- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a9d3a8: Notify user if newer tool versions are available
by GitHub 25 Jul '18

25 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9d3a82f1bf8bbb9c8fb12bf4edec90105b59dba https://github.com/galaxyproject/galaxy/commit/a9d3a82f1bf8bbb9c8fb12bf4ede… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Notify user if newer tool versions are available Commit: 84159d37cc44146716cc0f59df0a149aa5b0539e https://github.com/galaxyproject/galaxy/commit/84159d37cc44146716cc0f59df0a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6533 from guerler/new_tool_version Notify if newer tool version is available Compare: https://github.com/galaxyproject/galaxy/compare/d5a057fe37b5...84159d37cc44 **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] 61fdb0: Return a json blob containing redirect URI in OIDC...
by GitHub 24 Jul '18

24 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61fdb0ba831bc5dd9ed17b238730264e560bfbcd https://github.com/galaxyproject/galaxy/commit/61fdb0ba831bc5dd9ed17b238730… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Return a json blob containing redirect URI in OIDC login controller instead of redirecting users. Commit: d5a057fe37b57343bcc023509e00a3c633aab32a https://github.com/galaxyproject/galaxy/commit/d5a057fe37b57343bcc023509e00… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #6517 from VJalili/authn_controller2 Return a json blob containing redirect URI in OIDC login controller Compare: https://github.com/galaxyproject/galaxy/compare/e8cf719d4e43...d5a057fe37b5 **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] 1b52d2: Fix a bug in cloud storage api calling a non-exist...
by GitHub 24 Jul '18

24 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b52d247b4d12a5a000c72cf8c78f6856562d6af https://github.com/galaxyproject/galaxy/commit/1b52d247b4d12a5a000c72cf8c78… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Fix a bug in cloud storage api calling a non-existing function from manager. Commit: d2adf34f96e3ffc96ef5b0a63198ab525a5bc602 https://github.com/galaxyproject/galaxy/commit/d2adf34f96e3ffc96ef5b0a63198… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Use signed URLs to copy data from cloud to Galaxy, instead of staging them. Commit: 8f35166746f9f7b155bf98b37e41278d7f3a2389 https://github.com/galaxyproject/galaxy/commit/8f35166746f9f7b155bf98b37e41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update error message of failing to copy from cloud to Galaxy. Commit: 13ae24ce01c22078a2d7a16a730bd9c99e301c98 https://github.com/galaxyproject/galaxy/commit/13ae24ce01c22078a2d7a16a730b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add `SIGNED_URL_TTL` in cloud storage manager. Commit: a146aeac63fa9513f0232f69337a782a48a2e17f https://github.com/galaxyproject/galaxy/commit/a146aeac63fa9513f0232f69337a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix lint issues: remove unused imports and add a missing blank line. Commit: be4e4d3dae178243db0ca6b6ddd6f68bbe947d21 https://github.com/galaxyproject/galaxy/commit/be4e4d3dae178243db0ca6b6ddd6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 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: ----------- Rename API: from `copy-from` to `upload`, and update docs. Commit: a6cf909fd064bb37491c0b8e44090ef814dc51aa https://github.com/galaxyproject/galaxy/commit/a6cf909fd064bb37491c0b8e4409… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 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: ----------- Rename API: from `copy-to` to `download`, and update docs. Commit: 3e7bfc8069c20057d0fc8fff81cd0c10fe8617f0 https://github.com/galaxyproject/galaxy/commit/3e7bfc8069c20057d0fc8fff81cd… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Append `job_errors` to cloud upload api error messages. Commit: 0dde5d3253e81af3beb13e515f765b9cdcb10771 https://github.com/galaxyproject/galaxy/commit/0dde5d3253e81af3beb13e515f76… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud storage Upload API and manager to take a list of objects. Commit: 99f9d72fd462b51e67e97157a0445fcd576ca660 https://github.com/galaxyproject/galaxy/commit/99f9d72fd462b51e67e97157a044… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- remove an extra blank line in cloud api. Commit: 46e18dc2230ae618c000e34dc56c9619b43d768c https://github.com/galaxyproject/galaxy/commit/46e18dc2230ae618c000e34dc56c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Inlined upload_tool pointer. Commit: 559730c950d5bd51882acb072814846b5b52bcb8 https://github.com/galaxyproject/galaxy/commit/559730c950d5bd51882acb072814… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add `input_args` to cloud upload API and manager. Commit: 1a8be699d9f4c08c5865fb327d8b2b265ad87ac8 https://github.com/galaxyproject/galaxy/commit/1a8be699d9f4c08c5865fb327d8b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Make static the `_configure_provider` method in cloud storage manager. Commit: 87959ecb8fb5250e0ddae3cd5bc51e819308087e https://github.com/galaxyproject/galaxy/commit/87959ecb8fb5250e0ddae3cd5bc5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Change the default value of `input_args` from empty dict to None. Commit: 87320ccd1275c1ae7dbbaf234e73a211f81325b8 https://github.com/galaxyproject/galaxy/commit/87320ccd1275c1ae7dbbaf234e73… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update method docs in cloud manager. Commit: e697ec51b4dab8db9827287e3dcb1ad911a7c088 https://github.com/galaxyproject/galaxy/commit/e697ec51b4dab8db9827287e3dcb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug handling missing `input_args`. Commit: 6e3cb8888a4b0cd88d34d0a47b13b1cc268b0566 https://github.com/galaxyproject/galaxy/commit/6e3cb8888a4b0cd88d34d0a47b13… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Surround an object `get` in cloud storage manager in a try-catch block. Commit: e8cf719d4e4360c79814fd591c6aabd828b4b071 https://github.com/galaxyproject/galaxy/commit/e8cf719d4e4360c79814fd591c6a… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-23 (Mon, 23 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 #6519 from VJalili/improve_cloud_storage_api Improvements to Cloud Storage Manager Compare: https://github.com/galaxyproject/galaxy/compare/4f1e2bf4f862...e8cf719d4e43 **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] a8b989: Fix warning in CONVERTER_bam_to_bigwig_0 and CONVE...
by GitHub 23 Jul '18

