July 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f9ba8d: Allow setting tags on targets & contents in data f...
by GitHub 17 Jul '18

17 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9ba8d3823854e00e321b7776056d381132b0346 https://github.com/galaxyproject/galaxy/commit/f9ba8d3823854e00e321b7776056… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_dataset_collections.py M test/api/test_tools_upload.py Log Message: ----------- Allow setting tags on targets & contents in data fetch API. Rebased with default argument handling improvements suggested by Marius. Commit: 31d331379188e11fe95cdbfe5d8f1035dd511b63 https://github.com/galaxyproject/galaxy/commit/31d331379188e11fe95cdbfe5d8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Minor typo in new text (or -> of), and two bonus old typo fixes. Commit: 4719c4a3f1296d179e5e1dc107156ec5fae305ed https://github.com/galaxyproject/galaxy/commit/4719c4a3f1296d179e5e1dc10715… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_dataset_collections.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6499 from jmchilton/upload_tags_api Allow setting tags on targets & contents in data fetch API. Compare: https://github.com/galaxyproject/galaxy/compare/3c4eb54a9a87...4719c4a3f129 **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] 239c7c: Optimize setting large numbers of HIDs for collect...
by GitHub 17 Jul '18

17 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 239c7c920634c1074505cb9a2ebb1b263b852c2d https://github.com/galaxyproject/galaxy/commit/239c7c920634c1074505cb9a2ebb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Optimize setting large numbers of HIDs for collection outputs. Commit: 3c4eb54a9a877ff213f22315019ae17b33da5c09 https://github.com/galaxyproject/galaxy/commit/3c4eb54a9a877ff213f22315019a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6394 from jmchilton/collection_opt Optimize setting large numbers of HIDs for collection outputs. Compare: https://github.com/galaxyproject/galaxy/compare/2f9520e6a239...3c4eb54a9a87 **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] 43c9c9: Remove deprecated AOL openid backend.
by GitHub 17 Jul '18

17 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43c9c9624a4f5ed7f27c0bdc576dcf6467287633 https://github.com/galaxyproject/galaxy/commit/43c9c9624a4f5ed7f27c0bdc576d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/openid_conf.xml.sample R openid/aol.xml Log Message: ----------- Remove deprecated AOL openid backend. Commit: 2f9520e6a2394b528b3a31a541cc33fb70dee2fa https://github.com/galaxyproject/galaxy/commit/2f9520e6a2394b528b3a31a541cc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M config/openid_conf.xml.sample R openid/aol.xml Log Message: ----------- Merge pull request #6505 from VJalili/remove_deprecated_openid_backends Remove the deprecated AOL openid backend. Compare: https://github.com/galaxyproject/galaxy/compare/188015b13830...2f9520e6a239 **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] 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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