- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] aba31b: [17.01] Restrict workflow scheduling within a hist...
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aba31bc0d484f3729b46a10b2b357b92fa826fae https://github.com/galaxyproject/galaxy/commit/aba31bc0d484f3729b46a10b2b35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Lets revisit the problem that background scheduling workflows (as is the default UI behavior as of 16.10) makes it easier for histories to contain datasets interleaved from different workflow invocations under certain reasonable conditions (https://github.com/galaxyproject/galaxy/issues/3474) Considering only a four year old workflow and tool feature set (no collection operations, no dynamic dataset discovery, only tool and input workflow modules), all workflows can and will fully schedule on the first scheduling iteration. Under those circumstances, this solution is functionally equivalent to history_local_serial_workflow_scheduling introduced #3520 - but should be more performant because all such workflows fully schedule in the first iteration and the double loop introduced here https://github.com/galaxyproject/galaxy/pull/3520/files#diff-d7e80a366f3965… is avoided for each workflow invocation for each iteration. This addresses both concerns I outlined [here](https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-2893…. For workflows that use certain classes of newer tools or newer workflow features - I'd argue this approach will not degrade as harshly as enabling history_local_serial_workflow_scheduling. For instance, imagine a workflow with a dynamic dataset collection output step (such as used by IUC tools Deseq2, Trinity, Stacks, and various Mothur tools) half way through that takes 24 hour of queue time to reach. Now imagine a user running 5 such workflows at once. - Without this and without history_local_serial_workflow_scheduling, the 5 workflows will each run as fast as possible and the UI will show as much of each workflow as can be scheduled but the order of the datsets may be shuffled. The workflows will be complete for the users in 48 hours. - With history_local_serial_workflow_scheduling enabled, only 1 workflow will be scheduled only half way for the first 24 hours and the user will be given no visual indication for why the other workflows are not running for 1 day. The final workflow output will take nearly a week to be complete for the users. - With this enabled - the new default in this commit - each workflow will be scheduled in two chunks but these chunks will be contingious and it should be fairly clear to the user what tool caused the discontinuity of the datasets in the history. So things are still mostly ordered, but the draw backs of history_local_serial_workflow_scheduling are avoided entirely. Namely, the other four workflows aren't hidden from the user without a UI indication and the workflows will still only take 48 hours to be complete and outputs ready for the user. The only drawback of this new default behavior is that you could potentially see some performance improvements by scheduling multiple workflow invocations within one history - but this was never a design goal in my mind when implementing background scheduling and under typical Galaxy use cases I don't think this would be worth the UI problems. So, the older behavior can be re-enabled by setting parallelize_workflow_scheduling_within_histories to True in galaxy.ini but it won't be on by default or really recommended if the Galaxy UI is being used. Commit: 07887be3a162678859e32c063dae024f0a8da25c https://github.com/galaxyproject/galaxy/commit/07887be3a162678859e32c063dae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge pull request #3820 from jmchilton/fixed_history_handler [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Commit: 190d1901a43a284c478876d2ec3567a1cc1af5a5 https://github.com/galaxyproject/galaxy/commit/190d1901a43a284c478876d2ec35… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dfbb80dd8b21...190d1901a43a

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[galaxyproject/galaxy] aba31b: [17.01] Restrict workflow scheduling within a hist...
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: aba31bc0d484f3729b46a10b2b357b92fa826fae https://github.com/galaxyproject/galaxy/commit/aba31bc0d484f3729b46a10b2b35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Lets revisit the problem that background scheduling workflows (as is the default UI behavior as of 16.10) makes it easier for histories to contain datasets interleaved from different workflow invocations under certain reasonable conditions (https://github.com/galaxyproject/galaxy/issues/3474) Considering only a four year old workflow and tool feature set (no collection operations, no dynamic dataset discovery, only tool and input workflow modules), all workflows can and will fully schedule on the first scheduling iteration. Under those circumstances, this solution is functionally equivalent to history_local_serial_workflow_scheduling introduced #3520 - but should be more performant because all such workflows fully schedule in the first iteration and the double loop introduced here https://github.com/galaxyproject/galaxy/pull/3520/files#diff-d7e80a366f3965… is avoided for each workflow invocation for each iteration. This addresses both concerns I outlined [here](https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-2893…. For workflows that use certain classes of newer tools or newer workflow features - I'd argue this approach will not degrade as harshly as enabling history_local_serial_workflow_scheduling. For instance, imagine a workflow with a dynamic dataset collection output step (such as used by IUC tools Deseq2, Trinity, Stacks, and various Mothur tools) half way through that takes 24 hour of queue time to reach. Now imagine a user running 5 such workflows at once. - Without this and without history_local_serial_workflow_scheduling, the 5 workflows will each run as fast as possible and the UI will show as much of each workflow as can be scheduled but the order of the datsets may be shuffled. The workflows will be complete for the users in 48 hours. - With history_local_serial_workflow_scheduling enabled, only 1 workflow will be scheduled only half way for the first 24 hours and the user will be given no visual indication for why the other workflows are not running for 1 day. The final workflow output will take nearly a week to be complete for the users. - With this enabled - the new default in this commit - each workflow will be scheduled in two chunks but these chunks will be contingious and it should be fairly clear to the user what tool caused the discontinuity of the datasets in the history. So things are still mostly ordered, but the draw backs of history_local_serial_workflow_scheduling are avoided entirely. Namely, the other four workflows aren't hidden from the user without a UI indication and the workflows will still only take 48 hours to be complete and outputs ready for the user. The only drawback of this new default behavior is that you could potentially see some performance improvements by scheduling multiple workflow invocations within one history - but this was never a design goal in my mind when implementing background scheduling and under typical Galaxy use cases I don't think this would be worth the UI problems. So, the older behavior can be re-enabled by setting parallelize_workflow_scheduling_within_histories to True in galaxy.ini but it won't be on by default or really recommended if the Galaxy UI is being used. Commit: 07887be3a162678859e32c063dae024f0a8da25c https://github.com/galaxyproject/galaxy/commit/07887be3a162678859e32c063dae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge pull request #3820 from jmchilton/fixed_history_handler [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Commit: dd439530509f12ede24f8e9763f2bdb5314e2c13 https://github.com/galaxyproject/galaxy/commit/dd439530509f12ede24f8e9763f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Compare: https://github.com/galaxyproject/galaxy/compare/52b5e62de498...dd439530509f

