galaxy-commits November 2017

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[galaxyproject/usegalaxy-playbook] c63497: Update Test and Main to use HTTP/2.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c6349702456fd638e79f94840f1fc463ee182c11 https://github.com/galaxyproject/usegalaxy-playbook/commit/c6349702456fd638… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M env/main/templates/nginx/usegalaxy.j2 M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Update Test and Main to use HTTP/2.

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[galaxyproject/galaxy] 0ff639: More debugging in workflows API tests.
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ff639a29c6179e530c977b358cebf229c76139d https://github.com/galaxyproject/galaxy/commit/0ff639a29c6179e530c977b358ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- More debugging in workflows API tests. Commit: 4e9ee22ebcd5cc358d1b86f60e957846f35765a5 https://github.com/galaxyproject/galaxy/commit/4e9ee22ebcd5cc358d1b86f60e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflow_extraction.py M test/base/populators.py Log Message: ----------- More verbose workflow extraction test cases. Commit: 0e0894bbba8ee1d8b7c6946a5a42695fa6bd0858 https://github.com/galaxyproject/galaxy/commit/0e0894bbba8ee1d8b7c6946a5a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Refactoring history contents API. Commit: 8c1658f61a12b9c1e2efdb04ee3530c1272b0bde https://github.com/galaxyproject/galaxy/commit/8c1658f61a12b9c1e2efdb04ee35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Mixin for uses create and update time. Commit: c076b3b6c5bf5ac9d374d56d42c9a91c352688ce https://github.com/galaxyproject/galaxy/commit/c076b3b6c5bf5ac9d374d56d42c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Refactor workflow testing toward reuse via "populators". Should allow more functionality to be shared between vanilla API tests and integration tests for various workflow scheduling options. Commit: 55aa7bce5540469fad266f1166c9a2e7365030d4 https://github.com/galaxyproject/galaxy/commit/55aa7bce5540469fad266f1166c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_tools.py A test/functional/tools/output_filter_with_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test cases for mapping for outputs with filter statements. Checked through tools-iuc and I couldn't find any tools that use the actual input data parameters in filter statements so I think it is a fairly good approximation to assume that all mapped jobs will either filter or not at least with current execution model. Commit: d5f98f49045bca351e982f17cac9386308089eeb https://github.com/galaxyproject/galaxy/commit/d5f98f49045bca351e982f17cac9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/base/populators.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Formalize workflow invocation and invocation step outputs. Workflow Invocations -------------------- The workflow invocation outputs half of this is relatively straight forward. It is modelled somewhat on job outputs, output datasets and output dataset collections are now tracked for each workflow invocation and exposed via the workflow invocation API. This required adding new tables (linked to WorkflowInvocations and WorkflowOutputs) that track these output associations. Previously one could imagine backtracking this information for simple tool steps via the WorkflowInvocationStep -> Job table, but for steps that have many jobs (i.e. mapping over a collection) or for non-tool steps such information was more difficult to recover (and simply couldn't be recovered from the API at all or even internally without significant knowledge of the underlying workflow). Workflow Invocation Steps ------------------------- Tracking the outputs of WorkflowInvocationSteps was not previously done at all, one would have to follow the Job table as well. A signficant downside to this is that one cannot map over empty collections in a workflow - since no such job would exist. Tracking job outputs for WorkflowInvocationSteps is not a simple matter of just attaching outputs to an existing table because we had no concept of a workflow step tracked - since there could be many WorklfowInvocationSteps corresponding to the same combination of WorkflowInvocation and WorkflowStep. That should feel wrong and that is because it is - when collections were added the possiblity of having many jobs for the same combination of WorkflowInvocation and WorkflowStep was added. I should have split WorkflowInvocationSteps into WorkflowInvocationSteps and WorkflowInvocationStepJobAssociations at that time but didn't. This commit now does it - effectively normalizing the ``workflow_invocation_step`` table by introducing the new ``wo rkflow_invocation_step_job_association`` table. Splitting up the WorkflowInvocationStep table this way allows recovering the mapped over output (e.g. the implicitly created collection from all the jobs) as well the outputs from the individual jobs (by walking WorkflowInvocationStep -> WorkflowInvocationStepJobAssociation -> Job -> JobToOutput*Association). This split up involves failrly substantial changes to the workflow module interface. Any place a list of WorkflowInvocationSteps was assumed, I reworked it to just expect a single WorkflowInvocationStep. I vastly simplified recover_mapping to just use the persisted outputs (this was needed in order to also implment empty collection mapping