23 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8b9899681939286a03badd85c9c71f972958a18 https://github.com/galaxyproject/galaxy/commit/a8b9899681939286a03badd85c9c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Since v2.27.0 (see https://github.com/arq5x/bedtools2/commit/4d188435777cfbd6ada7394ee78fde37f… ), `bedtools genomecov` emits this warning: ``` ***** *****WARNING: Genome (-g) files are ignored when BAM input is provided. ***** ``` if both `-ibam` and `-g` option are specified, which causes the converters to always fail. Also: - Add `detect_errors="aggressive"` to `<command/>` to prevent future warnings from creating other issues. - Fix input format in `CONVERTER_sam_to_bigwig_0`. Commit: 50b34185394cc38159c33ca98b74e1418a7b1e55 https://github.com/galaxyproject/galaxy/commit/50b34185394cc38159c33ca98b74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #6528 from nsoranzo/release_18.05_fix_CONVERTER_bam_to_bigwig_0 [18.05] Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Commit: 4f1e2bf4f862c87d65be59186a053fbd6bc83866 https://github.com/galaxyproject/galaxy/commit/4f1e2bf4f862c87d65be59186a05… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2d1471efb40c...4f1e2bf4f862 **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] 8c3d7f: Removal of unreachable exit()
by GitHub 23 Jul '18

23 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c3d7f60f4911183f74b60c36caa949b38867bf3 https://github.com/galaxyproject/galaxy/commit/8c3d7f60f4911183f74b60c36caa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/web/stack/transport.py Log Message: ----------- Removal of unreachable exit() Commit: 2d1471efb40c023c606286ab21527811b25bed2a https://github.com/galaxyproject/galaxy/commit/2d1471efb40c023c606286ab2152… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/web/stack/transport.py Log Message: ----------- Merge pull request #6529 from dannon/unreachable_code Removal of unreachable exit() Compare: https://github.com/galaxyproject/galaxy/compare/3b629f02933c...2d1471efb40c **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] a8b989: Fix warning in CONVERTER_bam_to_bigwig_0 and CONVE...
by GitHub 23 Jul '18