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[galaxyproject/galaxy] aba31b: [17.01] Restrict workflow scheduling within a hist...
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: aba31bc0d484f3729b46a10b2b357b92fa826fae https://github.com/galaxyproject/galaxy/commit/aba31bc0d484f3729b46a10b2b35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Lets revisit the problem that background scheduling workflows (as is the default UI behavior as of 16.10) makes it easier for histories to contain datasets interleaved from different workflow invocations under certain reasonable conditions (https://github.com/galaxyproject/galaxy/issues/3474) Considering only a four year old workflow and tool feature set (no collection operations, no dynamic dataset discovery, only tool and input workflow modules), all workflows can and will fully schedule on the first scheduling iteration. Under those circumstances, this solution is functionally equivalent to history_local_serial_workflow_scheduling introduced #3520 - but should be more performant because all such workflows fully schedule in the first iteration and the double loop introduced here https://github.com/galaxyproject/galaxy/pull/3520/files#diff-d7e80a366f3965… is avoided for each workflow invocation for each iteration. This addresses both concerns I outlined [here](https://github.com/galaxyproject/galaxy/issues/3816#issuecomment-2893…. For workflows that use certain classes of newer tools or newer workflow features - I'd argue this approach will not degrade as harshly as enabling history_local_serial_workflow_scheduling. For instance, imagine a workflow with a dynamic dataset collection output step (such as used by IUC tools Deseq2, Trinity, Stacks, and various Mothur tools) half way through that takes 24 hour of queue time to reach. Now imagine a user running 5 such workflows at once. - Without this and without history_local_serial_workflow_scheduling, the 5 workflows will each run as fast as possible and the UI will show as much of each workflow as can be scheduled but the order of the datsets may be shuffled. The workflows will be complete for the users in 48 hours. - With history_local_serial_workflow_scheduling enabled, only 1 workflow will be scheduled only half way for the first 24 hours and the user will be given no visual indication for why the other workflows are not running for 1 day. The final workflow output will take nearly a week to be complete for the users. - With this enabled - the new default in this commit - each workflow will be scheduled in two chunks but these chunks will be contingious and it should be fairly clear to the user what tool caused the discontinuity of the datasets in the history. So things are still mostly ordered, but the draw backs of history_local_serial_workflow_scheduling are avoided entirely. Namely, the other four workflows aren't hidden from the user without a UI indication and the workflows will still only take 48 hours to be complete and outputs ready for the user. The only drawback of this new default behavior is that you could potentially see some performance improvements by scheduling multiple workflow invocations within one history - but this was never a design goal in my mind when implementing background scheduling and under typical Galaxy use cases I don't think this would be worth the UI problems. So, the older behavior can be re-enabled by setting parallelize_workflow_scheduling_within_histories to True in galaxy.ini but it won't be on by default or really recommended if the Galaxy UI is being used. Commit: 07887be3a162678859e32c063dae024f0a8da25c https://github.com/galaxyproject/galaxy/commit/07887be3a162678859e32c063dae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge pull request #3820 from jmchilton/fixed_history_handler [17.01] Restrict workflow scheduling within a history to a fixed, random handler. Compare: https://github.com/galaxyproject/galaxy/compare/8f8526bf307d...07887be3a162

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[galaxyproject/galaxy] c9f602: Update datatypes_conf.xml.sample
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9f602d434104423078d2f0661e6acd8aa5c359b https://github.com/galaxyproject/galaxy/commit/c9f602d434104423078d2f0661e6… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update datatypes_conf.xml.sample Oups, I did it again :) Just add the sniffer for the mzData datatype Commit: dfbb80dd8b21f87af217fce49d14df396517c6d9 https://github.com/galaxyproject/galaxy/commit/dfbb80dd8b21f87af217fce49d14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3852 from lecorguille/patch-1 Update datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/200e475bc7cd...dfbb80dd8b21

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[galaxyproject/galaxy] 185aa3: Log when workflow scheduling is delayed about why.
by GitHub 31 Mar '17

31 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 185aa3968bd38cfe021f7bcec9bae02c12ae4c0b https://github.com/galaxyproject/galaxy/commit/185aa3968bd38cfe021f7bcec9ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Log when workflow scheduling is delayed about why. Currently the logs contain fairly uninformative step delayed messages that don't allow admins to understand why parts of the workflow are being delayed during scheduling. Here are some examples of before and after. When running the test: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_pause ``` Before these lines would show up: ``` galaxy.workflow.run DEBUG 2017-03-30 09:23:47,327 Workflow step 2 of invocation 1 invoked (174.149 ms) galaxy.workflow.run DEBUG 2017-03-30 09:23:47,347 Workflow step 3 of invocation 1 invoked (19.355 ms) galaxy.workflow.run DEBUG 2017-03-30 09:23:47,364 Workflow step 4 of invocation 1 delayed (16.262 ms) ``` Now these same lines are as follows: ``` galaxy.workflow.run DEBUG 2017-03-30 09:19:28,601 Workflow step 2 of invocation 1 invoked (172.849 ms) galaxy.workflow.run DEBUG 2017-03-30 09:19:28,619 Marking step 3 outputs delayed (executing pause step) galaxy.workflow.run DEBUG 2017-03-30 09:19:28,620 Workflow step 3 of invocation 1 invoked (17.999 ms) galaxy.workflow.run DEBUG 2017-03-30 09:19:28,633 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (13.398 ms) ``` Also, when running the test: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections_3 ``` Before these lines would be printed: ``` galaxy.workflow.run DEBUG 2017-03-30 09:25:35,910 Workflow step 4 of invocation 1 invoked (281.479 ms) galaxy.workflow.run DEBUG 2017-03-30 09:25:35,937 Workflow step 5 of invocation 1 delayed (25.904 ms) galaxy.workflow.run DEBUG 2017-03-30 09:25:35,970 Workflow step 6 of invocation 1 delayed (32.597 ms) ``` Now these same lines are as follows: ``` galaxy.workflow.run DEBUG 2017-03-30 09:27:54,270 Workflow step 4 of invocation 1 invoked (295.826 ms) galaxy.workflow.run DEBUG 2017-03-30 09:27:54,315 Workflow step 5 of invocation 1 delayed (dependent collection [1] not yet populated with datasets) (44.581 ms) galaxy.workflow.run DEBUG 2017-03-30 09:27:54,326 Workflow step 6 of invocation 1 delayed (dependent step [5] delayed, so this step must be delayed) (10.804 ms) ``` When running workflows with steps that depend explicitly on other steps (instead of implicitly between dataset connections), lines such as: ``` galaxy.workflow.run DEBUG 2017-03-30 09:33:52,966 Marking step 3 outputs delayed (workflow paused at this step waiting for review) galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (0.157 ms) galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 5 of invocation 1 delayed (depends on step [4] but that step has not been invoked yet) (0.084 ms) ``` and ``` galaxy.workflow.run DEBUG 2017-03-30 09:33:57,090 Workflow step 5 of invocation 1 delayed (depends on step [4] but one or more jobs created from that step have not finished yet) (0.144 ms) ``` now may appear. Commit: b8692309484c3a671145684277201ed7aaf444dd https://github.com/galaxyproject/galaxy/commit/b8692309484c3a67114568427720… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Re-arrange workflow scheduling logic according to @nsoranzo's suggestions. Commit: 200e475bc7cd340401f46028fc234a1e7c2ad87c https://github.com/galaxyproject/galaxy/commit/200e475bc7cd340401f46028fc23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3849 from jmchilton/improved_scheduling_delay_logging Log reason when workflow scheduling of a step is delayed. Compare: https://github.com/galaxyproject/galaxy/compare/90ac2f435662...200e475bc7cd