in workflows). This also fixes a bug (or implements a missing feature) where Subworkflow moudles had no recover_mapping methods - so for instance if a tool that produces dynamic collections appeared anywhere in a workflow after a subworkflow step - that workflow would not complete scheduling properly. Now that we have a way to reference the set of jobs corresponding to a workflow step within an invocation, we can start to track partial scheduling of such steps. This is outlined in https://github.com/galaxyproject/galaxy/issues/3883 and refactoring toward this goal is included here - including adding a state to WorkflowInvocationStep so Galaxy can determine if it has started scheduling this step and an index when scheduling jobs so it can tell how far into a scheduling things have gone as well as augmenting the tool executor to take a maximum number of jobs to execute and allow recovery of existing jobs for collection building purposes. *Applications* These changes will enable: - A simple, consistent API for finding workflow outputs that can be consumed by Planemo for testing workflows. - Mapping over empty collections in workflows. - Re-scheduling workflow invocations that include subworkflow steps. - Partial scheduling within steps requiring a large number of jobs when scheduling workflow invocations. Commit: 64835c1e72eea545269260256c7a238a4e5ea7fe https://github.com/galaxyproject/galaxy/commit/64835c1e72eea545269260256c7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Three new worklfow test cases to verify mapping over workflows is possible. - Simple mapping over an input dataset. - Mapping that produces nested collections. - Mapping over subworkflows. Commit: 0185e04a5beaf951bb20d670d9421d988d70bb29 https://github.com/galaxyproject/galaxy/commit/0185e04a5beaf951bb20d670d942… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test recover_mapping in conjunction with subworkflow executions. Commit: 9e471d3e97a6d6b6893ed243b6a48108076899c4 https://github.com/galaxyproject/galaxy/commit/9e471d3e97a6d6b6893ed243b6a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/populators.py A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow mapping over empty collections. If one maps a tool over an empty collection, one should get an empty output collection for each of the tool's outputs. This should have always been a valid operation I think, the code just wasn't quite structured right when the collection work was merged - there were too many places I was assuming the existence of at least one actual output or input that was mapped over to continue going. This reworks all of that and seems to handle empty collections appropriately. Fixes #4025 (not being informing the user of the operation, but actually by allowing the operation - which it should be allowed I think). Commit: 53cba4aa74b0d2543445824a7636f92249baa150 https://github.com/galaxyproject/galaxy/commit/53cba4aa74b0d2543445824a7636… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Refactor collection manager into smaller, more focused methods. Stronger assertions to verify arguments are correct. Commit: 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 https://github.com/galaxyproject/galaxy/commit/78babab6455f4cd1c51aed0b1ddf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/unit/dataset_collections/test_matching.py Log Message: ----------- Pre-build collections during mapping to be more recoverable. Create mapped over collections ahead of time instead of at the end only if they are valid. - This way if there is a problem that problem can be reported in the state of the mapped collection. - This way datasets can just be hidden instead of displayed and then hidden (fixes #1790). - I think this should improve performance and prevent locks because we no longer have conflicting threads trying to write dataset state. - We populate the collection as we go so we can recover and continue scheduling the mapped step (needed for #3883) Commit: 40fd72a1980bd2df5ea116aae1016c8bad6c3ca1 https://github.com/galaxyproject/galaxy/commit/40fd72a1980bd2df5ea116aae101… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_scheduling_options.py Log Message: ----------- Allow rescheduling of single workflow steps. Implement maximum_workflow_jobs_per_scheduling_iteration to test this and mitigate memory issues associated with scheduling large workflow steps (maybe). Fixes #3883. Commit: d69962e7f4de38963401a032ada5131e6190b5e5 https://github.com/galaxyproject/galaxy/commit/d69962e7f4de38963401a032ada5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/db_shell.py M test/api/test_history_contents.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Implement model abstraction for ``ImplicitCollectionJobs``. These aggregate all the jobs contributing to an implicitly created HistoryDatasetCollectionAssociation. - Model enhancements that allow this. - API endpoint for jobs summary of history content (somewhat uniform across HDAs and HDCAs just for consistency). - Test cases. - Rework history contents API a bit to eliminate more costly state summary checks by default. Commit: e82012bde154c456f24743f3b61c0ed9ffc7eca2 https://github.com/galaxyproject/galaxy/commit/e82012bde154c456f24743f3b61c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M lib/galaxy/tools/execute.py Log Message: ----------- Undo splitting WorkflowInvocationStep... ... this concept of ImplicitCollectionJobs makes more sense for tracking collections of implicitly created jobs. Commit: 0dceb5a553d589324d4a9a97ec5f7629bc379b48 https://github.com/galaxyproject/galaxy/commit/0dceb5a553d589324d4a9a97ec5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdcas.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py M test/api/test_dataset_collections.py Log Message: ----------- Add element count to DatasetCollection objects. There are no places where this count is not set atomically in one thread so this should not have any performance downsides versus the older approach of calculating it on the fly (which was very expensive). Commit: ca09e803aeaf856556433e69bf5a48f8bab60c5d https://github.com/galaxyproject/galaxy/commit/ca09e803aeaf856556433e69bf5a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/api/test_tools.py M test/base/populators.py M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Dataset collection state UX test case. Commit: 5a9f0dd11eb0ba0abfed29ae9da1d0a5a5a01360 https://github.com/galaxyproject/galaxy/commit/5a9f0dd11eb0ba0abfed29ae9da1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js A client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/base.less M client/galaxy/style/less/list-item.less M lib/galaxy/managers/jobs.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add job state tracking to the GUI. - ``populated`` in the API response is gone - it was very expensive on the backend to calculate. - Eliminate GUI "thread" fetching ``element_count`` for collections after the panel is loaded, this value is now available at load time thanks to recent state change optimizations on the backend. - Track job state and implicit collection job states over time in a new "thread". - New different colors of job states, add progress bar for multiple jobs. Commit: e7e659cabcf2a5928ab58e73715c0959c78cc997 https://github.com/galaxyproject/galaxy/commit/e7e659cabcf2a5928ab58e73715c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/style/less/dataset.less Log Message: ----------- Better dataset loading description. Commit: 075d8c1d0ab7dca9c8573fe69a5ef7ec18ab2202 https://github.com/galaxyproject/galaxy/commit/075d8c1d0ab7dca9c8573fe69a5e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py R lib/galaxy/model/migrate/versions/0136_record_workflow_outputs.py Log Message: ----------- Rename huge database migration to reflect new PR topic. Commit: 8fa5496ba59e39ce4d16bd7c8da1d92989c7f5da https://github.com/galaxyproject/galaxy/commit/8fa5496ba59e39ce4d16bd7c8da1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Restructure collection state GUI tests to separate flakey tests of running state out. Paste just sometimes randomly hangs when it is not supposed to. Commit: c47d8992ba52e5af8eae635a4ce50cca8a6d02c9 https://github.com/galaxyproject/galaxy/commit/c47d8992ba52e5af8eae635a4ce5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css Log Message: ----------- Repack client. Commit: 9ef4e3bd70d3abe7b36388e9d9e52c609749002d https://github.com/galaxyproject/galaxy/commit/9ef4e3bd70d3abe7b36388e9d9e5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js A client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/list-item.less M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M scripts/db_shell.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_scheduling_options.py M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py M test/unit/dataset_collections/test_matching.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #5013 from jmchilton/workflow_and_collection_state Improved Collection and Workflow State with Applications Compare: https://github.com/galaxyproject/galaxy/compare/711107473fa5...9ef4e3bd70d3

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[galaxyproject/galaxy] d074b2: Standard naming for components. TODO: organizatio...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d074b22f296c8ce76a1c982fa63eab60ed74a1e2 https://github.com/galaxyproject/galaxy/commit/d074b22f296c8ce76a1c982fa63e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue R client/galaxy/scripts/components/citations.vue R client/galaxy/scripts/components/history-import.vue R client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Standard naming for components. TODO: organization, and re-add citations (working around case-insensitivity here) Commit: 15053783bf52b914830d9afdf4fa1435ec4d8b28 https://github.com/galaxyproject/galaxy/commit/15053783bf52b914830d9afdf4fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: A client/galaxy/scripts/components/Citations.vue Log Message: ----------- Case insensitive filesystems are a terrible idea. Commit: 79b9795f7df223598ec81661bcb2a914fce7fc1c https://github.com/galaxyproject/galaxy/commit/79b9795f7df223598ec81661bcb2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Build client. Commit: 711107473fa5bd0875ae6bc1c74c9e1b4f2e9999 https://github.com/galaxyproject/galaxy/commit/711107473fa5bd0875ae6bc1c74c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue R client/galaxy/scripts/components/citations.vue R client/galaxy/scripts/components/history-import.vue R client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5092 from dannon/vue_component_standardized_naming Vue component standardized naming Compare: https://github.com/galaxyproject/galaxy/compare/3e7973940a67...711107473fa5

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[galaxyproject/galaxy] 3c20f3: Attempt to make data manager integration test more...
