- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] c56cae: Swap hidden to d-* utilities for bs4 (this one wil...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/bs4_welcome_tweaks Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c56cae93d9901f2bfe79c3d86053edf96eed38b6 https://github.com/galaxyproject/usegalaxy-playbook/commit/c56cae93d9901f2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Swap hidden to d-* utilities for bs4 (this one will not work without bs4)

1 0

[galaxyproject/usegalaxy-playbook] 169ef8: Swap col-xs-N to col-sm-N for bootstrap4 changes. ...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/bs4_welcome_tweaks Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 169ef847fb90bf78a2c067358c1981d1db0a2a96 https://github.com/galaxyproject/usegalaxy-playbook/commit/169ef847fb90bf78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Swap col-xs-N to col-sm-N for bootstrap4 changes. Safe to deploy against bs3 as well.

1 0

[galaxyproject/usegalaxy-playbook] 7590c6: Updated mothur suite to version 1.39.5
by GitHub 04 Apr '18

04 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7590c6f3a09e22dbbc8862e14aaeac1c5852f951 https://github.com/galaxyproject/usegalaxy-playbook/commit/7590c6f3a09e22db… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 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/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated mothur suite to version 1.39.5

1 0

[galaxyproject/galaxy] 506de0: Skip new script tests in dev branch, they are brea...
by GitHub 04 Apr '18

04 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 506de02ec462d217220a531a8e40c0e02dbedcd7 https://github.com/galaxyproject/galaxy/commit/506de02ec462d217220a531a8e40… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: 1da06ba2b34a59ab6ea2dd4f1bd765142b423d63 https://github.com/galaxyproject/galaxy/commit/1da06ba2b34a59ab6ea2dd4f1bd7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5839 from jmchilton/integration_test_fixes Skip new script tests in dev branch, they are breaking integration suite. Compare: https://github.com/galaxyproject/galaxy/compare/fbd5541e4edd...1da06ba2b34a

1 0

[galaxyproject/galaxy] 0043f2: Remove unused template file.
by GitHub 04 Apr '18

04 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0043f2f3a0044e359522f2fe6e485469b008f330 https://github.com/galaxyproject/galaxy/commit/0043f2f3a0044e359522f2fe6e48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: R templates/admin/view_data_tables_registry.mako Log Message: ----------- Remove unused template file. Commit: 4e4dbc88233d5309dfd5cc9b0923cc0e0d178ac7 https://github.com/galaxyproject/galaxy/commit/4e4dbc88233d5309dfd5cc9b0923… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_admin_app.py Log Message: ----------- Expand selenium test coverage. Initial admin app tests including screenshots of display applications, data tables, data types, and job management. Commit: fbd5541e4edd57870da924a2de11c2675b1d7bc4 https://github.com/galaxyproject/galaxy/commit/fbd5541e4edd57870da924a2de11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_admin_app.py Log Message: ----------- Merge pull request #5836 from jmchilton/selenium_admin_init Initial Selenium Test Coverage for Admin App Compare: https://github.com/galaxyproject/galaxy/compare/c9881fdc5ca7...fbd5541e4edd

1 0

[galaxyproject/galaxy] 8fa866: Small improvements to scripts/grt/export.py for te...
by GitHub 03 Apr '18