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[galaxyproject/galaxy] 64f8e1: Stricter checks for GFF/GFF3/GTF sniffing
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64f8e1cf3c27d86f625736ecd0438df7d329ca2d https://github.com/galaxyproject/galaxy/commit/64f8e1cf3c27d86f625736ecd043… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Stricter checks for GFF/GFF3/GTF sniffing Check frame column in Gff.sniff() and Gtf.sniff() . Parse attributes column in Gff3.sniff() with a specific function to prevent non-compliant GTF files being recognised as GFF3. Commit: 32e8a2023deef55db60c61910321e366f40396d6 https://github.com/galaxyproject/galaxy/commit/32e8a2023deef55db60c61910321… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix import order for lib/galaxy/datatypes/util/gff_util.py Commit: 90ac2f43566220cd82a771afd2040a1410addb4a https://github.com/galaxyproject/galaxy/commit/90ac2f43566220cd82a771afd204… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #3832 from nsoranzo/gff_sniff_fix Stricter checks for GFF/GFF3/GTF sniffing Compare: https://github.com/galaxyproject/galaxy/compare/3d2833fdb72b...90ac2f435662

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[galaxyproject/galaxy] 5e11b5: Add the possibility to uninstall conda environment...
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e11b54da59e09f9e31b71c00f3ecaf99842a0c5 https://github.com/galaxyproject/galaxy/commit/5e11b54da59e09f9e31b71c00f3e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add the possibility to uninstall conda environments that are not in use by Galaxy Commit: 9ecb71ecf76df08fee7829e28db081ec2dc3fb0a https://github.com/galaxyproject/galaxy/commit/9ecb71ecf76df08fee7829e28db0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Build toolbox_requirements_status only once (thanks for the review @nsoranzo) Commit: 69e2af50317abefa98748b8fc84db2870552b589 https://github.com/galaxyproject/galaxy/commit/69e2af50317abefa98748b8fc84d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Restore render_tool_centric_table function Commit: 3d2833fdb72b9d967d4ec05581c7e0c1aa3a81a1 https://github.com/galaxyproject/galaxy/commit/3d2833fdb72b9d967d4ec05581c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Merge pull request #3750 from mvdbeek/remove_unused_envs Add the possibility to uninstall conda environments that are not in u… Compare: https://github.com/galaxyproject/galaxy/compare/94c357f608f9...3d2833fdb72b