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c20f3285a123a243eed57040da3966800ca2438 https://github.com/galaxyproject/galaxy/commit/3c20f3285a123a243eed57040da3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_data_manager_table_reload.py Log Message: ----------- Attempt to make data manager integration test more robust. Increase the timeout - this test fails on Jenkins every now and then and reports the DM job is still queued. I assume this is because of conda_auto_install setting up the requirements for this data manager and the logs seem consistent with that assumption. I also added data manager json type to the sample so this warning goes away: ``` galaxy.model WARNING 2017-11-30 06:39:59,335 Datatype class not found for extension 'data_manager_json' ``` Commit: 3e7973940a67e30506973070ced00e471b914b31 https://github.com/galaxyproject/galaxy/commit/3e7973940a67e30506973070ced0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_data_manager_table_reload.py Log Message: ----------- Merge pull request #5098 from jmchilton/reload_dm_test_robust Attempt to make data manager integration test more robust. Compare: https://github.com/galaxyproject/galaxy/compare/baba3417d08d...3e7973940a67

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[galaxyproject/galaxy] 7dc5fd: Update Jupyter IE default image
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/ie Home: https://github.com/galaxyproject/galaxy Commit: 7dc5fd9b77c330cc6c9643c7622294a24d78df99 https://github.com/galaxyproject/galaxy/commit/7dc5fd9b77c330cc6c9643c76222… Author: Enis Afgan <afgane(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Update Jupyter IE default image

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[galaxyproject/usegalaxy-playbook] 98aeb5: Install augustus 3.2.3
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98aeb5b7d8689e9fff6e2b2b3793235e0b7d1ab8 https://github.com/galaxyproject/usegalaxy-playbook/commit/98aeb5b7d8689e9f… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Install augustus 3.2.3

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[galaxyproject/usegalaxy-playbook] fa4cbb: Fix test installer access
by GitHub 30 Nov '17

30 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fa4cbb59187be6d3c6e46ba2e18e6efcab809caf https://github.com/galaxyproject/usegalaxy-playbook/commit/fa4cbb59187be6d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Fix test installer access

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[galaxyproject/galaxy] ef8ed0: support separate dsn for sentry
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ef8ed0ec3fce0f2e61cc0accfe1dcdb8dd79f97b https://github.com/galaxyproject/galaxy/commit/ef8ed0ec3fce0f2e61cc0accfe1d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M config/error_report.yml.sample M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- support separate dsn for sentry Commit: c6bf20df682a3dac10d4d6fd480d470ec5c8cbc8 https://github.com/galaxyproject/galaxy/commit/c6bf20df682a3dac10d4d6fd480d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- ok, test cases require this to pass Commit: baba3417d08d282c98418e2e62a7167f458c86bd https://github.com/galaxyproject/galaxy/commit/baba3417d08d282c98418e2e62a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M config/error_report.yml.sample M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5056 from erasche/sentry-stuff Support separate DSN for job sentry error reports Compare: https://github.com/galaxyproject/galaxy/compare/75a6d434ee00...baba3417d08d

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[galaxyproject/galaxy] 687950: Add js history form view
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6879507fef3f6b6697f3e8364953b1fc4c9f1361 https://github.com/galaxyproject/galaxy/commit/6879507fef3f6b6697f3e8364953… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/history/options-menu.js Log Message: ----------- Add js history form view Commit: f776229db4b9f81868df35b1e76cf5d605a5b0d4 https://github.com/galaxyproject/galaxy/commit/f776229db4b9f81868df35b1e76c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add history import Commit: 3e4058f098446ffddefb4b426233fa00fd4307ff https://github.com/galaxyproject/galaxy/commit/3e4058f098446ffddefb4b426233… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M client/galaxy/style/less/ui.less 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/style/blue/base.css Log Message: ----------- Fix styling, fix data submission for history endpoint Commit: 358dee22ca45e88fbf727fb773616b1f90473540 https://github.com/galaxyproject/galaxy/commit/358dee22ca45e88fbf727fb77361… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js.map Log Message: ----------- Use global vars Commit: 2a122157c540e412b8d37540205b88801e6a0746 https://github.com/galaxyproject/galaxy/commit/2a122157c540e412b8d37540205b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: A client/galaxy/scripts/mvc/history/history-import.