65… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.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/history/options-menu.js Log Message: ----------- Merge pull request #4574 from dannon/history_options_fixes Fix delete option in history menu Compare: https://github.com/galaxyproject/galaxy/compare/2aeb4590d1c9...b3f0f36c89a0

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[galaxyproject/galaxy] b17fbf: Fix startup of galaxy when wehbooks dir is empty
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: b17fbfb968b8921729798c909220e522abfb29fd https://github.com/galaxyproject/galaxy/commit/b17fbfb968b8921729798c909220… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix startup of galaxy when wehbooks dir is empty Reported by @alpapan on gitter. Commit: c86bf78c6a966b52d3c9e21ffae71bbf134ecdb4 https://github.com/galaxyproject/galaxy/commit/c86bf78c6a966b52d3c9e21ffae7… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Merge pull request #4570 from mvdbeek/webhook_loading_fix [17.05] Bug: Fix startup of galaxy when wehbooks dir is empty Compare: https://github.com/galaxyproject/galaxy/compare/41fe55129a3a...c86bf78c6a96

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[galaxyproject/galaxy] e50e72: Implement IP address whitelisting
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e50e7239b58ef80f62c537096bdf642198aaa9cb https://github.com/galaxyproject/galaxy/commit/e50e7239b58ef80f62c537096bdf… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Implement IP address whitelisting Commit: 569bd6bedf17b1b1f73c964345dd41b3d29cf104 https://github.com/galaxyproject/galaxy/commit/569bd6bedf17b1b1f73c964345dd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Show a more useful error when one is available Commit: d1892fc4446474b14da33b6862002a7d54fd9fd2 https://github.com/galaxyproject/galaxy/commit/d1892fc4446474b14da33b686200… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- the library prefers unicode stuff Commit: 36758478d590664615f7fe8e32ef9f7879eb2284 https://github.com/galaxyproject/galaxy/commit/36758478d590664615f7fe8e32ef… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- non-URL things get passed to this function Commit: b620536dc25af3b68a28aade5682b6b7a92af15d https://github.com/galaxyproject/galaxy/commit/b620536dc25af3b68a28aade5682… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: 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: ----------- rebuild client Commit: cb416390781e546ce77b94f56cca73e48faed070 https://github.com/galaxyproject/galaxy/commit/cb416390781e546ce77b94f56cca… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- flake8 Commit: e8ea1104a7ec1775350d881d3f5eed9fb420b38e https://github.com/galaxyproject/galaxy/commit/e8ea1104a7ec1775350d881d3f5e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- add a test expecting failure Commit: 618d89b972258db5d2dafcb127ed3a6b473402ae https://github.com/galaxyproject/galaxy/commit/618d89b972258db5d2dafcb127ed… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- lint-import-order Commit: 4e2cd5fea628884d1dddd305e28f3ec81b509982 https://github.com/galaxyproject/galaxy/commit/4e2cd5fea628884d1dddd305e28f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js Log Message: ----------- rebuild client Commit: 2aeb4590d1c9c7bb86bb21b42d6fe20ffc8d59f8 https://github.com/galaxyproject/galaxy/commit/2aeb4590d1c9c7bb86bb21b42d6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/utils/uploadbox.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/library/library-foldertoolbar-view.js M static/scripts/utils/uploadbox.js M test/integration/test_upload_configuration_options.py Log Message: ----------- Merge pull request #4289 from erasche/local-network Local network access restrictions Compare: https://github.com/galaxyproject/galaxy/compare/74f7181eafa9...2aeb4590d1c9

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[galaxyproject/galaxy] 826877: Allow paramiko runner to recover from ssh timeout
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82687795413520b5a23e86b17bc3198df3803e39 https://github.com/galaxyproject/galaxy/commit/82687795413520b5a23e86b17bc3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Allow paramiko runner to recover from ssh timeout Commit: 74f7181eafa93eec8fb2bd21ccab5c1373e73c07 https://github.com/galaxyproject/galaxy/commit/74f7181eafa93eec8fb2bd21ccab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Merge pull request #4503 from mvdbeek/paramiko_long_running Allow paramiko cli to recover from ssh timeout Compare: https://github.com/galaxyproject/galaxy/compare/57ff68edd062...74f7181eafa9