23 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a8b9899681939286a03badd85c9c71f972958a18 https://github.com/galaxyproject/galaxy/commit/a8b9899681939286a03badd85c9c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Since v2.27.0 (see https://github.com/arq5x/bedtools2/commit/4d188435777cfbd6ada7394ee78fde37f… ), `bedtools genomecov` emits this warning: ``` ***** *****WARNING: Genome (-g) files are ignored when BAM input is provided. ***** ``` if both `-ibam` and `-g` option are specified, which causes the converters to always fail. Also: - Add `detect_errors="aggressive"` to `<command/>` to prevent future warnings from creating other issues. - Fix input format in `CONVERTER_sam_to_bigwig_0`. Commit: 50b34185394cc38159c33ca98b74e1418a7b1e55 https://github.com/galaxyproject/galaxy/commit/50b34185394cc38159c33ca98b74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #6528 from nsoranzo/release_18.05_fix_CONVERTER_bam_to_bigwig_0 [18.05] Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Compare: https://github.com/galaxyproject/galaxy/compare/ef702e1458f7...50b34185394c **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/usegalaxy-playbook] 11fe01: Update usegalaxy.org cert
by GitHub 21 Jul '18

21 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 11fe018f13a77d9237124faea748de94ad83a9a8 https://github.com/galaxyproject/usegalaxy-playbook/commit/11fe018f13a77d92… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M env/common/files/ssl/usegalaxy.org_cert.pem Log Message: ----------- Update usegalaxy.org cert **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] eeb672: More optimized HID generation - in one commit inst...
by GitHub 20 Jul '18

20 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eeb6722fe7f7f96ee3e459a2a66ae052c1d3517c https://github.com/galaxyproject/galaxy/commit/eeb6722fe7f7f96ee3e459a2a66a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- More optimized HID generation - in one commit instead of two. Before HID optimization: galaxy.tools.actions INFO 2018-07-18 11:10:20,164 Added output datasets to history (14.193 ms) galaxy.tools.actions INFO 2018-07-18 11:10:20,416 Added output datasets to history (17.583 ms) galaxy.tools.actions INFO 2018-07-18 11:10:20,675 Added output datasets to history (19.875 ms) galaxy.model.orm.engine_factory INFO 2018-07-18 11:10:21,734 Executed [445] SQL requests in for web request [/api/tools] (1036.418676ms) After HID optimization: galaxy.tools.actions INFO 2018-07-18 11:13:41,855 Added output datasets to history (6.049 ms) galaxy.tools.actions INFO 2018-07-18 11:13:42,018 Added output datasets to history (7.192 ms) galaxy.tools.actions INFO 2018-07-18 11:13:42,184 Added output datasets to history (10.277 ms) galaxy.tools.actions INFO 2018-07-18 11:13:42,344 Added output datasets to history (5.800 ms) galaxy.model.orm.engine_factory INFO 2018-07-18 11:13:43,179 Executed [434] SQL requests in for web request [/api/tools] (818.706274ms) Commit: 3b629f02933cc20ee3af779f1dd90219f73cda5f https://github.com/galaxyproject/galaxy/commit/3b629f02933cc20ee3af779f1dd9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #6516 from jmchilton/hid_opt More optimized HID generation - in one commit instead of two. Compare: https://github.com/galaxyproject/galaxy/compare/5a72bfdf8617...3b629f02933c **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] 423c74: Fix failing qunit tests in dev.
by GitHub 20 Jul '18

20 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 423c747a1f4fa898dcd80030c9402d8b6a232848 https://github.com/galaxyproject/galaxy/commit/423c747a1f4fa898dcd80030c940… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Fix failing qunit tests in dev. minor Commit: 5a72bfdf8617b2a79beeab8f243f5b41b71cdef7 https://github.com/galaxyproject/galaxy/commit/5a72bfdf8617b2a79beeab8f243f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #6520 from jmchilton/failing_qunit_tests Fix failing qunit tests in dev. Compare: https://github.com/galaxyproject/galaxy/compare/c7dd6c2a00f5...5a72bfdf8617 **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] af4bec: Rebuild CSS.
by GitHub 20 Jul '18

