- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c73c71: Swap for the constant time comparison algorithm
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c73c7130436097cb9c6db0e3ac24b39515ce5560 https://github.com/galaxyproject/galaxy/commit/c73c7130436097cb9c6db0e3ac24… Author: E Rasche <hxr(a)hx42.org> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Swap for the constant time comparison algorithm Commit: dbf6f58251719f721da13e2d605f616956391076 https://github.com/galaxyproject/galaxy/commit/dbf6f58251719f721da13e2d605f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Merge pull request #5719 from erasche/constant-time-sha-compare Swap for the constant time comparison algorithm Compare: https://github.com/galaxyproject/galaxy/compare/8e95830bca1f...dbf6f5825171

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[galaxyproject/galaxy] d5d1e4: Clarfify that nginx-extras needs to be install for...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d5d1e4b80d84ebafccfd1e8cc642dbcd1f020d55 https://github.com/galaxyproject/galaxy/commit/d5d1e4b80d84ebafccfd1e8cc642… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Clarfify that nginx-extras needs to be install for the upload_store directive to work Commit: 127d7b8c3c854db7a28c761aee0c3f2d2e211a6e https://github.com/galaxyproject/galaxy/commit/127d7b8c3c854db7a28c761aee0c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #5717 from mvdbeek/nginx_doc_update [18.01] Clarify that nginx-extras needs to be install for the upload_store d… Compare: https://github.com/galaxyproject/galaxy/compare/c58ca749c26b...127d7b8c3c85

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[galaxyproject/galaxy] 393e1d: Remove subclass="true" from Phylip datatype defini...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 393e1d85cf4f5c32a63ba8b08977e92f79dc8d48 https://github.com/galaxyproject/galaxy/commit/393e1d85cf4f5c32a63ba8b08977… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove subclass="true" from Phylip datatype definition Introduced in commit 3e63b63720c7c5b2fc672f1bfa9b66bb38851f54 . Commit: 8e95830bca1f2290314733d8723b71f871d52f96 https://github.com/galaxyproject/galaxy/commit/8e95830bca1f2290314733d8723b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5718 from nsoranzo/fix_phylip_datatype Remove subclass="true" from Phylip datatype definition Compare: https://github.com/galaxyproject/galaxy/compare/b821b6a68321...8e95830bca1f

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[galaxyproject/usegalaxy-playbook] 837c03: rev domain blacklist to the latest
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 837c03684890c3ddb206b3d433aab91295231493 https://github.com/galaxyproject/usegalaxy-playbook/commit/837c03684890c3dd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M env/common/files/galaxy/config/disposable_email_blacklist.conf Log Message: ----------- rev domain blacklist to the latest as provided by the https://github.com/martenson/disposable-email-domains project

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[galaxyproject/galaxy] 680cfe: Properly order @flakey and @selenium_test decorato...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 680cfec4c9145e27541744da85948b90c5413133 https://github.com/galaxyproject/galaxy/commit/680cfec4c9145e27541744da8594… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Properly order @flakey and @selenium_test decorators Commit: b821b6a683210391035be133a096ecec736c49cd https://github.com/galaxyproject/galaxy/commit/b821b6a683210391035be133a096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #5711 from nsoranzo/flakey_after_selenium_tests Properly order @flakey and @selenium_test decorators Compare: https://github.com/galaxyproject/galaxy/compare/7c8b24394081...b821b6a68321

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[galaxyproject/galaxy] 200160: Make problematic test test_library_to_collections ...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2001606d33cdbb8bf261f301399e688b6a116aa6 https://github.com/galaxyproject/galaxy/commit/2001606d33cdbb8bf261f301399e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Make problematic test test_library_to_collections more robust potentially. Now that #5701 has been merged we have some more clues on the problem with this test. It is dying on the second upload being changed here. I suspect what is happening is that we are waiting on a history to become okay but we make that check before the first upload has even finished - so there is some chance the history is okay because it is empty - so we are reopening the home page in the middle of the first upload and this is causing something odd to happen - something is popping up an empty alert. I'm not sure what is causing that alert but it isn't what we are testing with this test so it is best to really just wait on the uploads - as we do in other tests (see test_uploads.py for instance). history_panel_wait_for_hid_ok is a stronger assertion and is generally more robust and has better error reporting anyway so this should be a stability win all around. Commit: 7c8b243940810b075d57f5a6625acdabcc38a5fa https://github.com/galaxyproject/galaxy/commit/7c8b243940810b075d57f5a6625a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5710 from jmchilton/selenium_fixes_39 Make problematic test test_library_to_collections more robust. Compare: https://github.com/galaxyproject/galaxy/compare/6716848a3632...7c8b24394081