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[galaxyproject/galaxy] d10f74: The user controller functions for changing informa...
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality. Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915 https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here. Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Strip out unnecessary user address editing. Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452 https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Update docstring to explicitly mention this as a temporary endpoint. Commit: b46ac475a93fbf0da71272861677a00a3877b91b https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix verbiage in temporary method. Commit: 64036a441284151e1b1a3e9305537d526005ff3a https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge pull request #3656 from dannon/admin-userinfo-edit-fix [17.01] Admin user information editing Commit: 0636053901545a26662ed8f42a15bb67407f2231 https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use pgcalc when possible Commit: 895351cdf8e8867452d28dffb89a2067eabfadb3 https://github.com/galaxyproject/galaxy/commit/895351cdf8e8867452d28dffb89a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- initial working async recalc Commit: 45d75e3da55e43a4444c1a7982e1ea31e1aa5cb7 https://github.com/galaxyproject/galaxy/commit/45d75e3da55e43a4444c1a7982e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Encode userid in messages. Commit: c373bf27e79e48bc2e8ba983e9f08abde16db4df https://github.com/galaxyproject/galaxy/commit/c373bf27e79e48bc2e8ba983e9f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Change handling of declare in queue_async_task Commit: 00b1591f05af4743d8b16b7d1bbbbc99a3974adb https://github.com/galaxyproject/galaxy/commit/00b1591f05af4743d8b16b7d1bbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix inline doc Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11 https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- improve 17.01 get galaxy release notes Commit: 53c00df805e7ae7e509c08374bc941d31d20000d https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Rename send_local_controL_task, add at least a tiny bit of documentation. Commit: d4b677bc38b221678bc991e0fddc43622accb928 https://github.com/galaxyproject/galaxy/commit/d4b677bc38b221678bc991e0fddc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3669 from dannon/logout-recalc-improvements [17.01] Logout recalc improvements Commit: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21 https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3670 from martenson/fix-RN1701 [17.01] improve 17.01 get galaxy release notes Commit: 0997348a1c0a450986d376a96af024c73d4c7f37 https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix tool search idnex building for tools with / in id and not from TS Commit: c11cb3dd4572e7a4f1f814a31a45477f9ecd5ae9 https://github.com/galaxyproject/galaxy/commit/c11cb3dd4572e7a4f1f814a31a45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix typo spotted by :beer: :eyes: Commit: 169b45b138685164010043be95cefe8148c6f713 https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix step name display for 17.01 Commit: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930 https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #3680 from martenson/fix-id-indexing [17.01] fix tool search index building for tools with slash in id and not from TS Commit: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3681 from guerler/fix_name_display [17.01] Fix step name display for 17.01 Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- [17.01] Fix container resolver log statements exposing pointers. These log statements: ``` 2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None] 2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None] 2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>] ``` Become: ``` 2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None] 2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None] 2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]] ``` Rebased with suggestion from @nsoranzo :eagle::eyes: Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3 https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #3679 from jmchilton/fix_logs [17.01] Fix container resolver log statements exposing pointers. Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5 https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Annotate converters that appear to need galaxy on PYTHONPATH. Should fix #3499 (thanks for the explicit heads up @mvdbeek). Commit: 93a802bd450658f0c66d4226c626112e8163d5a6 https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c626… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes [17.01] Annotate converters that appear to need galaxy on PYTHONPATH. Commit: 02f3a2737dd1c48574df9bf8e51ce43e6789bf1e https://github.com/galaxyproject/galaxy/commit/02f3a2737dd1c48574df9bf8e51c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: 7988ae59f5b94b952bd1965b76250ad3f21525d6 https://github.com/galaxyproject/galaxy/commit/7988ae59f5b94b952bd1965b7625… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Allow display of install_resolver_checkbox when installing data manager tools by merging select_shed_tool_panel_config.mako functionality into select_tool_panel_section.mako (thx @nsoranzo for this suggestion). Commit: e8922295bd5753e0be262f141b25a05622972ee6 https://github.com/galaxyproject/galaxy/commit/e8922295bd5753e0be262f141b25… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove checks for `includes_tools_for_display_in_tool_panel` and `includes_tools_for_display_in_tool_panel` when determining if initiate_repository_installation.mako should be posted to. It is sufficient to check that select_tool_panel_section_button has been clicked. Commit: 2df727cb05d8d15e14a23a4f8c1da920bfde999d https://github.com/galaxyproject/galaxy/commit/2df727cb05d8d15e14a23a4f8c1d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Adjust wording of datatype converter install test. Commit: 1b9a2868a17899787bf65181f96892596b16b51b https://github.com/galaxyproject/galaxy/commit/1b9a2868a17899787bf65181f968… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows Commit: 376212eff900d28450165ddf715f3d9a29870ca9 https://github.com/galaxyproject/galaxy/commit/376212eff900d28450165ddf715f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix for uploading rdata datasets when explicitly declaring datatype. Now that ext's are forced to be all lowercase, you cannot upload a dataset with any uppercase characters in the extension. TODO: An additional fix directly for the upload tool/datatype widget should be pursued that will prevent these issues. Commit: fa37f67786b88b5d1c4138a142efccf3cc42d219 https://github.com/galaxyproject/galaxy/commit/fa37f67786b88b5d1c4138a142ef… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Commit: 7429ded33e1af8214f2ca20563698f73dd3869d3 https://github.com/galaxyproject/galaxy/commit/7429ded33e1af8214f2ca2056369… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix datetime import Commit: aaafbe956f343eb6d34dbdcec0b8b937e439334a https://github.com/galaxyproject/galaxy/commit/aaafbe956f343eb6d34dbdcec0b8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- add the activation functionality to API users controller it was invoked but not included resulting in errors Commit: 642956a899ea2b97348be698bd81dd11a85d113e https://github.com/galaxyproject/galaxy/commit/642956a899ea2b97348be698bd81… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- remove unused import Commit: 54fb1a433d061d398d67a0cb3e80ea1406226898 https://github.com/galaxyproject/galaxy/commit/54fb1a433d061d398d67a0cb3e80… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- only request verificaion when needed thanks @nsoranzo Commit: 56c710adbc1f10579511c506503493241df4176c https://github.com/galaxyproject/galaxy/commit/56c710adbc1f10579511c5065034… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- reqork the activation logic when email is changed thanks to @nsoranzo for help Commit: cfa3e29cadf0960f01735a2ad43b64ac9c17e031 https://github.com/galaxyproject/galaxy/commit/cfa3e29cadf0960f01735a2ad43b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge pull request #3686 from mvdbeek/datamanager_conda_install [17.01] Allow display of install_resolver_checkbox when installing data manag… Commit: 6ab5cc1caf8c9fc0d4ce311c43988d12ea2ae6bb https://github.com/galaxyproject/galaxy/commit/6ab5cc1caf8c9fc0d4ce311c4398… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-18 (Sat, 18 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3771 from martenson/fix-users-api [17.01] Fixes for users API Commit: e3e24facc72103dadeca2dc72c9d038f907eb10e https://github.com/galaxyproject/galaxy/commit/e3e24facc72103dadeca2dc72c9d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #3766 from blankenberg/17.01-rdata-upload-fix [17.01] Fix for uploading rdata datasets when explicitly declaring datatype. Commit: 12eb3838496f373e429235cd8e75117baf682005 https://github.com/galaxyproject/galaxy/commit/12eb3838496f373e429235cd8e75… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- fix xss thanks to @erasche Commit: 2528a89bd087786c458c86d6ac78c24e8fb7f51d https://github.com/galaxyproject/galaxy/commit/2528a89bd087786c458c86d6ac78… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids Commit: e3255fd3cb7c1b0cf9ce9fa82f0a4a9c39719f19 https://github.com/galaxyproject/galaxy/commit/e3255fd3cb7c1b0cf9ce9fa82f0a… Author: nekrut <anton(a)nekrut.org> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- made collection ops help sections slightly more readable Commit: d9c3a0bb57e63a1849bb3f55c056ae0384a2279a https://github.com/galaxyproject/galaxy/commit/d9c3a0bb57e63a1849bb3f55c056… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- Update unzip_collection.xml fixed typos identified by @mvdbeek Commit: 80ecc79a4cb8fa3dbaf9b3348216df6f9387a91c https://github.com/galaxyproject/galaxy/commit/80ecc79a4cb8fa3dbaf9b3348216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 Commit: 490e565611b5e3a22124d937e22cf0363afb62f6 https://github.com/galaxyproject/galaxy/commit/490e565611b5e3a22124d937e22c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3790 from galaxyproject/release_16.07 merge 16.07 into 16.10 Commit: ec88dda1e9c926341b87bc7e19b7b5842eb92ddb https://github.com/galaxyproject/galaxy/commit/ec88dda1e9c926341b87bc7e19b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3791 from galaxyproject/release_16.10 merge 16.10 into 17.01 Commit: c84b3ba0b8f9de983d43ea17c165856d23960911 https://github.com/galaxyproject/galaxy/commit/c84b3ba0b8f9de983d43ea17c165… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- Merge pull request #3788 from jmchilton/backport_collection_option_help_fixes [17.01] Backport collection operation help fixes Commit: 15aa0bd615726ed46fa7beec9a364bb3c11df9f2 https://github.com/galaxyproject/galaxy/commit/15aa0bd615726ed46fa7beec9a36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix problem with cleaning up jobs in local runner. Fixes #3801 (broken in b78287f as part of #3291). Commit: 65cbddee7c3bc2d772686b261aaf853f84f76235 https://github.com/galaxyproject/galaxy/commit/65cbddee7c3bc2d772686b261aaf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #3803 from jmchilton/1701_fixes_0 [17.01] Fix problem with cleaning up jobs in local runner. Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2 https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: 3068c9f053554c448a30388d46b91a6979e39cb7 https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment. Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822. Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559 https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3824 from jmchilton/more_tool_env_fixes [17.01] More CONVERTER fixes for restricting tools' Python environment. Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Commit: 4beb98e973000e0bd51b06ad35301ddb8b905ec1 https://github.com/galaxyproject/galaxy/commit/4beb98e973000e0bd51b06ad3530… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- [17.01] By default, do not allow workflow invocations to schedule indefinitely. Give up after a month but allow admins to reduce this amount as well. Commit: 8f8526bf307d083c64330859793c112a9823b5d8 https://github.com/galaxyproject/galaxy/commit/8f8526bf307d083c64330859793c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge pull request #3659 from jmchilton/1701_maximum_workflow_invocation_duration [17.01] By default, do not allow workflow invocations to schedule indefinitely. Commit: 52b5e62de498f08ccd55f792d555c884f8bd6e98 https://github.com/galaxyproject/galaxy/commit/52b5e62de498f08ccd55f792d555… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M display_applications/igv/bigwig.xml M doc/source/releases/17.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/run.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako A templates/webapps/galaxy/user/manage_info.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Compare: https://github.com/galaxyproject/galaxy/compare/3a2ff46c2817...52b5e62de498

