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[galaxyproject/galaxy] 825d7f: Allow from_param to reference a child collection
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 825d7f6fa74384d195739fe7ac0bf4e1d5b9c1cf https://github.com/galaxyproject/galaxy/commit/825d7f6fa74384d195739fe7ac0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: 50c98701b7682d8878cbc2fa1acdc3f28abdad0e https://github.com/galaxyproject/galaxy/commit/50c98701b7682d8878cbc2fa1acd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 99889af1d52a263737dca3c7461baa5ce4fe8ad7 https://github.com/galaxyproject/galaxy/commit/99889af1d52a263737dca3c7461b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: f690386f0b88fa4f5f94b83e4dea8c97f60747fd https://github.com/galaxyproject/galaxy/commit/f690386f0b88fa4f5f94b83e4dea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Drop unused COLLECTION_ATTRIBUTES Commit: 2f6c184e6f5c614e36f8100648b1a5f5a8f6ac94 https://github.com/galaxyproject/galaxy/commit/2f6c184e6f5c614e36f8100648b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6253 from mvdbeek/mapping_over_from_param_fixes Mapping over from_param fixes Compare: https://github.com/galaxyproject/galaxy/compare/9cf66df7a7af...2f6c184e6f5c **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] 4c4aa1: Update @erasche's name
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c4aa11ad469a3a66c1bfa03fb6985a9b0033498 https://github.com/galaxyproject/galaxy/commit/4c4aa11ad469a3a66c1bfa03fb69… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update @erasche's name Commit: 73fb6785fd7ddd9cf14d41b1f5496b0a2f9a9563 https://github.com/galaxyproject/galaxy/commit/73fb6785fd7ddd9cf14d41b1f549… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clarify how +1 votes on PRs can be expressed Commit: 9cf66df7a7af0d28b627ad9f24b395a4579cc988 https://github.com/galaxyproject/galaxy/commit/9cf66df7a7af0d28b627ad9f24b3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #6171 from nsoranzo/pr_approval [PROCEDURES] Clarify how +1 votes on PRs can be expressed v.3 Compare: https://github.com/galaxyproject/galaxy/compare/1954c9dc633b...9cf66df7a7af **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] e95052: add sbml datatype
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e950520ab0a5c47296d023d9f20ffbdc55125996 https://github.com/galaxyproject/galaxy/commit/e950520ab0a5c47296d023d9f20f… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/xml.py Log Message: ----------- add sbml datatype Commit: 9c17828e9616161a63ea6c7dfd4ebf0fb64bcae9 https://github.com/galaxyproject/galaxy/commit/9c17828e9616161a63ea6c7dfd4e… Author: MONJEAUD Cyril <Cyril.Monjeaud(a)irisa.fr> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- Add edam format Commit: 21aa40addfb21c22dad676aebe041c77cc4ffd92 https://github.com/galaxyproject/galaxy/commit/21aa40addfb21c22dad676aebe04… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add edam data Commit: fcc5b207ab77a29e17ab13d0ba0d38a420ced659 https://github.com/galaxyproject/galaxy/commit/fcc5b207ab77a29e17ab13d0ba0d… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- fix conflicts Commit: e57ff42e2ef8e61dd5d49e7f91a9ecabcd484706 https://github.com/galaxyproject/galaxy/commit/e57ff42e2ef8e61dd5d49e7f91a9… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add blank line Commit: 1954c9dc633bdf72df446a16f7ec2f2150f92e60 https://github.com/galaxyproject/galaxy/commit/1954c9dc633bdf72df446a16f7ec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/xml.py Log Message: ----------- Merge pull request #6201 from cmonjeau/add_sbml_datatype New datatype: SBML Compare: https://github.com/galaxyproject/galaxy/compare/5ba71f580fc8...1954c9dc633b **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/infrastructure-playbook] 1f3c6d: Add libGL on nodes for PyQt5 conda package
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1f3c6d7f6e442eb8d9015be1048a2f2e49cf7135 https://github.com/galaxyproject/infrastructure-playbook/commit/1f3c6d7f6e4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Add libGL on nodes for PyQt5 conda package **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] 30b5e5: Enable dynamic reload of dynamic job rules when co...