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[galaxyproject/galaxy] be0206: Set the role type to SYSTEM for auto generated rol...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: be02063c3fbec79a7e146ef87dbc6e99c80e7754 https://github.com/galaxyproject/galaxy/commit/be02063c3fbec79a7e146ef87dbc… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Set the role type to SYSTEM for auto generated roles, which is similar to the default behavior Commit: c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999 https://github.com/galaxyproject/galaxy/commit/c58ca749c26bbb3c4ca8750f2c37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #5709 from scholtalbers/fix/default_ldap_role_type [18.01] Fix/default role type on auto created roles Compare: https://github.com/galaxyproject/galaxy/compare/ebb7be8d0ec3...c58ca749c26b

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[galaxyproject/infrastructure-playbook] 8f2240: Enable GCC2019 redirect on Hub
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8f224099bde598ead8fd29402b25ed3ec7089f11 https://github.com/galaxyproject/infrastructure-playbook/commit/8f224099bde… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: A env/galaxy/group_vars/sslservers M env/galaxy/templates/nginx/galaxyproject.j2 Log Message: ----------- Enable GCC2019 redirect on Hub

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[galaxyproject/galaxy] d85a53: Don't retry skipped tests.
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d85a53cf13afb39f62e87f1fb2deaed03c4f47e0 https://github.com/galaxyproject/galaxy/commit/d85a53cf13afb39f62e87f1fb2de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Don't retry skipped tests. Wasting time on these when running Selenium tests on Jenkins. Commit: b5a8260765005ef87f39ed717ff65daf7e73ff18 https://github.com/galaxyproject/galaxy/commit/b5a8260765005ef87f39ed717ff6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Print a statement when retrying Selenium test functions. Pointed out by @nsoranzo (https://github.com/galaxyproject/galaxy/pull/5708#discussion_r175054796) that there isn't mmuch of an indication this is occurring otherwise. Commit: 6716848a363238e1dc481ee2025caada11560a9c https://github.com/galaxyproject/galaxy/commit/6716848a363238e1dc481ee2025c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5708 from jmchilton/selenium_fixes_38 Don't retry skipped tests. Compare: https://github.com/galaxyproject/galaxy/compare/2bbd08ce14d0...6716848a3632

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[galaxyproject/galaxy] 506f04: Potential fix for occasional waiting on popups to ...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 506f0438aa3e2768afd68e6dd117cd85719385bd https://github.com/galaxyproject/galaxy/commit/506f0438aa3e2768afd68e6dd117… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Potential fix for occasional waiting on popups to clear. Created this wait type but never actually used it - now I do and I'm extending it from the initial 10 because of (https://jenkins.galaxyproject.org/job/docker-selenium/1691/artifact/1691-te…) Commit: 2bbd08ce14d09c8c4f409350739649cee41980b6 https://github.com/galaxyproject/galaxy/commit/2bbd08ce14d09c8c4f4093507396… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #5707 from jmchilton/selenium_fixes_37 Potential fix for occasional waiting on popups to clear. Compare: https://github.com/galaxyproject/galaxy/compare/d783ec5daf46...2bbd08ce14d0

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[galaxyproject/galaxy] f93044: Make collection builder tests more robust against ...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f93044d5836dee02e6984caa54b6e7b5b4a04fcb https://github.com/galaxyproject/galaxy/commit/f93044d5836dee02e6984caa54b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Make collection builder tests more robust against potential history panel glitches. Commit: d783ec5daf4637747d9d435be6cfa69f9062dd0f https://github.com/galaxyproject/galaxy/commit/d783ec5daf4637747d9d435be6cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #5705 from jmchilton/more_robust_collection_builder_test Make collection builder tests more robust against potential history panel glitches. Compare: https://github.com/galaxyproject/galaxy/compare/63f3b0c0041e...d783ec5daf46