03 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/hash_util.py M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Small improvements to scripts/grt/export.py for testing. - Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this). - Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell. Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48 https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/communication/communication_server.py M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A test/integration/test_scripts.py Log Message: ----------- Unification of Galaxy configuration parsing for scripts/* Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4 https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/sync_reports_config.py M scripts/transfer.py Log Message: ----------- Mark scripts/* that don't work with YAML configuraiton options as deprecated. Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119 https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh Log Message: ----------- Remove unused and unuseful scripts. Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2 https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh Log Message: ----------- Drop data library whoosh/lucene scripts. We don't set that config option in Galaxy anymore so these are broken anyway. Commit: fea7953410a4145f45afbe1656735febcf390a92 https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe165673… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py Log Message: ----------- Remove two scripts - dataset purging hasn't worked this way for a very long time. Commit: b14928d97203d4d459c289c393589e4f4120e3e4 https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c39358… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Cleanup script integration tests. Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2 https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Cleanup incorrect FIXME - spotted by @nsoranzo. Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40 https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Fix missing ENV information in config parameter args. Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Bring in @nsoranzo's requested changes for config_file_from_args, etc. Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394 https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py M test/integration/test_scripts.py Log Message: ----------- More grt fixes - spotted by @nsoranzo. Commit: a1f0e1772ec5280a0523f2218008933f768e886e https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f2218008… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Redact help for --config-section option for @nsoranzo. Kept the string in the file for in-code documentation but hiding it from users. Commit: 62d4582ef6913a4c681db2a08369a7757523de42 https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py Log Message: ----------- Touch up script unification PR based on @natefoo comments. Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M Makefile M client/README.md Log Message: ----------- Clarify make targets, update client/README Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious. Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Articles are important. Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff076… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Reflow text Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference. Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Better re-use of `tool` attribute Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Simplify get_datatype_by_extension() method Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Erase trello from Contributing. Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M client/README.md Log Message: ----------- Proofreading - thanks @nsoranzo Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d00… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications [18.01] Client related readme/makefile clarifications Commit: 288d13b60681a3729fd38c09b41763b520239317 https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b417… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix metadata setting for CRAM files Should fix https://github.com/galaxyproject/galaxy/issues/5801. Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app() Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Handle an empty datatypes_registry Also transform it to an object attribute for re-use. Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes [18.01] Use app.datatypes_registry in ValidationContext.from_app() Commit: 241fadc98159f206b26938ba5626c1f24b1120c2 https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5805 from mvdbeek/fix_cram_metadata [18.01] Fix metadata setting for CRAM files Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge pull request #5769 from jmchilton/unify_scripts [18.01] Fix scripts/ for YAML/ENV configuration processing Commit: c9881fdc5ca751e70248e199b487e98734c39e07 https://github.com/galaxyproject/galaxy/commit/c9881fdc5ca751e70248e199b487… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/62338abbd61f...c9881fdc5ca7

1 0

[galaxyproject/galaxy] e7ecab: If psycopg2-binary is installed (as might be if sw...
by GitHub 02 Apr '18

02 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7ecab77349ee430d4d95978c7a71c0ae54b1d77 https://github.com/galaxyproject/galaxy/commit/e7ecab77349ee430d4d95978c7a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- If psycopg2-binary is installed (as might be if switching between branches), uninstalling psycopg2 will leave psycopg2-binary installed but in a broken state. If we're removing psycopg2, we need to remove psycopg2-binary at the same time, leaving psycopg2-binary to be correctly installed afterwards. Commit: 62338abbd61f7ca6b854ce0954c8cdebf2442c65 https://github.com/galaxyproject/galaxy/commit/62338abbd61f7ca6b854ce0954c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5825 from dannon/psycopg2-binary-handling-touchup psycopg2-binary handling tweak Compare: https://github.com/galaxyproject/galaxy/compare/30337f40d4bc...62338abbd61f

1 0

[galaxyproject/galaxy] 19c652: Exclude the JS GIE proxy's node modules from linti...
by GitHub 02 Apr '18

02 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19c652cdb4ad6e444fa95be10d815fc5617e4e39 https://github.com/galaxyproject/galaxy/commit/19c652cdb4ad6e444fa95be10d81… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Exclude the JS GIE proxy's node modules from linting. Commit: 30337f40d4bc46089e0d3f79cedca2301d14123f https://github.com/galaxyproject/galaxy/commit/30337f40d4bc46089e0d3f79cedc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #5826 from natefoo/flake8-exclude-proxy Exclude the JS GIE proxy's node modules from linting Compare: https://github.com/galaxyproject/galaxy/compare/a8072a1d8bf2...30337f40d4bc

1 0

[galaxyproject/galaxy] 03287e: Bugfix in upload_common -- ensure hda is added to ...
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03287ed195d65ce305e6414ed3659e43c9ac8444 https://github.com/galaxyproject/galaxy/commit/03287ed195d65ce305e6414ed365… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Bugfix in upload_common -- ensure hda is added to a session prior to state setting. Commit: a8072a1d8bf2bf5e232649df61fc6f954164fca3 https://github.com/galaxyproject/galaxy/commit/a8072a1d8bf2bf5e232649df61fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Merge pull request #5816 from dannon/upload_common_bugfix Bugfix in upload_common -- ensure hda is added to a session Compare: https://github.com/galaxyproject/galaxy/compare/e552bc4cbb59...a8072a1d8bf2