20 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af4becedd2736e3bae7790d98367a341b021faff https://github.com/galaxyproject/galaxy/commit/af4becedd2736e3bae7790d98367… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Rebuild CSS. If we're going to keep this file in the tree it should be updated against current sources then I believe. Commit: c7dd6c2a00f59c053ffbccfc5d6ca52f00fde0a8 https://github.com/galaxyproject/galaxy/commit/c7dd6c2a00f59c053ffbccfc5d6c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Merge pull request #6521 from jmchilton/css_rebuild Rebuild CSS against latest dev Compare: https://github.com/galaxyproject/galaxy/compare/b39bebb6a694...c7dd6c2a00f5 **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] 8d687b: Cache chrom_info generation when mapping over coll...
by GitHub 20 Jul '18

20 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d687bc3b7e2e4496b464e28c0961ba9fe2ad691 https://github.com/galaxyproject/galaxy/commit/8d687bc3b7e2e4496b464e28c096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cache chrom_info generation when mapping over collections. Eliminates several SQL queries per job and 20ms off the time it takes to create a job (about 10% for simple jobs). Timings below based on a branch with other optimizations so this will probably represent a smaller percent of runtime in dev until it catches up but the idea is pretty self contained unlike some other work in local my branch. Before chrom_info cache: ``` galaxy.tools.actions INFO 2018-07-18 14:59:35,041 Collected inputs for tool execute (14.586 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,069 setup execute (28.450 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,071 Handled output named out_file1 for tool cat_data_and_sleep (1.082 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,077 Added output datasets to history (5.986 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,104 Flushed output datasets (27.165 ms) ... galaxy.tools.actions INFO 2018-07-18 14:59:35,183 Collected inputs for tool execute (9.299 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,210 setup execute (26.842 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,211 Handled output named out_file1 for tool cat_data_and_sleep (1.375 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,217 Added output datasets to history (5.168 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,244 Flushed output datasets (27.395 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:59:36,033 Executed [417] SQL requests in for web request [/api/tools] (807.188749(s)ms) ``` ``` galaxy.tools.actions INFO 2018-07-18 14:58:20,505 Collected inputs for tool execute (8.643 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,533 setup execute (27.325 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,534 Handled output named out_file1 for tool cat_data_and_sleep (1.201 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,539 Added output datasets to history (4.913 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,565 Flushed output datasets (25.520 ms) ... galaxy.tools.actions INFO 2018-07-18 14:58:20,641 Collected inputs for tool execute (7.044 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,669 setup execute (27.744 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,670 Handled output named out_file1 for tool cat_data_and_sleep (0.990 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,674 Added output datasets to history (4.727 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,701 Flushed output datasets (26.265 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:58:21,480 Executed [417] SQL requests in for web request [/api/tools] (796.465635(s)ms) ``` After chrom_info cache: ``` ... galaxy.tools.actions INFO 2018-07-18 14:56:21,486 Collected inputs for tool execute (9.792 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,487 setup execute (0.399 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,488 Handled output named out_file1 for tool cat_data_and_sleep (1.068 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,497 Added output datasets to history (9.218 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,522 Flushed output datasets (24.905 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:56:22,352 Executed [381] SQL requests in for web request [/api/tools] (684.080839(s)ms) ``` ``` galaxy.tools.actions INFO 2018-07-18 14:55:27,979 Collected inputs for tool execute (8.400 ms) galaxy.tools.actions INFO 2018-07-18 14:55:27,979 setup execute (0.462 ms) galaxy.tools.actions INFO 2018-07-18 14:55:27,980 Handled output named out_file1 for tool cat_data_and_sleep (1.208 ms) galaxy.tools.actions INFO 2018-07-18 14:55:27,991 Added output datasets to history (10.558 ms) galaxy.tools.actions INFO 2018-07-18 14:55:28,016 Flushed output datasets (24.182 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:55:28,838 Executed [381] SQL requests in for web request [/api/tools] (714.353323(s)ms) ``` Commit: b39bebb6a694af2cd50cee8c416443e7dcb501cf https://github.com/galaxyproject/galaxy/commit/b39bebb6a694af2cd50cee8c4164… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6515 from jmchilton/chrom_info_cache Cache chrom_info generation when mapping over collections. Compare: https://github.com/galaxyproject/galaxy/compare/20f10fe6db8c...b39bebb6a694 **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] 8d3f1b: Merge branch 'dev' into data_column_1
by GitHub 18 Jul '18