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[galaxyproject/usegalaxy-playbook] 5a7643: Added new slide to slide rotation.
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5a7643266b41a39c8d94a60eb13786bce321ee47 https://github.com/galaxyproject/usegalaxy-playbook/commit/5a7643266b41a39c… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: A env/common/files/galaxy/static/welcome_img/gccbosc2018_ext.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Added new slide to slide rotation.

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[galaxyproject/galaxy] aadf82: Fix for merging of HDA & DCE models into one model...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aadf828d15a599b4b8e550ea912ad65c149ba561 https://github.com/galaxyproject/galaxy/commit/aadf828d15a599b4b8e550ea912a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix for merging of HDA & DCE models into one model in the client. I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way. Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure. Commit: 63f3b0c0041e99ded69215062714f7293bb77302 https://github.com/galaxyproject/galaxy/commit/63f3b0c0041e99ded69215062714… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Merge pull request #5703 from jmchilton/unwind_client_model_merge_issues_maybe_but_who_knows_how_are_the_tests Fix for merging of HDA & DCE models into one model in the client. Compare: https://github.com/galaxyproject/galaxy/compare/1df477b9218a...63f3b0c0041e

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[galaxyproject/usegalaxy-playbook] bf9461: Reenable GenomeSpace tools
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bf9461f8026ab5f758a85f5f9f75f36e55589e84 https://github.com/galaxyproject/usegalaxy-playbook/commit/bf9461f8026ab5f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Reenable GenomeSpace tools Commit: b040873ac80688dd749c77e99b9f7ec8c24898bc https://github.com/galaxyproject/usegalaxy-playbook/commit/b040873ac80688dd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2f2df6a844b0...…

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[galaxyproject/galaxy] dd20f6: Don't let Selenium driver failures during debuggin...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd20f640beedeeec10d091f4d5c6279b5b40132b https://github.com/galaxyproject/galaxy/commit/dd20f640beedeeec10d091f4d5c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Don't let Selenium driver failures during debugging mask underlying errors. https://jenkins.galaxyproject.org/job/docker-selenium/1665/testReport/selen… Commit: 1df477b9218a94ad25ab5219c0bc3a972aba2ef9 https://github.com/galaxyproject/galaxy/commit/1df477b9218a94ad25ab5219c0bc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5701 from jmchilton/screenshot_exception Don't let failure to save Selenium screenshot for debugging mask underlying errors. Compare: https://github.com/galaxyproject/galaxy/compare/8366d2b5fa32...1df477b9218a

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[galaxyproject/galaxy] 0ec022: Do not show composite datatypes for regular datase...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ec0226e0c893bf9ea785350c749a284b07dae3d https://github.com/galaxyproject/galaxy/commit/0ec0226e0c893bf9ea785350c749… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Do not show composite datatypes for regular dataset upload in the dropdown shown on each row. Mirroring what is done already in `client/galaxy/scripts/mvc/upload/default/default-view.js` Commit: 8366d2b5fa32c5697306139426d85df86dac0782 https://github.com/galaxyproject/galaxy/commit/8366d2b5fa32c5697306139426d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #5700 from nsoranzo/dont_show_composite_datatypes Do not show composite datatypes for regular dataset upload Compare: https://github.com/galaxyproject/galaxy/compare/16751cd6ab9d...8366d2b5fa32

