- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5e6a25: Allow LDAP options not starting with OPT_
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 5e6a2572f8bfabd6c674ff218d8a3ee1f9f22615 https://github.com/galaxyproject/galaxy/commit/5e6a2572f8bfabd6c674ff218d8a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Allow LDAP options not starting with OPT_ Fix https://github.com/galaxyproject/galaxy/issues/5486 Commit: af7b0ab1b65f5a54b8a8adda1c095fc9a8c2e912 https://github.com/galaxyproject/galaxy/commit/af7b0ab1b65f5a54b8a8adda1c09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #5556 from nsoranzo/release_18.01_fix_5486 [18.01] Allow LDAP options not starting with OPT_ Compare: https://github.com/galaxyproject/galaxy/compare/e7f7d5e29a0f...af7b0ab1b65f

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[galaxyproject/galaxy] b84da7: Allow per-request SQL debugging via URL parameter.
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b84da7a07a7b53f7770d6dc015ff0829305e3075 https://github.com/galaxyproject/galaxy/commit/b84da7a07a7b53f7770d6dc015ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow per-request SQL debugging via URL parameter. This has been super helpful in debugging the SQL generated by Galaxy for recent PRs. To use this simply enable the middleware, use your browser's network logger to find the URL of interest, copy the URL into the browser address bar and add ``?debug_sql=1`` to it. You will then see the sql in the logs only for that request and for every statement in that request. Simply turning all logging on results in a deluge of logging I've never been able to grok and that is very hard to ping to particular request. Slow request logging is great but it doesn't make this kind of per-query full profile of the SQL generated as easy as this approach and isn't great at debugging performance problems when the result from a large number of small requests (you'd have to set a very low threshold to make sure you are logging every query and then it is no different from the full log). Commit: 0c7dcc37c96617a6a98d1f061c051bee678e8c67 https://github.com/galaxyproject/galaxy/commit/0c7dcc37c96617a6a98d1f061c05… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5539 from jmchilton/per_request_sql_debugging Add middleware and instrumentation to allow per-request SQL debugging. Compare: https://github.com/galaxyproject/galaxy/compare/ca7cbaf2bffb...0c7dcc37c966

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[galaxyproject/galaxy] d964d5: [18.01] Do not reload page when deleting collectio...
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d964d594a5314b85def7676f5ae39c949420f4f0 https://github.com/galaxyproject/galaxy/commit/d964d594a5314b85def7676f5ae3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- [18.01] Do not reload page when deleting collections. Fixes #5499 reported by @mvdbeek (thanks for catching that). Commit: e7f7d5e29a0fc746625d5c8634d8976d4c2b667c https://github.com/galaxyproject/galaxy/commit/e7f7d5e29a0fc746625d5c8634d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Merge pull request #5558 from jmchilton/deletion_cleanup_1 [18.01] Do not reload page when deleting collections. Compare: https://github.com/galaxyproject/galaxy/compare/0d029b39ac9a...e7f7d5e29a0f

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[galaxyproject/galaxy] 19eee5: added fasta.gz
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19eee525a166b6c9abf03e5a91fd69a356447c20 https://github.com/galaxyproject/galaxy/commit/19eee525a166b6c9abf03e5a91fd… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- added fasta.gz Commit: 0c2c9ba49e70f19cd4ec9f4c93bf19af14fa348e https://github.com/galaxyproject/galaxy/commit/0c2c9ba49e70f19cd4ec9f4c93bf… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fixed flake8 errors Commit: 84e818577a162b507fa4f1a69006fdee20ad8e5f https://github.com/galaxyproject/galaxy/commit/84e818577a162b507fa4f1a69006… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- removing stray whitespace Commit: 4390cd4142605efbf062126fdf0082940d7dfe30 https://github.com/galaxyproject/galaxy/commit/4390cd4142605efbf062126fdf00… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fixed name of fastagz->fasta converter Commit: 6359262b3ce3632bd859278201bcd9e6e893fba9 https://github.com/galaxyproject/galaxy/commit/6359262b3ce3632bd859278201bc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fix copypasta Commit: 55a405f18a1b493c7e0249f8e56b12b254603d3c https://github.com/galaxyproject/galaxy/commit/55a405f18a1b493c7e0249f8e56b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fix more fasta copypasta Commit: ca7cbaf2bffb4b1a622386e5651acf396db65cfd https://github.com/galaxyproject/galaxy/commit/ca7cbaf2bffb4b1a622386e5651a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #5553 from nekrut/fasta_gz added fasta.gz Compare: https://github.com/galaxyproject/galaxy/compare/a5bea5f885fb...ca7cbaf2bffb

