- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e7bfd6: Set detect_errors to aggressive
by GitHub 17 Jul '18

17 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7bfd6c552ec6d65338bf9319cfcb9bca4e7264a https://github.com/galaxyproject/galaxy/commit/e7bfd6c552ec6d65338bf9319cfc… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-07-14 (Sat, 14 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Set detect_errors to aggressive As per the [documentation](https://docs.galaxyproject.org/en/master/dev/schema.html#too… leaving the tool without `detect_errors` and without a `profile` set to greater than or equal to `16.04` invokes the old behaviour where any output to `stderr` denotes failure. When provided with a BAM format input file and the `-g` option, `bedtools` outputs a warning to `stderr` stating that it will ignore the provided genome, triggering a tool failure. Commit: 188015b138307f08ad75078466587183527e28c5 https://github.com/galaxyproject/galaxy/commit/188015b138307f08ad7507846658… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #6502 from pvanheus/patch-3 Fix bam to bigwig error detection. Compare: https://github.com/galaxyproject/galaxy/compare/347e3124f462...188015b13830 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 66af9c: Make upload tool python3 compatible
by GitHub 17 Jul '18

17 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66af9ce96111685e8fe22c48aa7d0e6471027c64 https://github.com/galaxyproject/galaxy/commit/66af9ce96111685e8fe22c48aa7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/web/framework/base.py M tools/data_source/upload.py Log Message: ----------- Make upload tool python3 compatible Commit: 8ce663addbb9f8cde2bd411ab45f097cffa017e8 https://github.com/galaxyproject/galaxy/commit/8ce663addbb9f8cde2bd411ab45f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Consistently use webob.compat.cgi_FieldStorage This works around bugs in python3 cgi.FieldStorage. Commit: a729faab8ba5e82e33baa837e804afd747532a9d https://github.com/galaxyproject/galaxy/commit/a729faab8ba5e82e33baa837e804… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/web/framework/middleware/batch.py Log Message: ----------- Fix batch api middleware Commit: 28cca49747d29bacbb0751df34475a47cd045cd9 https://github.com/galaxyproject/galaxy/commit/28cca49747d29bacbb0751df3447… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Remove WebOb pin in Pipfile Commit: ca8547ce1d729249f8ff07962e8e96d4f017a556 https://github.com/galaxyproject/galaxy/commit/ca8547ce1d729249f8ff07962e8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Inject `self` and `obj` into global scope The list comprehension code in `transform_lines` gets its own local scope, so just copying the local scope into the eval functions local scope doesn't work. Commit: c5fa023c26fafa53ea9da477243b13b3e6b85278 https://github.com/galaxyproject/galaxy/commit/c5fa023c26fafa53ea9da477243b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Use webob.compat's FieldStorage in the remaining codebase Commit: a65cd29c366035fb8b26e2274046e8c96e3cab33 https://github.com/galaxyproject/galaxy/commit/a65cd29c366035fb8b26e2274046… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Patch webob.compat.cgi_FieldStorage instead of overwrite it Commit: c6c34beb812a966c224c30c17e675d6dfd278248 https://github.com/galaxyproject/galaxy/commit/c6c34beb812a966c224c30c17e67… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M tox.ini Log Message: ----------- Add py34-unit to default tox tests Commit: 9d886c866da5a04e51e5ff6887867393a009257d https://github.com/galaxyproject/galaxy/commit/9d886c866da5a04e51e5ff688786… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Use six.moves for urlparse import Commit: 347e3124f4628cde3ad9f6ba169ecf1d2a0a0e4e https://github.com/galaxyproject/galaxy/commit/347e3124f4628cde3ad9f6ba169e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/api/repositories.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge pull request #6467 from mvdbeek/fix_upload_tool_py3 Make upload tool python3 compatible Compare: https://github.com/galaxyproject/galaxy/compare/051bc9507313...347e3124f462 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8a8527: Fix and docs for advanced container options in job...