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[galaxyproject/galaxy] 39d7e2: Close file handles
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 39d7e2e7397441fde631b25e4c1e7ec8e1ccc3a6 https://github.com/galaxyproject/galaxy/commit/39d7e2e7397441fde631b25e4c1e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Close file handles Commit: 67330b2751f58e5c8f0a6ef8d1262c8207c9ea63 https://github.com/galaxyproject/galaxy/commit/67330b2751f58e5c8f0a6ef8d126… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Fix upload param to specify datatype Also use higher level `tools_post()` method of the dataset populator instead of `_post()`. Commit: b6944c5ad6c542054649e4bdb3df2c35a884fab3 https://github.com/galaxyproject/galaxy/commit/b6944c5ad6c542054649e4bdb3df… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Remove leftover log statements Commit: 6c3c076ef1d773c156ff6a4b318a4b183ae6ede7 https://github.com/galaxyproject/galaxy/commit/6c3c076ef1d773c156ff6a4b318a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Sort files and subdirectories when fetching an FTP directory Commit: 0944aee34910b3ecbb65168a45a8e06ca98b4fcc https://github.com/galaxyproject/galaxy/commit/0944aee34910b3ecbb65168a45a8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M test/base/populators.py Log Message: ----------- Add velvet to the datatypes allowed for upload It was already allowed in `test/functional/tools/sample_datatypes_conf.xml` This will stop the skipping of tests requiring the `velvet` datatype, like `ToolsUploadTestCase.test_composite_datatype` in `test/api/test_tools_upload.py` . Commit: 5ae52b7f0616a43a08c5849d118adf152932e42b https://github.com/galaxyproject/galaxy/commit/5ae52b7f0616a43a08c5849d118a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Try to fix occasionally failing integration test See https://jenkins.galaxyproject.org/job/docker-integration/4293/testReport/ju… It seems `get_history_collection_details()` was called before the collection was completely populated. Also small fixes for a typo and class documentation found while researching the origin of the bug. Commit: 16751cd6ab9ddbc8f28b9bddab55b901c4c6576e https://github.com/galaxyproject/galaxy/commit/16751cd6ab9ddbc8f28b9bddab55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Merge pull request #5691 from nsoranzo/test_fixes Various test fixes Compare: https://github.com/galaxyproject/galaxy/compare/0f3259c4b1f9...16751cd6ab9d