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[galaxyproject/galaxy] 4beb98: [17.01] By default, do not allow workflow invocati...
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4beb98e973000e0bd51b06ad35301ddb8b905ec1 https://github.com/galaxyproject/galaxy/commit/4beb98e973000e0bd51b06ad3530… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- [17.01] By default, do not allow workflow invocations to schedule indefinitely. Give up after a month but allow admins to reduce this amount as well. Commit: 8f8526bf307d083c64330859793c112a9823b5d8 https://github.com/galaxyproject/galaxy/commit/8f8526bf307d083c64330859793c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge pull request #3659 from jmchilton/1701_maximum_workflow_invocation_duration [17.01] By default, do not allow workflow invocations to schedule indefinitely. Commit: 94c357f608f93ccf9c0494e07599cae85c15782d https://github.com/galaxyproject/galaxy/commit/94c357f608f93ccf9c0494e07599… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/10e89cfc8515...94c357f608f9

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[galaxyproject/galaxy] 4beb98: [17.01] By default, do not allow workflow invocati...
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 4beb98e973000e0bd51b06ad35301ddb8b905ec1 https://github.com/galaxyproject/galaxy/commit/4beb98e973000e0bd51b06ad3530… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- [17.01] By default, do not allow workflow invocations to schedule indefinitely. Give up after a month but allow admins to reduce this amount as well. Commit: 8f8526bf307d083c64330859793c112a9823b5d8 https://github.com/galaxyproject/galaxy/commit/8f8526bf307d083c64330859793c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge pull request #3659 from jmchilton/1701_maximum_workflow_invocation_duration [17.01] By default, do not allow workflow invocations to schedule indefinitely. Compare: https://github.com/galaxyproject/galaxy/compare/a2b5c41de005...8f8526bf307d

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[galaxyproject/usegalaxy-playbook] 2d30ae: remove game from slides
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2d30ae8bc3cd4408c5814f7a7738f4df2823d99d https://github.com/galaxyproject/usegalaxy-playbook/commit/2d30ae8bc3cd4408… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- remove game from slides Commit: d3df934c0c0672f040c99aca5d38faf02754b7ca https://github.com/galaxyproject/usegalaxy-playbook/commit/d3df934c0c0672f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- change link from nekrut wiki to hub Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/9200160c4815...…

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[galaxyproject/infrastructure-playbook] e83536: add TS rewrites
by GitHub 30 Mar '17