1 0

[galaxyproject/galaxy] 9e71e1: Allow anonymous users to view their jobs via the A...
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e71e1d2f0e7c6586b3f5946edb033466a495258 https://github.com/galaxyproject/galaxy/commit/9e71e1d2f0e7c6586b3f5946edb0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Allow anonymous users to view their jobs via the API. Commit: 083bdcbdd84da29b1e2692058bbebd6426e8b2ae https://github.com/galaxyproject/galaxy/commit/083bdcbdd84da29b1e2692058bbe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Rule-based Collection Builder Vue-based component for defining collections by applying rules to a list of files or more general spreadsheet style information (e.g. sample sheets or tabular data from data sources containing URL or FTP file paths for files along with metadata). The widget is fairly complex but very broadly is broken into two panes - one to preview how rules are applied to build up tabular data defining collections (each row corresponding to a file with columns for metadata and such) and one that displays defined rules and allows for editing of these rules and creation of new ones. The goal behind defining rules this way instead of allowing the user to interact with the spreadsheet display directly is to enable scaling up collection creation. If a user wishes to upload hundreds of datasets - interacting with a widget directly for each input doesn't scale well and would be error prone. If a user wishes to upload hundreds of thousands of datasets - even loading this information in the GUI may not scale (though I've been impressed with the performance so far of this approach) and so we can potentially just display a preview of some of the rows and process the final set of rules on the backend. Since we can handle an arbitrary number of columns this way, we can define multiple list identifiers per file and so we can easily construct nested lists. Hence this allows creation of not just potentially larger collections but arbitrarily complex lists as well. Paired identifiers via indicator columns are also implemented. In order to operate over lists of datasets directly - the multi-select history widget now has a new option "Build Collection from Rules" along side the other collection builders. This mode uses the well established dataset collection API to build collections from HDAs. In order to operate on lists of FTP files or URLs - the upload widget has a new tab "Rule-based" tab that allows users to paste in tabular data or select a history dataset and then send this tabular data to the new builder widget. This will be extended to include FTP directories for instance over time. This mode uses the new data fetch API to build collections and handle uploads of arbitrary collections of files. The preview of the tabular data generated via rules is done via [Handsontable](https://handsontable.com/) - a JavaScript spreadsheet widget with a VueJS [wrapper component](https://github.com/handsontable/vue-handsontable-official). This turns out to be a fairly nice application for reactive components - as rules are added or modified the spreadsheet just naturally updates. In my hands the widget scales very nicely - I've uploaded files with tens of thousands of rows and rules modifying the data and changing the spreadsheet do not seem to cause siignificant delays in the web browser. Commit: ebf08c16493b8fd3e770bf3c33c1f3eea55dd374 https://github.com/galaxyproject/galaxy/commit/ebf08c16493b8fd3e770bf3c33c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Fix production build of vue-handsontable Commit: cfa1208a79dcd0bdda5c7632366c2bd2b6deea0d https://github.com/galaxyproject/galaxy/commit/cfa1208a79dcd0bdda5c7632366c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/yarn.lock Log Message: ----------- Yarn lock w/ new deps. Commit: b32e78f338fcbd586f77c64f0fa18aee6ce23d1b https://github.com/galaxyproject/galaxy/commit/b32e78f338fcbd586f77c64f0fa1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix upload view initialization. Commit: 1c04bbe9f6a95c1c8050bc5a8cd69bd8030cf350 https://github.com/galaxyproject/galaxy/commit/1c04bbe9f6a95c1c8050bc5a8cd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/.babelrc M client/package.json M client/yarn.lock Log Message: ----------- Add babel plugin for vue template preprocessing. This allows precompilation without a vue runtime for nested local components in vue SFCs, and other situations. Commit: e552bc4cbb592eb2fcb4658e287026a742aab286 https://github.com/galaxyproject/galaxy/commit/e552bc4cbb592eb2fcb4658e2870… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/.babelrc A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/api/jobs.py A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5365 from jmchilton/rule_based_uploader Rule-based Uploader / Builder Compare: https://github.com/galaxyproject/galaxy/compare/ac74b7ffb221...e552bc4cbb59

1 0