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[galaxyproject/galaxy] 059b04: Improve error logging for API-based testing.
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 059b0437f725732f97900366c3af48e6c19ed816 https://github.com/galaxyproject/galaxy/commit/059b0437f725732f97900366c3af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/base/populators.py Log Message: ----------- Improve error logging for API-based testing. ``` ====================================================================== FAIL: test_recover_mapping_in_subworkflow (api.test_workflows.WorkflowsApiTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/api/test_workflows.py", line 1467, in test_recover_mapping_in_subworkflow """, history_id=history_id, wait=True) File "/Users/john/workspace/galaxy/test/api/test_workflows.py", line 251, in _run_jobs self.workflow_populator.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=assert_ok) File "/Users/john/workspace/galaxy/test/base/populators.py", line 445, in wait_for_workflow self.wait_for_invocation(workflow_id, invocation_id, timeout=timeout) File "/Users/john/workspace/galaxy/test/base/populators.py", line 440, in wait_for_invocation return wait_on_state(lambda: self._get(url), desc="workflow invocation state", timeout=timeout) File "/Users/john/workspace/galaxy/test/base/populators.py", line 810, in wait_on_state raise TimeoutAssertionError("%s Current response containing state [%s]." % (e.message, response.json())) TimeoutAssertionError: Timed out after 60.25 seconds waiting on workflow invocation state. Current response containing state [{u'inputs': {u'0': {u'src': u'hda', u'id': u'adb5f5c93f827949', u'uuid': u'de3d999f-d993-447f-a7c4-0389a358034f'}}, u'update_time': u'2018-03-14T15:58:08.615444', u'uuid': u'7b0fc935-27a0-11e8-b255-784f435ea615', u'outputs': {}, u'history_id': u'adb5f5c93f827949', u'workflow_id': u'529fd61ab1c6cc36', u'output_collections': {}, u'state': u'ready', u'steps': [{u'workflow_step_label': u'outer_input', u'update_time': u'2018-03-14T15:58:05.629190', u'job_id': None, u'state': u'scheduled', u'workflow_step_uuid': u'afafbeb3-c3d8-49c8-ae21-5add12558c90', u'order_index': 0, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'cb6e11b662890a90', u'id': u'adb5f5c93f827949'}, {u'workflow_step_label': u'first_cat', u'update_time': u'2018-03-14T15:58:06.015192', u'job_id': u'529fd61ab1c6cc36', u'state': u'scheduled', u'workflow_step_uuid': u'6a 5b3ac3-bacf-4e97-bcca-57ea8d8161dd', u'order_index': 1, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'cb227cec8ca83994', u'id': u'529fd61ab1c6cc36'}, {u'workflow_step_label': u'nested_workflow', u'update_time': u'2018-03-14T15:58:06.770332', u'job_id': None, u'state': u'scheduled', u'workflow_step_uuid': u'55640d5d-5e8d-490f-9d68-736f66b1b65a', u'order_index': 2, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'f3f73e481f432006', u'id': u'd9abeb98649a6a7e'}, {u'workflow_step_label': u'second_cat', u'update_time': u'2018-03-14T15:58:06.770643', u'job_id': None, u'state': u'new', u'workflow_step_uuid': u'67beb950-271c-46f4-aca0-42dbe59c6d57', u'order_index': 3, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'2234cb1fd1df4331', u'id': u'cb6e11b662890a90'}], u'model_class': u'WorkflowInvocation', u'id': u'adb5f5c93f827949'}]. -------------------- >> begin captured stdout << --------------------- Executing git --work-tree test-data-cache/ad1daf4e1504da1acd42c088c6f49be6 --git-dir test-data-cache/ad1daf4e1504da1acd42c088c6f49be6/.git fetch && git --work-tree test-data-cache/ad1daf4e1504da1acd42c088c6f49be6 --git-dir test-data-cache/ad1daf4e1504da1acd42c088c6f49be6/.git merge origin/master Problem in history with id adb5f5c93f827949 - summary of history's datasets and jobs below. -------------------------------------- | 1 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 65 lines | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -</td></tr><tr><td>chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +</td></tr><tr><td>chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -</td></tr><tr><td>chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +</td></tr><tr><td>chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - Concatenate datasets on data 1 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 65 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -</td></tr><tr><td>chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +</td></tr><tr><td>chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -</td></tr><tr><td>chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +</td></tr><tr><td>chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 3 - Select random lines on data 2 (HID - NAME) | Dataset State: | running | Dataset Blurb: | queued | Dataset Info: | None | Peek: | None | Dataset Job Standard Output: | None | Dataset Job Standard Error: | None | -------------------------------------- | 4 - lines (HID - NAME) | Dataset Collection: {u'hid': 4, u'history_content_type': u'dataset_collection', u'populated_state_message': None, u'name': u'lines', u'populated': False, u'deleted': False, u'job_source_type': u'Job', u'history_id': u'adb5f5c93f827949', u'tags': [], u'element_count': None, u'job_source_id': u'f3f73e481f432006', u'visible': True, u'elements': [], u'collection_type': u'list', u'url': u'/api/histories/adb5f5c93f827949/contents/dataset_collections/adb5f5c93f827949', u'model_class': u'HistoryDatasetCollectionAssociation', u'type': u'collection', u'id': u'adb5f5c93f827949', u'populated_state': u'new'} | -------------------------------------- | Job d9abeb98649a6a7e | State: | running | Update Time: | 2018-03-14T15:58:09.483449 | Create Time: | 2018-03-14T15:58:06.139665 | -------------------------------------- | Job 529fd61ab1c6cc36 | State: | ok | Update Time: | 2018-03-14T15:58:08.633359 | Create Time: | 2018-03-14T15:58:05.706745 | -------------------------------------- | Job f3f73e481f432006 | State: | new | Update Time: | 2018-03-14T15:58:06.559809 | Create Time: | 2018-03-14T15:58:06.559799 | -------------------------------------- | Job adb5f5c93f827949 | State: | ok | Update Time: | 2018-03-14T15:58:04.602106 | Create Time: | 2018-03-14T15:58:00.368911 | -------------------------------------- ``` Commit: 0f3259c4b1f91b20965214d144b6705c802146ee https://github.com/galaxyproject/galaxy/commit/0f3259c4b1f91b20965214d144b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/base/populators.py Log Message: ----------- Merge pull request #5697 from jmchilton/api_test_logging Improve error logging for API-based testing. Compare: https://github.com/galaxyproject/galaxy/compare/2ace504daea6...0f3259c4b1f9