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30b5e50ba0079a7dd24d3334cacbde2e4b9c07dc https://github.com/galaxyproject/galaxy/commit/30b5e50ba0079a7dd24d3334cacb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/queue_worker.py A lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Enable dynamic reload of dynamic job rules when configured, using watchdog notifications. Commit: 91dbeebf5f4ea2fd94586a883616e6fc148940ae https://github.com/galaxyproject/galaxy/commit/91dbeebf5f4ea2fd94586a883616… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Fix non-Galaxy webapp unit tests Commit: 41a601d5375669bfb612b6a98e289fccd4eac8a9 https://github.com/galaxyproject/galaxy/commit/41a601d5375669bfb612b6a98e28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Watch any objects in job rule directories that are not python bytecode, rather than only watching python source. Commit: 8bd856da5120eb15053e1d32f1964aaa851626ad https://github.com/galaxyproject/galaxy/commit/8bd856da5120eb15053e1d32f196… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Ignore change events for dot files. This could be configurable if it's needed but I can't imagine when it would be. Prevents reloading on vim swapfile writes. Commit: 73ea1189e9fae103e367955fc62916e497074b38 https://github.com/galaxyproject/galaxy/commit/73ea1189e9fae103e367955fc629… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Avoid using builtins for variable names. file->file_path, dir->dir_path in generic watcher functions Commit: 1652c4221eacfac2a04955ee6fd4004c84f97ae6 https://github.com/galaxyproject/galaxy/commit/1652c4221eacfac2a04955ee6fd4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Merge pull request #8 from dannon/dynamic-rule-dynamic-reload Avoid using builtins for variable names. Commit: 5ba71f580fc861be9c924991a762f0917811b720 https://github.com/galaxyproject/galaxy/commit/5ba71f580fc861be9c924991a762… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/queue_worker.py A lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Merge pull request #6215 from natefoo/dynamic-rule-dynamic-reload Enable automatic reload of dynamic job rules on change Compare: https://github.com/galaxyproject/galaxy/compare/a5594551c092...5ba71f580fc8 **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] ba5e54: Enable cgroup metric on main
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ba5e549e1d61e9730825daea40aecbf701101e05 https://github.com/galaxyproject/usegalaxy-playbook/commit/ba5e549e1d61e973… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M env/main/files/galaxy/config/job_metrics_conf.xml Log Message: ----------- Enable cgroup metric on main **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] c1614b: Pause jobs with invalid inputs
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1614be1ef5abaab241bf9739fb99390a8954343 https://github.com/galaxyproject/galaxy/commit/c1614be1ef5abaab241bf9739fb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Pause jobs with invalid inputs Otherwise these jobs may hang around forever/until the admin does a cleanup. This is probably preferable for users as well, as the pause message gives a hint of why their job didn't start running. Fixes https://github.com/galaxyproject/galaxy/issues/6022 and would minimize maintenance as outlined in https://github.com/galaxyproject/galaxy/issues/5944. I'm working on tests, but one easy way to test this is create a collection through the list builder interface, then delete the source HDAs. Then run a workflow on the collection and without this commit the outputs get created but the job just hangs around indefinetely. With the PR the steps consuming the collection and the subsequent jobs will be paused. Set to paused Commit: 0e31f97269586b061ce58a9eac75743590e310a3 https://github.com/galaxyproject/galaxy/commit/0e31f97269586b061ce58a9eac75… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add a testcase for pausing jobs with deleted input Fix test Commit: ed0b087926c53f4c2c4293ff6443f997fafa9526 https://github.com/galaxyproject/galaxy/commit/ed0b087926c53f4c2c4293ff6443… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Fail jobs with purged inputs We can't resume these jobs anyway, so better to set them to failed. Also resets the info field for datasets produced by resumed jobs. Commit: f9a65a10eb10fd2942ca3306b461ba7dbae4aa09 https://github.com/galaxyproject/galaxy/commit/f9a65a10eb10fd2942ca3306b461… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Display the info field for paused jobs Commit: f8cc653b3051b93cea446317194fcdd88d1aa674 https://github.com/galaxyproject/galaxy/commit/f8cc653b3051b93cea446317194f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py M test/api/test_workflows.py Log Message: ----------- Pause job if input dataset state is paused Commit: ca31222cf87a471648876575f068f4e5ac3cba92 https://github.com/galaxyproject/galaxy/commit/ca31222cf87a471648876575f068… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Optimize job resume function Commit: c401f5a713c1774e2dd8d817de04d48e2864e40f https://github.com/galaxyproject/galaxy/commit/c401f5a713c1774e2dd8d817de04… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Use info style when displaying the reason for pausing a dataset Commit: a5594551c09250db0dac799711a0d5676817038c https://github.com/galaxyproject/galaxy/commit/a5594551c09250db0dac799711a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6036 from mvdbeek/kill_jobs_with_invalid_input Pause jobs with invalid inputs Compare: https://github.com/galaxyproject/galaxy/compare/f19f09b30f60...a5594551c092 **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] bac416: Rename disabled flag for consistency with existing...