30 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e8353672357a651d80e1ef562a4346718dbeb9fa https://github.com/galaxyproject/infrastructure-playbook/commit/e8353672357… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- add TS rewrites Commit: 2afa80ca68ee81b9098f42f98418b392e3a7c459 https://github.com/galaxyproject/infrastructure-playbook/commit/2afa80ca68e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M ansible.cfg M common_roles M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml A jetstreamdockerenv/README.md A jetstreamdockerenv/group_vars/all.yml A jetstreamdockerenv/group_vars/baseinstances.yml A jetstreamdockerenv/group_vars/imageinstances.yml A jetstreamdockerenv/inc_clouds_yaml.yml A jetstreamdockerenv/inc_delete.yml A jetstreamdockerenv/inc_spawn.yml A jetstreamdockerenv/inventory A jetstreamdockerenv/secret_group_vars/instances.yml A jetstreamdockerenv/snapshot_docker_base.yml A jetstreamdockerenv/snapshot_docker_image.yml A jetstreamdockerenv/ssh_config.jetstream_iu A jetstreamdockerenv/ssh_config.jetstream_tacc M roles/docker/README.md M roles/docker/defaults/main.yml M roles/docker/tasks/main.yml A roles/docker/tasks/ssl-ca.yml A roles/docker/tasks/ssl-client.yml M roles/docker/tasks/ssl-server.yml M taccenv/group_vars/galaxyservers.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Commit: 922a0a6e942aa677da4d28237be40169f9c11543 https://github.com/galaxyproject/infrastructure-playbook/commit/922a0a6e942… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M common_roles Log Message: ----------- update submodule Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/2c6e2d24d1…

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[galaxyproject/galaxy] 11860d: Attempt to improve the robustness and verboseness ...
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11860d55fb7a51985d4027e35b6a6ead78748cfa https://github.com/galaxyproject/galaxy/commit/11860d55fb7a51985d4027e35b6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test. - When registering, put a little pause in after clicking to ensure the browser has a chance to submit the request before continuing to check if indeed the user is logged in. - If the user doesn't appear to be logged in, dump the contents of the user menu out so we can see if a different user is logged in or if there is no log in. - Attempt to be more robust about conditions being waited on when clicking history option menu - in case clicks were being fired during jQuery transitions or something. xref #3838 Commit: 10e89cfc851526973b8234257ba9039b5961160f https://github.com/galaxyproject/galaxy/commit/10e89cfc851526973b8234257ba9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #3841 from jmchilton/selenium_fixes_7 Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test. Compare: https://github.com/galaxyproject/galaxy/compare/777db9829b41...10e89cfc8515

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[galaxyproject/galaxy] 606c32: Allow upload to collections.
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 606c32998f94a5e94921315a1be66d570e68c63d https://github.com/galaxyproject/galaxy/commit/606c32998f94a5e94921315a1be6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Allow upload to collections. - New upload tab for "Collections". - This has a new option to select "Collection Type" in footer. - Collection upload geared toward homogeneous datasets - must specify genome and file format for all files. - New button "Build" after all individual datasets have finished their upload to the server. - Clicking "Build" launches the appropriate collection builder for selected collection type. - By default, uploading a collection hides the original uploaded datasets (can be unchecked). Implement tests for all uploaded collection types. Commit: 777db9829b41a0ffde892ac9fe11846f5af93b91 https://github.com/galaxyproject/galaxy/commit/777db9829b41a0ffde892ac9fe11… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3696 from jmchilton/upload_collection Allow uploading to collections. Compare: https://github.com/galaxyproject/galaxy/compare/a0b4ab63d288...777db9829b41

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[galaxyproject/galaxy] 790a35: Properly handle multiple hidden datasets when popu...
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 790a35ea2e605c3b15e3e59df07f3febc9688f8d https://github.com/galaxyproject/galaxy/commit/790a35ea2e605c3b15e3e59df07f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly handle multiple hidden datasets when populating data select options Commit: a0b4ab63d288d04ddd7b4372090c1e956653f4e6 https://github.com/galaxyproject/galaxy/commit/a0b4ab63d288d04ddd7b4372090c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3842 from guerler/fix_hidden_datasets Properly handle multiple hidden datasets when populating data select options Compare: https://github.com/galaxyproject/galaxy/compare/ab11adfa501a...a0b4ab63d288

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[galaxyproject/galaxy] 371d27: Disable tool shed test function that fails frequen...
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 371d277c5514d0e7d033c8724f8d5cc58878f6bc https://github.com/galaxyproject/galaxy/commit/371d277c5514d0e7d033c8724f8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Disable tool shed test function that fails frequently on Jenkins. Commit: ab11adfa501ababc2d1f20e731727b8df787b803 https://github.com/galaxyproject/galaxy/commit/ab11adfa501ababc2d1f20e73172… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge pull request #3819 from jmchilton/disable_pesky_ts_test Disable tool shed test function that fails frequently on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/66ca698f5aa4...ab11adfa501a

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[galaxyproject/usegalaxy-playbook] 920016: Add a conda env for set_meta on handlers
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9200160c4815cb2dea25df3e6448993e4cecc167 https://github.com/galaxyproject/usegalaxy-playbook/commit/9200160c4815cb2d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M templates/supervisor/galaxy_handler.j2 Log Message: ----------- Add a conda env for set_meta on handlers

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[galaxyproject/usegalaxy-playbook] ed7a52: add IE files generated by run
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed7a52e63097edab6710737b6950348b69286033 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed7a52e63097edab… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako A production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml A production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js A production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako A production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako A production/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample A production/files/interactive_environments/plugins/neo/config/neo.ini.sample A production/files/interactive_environments/plugins/neo/config/neo.xml A production/files/interactive_environments/plugins/neo/static/js/neo.js A production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako A production/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/config/rstudio.xml M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/Dockerfile M production/files/interactive_environments/proxy/lib/main.js M production/files/interactive_environments/proxy/lib/mapper.js M production/files/interactive_environments/proxy/lib/proxy.js M production/files/interactive_environments/proxy/package.json Log Message: ----------- add IE files generated by run

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[galaxyproject/galaxy] d8af12: Update __init__.py
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2 https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: 3068c9f053554c448a30388d46b91a6979e39cb7 https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment. Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822. Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559 https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3824 from jmchilton/more_tool_env_fixes [17.01] More CONVERTER fixes for restricting tools' Python environment. Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Commit: 66ca698f5aa4e897a792fe47f81526ed703bc154 https://github.com/galaxyproject/galaxy/commit/66ca698f5aa4e897a792fe47f815… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3829 from galaxyproject/release_17.01 Merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/07be669ed0d3...66ca698f5aa4