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[galaxyproject/galaxy] 070889: Better logging for a broad swath of workflow API t...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07088907d3c2ba58986e1025dc1fea6fc6ed0911 https://github.com/galaxyproject/galaxy/commit/07088907d3c2ba58986e1025dc1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Better logging for a broad swath of workflow API tests. I did a few of these test conversions with 0ff639a29c6179e530c977b358cebf229c76139d but this covers many more the workflow API tests. The idea is to switch to this with statement and context manager that does a better job managing test histories including summarizing the history when problems occur (this summary will include job information after #5697). Commit: 2ace504daea607cc482d29d1bbdfefe53504d748 https://github.com/galaxyproject/galaxy/commit/2ace504daea607cc482d29d1bbdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #5699 from jmchilton/workflow_api_logging Better logging for a large number of workflow API tests. Compare: https://github.com/galaxyproject/galaxy/compare/1d9d39867c38...2ace504daea6

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[galaxyproject/galaxy] e806a3: Fix for running Yarn in Docker for tests that do n...
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e806a3d0e55cee2e72c59a87dba511583d2934a0 https://github.com/galaxyproject/galaxy/commit/e806a3d0e55cee2e72c59a87dba5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix for running Yarn in Docker for tests that do not need it. Commit: 1d9d39867c3842f9218a52eb15c9636342eeb4f1 https://github.com/galaxyproject/galaxy/commit/1d9d39867c3842f9218a52eb15c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5690 from jmchilton/skip_client_build_docker Fix for running Yarn in Docker for tests that do not need it. Compare: https://github.com/galaxyproject/galaxy/compare/c6993caabff5...1d9d39867c38

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[galaxyproject/usegalaxy-playbook] 2f2df6: Switch swarmscale to use new image
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2f2df6a844b0185c88482e2eb770b8acbce89959 https://github.com/galaxyproject/usegalaxy-playbook/commit/2f2df6a844b0185c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Switch swarmscale to use new image

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[galaxyproject/infrastructure-playbook] 9146d1: New Jetstream docker image
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9146d1938f4bfa8b4d894295f3a68e7f709792de https://github.com/galaxyproject/infrastructure-playbook/commit/9146d1938f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: A env/jsdocker/.snapshot_base.yml.swp M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/group_vars/baseinstances.yml M env/jsdocker/group_vars/imageinstances.yml Log Message: ----------- New Jetstream docker image

