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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.

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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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