- galaxy-commits - lists.galaxyproject.org

[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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