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[galaxyproject/galaxy] c83c38: Add basic structure to support chunked file upload...
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c83c38c723d76e4dd0f87b2c2fca08e88c515d87 https://github.com/galaxyproject/galaxy/commit/c83c38c723d76e4dd0f87b2c2fca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add basic structure to support chunked file uploads Commit: 2eb4fa5e4e06455a7fa6b079211b342b85aec808 https://github.com/galaxyproject/galaxy/commit/2eb4fa5e4e06455a7fa6b079211b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix debug statements Commit: 6de335391b9422b45b8bfc59f7d5860e6508623a https://github.com/galaxyproject/galaxy/commit/6de335391b9422b45b8bfc59f7d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Remove debugging script, submit actual data Commit: 96d3e8076d67adcfb18969ae5939e5b760f8ad6e https://github.com/galaxyproject/galaxy/commit/96d3e8076d67adcfb18969ae5939… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Modify progress handler to accomodate chunks Commit: 313f165c4a42303dbdcf795f62dfc705ffbcd4fe https://github.com/galaxyproject/galaxy/commit/313f165c4a42303dbdcf795f62df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use let instead of var for for-loops Commit: afe0b6a90e8a358dafc0f0700149cfaa3f3296d8 https://github.com/galaxyproject/galaxy/commit/afe0b6a90e8a358dafc0f0700149… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use regular debug statements instead of logger Commit: d9c9482685c040a03ba954ddd89818bd1e1ca0d7 https://github.com/galaxyproject/galaxy/commit/d9c9482685c040a03ba954ddd898… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reuse submission helper Commit: 309dfbf355c207b3b626076b5f9194e277bd8ec3 https://github.com/galaxyproject/galaxy/commit/309dfbf355c207b3b626076b5f91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Remove redundant log Commit: 8805d09c07b5eb8128283f7c205106592a9a29d2 https://github.com/galaxyproject/galaxy/commit/8805d09c07b5eb8128283f7c2051… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add file data name parameter Commit: ca2382576227d078cd5e95b1f9778f121fed9e5a https://github.com/galaxyproject/galaxy/commit/ca2382576227d078cd5e95b1f977… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix for collection handler Commit: ca2c300d943f9df45744ba3b02da23d245e0cfb4 https://github.com/galaxyproject/galaxy/commit/ca2c300d943f9df45744ba3b02da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reduce chunk size for testing, remove debug output Commit: 09bd90845677c9b36881bbaf6f84be63049bf00a https://github.com/galaxyproject/galaxy/commit/09bd90845677c9b36881bbaf6f84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix chunk sizes Commit: 5e26c0322a5338d0096abab1559f54227d75b6b0 https://github.com/galaxyproject/galaxy/commit/5e26c0322a5338d0096abab1559f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix comment Commit: 975bd2f36714622b2b34e06422c9bb93ecd33e45 https://github.com/galaxyproject/galaxy/commit/975bd2f36714622b2b34e06422c9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Submit file segments in request body, use header parameters Commit: c5337fe04a89cc6a3716469f13b0c7a5777ad5bc https://github.com/galaxyproject/galaxy/commit/c5337fe04a89cc6a3716469f13b0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Parse file and chunk data to post helper Commit: 488ce62aa3c870c4dd524ad7d07efc9f27acbafe https://github.com/galaxyproject/galaxy/commit/488ce62aa3c870c4dd524ad7d07e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use template literal, fix session id parsing Commit: 0f69eafc9d7ca185a505a7c75e5ffce14cb48e49 https://github.com/galaxyproject/galaxy/commit/0f69eafc9d7ca185a505a7c75e5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Rename header parameter Commit: b56bec033d111be265102deef262127cb574906e https://github.com/galaxyproject/galaxy/commit/b56bec033d111be265102deef262… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix template string Commit: 2b18782598848f109b58efa9b5364b9afccaee7e https://github.com/galaxyproject/galaxy/commit/2b18782598848f109b58efa9b536… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Parse nginx upload directory to client Commit: 39512626d2f35083d554d99d86030bf79f826844 https://github.com/galaxyproject/galaxy/commit/39512626d2f35083d554d99d8603… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reuse existing request helper for whole file submission Commit: 937fe619e61023b4fe786e4a7c2bfcbb52da7cfa https://github.com/galaxyproject/galaxy/commit/937fe619e61023b4fe786e4a7c2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix success response parsing Commit: bd9ce253383c8833a387e3895d032ad10fd0729d https://github.com/galaxyproject/galaxy/commit/bd9ce253383c8833a387e3895d03… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix comments Commit: ceedcb550fb23b045db0b1e32938df32e8d79be7 https://github.com/galaxyproject/galaxy/commit/ceedcb550fb23b045db0b1e32938… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Consolidate helpers Commit: dee0cef80f6e5e2a480a8a41a2ed6b2bcb7ca92f https://github.com/galaxyproject/galaxy/commit/dee0cef80f6e5e2a480a8a41a2ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js