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a85270629b80b4c4b306a9130293f25dc7a2da6 https://github.com/galaxyproject/galaxy/commit/8a85270629b80b4c4b306a913029… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix and docs for advanced container options in job_conf.xml. These options were added in #2790 but you know how @jmchilton is about documentation. The bug fix is to fix selecting the first valid option if multiple ones are present instead of just the first option which may be invalid given the other configured destination parameters. Commit: 051bc950731365b580d3569be8c0481f8bcecf86 https://github.com/galaxyproject/galaxy/commit/051bc950731365b580d3569be8c0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #6503 from jmchilton/destination_container_target_fixes Fix and docs for advanced container options in job_conf.xml. Compare: https://github.com/galaxyproject/galaxy/compare/9f352f77c0c7...051bc9507313 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 62482d: Use bootstrap vue classes for workflow import form
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62482dd9fda547ba22391cd210518316a0bbbf76 https://github.com/galaxyproject/galaxy/commit/62482dd9fda547ba22391cd21051… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Use bootstrap vue classes for workflow import form Commit: f8210d89ace977ec8857ef7205a778b5af0b680a https://github.com/galaxyproject/galaxy/commit/f8210d89ace977ec8857ef7205a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/WorkflowImport.vue M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow import Selenium tests for #6489. Commit: 86922d65572ee32b1498ccf422f3f52eb2405386 https://github.com/galaxyproject/galaxy/commit/86922d65572ee32b1498ccf422f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Explicitly specify bootstrapvue (works currently either way, due to bundling and the way these are included, but it might not forever -- best to be explicit) Commit: 9f352f77c0c7a747295ab9aa8e96afee9b13304a https://github.com/galaxyproject/galaxy/commit/9f352f77c0c7a747295ab9aa8e96… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/WorkflowImport.vue M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #6489 from guerler/workflow_import Use bootstrap vue classes for workflow import form Compare: https://github.com/galaxyproject/galaxy/compare/d661d99b12ed...9f352f77c0c7 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2097c9: Remove redundant endpoint to edit user info
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2097c9db787bc9803b391c9286a2a3f3561ba293 https://github.com/galaxyproject/galaxy/commit/2097c9db787bc9803b391c9286a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-14 (Sat, 14 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove redundant endpoint to edit user info Commit: d661d99b12ede64280dce8a597e7845abfd6dd10 https://github.com/galaxyproject/galaxy/commit/d661d99b12ede64280dce8a597e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #6501 from guerler/admin_user_info Remove redundant/duplicate endpoint to edit user info Compare: https://github.com/galaxyproject/galaxy/compare/6da93fc07102...d661d99b12ed **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9356ff: Rulebuilder: Special case auto URL schema detectio...
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9356ff88c3e6a786f494f2b2cba059fc24ea3f98 https://github.com/galaxyproject/galaxy/commit/9356ff88c3e6a786f494f2b2cba0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Rulebuilder: Special case auto URL schema detection for SRA inputs. @mblue9 has runs some tests and this prefix seems to serve the files considerably faster. Commit: 6da93fc07102d98a5f996ec9694e1465e2d45c3c https://github.com/galaxyproject/galaxy/commit/6da93fc07102d98a5f996ec9694e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6476 from jmchilton/sra_special_case Rulebuilder: Special case auto URL schema detection for SRA inputs. Compare: https://github.com/galaxyproject/galaxy/compare/a72954dfba7c...6da93fc07102 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 89c622: remove dead link
by GitHub 16 Jul '18

16 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89c62229c5af00ecc05df596129a53473a96db38 https://github.com/galaxyproject/galaxy/commit/89c62229c5af00ecc05df596129a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- remove dead link I did not find the original post Commit: a72954dfba7c69195a6845b4111d4a350e69d54f https://github.com/galaxyproject/galaxy/commit/a72954dfba7c69195a6845b4111d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6496 from martenson/remove-dead-link remove dead link Compare: https://github.com/galaxyproject/galaxy/compare/bc90d0a43591...a72954dfba7c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 59bd1b: Add unittest that catches https://github.com/galax...
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59bd1ba20a16ecf50586abec4b637c133eefb2a7 https://github.com/galaxyproject/galaxy/commit/59bd1ba20a16ecf50586abec4b63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Add unittest that catches https://github.com/galaxyproject/galaxy/issues/6495 Commit: 4610258b9c2fde78fb056bb9183eb67d12ec00a4 https://github.com/galaxyproject/galaxy/commit/4610258b9c2fde78fb056bb9183e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix job resume from history menu Commit: bc90d0a4359194fc79b5102f4e88a0cd9a36b1a8 https://github.com/galaxyproject/galaxy/commit/bc90d0a4359194fc79b5102f4e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #6498 from mvdbeek/fix_resume_from_history_panel Fix resume from history panel Compare: https://github.com/galaxyproject/galaxy/compare/4a8857e4f9da...bc90d0a43591 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4b0ae3: Added fix to ensure that original ftp files that h...
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4b0ae30a83aeb86a821ec15cfa87e6af7e160a03 https://github.com/galaxyproject/galaxy/commit/4b0ae30a83aeb86a821ec15cfa87… Author: takadonet <philipmabon(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 Commit: fd33c5c6d6aa2478654da74c7e80efdcf31e09a7 https://github.com/galaxyproject/galaxy/commit/fd33c5c6d6aa2478654da74c7e80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6497 from martenson/backport-takadonet [18.05] backport ftp purge fix Compare: https://github.com/galaxyproject/galaxy/compare/dfc996c8d6b8...fd33c5c6d6aa **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 77c344: Add webapp mapper for cloud upload API.