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/history/history-import.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 A static/scripts/mvc/history/history-import.js Log Message: ----------- Augment existing api endpoint, redirect post Commit: 0c615411c9a063ddfaeb6b2e2bfba1b783a1543f https://github.com/galaxyproject/galaxy/commit/0c615411c9a063ddfaeb6b2e2bfb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Consolidate endpoints Commit: 4fd3021330f9d1ec4061807fe739933140f63e91 https://github.com/galaxyproject/galaxy/commit/4fd3021330f9d1ec4061807fe739… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-import.js M static/maps/mvc/history/history-import.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/history/history-import.js Log Message: ----------- Remove debug helper Commit: cf66742b4c1ab6d2c5bef8b5064679b5e7963b0a https://github.com/galaxyproject/galaxy/commit/cf66742b4c1ab6d2c5bef8b50646… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/utils/ajax-queue.js M config/galaxy.ini.sample M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/hash_util.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/controllers/library.py R lib/galaxy/webapps/galaxy/controllers/library_admin.py R lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/hg_util.py M run_tests.sh M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/utils/ajax-queue.js R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M test/base/populators.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: b96398027e648d8c1c42180c162fbae3c73e31f5 https://github.com/galaxyproject/galaxy/commit/b96398027e648d8c1c42180c162f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Consistent strings Commit: 8f7dee460e7f90fa945cb6a1ff31c7aa81a4505b https://github.com/galaxyproject/galaxy/commit/8f7dee460e7f90fa945cb6a1ff31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py A lib/galaxy/util/script.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/controllers/history.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/root.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/authenticate.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/schedulers/core.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/utility_containers/__init__.py M run_tests.sh M scripts/common_startup.sh M scripts/functional_tests.py M scripts/manage_tool_dependencies.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map A static/maps/mvc/history/history-item-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-node.js M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako R templates/search/index.mako M templates/show_params.mako M templates/user/register.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_data_manager_table_reload.py A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/microbial_import.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: 2623bf369cae8b658118defad6fbf0dc825c2b73 https://github.com/galaxyproject/galaxy/commit/2623bf369cae8b658118defad6fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .travis.yml M Makefile A client/galaxy/scripts/apps/admin-toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/library.js A client/galaxy/scripts/apps/masthead.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/viz.js A client/galaxy/scripts/apps/workflow.js A client/galaxy/scripts/components/citations.vue A client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/panel.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/style/less/base.less M client/gulpfile.js A client/karma.config.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M run_tests.sh M static/maps/galaxy.library.js.map M static/maps/layout/panel.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/citation/citation-view.js.map A static/maps/mvc/citations.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map A static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/library.bundled.js A static/scripts/bundled/library.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 A static/scripts/bundled/masthead.bundled.js A static/scripts/bundled/masthead.bundled.js.map A static/scripts/bundled/viz.bundled.js A static/scripts/bundled/viz.bundled.js.map A static/scripts/bundled/workflow.bundled.js A static/scripts/bundled/workflow.