A client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/ui.less M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample R config/plugins/visualizations/charts/config/charts.xml R 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lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/qname_sorted.bam 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/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/multi_output_recurse.xml M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into chunk_uploads Commit: ecc6ac5dbf58c351e71a10835641c988ec1d0d48 https://github.com/galaxyproject/galaxy/commit/ecc6ac5dbf58c351e71a10835641… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/managers/configuration.py Log Message: ----------- Default to 100 in configuration manager Commit: d6a3964c5b41f0a9a268a1c5182fa23798526a55 https://github.com/galaxyproject/galaxy/commit/d6a3964c5b41f0a9a268a1c5182f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Add additional checks, use join Commit: 3f56aeb3cf1e2d5f6eba961f1a6925b35e836cb4 https://github.com/galaxyproject/galaxy/commit/3f56aeb3cf1e2d5f6eba961f1a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Re-use regex to validate session id Commit: 51a135bbaaee7a65619a802e5506ecd1fd27df8b https://github.com/galaxyproject/galaxy/commit/51a135bbaaee7a65619a802e5506… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Read chunks of chunks when writing target file Commit: 529e98ef04e67a5068b55efd54d946aca126527f https://github.com/galaxyproject/galaxy/commit/529e98ef04e67a5068b55efd54d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Rely on automated file closing, add new line Commit: a4287f1212050c7ff068ad161ce2d17cd65bd7cb https://github.com/galaxyproject/galaxy/commit/a4287f1212050c7ff068ad161ce2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/config.py M test/base/driver_util.py Log Message: ----------- Test chunked uploads Commit: a137420c42206fdf9482615ff292ba3d1546f22f https://github.com/galaxyproject/galaxy/commit/a137420c42206fdf9482615ff292… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use ceil instead of floor Commit: 2dba72fb2f850c9fb7ab940be7ae7bef5626acd9 https://github.com/galaxyproject/galaxy/commit/2dba72fb2f850c9fb7ab940be7ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Align chunk size check Commit: 22dd4a8a64820711abe91b6e1f75d2da52144b8a https://github.com/galaxyproject/galaxy/commit/22dd4a8a64820711abe91b6e1f75… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Fix lint Commit: 7589bbbb4dd556e41988ff6a6327e004b53e5ef9 https://github.com/galaxyproject/galaxy/commit/7589bbbb4dd556e41988ff6a6327… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/uploads.py M test/base/driver_util.py Log Message: ----------- Specify chunk size in bytes instead of megabytes Commit: 71c88092c0a4fcd3ccb02e652c024591e004e7f8 https://github.com/galaxyproject/galaxy/commit/71c88092c0a4fcd3ccb02e652c02… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Remove unused import Commit: 8d1e0fccc2f116674250a1b977168beef2cbd238 https://github.com/galaxyproject/galaxy/commit/8d1e0fccc2f116674250a1b97716… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add chunk size config option to schema Commit: 941017b04a3092556d525130e40c8e242860d828 https://github.com/galaxyproject/galaxy/commit/941017b04a3092556d525130e40c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Moderate chunk size for upload tests Commit: 759511479f86b95575ca8b5f3bcf06d6acecf56f https://github.com/galaxyproject/galaxy/commit/759511479f86b95575ca8b5f3bcf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix typo Commit: fcd00166e279cdd216deee8921449070192b19b9 https://github.com/galaxyproject/galaxy/commit/fcd00166e279cdd216deee892144… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Client format Commit: c6993caabff5aa0dcdbb2150a2f18fb9566aae84 https://github.com/galaxyproject/galaxy/commit/c6993caabff5aa0dcdbb2150a2f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/decorators.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/root.py M test/base/driver_util.py Log Message: ----------- Merge branch 'chunk_uploads' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5f73d7fbbd2c...c6993caabff5

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[galaxyproject/galaxy] 8833d1: add security announcement to the rn
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 8833d1a8a49d7b6d4a9c849b0335d3260564b351 https://github.com/galaxyproject/galaxy/commit/8833d1a8a49d7b6d4a9c849b0335… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn

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[galaxyproject/galaxy] 73e61f: add security announcement to the rn
by GitHub 13 Mar '18

13 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: ebb7be8d0ec3944eb945f5cc6e57087328e69d5e https://github.com/galaxyproject/galaxy/commit/ebb7be8d0ec3944eb945f5cc6e57… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5688 from martenson/security-rn [18.01] backport add security announcement to the release notes Compare: https://github.com/galaxyproject/galaxy/compare/0182d8d0bec3...ebb7be8d0ec3

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