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77c34446728f414491dd7a14fc5992800d9ae32a https://github.com/galaxyproject/galaxy/commit/77c34446728f414491dd7a14fc59… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add webapp mapper for cloud upload API. Commit: 92830a1c155450a68bdd5d214d3f432f00056a1c https://github.com/galaxyproject/galaxy/commit/92830a1c155450a68bdd5d214d3f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Implement cloud upload API. Commit: 4e23c5e67dbc57ff03512f65549d6ea097a70deb https://github.com/galaxyproject/galaxy/commit/4e23c5e67dbc57ff03512f65549d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Implement logic of uploading dataset(s) to cloud in the cloud manager. Commit: 62d67c9c401c2c5c1547457fe82229cf97e7e0ff https://github.com/galaxyproject/galaxy/commit/62d67c9c401c2c5c1547457fe822… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Check for missing arguments from payload in cloud upload api. Commit: 63be2dba410c1d1cc17e6e4a1030d100bf5eaf6b https://github.com/galaxyproject/galaxy/commit/63be2dba410c1d1cc17e6e4a1030… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Assert the validity of provided history ID in cloud upload API. Commit: 6a9ce39a2147b0b2449e4eaf73fb6e54399b5976 https://github.com/galaxyproject/galaxy/commit/6a9ce39a2147b0b2449e4eaf73fb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Assert the validity of provided dataset ID(s). Commit: ff42cc7b0684c47191a94e4d1a016dcbc7ef21b1 https://github.com/galaxyproject/galaxy/commit/ff42cc7b0684c47191a94e4d1a01… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- In cloud upload API, handle overwriting an existing object. Commit: f1b9a23c939f20718b430916e5e5fdd4d9b2a330 https://github.com/galaxyproject/galaxy/commit/f1b9a23c939f20718b430916e5e5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Use named arguments in cloud upload API when calling its manager. Commit: 35a30219f652741e20f6810b42c21dbf3e74e0c0 https://github.com/galaxyproject/galaxy/commit/35a30219f652741e20f6810b42c2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in cloud upload API. Commit: 17ab3e8d2dff82996264a3404fda800a707b8487 https://github.com/galaxyproject/galaxy/commit/17ab3e8d2dff82996264a3404fda… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud upload API description. Commit: 0ed19ad7b0402c7be544a358386b80377d63d85c https://github.com/galaxyproject/galaxy/commit/0ed19ad7b0402c7be544a358386b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud upload API description. Commit: 3b74bd899c323f99135362a23f64726cd09ee331 https://github.com/galaxyproject/galaxy/commit/3b74bd899c323f99135362a23f64… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix bugs related to import order and boolean assert in cloud upload API. Commit: c7c7691c98b2ef2cdeee5bf7661b9415e6eebf86 https://github.com/galaxyproject/galaxy/commit/c7c7691c98b2ef2cdeee5bf7661b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/Sharing.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/communication-server-view.js A client/galaxy/scripts/layout/data.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M 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test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into upload_to_cloud Commit: 5b1b4314a3ac140779146286f4dc2cfd5fad6807 https://github.com/galaxyproject/galaxy/commit/5b1b4314a3ac140779146286f4dc… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor the API end point from `upload` to `copy_to`. Commit: 97fd2088faa0eda1275448d7552a47c801ab9a4b https://github.com/galaxyproject/galaxy/commit/97fd2088faa0eda1275448d7552a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add cloud storage `copy_to` API. Commit: 7e8be2ff53e9f6f781618c2182d9b3d58675c47e https://github.com/galaxyproject/galaxy/commit/7e8be2ff53e9f6f781618c2182d9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add cloud-based storage `copy-to` manager. Commit: b3f1a7cf9cdc29bcc52a6d7f5c35fc6ecfa02878 https://github.com/galaxyproject/galaxy/commit/b3f1a7cf9cdc29bcc52a6d7f5c35… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Doc style updates; copy-to return dict with copied datasets Commit: 4a8857e4f9daf15101270724375dad14c4897e6c https://github.com/galaxyproject/galaxy/commit/4a8857e4f9daf15101270724375d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6078 from VJalili/upload_to_cloud Upload data to a cloud-based storage Compare: https://github.com/galaxyproject/galaxy/compare/2abb01b6cbb1...4a8857e4f9da **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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