by GitHub 01 Jun '18

01 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bac4169d178eeace51cfdf62d979f8a14ce04101 https://github.com/galaxyproject/galaxy/commit/bac4169d178eeace51cfdf62d979… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Rename disabled flag for consistency with existing naming Commit: 5ae57e28667524086595483ff04674b010d067b1 https://github.com/galaxyproject/galaxy/commit/5ae57e28667524086595483ff046… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Use new collapsible flag in rules editor Commit: fb6dbb27026abfa8832dc821633214882e8ee6e9 https://github.com/galaxyproject/galaxy/commit/fb6dbb27026abfa8832dc8216332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse unmodified options Commit: 292a2096424a207a943457d00bf6540fc84e6a3d https://github.com/galaxyproject/galaxy/commit/292a2096424a207a943457d00bf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js Log Message: ----------- Remove input specific options handling, unify input update mechanism Commit: d0187ac206219c0fb0cb4767f6c1b5d0dcc68e1f https://github.com/galaxyproject/galaxy/commit/d0187ac206219c0fb0cb4767f6c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js Log Message: ----------- Adjust update handler for list inputs Commit: f3ccf42cab1cca514d4e8e159b4b1338090beaea https://github.com/galaxyproject/galaxy/commit/f3ccf42cab1cca514d4e8e159b4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Adjust handling in text select field Commit: 94220c0ac1c0c2273213355343b7164832d31a1a https://github.com/galaxyproject/galaxy/commit/94220c0ac1c0c2273213355343b7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Adjust update caller in rules editor Commit: c8afba470be865acc96af1d532876b580e1739a6 https://github.com/galaxyproject/galaxy/commit/c8afba470be865acc96af1d53287… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Move options handling into selection fields Commit: 3df2a94dbd9d37c99bde75ef637866683a231618 https://github.com/galaxyproject/galaxy/commit/3df2a94dbd9d37c99bde75ef6378… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Fix library dataset selector Commit: 0bad91c59295626bd577662ac2c80f16868a6a6b https://github.com/galaxyproject/galaxy/commit/0bad91c59295626bd577662ac2c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse data as is to select field Commit: 0022615418af51ea6d8b1b00a12855ad4191177c https://github.com/galaxyproject/galaxy/commit/0022615418af51ea6d8b1b00a128… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Handle alternative option formatting in text select wrapper Commit: cb98bb23f3121708efa8d948b5e3e39426f2b773 https://github.com/galaxyproject/galaxy/commit/cb98bb23f3121708efa8d948b5e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js Log Message: ----------- Adjust drilldown handler Commit: 5c65012f9c2e41b328483fc28b685ae736cc500a https://github.com/galaxyproject/galaxy/commit/5c65012f9c2e41b328483fc28b68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix list parameter style Commit: f19f09b30f607c3af922fcba16ebe0ab95996d2f https://github.com/galaxyproject/galaxy/commit/f19f09b30f607c3af922fcba16eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6248 from guerler/form_fix Align input element update mechanism Compare: https://github.com/galaxyproject/galaxy/compare/53d2664b0b7b...f19f09b30f60 **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] c0c8aa: Fix history shared with me 'view' link
by GitHub 31 May '18

31 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c0c8aad528d9164fb7aaf88c3a202c66044c0134 https://github.com/galaxyproject/galaxy/commit/c0c8aad528d9164fb7aaf88c3a20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history shared with me 'view' link Commit: 692465d4ec9a4493ae1326cbc8b118cf49f5cbff https://github.com/galaxyproject/galaxy/commit/692465d4ec9a4493ae1326cbc8b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Standard quotes. Commit: 8a0427a6e8eeffde3022ed1187b114265b73447f https://github.com/galaxyproject/galaxy/commit/8a0427a6e8eeffde3022ed1187b1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6257 from dannon/sharing_link_fix [18.05] Fix history shared with me 'view' link Compare: https://github.com/galaxyproject/galaxy/compare/44b42e7e7e01...8a0427a6e8ee **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/infrastructure-playbook] 8ecbb5: WIP Jetstream autoscaling