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[galaxyproject/galaxy] 144977: Prevent in-place editing if purge_source is false
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14497719ba6d3a9727563d15dbeacf2b537551f3 https://github.com/galaxyproject/galaxy/commit/14497719ba6d3a9727563d15dbea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Prevent in-place editing if purge_source is false When importing files from the FTP folder the admin can choose to prevent purging of imported files. In this case the source file should not be modified in-place by galaxy. This also modifies relevant bare `except:` statements and modifies the meaning of `in_place` in upload.py from no external chown script to do not edit files in place if we keep the source file. This fixes https://github.com/galaxyproject/galaxy/issues/4527. Commit: 62ef8b52aedb9b9b34403db83703083a0cddbaf9 https://github.com/galaxyproject/galaxy/commit/62ef8b52aedb9b9b34403db83703… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix sniffing for non-binary files Commit: 06db29413e838fd88a2ec84ede347f097be161e2 https://github.com/galaxyproject/galaxy/commit/06db29413e838fd88a2ec84ede34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Move instead of copying converted datasets when possible shutil.move tries to move files by renaming them. If that fails with OSError (due to permission or cross-filesystem rename) it falls back to copying files followed by removing them (https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279) By using shutil.move and catching permission problems we avoid an unnecessary copy if source and destination are on the same filesystem. Also avoids shutil.move if the upload tool is run as real-user which should fix https://github.com/galaxyproject/galaxy/issues/4300. Commit: 57ff68edd0627a58c1bdce645d666ad3243df8d2 https://github.com/galaxyproject/galaxy/commit/57ff68edd0627a58c1bdce645d66… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #4539 from mvdbeek/purge_source Prevent in-place editing of uploaded files if files are imported from the FTP folder Compare: https://github.com/galaxyproject/galaxy/compare/696a1eda3ca5...57ff68edd062

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[galaxyproject/usegalaxy-playbook] 319ff4: Switch main to use UCSC builds and chrom lengths i...
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 319ff47516accf3e70f7544ee21ca41d985228c1 https://github.com/galaxyproject/usegalaxy-playbook/commit/319ff47516accf3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/main/templates/galaxy/config/build_sites.yml.j2 Log Message: ----------- Switch main to use UCSC builds and chrom lengths in CVMFS

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[galaxyproject/usegalaxy-playbook] f3257f: Update Test and switch it to use UCSC builds and c...
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f3257f3677ece1445559d1c517876c5455a6776d https://github.com/galaxyproject/usegalaxy-playbook/commit/f3257f3677ece144… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M CHANGELOG.md M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/build_sites.yml.j2 Log Message: ----------- Update Test and switch it to use UCSC builds and chrom lengths in CVMFS.

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[galaxyproject/galaxy] 13ab2f: join with header: add test-data output files
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13ab2fd1a499d64f695e75ce4f6a96449fd8a75c https://github.com/galaxyproject/galaxy/commit/13ab2fd1a499d64f695e75ce4f6a… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed Log Message: ----------- join with header: add test-data output files Commit: 5cf405902bd86fd3f57d8b8ed12a1e06f3c89662 https://github.com/galaxyproject/galaxy/commit/5cf405902bd86fd3f57d8b8ed12a… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out5.tab M tools/filters/joiner.xml Log Message: ----------- join with header: add test Commit: 406c71acab0b0fea03dfa31712c06d066cb2a5c6 https://github.com/galaxyproject/galaxy/commit/406c71acab0b0fea03dfa31712c0… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/join.py M tools/filters/joiner.xml Log Message: ----------- join with header: test passed Commit: 712a7045e5a4b092d7ecb4de0e6f11544d10a956 https://github.com/galaxyproject/galaxy/commit/712a7045e5a4b092d7ecb4de0e6f… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/joiner_out7.tab M tools/filters/joiner.xml Log Message: ----------- join with header: add a regression test Commit: f8bc4076177d56c7b6beed9c975795b6c3a80dd0 https://github.com/galaxyproject/galaxy/commit/f8bc4076177d56c7b6beed9c9757… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/joiner_out6.tab M tools/filters/joiner.xml Log Message: ----------- join with header: add a use case with a fill value Commit: 222a7502e7672be3d433611269735e449daa0101 https://github.com/galaxyproject/galaxy/commit/222a7502e7672be3d43361126973… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/joiner.xml Log Message: ----------- join header: fix tool syntax Commit: 530827f6548e5b4360ac7d6a2e1569395ec8ec68 https://github.com/galaxyproject/galaxy/commit/530827f6548e5b4360ac7d6a2e15… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/join.py Log Message: ----------- join with header: flake import order fix Commit: d887cb17f0e330bed43d80073801568165746454 https://github.com/galaxyproject/galaxy/commit/d887cb17f0e330bed43d80073801… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M tools/filters/join.py M tools/filters/joiner.xml Log Message: ----------- Merge join_header into dev. Commit: 696a1eda3ca5695f9c0631c3f2f357c83b4a8995 https://github.com/galaxyproject/galaxy/commit/696a1eda3ca5695f9c0631c3f2f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M tools/filters/join.py M tools/filters/joiner.xml Log Message: ----------- Merge integration branch of 'header_join' into dev Compare: https://github.com/galaxyproject/galaxy/compare/20b935639670...696a1eda3ca5

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[galaxyproject/galaxy] 30b97f: refactor callback hell to use promises
by GitHub 07 Sep '17