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[galaxyproject/usegalaxy-playbook] 0af54a: Decrease client request size, increase staging req...
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0af54a769a5be23b38ce64e922504998675f12be https://github.com/galaxyproject/usegalaxy-playbook/commit/0af54a769a5be23b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M env/main/group_vars/galaxystagingservers.yml M env/main/group_vars/galaxywebservers.yml M env/main/group_vars/webservers.yml Log Message: ----------- Decrease client request size, increase staging request size

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[galaxyproject/infrastructure-playbook] 6ae3b1: update grafana
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6ae3b1a0c18f6ad7b428c5041b65b2b977d6a037 https://github.com/galaxyproject/infrastructure-playbook/commit/6ae3b1a0c18… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- update grafana Commit: f9205a79e9cf8791c9ab1b5d929e9bfaba208ebc https://github.com/galaxyproject/infrastructure-playbook/commit/f9205a79e9c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Merge pull request #20 from galaxyproject/grafana-update update grafana Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/669ca93ed1…

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[galaxyproject/infrastructure-playbook] 6ae3b1: update grafana
by GitHub 19 Feb '18

19 Feb '18

Branch: refs/heads/grafana-update Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6ae3b1a0c18f6ad7b428c5041b65b2b977d6a037 https://github.com/galaxyproject/infrastructure-playbook/commit/6ae3b1a0c18… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- update grafana

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[galaxyproject/galaxy] 9023dd: Ensure jobStateSummariesCollection exists; events ...
by GitHub 18 Feb '18

18 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9023dd4e2edc940be9fb718dd85a157cbb6f663f https://github.com/galaxyproject/galaxy/commit/9023dd4e2edc940be9fb718dd85a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 6211f8bd18eaf47703c92d27cf2b0025c94731b9 https://github.com/galaxyproject/galaxy/commit/6211f8bd18eaf47703c92d27cf2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Import cleanup; remove unnecessary try...catch statement, use const. Commit: eb03d877a83e74c3d2c0124ec5bf7b36bf680564 https://github.com/galaxyproject/galaxy/commit/eb03d877a83e74c3d2c0124ec5bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- More refactoring, removal of 'self' references in history-contents Commit: a5bea5f885fb5a5205bac518c895710e4b7f9965 https://github.com/galaxyproject/galaxy/commit/a5bea5f885fb5a5205bac518c895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5448 from dannon/multidelete_fix_and_refactor History contents refactoring Compare: https://github.com/galaxyproject/galaxy/compare/788934c3aa0c...a5bea5f885fb

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[galaxyproject/galaxy] 25952e: Map static content by default for Reports and Tool...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Map static content by default for Reports and Tool Shed webapps. Commit: fa93d4e04bccd31ba347bbb916b9c7b23b6c5c9d https://github.com/galaxyproject/galaxy/commit/fa93d4e04bccd31ba347bbb916b9… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Close tempfile handles. Commit: 5488cf29eabc835e8e7ee994035557392471c586 https://github.com/galaxyproject/galaxy/commit/5488cf29eabc835e8e7ee9940355… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5552 from davebx/18.01 [18.01] Close tempfile handles. Commit: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge pull request #5534 from natefoo/17.09-static-map-fix [17.09] Map static content by default for Reports and Tool Shed webapps Commit: 0d029b39ac9ae6bc21a6c1834fe6e05280d8e0d0 https://github.com/galaxyproject/galaxy/commit/0d029b39ac9ae6bc21a6c1834fe6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 788934c3aa0c4395dc479d1840a9869a2ee8b42a https://github.com/galaxyproject/galaxy/commit/788934c3aa0c4395dc479d1840a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Log Message: ----------- Merge branch 'release_18.01' into dev Conflicts: config/reports.yml.sample config/tool_shed.yml.sample Compare: https://github.com/galaxyproject/galaxy/compare/c9c2e968daba...788934c3aa0c

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[galaxyproject/galaxy] 25952e: Map static content by default for Reports and Tool...
by GitHub 16 Feb '18

16 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Map static content by default for Reports and Tool Shed webapps. Commit: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge pull request #5534 from natefoo/17.09-static-map-fix [17.09] Map static content by default for Reports and Tool Shed webapps Commit: 0d029b39ac9ae6bc21a6c1834fe6e05280d8e0d0 https://github.com/galaxyproject/galaxy/commit/0d029b39ac9ae6bc21a6c1834fe6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/5488cf29eabc...0d029b39ac9a

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