by GitHub 31 May '18

31 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8ecbb55376f5ae76d114fa506a67f58f5a772943 https://github.com/galaxyproject/infrastructure-playbook/commit/8ecbb55376f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M env/jsiu/group_vars/all.yml R env/jsiu/group_vars/controllers.yml A env/jsiu/group_vars/controllers/vars.yml A env/jsiu/group_vars/controllers/vault.yml A env/jsiu/slurmscale.yml A roles/slurmscale/defaults/main.yml A roles/slurmscale/files/ansible.cfg A roles/slurmscale/files/config.yml A roles/slurmscale/files/group_vars/all/cluster.yml A roles/slurmscale/files/group_vars/all/spawn.yml A roles/slurmscale/files/group_vars/jetstream-large.yml A roles/slurmscale/files/group_vars/jetstream-medium.yml A roles/slurmscale/files/group_vars/jetstream-small.yml A roles/slurmscale/files/inventory/flavors A roles/slurmscale/files/inventory/openstack_inventory.py A roles/slurmscale/files/spawn.yml A roles/slurmscale/files/start.yml A roles/slurmscale/files/stop.yml A roles/slurmscale/files/templates/auto.jetstream.j2 A roles/slurmscale/files/templates/slurm/slurm.conf.j2 A roles/slurmscale/tasks/main.yml A roles/slurmscale/templates/group_vars/all/cloud.yml.j2 A roles/slurmscale/templates/slurm_resume.sh.j2 A roles/slurmscale/templates/slurm_suspend.sh.j2 Log Message: ----------- WIP Jetstream autoscaling **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] 94ae2e: permit actual numbers in conf file
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 94ae2e6a958e611c6cdcfe56dc72d47f2dfb66c3 https://github.com/galaxyproject/galaxy/commit/94ae2e6a958e611c6cdcfe56dc72… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- permit actual numbers in conf file Commit: 53d2664b0b7bafc5d91243ad897e7fcd3ab1c13a https://github.com/galaxyproject/galaxy/commit/53d2664b0b7bafc5d91243ad897e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- Merge pull request #6200 from erasche/grt-asdf Permit numeric values of GRT instance ID in config Compare: https://github.com/galaxyproject/galaxy/compare/06d0fcc0de1a...53d2664b0b7b **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] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 44b42e7e7e01c8471777cf87251499f3bbfbf3f9 https://github.com/galaxyproject/galaxy/commit/44b42e7e7e01c8471777cf872514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 06d0fcc0de1a7634df5cb71f4225e11af2ebb345 https://github.com/galaxyproject/galaxy/commit/06d0fcc0de1a7634df5cb71f4225… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fb78fabcd757...06d0fcc0de1a **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] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 44b42e7e7e01c8471777cf87251499f3bbfbf3f9 https://github.com/galaxyproject/galaxy/commit/44b42e7e7e01c8471777cf872514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c9641e1f1384...44b42e7e7e01 **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] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 44b42e7e7e01c8471777cf87251499f3bbfbf3f9 https://github.com/galaxyproject/galaxy/commit/44b42e7e7e01c8471777cf872514… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c9641e1f1384...44b42e7e7e01 **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] 89bf97: Link downlaod attributes are well supported and sh...