18 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d3f1b7fbbe1d9acc7d93bc70a27e3f52c8cf9ae https://github.com/galaxyproject/galaxy/commit/8d3f1b7fbbe1d9acc7d93bc70a27… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M config/datatypes_conf.xml.sample M config/plugins/visualizations/msa/config/msa.xml M lib/galaxy/datatypes/binary.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/grt/export.py M test/api/test_jobs.py Log Message: ----------- Merge branch 'dev' into data_column_1 Commit: df17fad74a160ed8e8c71097d027b418af9c67e7 https://github.com/galaxyproject/galaxy/commit/df17fad74a160ed8e8c71097d027… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M test/api/test_tools.py Log Message: ----------- Merge branch 'dev' into data_column_1 Commit: ca57b770901c0204e63dec836856cf75dae09acb https://github.com/galaxyproject/galaxy/commit/ca57b770901c0204e63dec836856… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-06-24 (Sun, 24 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- fix data_column cast error when multiple is false Commit: 88132f9d1609f2e6bf804d9e148e397cd0c2aeee https://github.com/galaxyproject/galaxy/commit/88132f9d1609f2e6bf804d9e148e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: A test-data/11.tabular A test-data/configfile.json A test/functional/tools/column_param_configfile.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test dumping multiple="false" data_column param as json Tests https://github.com/galaxyproject/galaxy/pull/6389 Commit: 2da83ae3fef08703016fb9567807e04d0baeb084 https://github.com/galaxyproject/galaxy/commit/2da83ae3fef08703016fb9567807… Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: A test-data/11.tabular A test-data/configfile.json A test/functional/tools/column_param_configfile.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1 from mvdbeek/qiagu-data_column_1 Test dumping multiple="false" data_column param as json Commit: c9df2ef9be73cf12644cb436cf7d4d23c7308174 https://github.com/galaxyproject/galaxy/commit/c9df2ef9be73cf12644cb436cf7d… Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M test-data/configfile.json Log Message: ----------- Update configfile.json Commit: 53709df8cfb8fd384d60d221786c4167d7aa9658 https://github.com/galaxyproject/galaxy/commit/53709df8cfb8fd384d60d221786c… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M test-data/configfile.json Log Message: ----------- Revert "Update configfile.json" This reverts commit c9df2ef9be73cf12644cb436cf7d4d23c7308174. Commit: 20f10fe6db8ceb73c843c2a5609ab5fa5cf2f4ba https://github.com/galaxyproject/galaxy/commit/20f10fe6db8ceb73c843c2a5609a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py A test-data/11.tabular A test-data/configfile.json A test/functional/tools/column_param_configfile.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6389 from qiagu/data_column_1 fix data_column cast error when multiple is false Compare: https://github.com/galaxyproject/galaxy/compare/adb082a805d2...20f10fe6db8c **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] bc712c: Changing menu tabs without hard refresh
by GitHub 18 Jul '18

18 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc712cae907ded706954deeb417e7c66e3a5f533 https://github.com/galaxyproject/galaxy/commit/bc712cae907ded706954deeb417e… Author: Alexandru Mahmoud <amahmou4(a)jhu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- Changing menu tabs without hard refresh Commit: 0a2f77c4926c51f17541492d9ada6971f865e09e https://github.com/galaxyproject/galaxy/commit/0a2f77c4926c51f17541492d9ada… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Minor formatting. Commit: adb082a805d28985d4e24c7700417f4822f8acfa https://github.com/galaxyproject/galaxy/commit/adb082a805d28985d4e24c770041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge branch 'soft-page-change' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e794443f4886...adb082a805d2 **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] 267c23: Fix for supplying multiple actual uploads to the u...
by GitHub 18 Jul '18