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[galaxyproject/galaxy] 21e573: Fix for EtherCalc IE image specification.
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21e5731355ebcbba2bb4280844091576c7700abf https://github.com/galaxyproject/galaxy/commit/21e5731355ebcbba2bb428084409… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample Log Message: ----------- Fix for EtherCalc IE image specification. Will allow EtherCalc to work in 17.05. Commit: 07be669ed0d392fde70a79aa442bae028cfe3fcd https://github.com/galaxyproject/galaxy/commit/07be669ed0d392fde70a79aa442b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample Log Message: ----------- Merge pull request #3825 from blankenberg/ethercalc Fix for EtherCalc IE image specification. Compare: https://github.com/galaxyproject/galaxy/compare/c24ed4f8fa2f...07be669ed0d3

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[galaxyproject/galaxy] 1fbdb3: Have IGV bigWig display application make use of bu...
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Compare: https://github.com/galaxyproject/galaxy/compare/70b22dffc288...a2b5c41de005

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[galaxyproject/galaxy] f17435: fix link to galaxy logo
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f174358b9542610ffa4c00588096a4e80583ae0a https://github.com/galaxyproject/galaxy/commit/f174358b9542610ffa4c00588096… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/releases/_header.rst Log Message: ----------- fix link to galaxy logo Commit: 85093dc13ad06eb8d4896f01d934846cd57c1473 https://github.com/galaxyproject/galaxy/commit/85093dc13ad06eb8d4896f01d934… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- reword topic Commit: e02e2cb09e245ab5cbbe48d532e4f3ffe9a1612a https://github.com/galaxyproject/galaxy/commit/e02e2cb09e245ab5cbbe48d532e4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/index.rst Log Message: ----------- improve doc-build-urself docs Commit: b4feb85f11280935b0ce13ea5d3693122f4319e8 https://github.com/galaxyproject/galaxy/commit/b4feb85f11280935b0ce13ea5d36… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/ts_api_doc.rst Log Message: ----------- improve accessibility of API docs for both Galaxy and TS Commit: bdcf4807ce5f2d3c1f12cd23120f4f5ec55f0067 https://github.com/galaxyproject/galaxy/commit/bdcf4807ce5f2d3c1f12cd23120f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md Log Message: ----------- add basic Reports documentation Commit: c24ed4f8fa2f277757eccb8e5cdb7d324a3a3521 https://github.com/galaxyproject/galaxy/commit/c24ed4f8fa2f277757eccb8e5cdb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst Log Message: ----------- Merge pull request #3812 from martenson/admin-docs-imp api & reports documentation improvements Compare: https://github.com/galaxyproject/galaxy/compare/cfd8ec776e69...c24ed4f8fa2f

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[galaxyproject/galaxy] b18736: Updating Cytoscape viewer in Viz/Charts, replacing...
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b18736d82447637d7257f3fd406e1c40a02afed0 https://github.com/galaxyproject/galaxy/commit/b18736d82447637d7257f3fd406e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating Cytoscape viewer in Viz/Charts, replacing the previous 'basic' folder name to 'viewer' and updating the wrapper.js file Commit: 69b9b575172086376657433ff0a066bf732d4e4d https://github.com/galaxyproject/galaxy/commit/69b9b575172086376657433ff0a0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding basic options like layout name and curve style for cytoscape graphs Commit: 504f4ac670b3135b9df885d9d884d176dc494768 https://github.com/galaxyproject/galaxy/commit/504f4ac670b3135b9df885d9d884… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding min and max zoom settings for graphs Commit: b437be2c566c431267d814b7718380969b8bd3b7 https://github.com/galaxyproject/galaxy/commit/b437be2c566c431267d814b77183… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding SIF to JSON converter for Cytoscape viewer Commit: 2275d098eeeaeb115fa69b0d1fa7856f7bfa4d18 https://github.com/galaxyproject/galaxy/commit/2275d098eeeaeb115fa69b0d1fa7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph resize property for window resize Commit: 56338972b9767b9e0be474d99b8f4ea915e6dd96 https://github.com/galaxyproject/galaxy/commit/56338972b9767b9e0be474d99b8f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Extending the sif to json converter to allow single nodes to be plotted Commit: c6bd499d001b667f20bd4caf99612a3d56b200c1 https://github.com/galaxyproject/galaxy/commit/c6bd499d001b667f20bd4caf9961… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding node text and colors for graphs Commit: 2a6391550b2256c18f2671b2260f58746b507db7 https://github.com/galaxyproject/galaxy/commit/2a6391550b2256c18f2671b2260f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding directed/undirected attribute for graphs Commit: 9f42821f57c3126826ebc773407ac02084a965ea https://github.com/galaxyproject/galaxy/commit/9f42821f57c3126826ebc773407a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Breadth First Search for cytoscape graphs. Tapping any node plays BFS Commit: a2affcc618ae5ec8d0f36e55a0f7ef15de53ef68 https://github.com/galaxyproject/galaxy/commit/a2affcc618ae5ec8d0f36e55a0f7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Depth First Search for cytoscape graphs Commit: c658ef3c7efd56986c096dc71a73c06260351ccc https://github.com/galaxyproject/galaxy/commit/c658ef3c7efd56986c096dc71a73… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-19 (Sun, 19 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Kruskal algorithm for graphs and color choosing scheme for highlighted edges Commit: 0d95b4e2079aa0d442a2e030fe7606c7627bd1e6 https://github.com/galaxyproject/galaxy/commit/0d95b4e2079aa0d442a2e030fe76… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph traversal types Commit: cbc7dd17fcf3bfe9eecdd8a0577a6d63e565f509 https://github.com/galaxyproject/galaxy/commit/cbc7dd17fcf3bfe9eecdd8a0577a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing unused if else Commit: 50417de1b4971db4fe42b1c797024081c66deef5 https://github.com/galaxyproject/galaxy/commit/50417de1b4971db4fe42b1c79702… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding A* search algorithm for finding shortest distance between root and destination Commit: 50a51575f1d4f0a7ccc8c476ab0ad7de2ffca3c8 https://github.com/galaxyproject/galaxy/commit/50a51575f1d4f0a7ccc8c476ab0a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M 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test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merging with dev Commit: 086dfd71ca4b82a7aeb2421cb2a08e76975639b3 https://github.com/galaxyproject/galaxy/commit/086dfd71ca4b82a7aeb2421cb2a0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing tabs and updating time out for path animation Commit: 04941d0aea0be51fd169cb332070f6a420b71d0c https://github.com/galaxyproject/galaxy/commit/04941d0aea0be51fd169cb332070… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Fixing review comments- removing sliders for colors and zoom and adding color pickers, updating values for min and max zoom and replacing logo of the plugin Commit: f1206a8e352b9ef4288aa08bd18ac6b3387c790e https://github.com/galaxyproject/galaxy/commit/f1206a8e352b9ef4288aa08bd18a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map Log Message: ----------- Updating library files Commit: 90c534570876c0f76a02458433960d9923a96ec3 https://github.com/galaxyproject/galaxy/commit/90c534570876c0f76a0245843396… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M 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config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding styles for selected nodes and updating default colors for nodes, edges and higlighted elements Commit: 0809c19c36cf5f73f60928bd11c6a091c96e06b2 https://github.com/galaxyproject/galaxy/commit/0809c19c36cf5f73f60928bd11c6… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M 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static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merging with dev Commit: cfd8ec776e692fe2706c1bd7cc40dcf1a8c56832 https://github.com/galaxyproject/galaxy/commit/cfd8ec776e692fe2706c1bd7cc40… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #3817 from bgruening/cytoscape Cytoscape as the Galaxy charts plugin Compare: https://github.com/galaxyproject/galaxy/compare/db09acb02637...cfd8ec776e69