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89bf971aa8cee76bc624536e0896de38556d806c https://github.com/galaxyproject/galaxy/commit/89bf971aa8cee76bc624536e0896… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Link downlaod attributes are well supported and should work here, allowing us to actually name the downloads. Commit: a5840a89bb71c0c17373c7fdac5498f886483b2c https://github.com/galaxyproject/galaxy/commit/a5840a89bb71c0c17373c7fdac54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Refactoring, cleanup, a few bugfixes. Commit: 1656b48323a3110134d0ba3fcc86c54923a75fdc https://github.com/galaxyproject/galaxy/commit/1656b48323a3110134d0ba3fcc86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Minor filename handling tweak, more explicitly better support empty default Commit: 60b5cc5341f2bedd97f6a1da8e187edb1584e2b6 https://github.com/galaxyproject/galaxy/commit/60b5cc5341f2bedd97f6a1da8e18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- SVG download titles, more minor refactoring/reuse Commit: ddb6b8692d0eecdaba27a00921875223cef387ef https://github.com/galaxyproject/galaxy/commit/ddb6b8692d0eecdaba27a0092187… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Formatting fixes. Commit: fb78fabcd757b80cbe063cddab104f17e2b3a4e2 https://github.com/galaxyproject/galaxy/commit/fb78fabcd757b80cbe063cddab10… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Merge pull request #6216 from dannon/chart_download_fix Charts filename download fix Compare: https://github.com/galaxyproject/galaxy/compare/fd25d51b8e47...fb78fabcd757 **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] ce9b67: Hack paster args to not duplicate pid file stuff f...
by GitHub 31 May '18

31 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: ce9b671bd4747cd29af9dc25074b0831bb3068e1 https://github.com/galaxyproject/galaxy/commit/ce9b671bd4747cd29af9dc25074b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Hack paster args to not duplicate pid file stuff for RUN_ALL. Commit: 88c94fc49b3f5869b6746bb0fe8f3248e33f440e https://github.com/galaxyproject/galaxy/commit/88c94fc49b3f5869b6746bb0fe8f… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Set pid and log file for paster in server_args This avoids setting log and pid file in paster_args so that with GALAXY_RUN_ALL they can be set individually, but ensures they are set when running paster otherwise. Commit: b137d5cf3461d4d7edb10b8510e36aa02fce6797 https://github.com/galaxyproject/galaxy/commit/b137d5cf3461d4d7edb10b8510e3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6239 from lparsons/fix_paster_args [18.01] Hack paster args to not duplicate pid file stuff for RUN_ALL. Compare: https://github.com/galaxyproject/galaxy/compare/0718a083badc...b137d5cf3461 **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] 340a1a: Test Jetstream autoscaling
by GitHub 31 May '18

31 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 340a1a2402fe9aec74c43f83af5dddf487da1f50 https://github.com/galaxyproject/usegalaxy-playbook/commit/340a1a2402fe9aec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Test Jetstream autoscaling **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] ac7c6e: Refactor to match domain name (follow-up to #6244)
by GitHub 31 May '18

31 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac7c6e5d947f42054105b25fe33e490152dd7d2f https://github.com/galaxyproject/galaxy/commit/ac7c6e5d947f42054105b25fe33e… Author: Katrin Leinweber <9948149+katrinleinweber(a)users.noreply.github.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/managers/citations.py Log Message: ----------- Refactor to match domain name (follow-up to #6244) Commit: fd25d51b8e47bda031aa6a490c6e73741ab15fe9 https://github.com/galaxyproject/galaxy/commit/fd25d51b8e47bda031aa6a490c6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/managers/citations.py Log Message: ----------- Merge pull request #6252 from katrinleinweber/patch-1 Refactor dx_url to doi_url to match domain name Compare: https://github.com/galaxyproject/galaxy/compare/27106c59e5d6...fd25d51b8e47 **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] 03a815: Some more upload/sniff tests.