07 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30b97f1f1ea9987f967e9774f65ed2e3d8450a3b https://github.com/galaxyproject/galaxy/commit/30b97f1f1ea9987f967e9774f65e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- refactor callback hell to use promises Commit: cf09a25fdc742998d5bd71deca32527a947c6812 https://github.com/galaxyproject/galaxy/commit/cf09a25fdc742998d5bd71deca32… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix import of collections to datalibs I swear I fixed this before Commit: 20b935639670d171eadb96b3406d00174d978ae6 https://github.com/galaxyproject/galaxy/commit/20b935639670d171eadb96b3406d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4568 from martenson/fix-collection-import Fix datalib collection import Compare: https://github.com/galaxyproject/galaxy/compare/8f7d2374cac0...20b935639670

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[galaxyproject/galaxy] 49eadb: Increase the robustness of Selenium workflow manag...
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49eadb682ac5b2662dbe603cea4f0ba68cf59eec https://github.com/galaxyproject/galaxy/commit/49eadb682ac5b2662dbe603cea4f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Increase the robustness of Selenium workflow management tests. Next Selenium build encountered a few different problems with importing workflows from URL: - https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors… - https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors… - https://jenkins.galaxyproject.org/job/selenium/213/artifact/213-test-errors… On full test retry, only one of these actually caused a test error but we shouldn't have to depend on the test re-running stuff. Commit: 8f7d2374cac0fcf44b2f878490d912e9bb98a8ec https://github.com/galaxyproject/galaxy/commit/8f7d2374cac0fcf44b2f878490d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4564 from jmchilton/selenium_fixes_20 Increase the robustness of Selenium workflow management tests. Compare: https://github.com/galaxyproject/galaxy/compare/e8ee2741f909...8f7d2374cac0

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[galaxyproject/galaxy] 095c10: add logging to ts index building
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 095c1045b6605756934ef9524907d6cb73c4baf9 https://github.com/galaxyproject/galaxy/commit/095c1045b6605756934ef9524907… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- add logging to ts index building Commit: e8ee2741f9093496aa68c2afe435aa9fc7dd8fcc https://github.com/galaxyproject/galaxy/commit/e8ee2741f9093496aa68c2afe435… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #4567 from martenson/index-refresh-logging add logging to ts index building Compare: https://github.com/galaxyproject/galaxy/compare/eb799267ee35...e8ee2741f909

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[galaxyproject/galaxy] 47ba64: 2017-08 Security Patch
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 5a18464d547d7497285ee25067050ee4cd665eda https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9 https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 759780b72c03efd6563c0c53efc9edff9505979c https://github.com/galaxyproject/galaxy/commit/759780b72c03efd6563c0c53efc9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 41fe55129a3af95d7ef84ecb387b954b14509843 https://github.com/galaxyproject/galaxy/commit/41fe55129a3af95d7ef84ecb387b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: lib/galaxy/datatypes/data.py Commit: eb799267ee35da3b5b9dbef8a58ed8107aeb16ae https://github.com/galaxyproject/galaxy/commit/eb799267ee35da3b5b9dbef8a58e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a95566b36c18...eb799267ee35

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[galaxyproject/galaxy] 47ba64: 2017-08 Security Patch
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 5a18464d547d7497285ee25067050ee4cd665eda https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9 https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 759780b72c03efd6563c0c53efc9edff9505979c https://github.com/galaxyproject/galaxy/commit/759780b72c03efd6563c0c53efc9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 41fe55129a3af95d7ef84ecb387b954b14509843 https://github.com/galaxyproject/galaxy/commit/41fe55129a3af95d7ef84ecb387b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: lib/galaxy/datatypes/data.py Compare: https://github.com/galaxyproject/galaxy/compare/1d485390b0af...41fe55129a3a

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[galaxyproject/galaxy] 580811: Potential fix for transiently failing Selenium pub...
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 580811d7405f4566bfb8cb62e3bff5c7cc0e80a7 https://github.com/galaxyproject/galaxy/commit/580811d7405f4566bfb8cb62e3bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Potential fix for transiently failing Selenium published histories test. The the [latest Selenium test execution](https://jenkins.galaxyproject.org/job/selenium/212/testReport/) most of the published histories tests failed. It looks like this is because of the three histories that were supposed to be published, only 2 were actually published. My best guess for what happeend was that the click of the button to publish the history occurred but the next Selenium command happened so quickly that the page had not gotten a chance to respond to the click. This tweaked approach to publishing histories ensures we stay on the page until the "unpublish" link appears - this will either fix the problem or rule this theory out as the explanation. Commit: a95566b36c18667cca73286f463b89fabeb8fbf8 https://github.com/galaxyproject/galaxy/commit/a95566b36c18667cca73286f463b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4562 from jmchilton/selenium_fixes_19 Potential fix for transiently failing Selenium published histories test. Compare: https://github.com/galaxyproject/galaxy/compare/37802abee2b5...a95566b36c18

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[galaxyproject/galaxy] 47ba64: 2017-08 Security Patch
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9 https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 759780b72c03efd6563c0c53efc9edff9505979c https://github.com/galaxyproject/galaxy/commit/759780b72c03efd6563c0c53efc9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/5a18464d547d...759780b72c03

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[galaxyproject/galaxy] 02c779: [16.01] Backport uwsgi fix from #2836.
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9 https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/47ba644de78d...140c570517df

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