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[galaxyproject/galaxy] d270a2: Allow non-ready jobs in collection builder.
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d270a21908a8b1d203ac653d96177ae921cb5a5d https://github.com/galaxyproject/galaxy/commit/d270a21908a8b1d203ac653d9617… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/history/history-view-edit.js M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Allow non-ready jobs in collection builder. This includes two parallel changes to the Selenium tests. - It adds a decorator to allow retrying certain atomic actions that may occur during jQuery transitions automatically. - It refactors things to allow waiting on HIDs to become visible instead of just green. Commit: 3d13a2bb4f75f2224f24511aa96c9f97d8ff3e44 https://github.com/galaxyproject/galaxy/commit/3d13a2bb4f75f2224f24511aa96c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix transiently failing Selenium test of tool form re-running. Reworks addition of staleness checkers introduced in #3780. Commit: c9d06aeb41d9e15c07dddf4fff67630f2ee2237d https://github.com/galaxyproject/galaxy/commit/c9d06aeb41d9e15c07dddf4fff67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M test/api/test_history_contents.py Log Message: ----------- Allow collection creation API to hide original datasets during creation. Commit: 5fa546749bcc7b5a8c2579c46a1360217d4883c8 https://github.com/galaxyproject/galaxy/commit/5fa546749bcc7b5a8c2579c46a13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/style/less/ui/paired-collection-creator.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/style/blue/base.css Log Message: ----------- Allow collection builders to hide original datasets. Commit: 82ca6931c02b1a4b13fe9dc4e86c7ace6029f5d5 https://github.com/galaxyproject/galaxy/commit/82ca6931c02b1a4b13fe9dc4e86c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py Log Message: ----------- More test cases for collection builders. - Add test case for building paired lists. - Add tests for new hide original datasets functionality for lists and paired lists. Commit: 810a96caef678462369604afd2a52b5c25c9268c https://github.com/galaxyproject/galaxy/commit/810a96caef678462369604afd2a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge branch 'dev' into collection_builder_enhancements Commit: db09acb0263751560714c74d9f7c9ea6fed649ae https://github.com/galaxyproject/galaxy/commit/db09acb0263751560714c74d9f7c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/style/blue/base.css M test/api/test_history_contents.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3806 from jmchilton/collection_builder_enhancements Small enhancements for collection builders Compare: https://github.com/galaxyproject/galaxy/compare/967d0b6c0aef...db09acb02637

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[galaxyproject/usegalaxy-playbook] 7f263c: Update Pulsar on Test, resolve dependencies on Bri...
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7f263c2773615da2c8a60045b1ec739d228bdc16 https://github.com/galaxyproject/usegalaxy-playbook/commit/7f263c2773615da2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M files/galaxy/common/dynamic_rules/bridges_select.py M files/pulsar/common/config/bridges_dependency_resolvers_conf.xml M stage/group_vars/pulsarservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Update Pulsar on Test, resolve dependencies on Bridges using conda (after modules) and run rnaSPAdes on Bridges Commit: 49a1769f06256411fcbf0c92a2f4625746bcd26e https://github.com/galaxyproject/usegalaxy-playbook/commit/49a1769f06256411… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml A roles/galaxyprojectdotorg.interactive_environments/templates/generic_apache.conf.j2 A roles/galaxyprojectdotorg.interactive_environments/templates/generic_nginx.conf.j2 M roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2 M roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2 M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M stage/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M stage/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M stage/files/interactive_environments/plugins/common/templates/ie.mako A stage/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample A stage/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml A stage/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js A stage/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako A stage/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M stage/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M stage/files/interactive_environments/plugins/jupyter/config/jupyter.xml M stage/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M stage/files/interactive_environments/plugins/jupyter/templates/jupyter.mako A stage/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample A stage/files/interactive_environments/plugins/neo/config/neo.ini.sample A stage/files/interactive_environments/plugins/neo/config/neo.xml A stage/files/interactive_environments/plugins/neo/static/js/neo.js A stage/files/interactive_environments/plugins/neo/templates/neo.mako M stage/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M stage/files/interactive_environments/plugins/phinch/static/js/phinch.js M stage/files/interactive_environments/plugins/phinch/templates/phinch.mako A stage/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M stage/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M stage/files/interactive_environments/plugins/rstudio/config/rstudio.xml M stage/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M stage/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/Dockerfile M stage/files/interactive_environments/proxy/lib/main.js M stage/files/interactive_environments/proxy/lib/mapper.js M stage/files/interactive_environments/proxy/lib/proxy.js M stage/files/interactive_environments/proxy/package.json M stage/galaxy_version.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update galaxyprojectdotorg.interactive_environments and enable the ethercalc GIE on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4324d0b90e77...…

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