18 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 267c2320769ad68fc2df0b10b92cf94641c24e15 https://github.com/galaxyproject/galaxy/commit/267c2320769ad68fc2df0b10b92c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/data_fetch.xml M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix for supplying multiple actual uploads to the upload 2.0 tool. Commit: 8d5a4c3625e96bb7e5c879cadcf1980217801481 https://github.com/galaxyproject/galaxy/commit/8d5a4c3625e96bb7e5c879cadcf1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Transition API tests from upload datasets and assembling collecitons to uploading collections. Should be a lot more efficient. Commit: 9f73bc89854420a4f28188fbcefad7999689ca6b https://github.com/galaxyproject/galaxy/commit/9f73bc89854420a4f28188fbcefa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Repsonse->response Commit: 5171b9bd497cb07c3e7ab940230c97916ab29f6a https://github.com/galaxyproject/galaxy/commit/5171b9bd497cb07c3e7ab940230c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M test/base/populators.py M test/integration/test_scripts.py Log Message: ----------- A couple more typos. Commit: e794443f488649c8bb1d1d0825e4a113dacee26c https://github.com/galaxyproject/galaxy/commit/e794443f488649c8bb1d1d0825e4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/data_fetch.xml M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/integration/test_scripts.py Log Message: ----------- Merge pull request #6294 from jmchilton/better_tool_tests Upload collections directly for tests. Compare: https://github.com/galaxyproject/galaxy/compare/6c668774f7ca...e794443f4886 **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 18 Jul '18

18 Jul '18

Branch: refs/heads/dev 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 Commit: 7b8e4f9e740725861951535d59e50243e4a0b2e0 https://github.com/galaxyproject/galaxy/commit/7b8e4f9e740725861951535d59e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Fix empty datatypes. Commit: ef702e1458f746299710e9ce5afb7b350b61f91c https://github.com/galaxyproject/galaxy/commit/ef702e1458f746299710e9ce5afb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Merge pull request #6510 from nsoranzo/release_18.05_backport_29f8e29b0bf5d50c0b735aa707d2a61623cc805b [18.05] Fix infinite loop in uploads Commit: 6c668774f7cac2098bc32a3123471a0eb62f384c https://github.com/galaxyproject/galaxy/commit/6c668774f7cac2098bc32a312347… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-18 (Wed, 18 Jul 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e8b437dfd8e0...6c668774f7ca **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] 489839: Integrate tagging into the rule builder.
by GitHub 18 Jul '18

18 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 489839cb638df8648041cc6197a61faf9cfc7a6a https://github.com/galaxyproject/galaxy/commit/489839cb638df8648041cc6197a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Integrate tagging into the rule builder. - Allow specifying name tags, group tags, and "general" tags on stand-alone datasets and collection content datasets. - Allow reusing the collection name as a name tag during upload for the whole collection. In this context I think the name tag is especially useful and will typically be the same name as the collection so the UI is kept simple by making it a checkbox. Commit: 26b5891908757648eed5ce9be3cccbe7104ad7d3 https://github.com/galaxyproject/galaxy/commit/26b5891908757648eed5ce9be3cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Client-format Commit: e8b437dfd8e07f88f48a5872ce18693343f33573 https://github.com/galaxyproject/galaxy/commit/e8b437dfd8e07f88f48a5872ce18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge branch 'rule_builder_tags' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4719c4a3f129...e8b437dfd8e0 **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] 7b8e4f: Fix empty datatypes.
by GitHub 17 Jul '18

17 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 7b8e4f9e740725861951535d59e50243e4a0b2e0 https://github.com/galaxyproject/galaxy/commit/7b8e4f9e740725861951535d59e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Fix empty datatypes. Commit: ef702e1458f746299710e9ce5afb7b350b61f91c https://github.com/galaxyproject/galaxy/commit/ef702e1458f746299710e9ce5afb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Merge pull request #6510 from nsoranzo/release_18.05_backport_29f8e29b0bf5d50c0b735aa707d2a61623cc805b [18.05] Fix infinite loop in uploads Compare: https://github.com/galaxyproject/galaxy/compare/fd33c5c6d6aa...ef702e1458f7 **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] 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.

1 0

[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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