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03a815a2c379186237a9978d0f3af32f1e69c933 https://github.com/galaxyproject/galaxy/commit/03a815a2c379186237a9978d0f3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.tiff A test-data/1.tiff M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Some more upload/sniff tests. Commit: 27106c59e5d6d3583f1a11adec1ddd26d0114da1 https://github.com/galaxyproject/galaxy/commit/27106c59e5d6d3583f1a11adec1d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.tiff A test-data/1.tiff M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Merge pull request #6212 from jmchilton/tiff_tests Some more upload/sniff tests. Compare: https://github.com/galaxyproject/galaxy/compare/a79d6fae43be...27106c59e5d6 **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] f99f86: Hyperlink DOIs against preferred resolver
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f99f8667bcfceea21101d0690d2ba6f5630d34cf https://github.com/galaxyproject/galaxy/commit/f99f8667bcfceea21101d0690d2b… Author: Katrin Leinweber <kalei(a)posteo.de> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/managers/citations.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M tools/sr_mapping/bfast_wrapper.xml Log Message: ----------- Hyperlink DOIs against preferred resolver Commit: a79d6fae43be20dbf79d57e8067a022f877b57be https://github.com/galaxyproject/galaxy/commit/a79d6fae43be20dbf79d57e8067a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/managers/citations.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M tools/sr_mapping/bfast_wrapper.xml Log Message: ----------- Merge pull request #6244 from katrinleinweber/resolve-DOIs-securely Hyperlink DOIs against preferred resolver Compare: https://github.com/galaxyproject/galaxy/compare/8fcc9332448a...a79d6fae43be **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] 3b27d2: Strip busted history structure view -- we're goign...
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b27d249b2876a8e88691dad2fe42213f8943893 https://github.com/galaxyproject/galaxy/commit/3b27d249b2876a8e88691dad2fe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/mvc/history/history-structure-view.js M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/structure.mako Log Message: ----------- Strip busted history structure view -- we're goign to start from scratch here Commit: 8d9a21c4e9eeab4f1b947b66688658941c482340 https://github.com/galaxyproject/galaxy/commit/8d9a21c4e9eeab4f1b947b666886… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove unused import. Commit: 8fcc9332448add1e55fd6b5831da80b336d63078 https://github.com/galaxyproject/galaxy/commit/8fcc9332448add1e55fd6b5831da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/mvc/history/history-structure-view.js M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/structure.mako Log Message: ----------- Merge pull request #6241 from dannon/history_structure_cleanup Strip legacy history structure view Compare: https://github.com/galaxyproject/galaxy/compare/9b4697d3eda8...8fcc9332448a **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] b17beb: Move smart_str() calls inside pbkdf2_bin()
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b17bebcb30cd131ee1aab0f9bebeae5a9f3e6b04 https://github.com/galaxyproject/galaxy/commit/b17bebcb30cd131ee1aab0f9bebe… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Move smart_str() calls inside pbkdf2_bin() Commit: 6b21a35319a2916e9d4fa552ac32d8766d0b7c4e https://github.com/galaxyproject/galaxy/commit/6b21a35319a2916e9d4fa552ac32… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Use unicodify() Commit: 7b5e1903f13de4a245a04d42254f68ac81bfeecd https://github.com/galaxyproject/galaxy/commit/7b5e1903f13de4a245a04d42254f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Make pbkdf2_bin() faster `digest` was needlessly recalculated as `bytearray(u)` in the internal loop, instead make `_pseudorandom()` return both the bytestring and the list of character ordinals. Commit: 2ebe88718aa4c4b6bafcfd7dfc0d29bccf9df614 https://github.com/galaxyproject/galaxy/commit/2ebe88718aa4c4b6bafcfd7dfc0d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Unicodify bytearrays Commit: 9b4697d3eda8243ada0908a03b2e8810642eec04 https://github.com/galaxyproject/galaxy/commit/9b4697d3eda8243ada0908a03b2e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #6242 from nsoranzo/python3 Password encoding improvements Compare: https://github.com/galaxyproject/galaxy/compare/d4cb7c614ecb...9b4697d3eda8 **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] 6702fa: Remove defunct sharing column link
