September 2017 - galaxy-commits - lists.galaxyproject.org

[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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