by GitHub 28 May '18

28 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 6702fa45cda22b3cc2d820d1075f2b02ae65abe5 https://github.com/galaxyproject/galaxy/commit/6702fa45cda22b3cc2d820d1075f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove defunct sharing column link Commit: 02feb1735086c8aca9feff740139bdebc1bc91d5 https://github.com/galaxyproject/galaxy/commit/02feb1735086c8aca9feff740139… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Fix broken collection_type_source tool and test. The tool wouldn't load after 8af243c176fd9c261277327750aaa71806add4ef and that caused the relevant tests to "SKIP" instead of failing outright. ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_collection_type_source Commit: 221897be04bff63a0ca91646bbb1d82d4cf3ea84 https://github.com/galaxyproject/galaxy/commit/221897be04bff63a0ca91646bbb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-26 (Sat, 26 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #6177 from guerler/remove_defunct_link [18.05] Remove defunct sharing column link Commit: c9641e1f13847fc7713a359076597217bf7c664a https://github.com/galaxyproject/galaxy/commit/c9641e1f13847fc7713a35907659… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-27 (Sun, 27 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #6227 from jmchilton/collection_type_source_regression [18.05] Fix broken collection_type_source tool and test. Compare: https://github.com/galaxyproject/galaxy/compare/e91f91b5f217...c9641e1f1384 **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] 6702fa: Remove defunct sharing column link
by GitHub 28 May '18

28 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6702fa45cda22b3cc2d820d1075f2b02ae65abe5 https://github.com/galaxyproject/galaxy/commit/6702fa45cda22b3cc2d820d1075f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove defunct sharing column link Commit: 02feb1735086c8aca9feff740139bdebc1bc91d5 https://github.com/galaxyproject/galaxy/commit/02feb1735086c8aca9feff740139… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Fix broken collection_type_source tool and test. The tool wouldn't load after 8af243c176fd9c261277327750aaa71806add4ef and that caused the relevant tests to "SKIP" instead of failing outright. ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_collection_type_source Commit: 221897be04bff63a0ca91646bbb1d82d4cf3ea84 https://github.com/galaxyproject/galaxy/commit/221897be04bff63a0ca91646bbb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-26 (Sat, 26 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #6177 from guerler/remove_defunct_link [18.05] Remove defunct sharing column link Commit: c9641e1f13847fc7713a359076597217bf7c664a https://github.com/galaxyproject/galaxy/commit/c9641e1f13847fc7713a35907659… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-27 (Sun, 27 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #6227 from jmchilton/collection_type_source_regression [18.05] Fix broken collection_type_source tool and test. Commit: d4cb7c614ecb2cc3193de89a87a1fe9661975d21 https://github.com/galaxyproject/galaxy/commit/d4cb7c614ecb2cc3193de89a87a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/820712144000...d4cb7c614ecb **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] 02feb1: Fix broken collection_type_source tool and test.
by GitHub 27 May '18

27 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 02feb1735086c8aca9feff740139bdebc1bc91d5 https://github.com/galaxyproject/galaxy/commit/02feb1735086c8aca9feff740139… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Fix broken collection_type_source tool and test. The tool wouldn't load after 8af243c176fd9c261277327750aaa71806add4ef and that caused the relevant tests to "SKIP" instead of failing outright. ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_collection_type_source Commit: c9641e1f13847fc7713a359076597217bf7c664a https://github.com/galaxyproject/galaxy/commit/c9641e1f13847fc7713a35907659… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-27 (Sun, 27 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #6227 from jmchilton/collection_type_source_regression [18.05] Fix broken collection_type_source tool and test. Compare: https://github.com/galaxyproject/galaxy/compare/221897be04bf...c9641e1f1384 **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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