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/panel.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js A static/scripts/libs/vue.js R static/scripts/mvc/citation/citation-model.js R static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/citations.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/workflow/editor.mako R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js M tox.ini Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: cb044bd45263341aede9866f219600a2caddfe55 https://github.com/galaxyproject/galaxy/commit/cb044bd45263341aede9866f2196… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/library.bundled.js M static/scripts/bundled/library.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/bundled/masthead.bundled.js M static/scripts/bundled/masthead.bundled.js.map M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js M static/scripts/bundled/workflow.bundled.js.map Log Message: ----------- Transform history import to vue component Commit: 4cf8ad218467b310652b7c2e37190cf56ca68820 https://github.com/galaxyproject/galaxy/commit/4cf8ad218467b310652b7c2e3719… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: R client/galaxy/scripts/mvc/history/history-import.js R static/maps/mvc/history/history-import.js.map Log Message: ----------- Remove former backbone view for history imports Commit: 4ecf7a05b4d8bd6c20b8f73920c1e36436918c61 https://github.com/galaxyproject/galaxy/commit/4ecf7a05b4d8bd6c20b8f73920c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-22 (Wed, 22 Nov 2017) Changed paths: M .gitignore M client/gulpfile.js M client/webpack.config.js R static/maps/admin.toolshed.js.map R static/maps/analysis.js.map R static/maps/app.js.map R static/maps/app/analysis.js.map R static/maps/galaxy-app-base.js.map R static/maps/galaxy.interactive_environments.js.map R static/maps/galaxy.js.map R static/maps/galaxy.menu.js.map R static/maps/galaxy.pages.js.map R static/maps/i18n.js.map R static/maps/layout/generic-nav-view.js.map R static/maps/layout/masthead.js.map R static/maps/layout/menu.js.map R static/maps/layout/modal.js.map R static/maps/layout/page.js.map R static/maps/layout/router.js.map R static/maps/layout/scratchbook.js.map R static/maps/libs/backbone.js.map R static/maps/libs/bbi/bigwig.js.map R static/maps/libs/bbi/jquery-ajax-native.js.map R static/maps/libs/bbi/jszlib.js.map R static/maps/libs/bbi/spans.js.map R static/maps/libs/bibtex.js.map R static/maps/libs/bootstrap-tour.js.map R static/maps/libs/bootstrap.js.map R static/maps/libs/common-libs.js.map R static/maps/libs/d3.js.map R static/maps/libs/farbtastic.js.map R static/maps/libs/jquery.complexify.js.map R static/maps/libs/jquery.sparklines.js.map R static/maps/libs/jquery/jquery-ui.js.map R static/maps/libs/jquery/jquery.autocomplete.js.map R static/maps/libs/jquery/jquery.complexify.js.map R static/maps/libs/jquery/jquery.cookie.js.map R static/maps/libs/jquery/jquery.dynatree.js.map R static/maps/libs/jquery/jquery.event.drag.js.map R static/maps/libs/jquery/jquery.event.drop.js.map R static/maps/libs/jquery/jquery.event.hover.js.map R static/maps/libs/jquery/jquery.form.js.map R static/maps/libs/jquery/jquery.js.map R static/maps/libs/jquery/jquery.migrate.js.map R static/maps/libs/jquery/jquery.mousewheel.js.map R static/maps/libs/jquery/jquery.rating.js.map R static/maps/libs/jquery/jquery.wymeditor.js.map R static/maps/libs/jquery/jstorage.js.map R static/maps/libs/jquery/jstree.js.map R static/maps/libs/jquery/select2.js.map R static/maps/libs/raven.js.map R static/maps/libs/require.js.map R static/maps/libs/showdown.js.map R static/maps/libs/toastr.js.map R static/maps/libs/underscore.js.map R static/maps/mvc/annotation.js.map R static/maps/mvc/base-mvc.js.map R static/maps/mvc/base/controlled-fetch-collection.js.map R static/maps/mvc/collection/base-creator.js.map R static/maps/mvc/collection/collection-li-edit.js.map R static/maps/mvc/collection/collection-li.js.map R static/maps/mvc/collection/collection-model.js.map R static/maps/mvc/collection/collection-view-edit.js.map R static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/collection/list-collection-creator.js.map R static/maps/mvc/collection/list-of-pairs-collection-creator.js.map R static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/collection/paired-collection-creator.js.map R static/maps/mvc/dataset/data.js.map R static/maps/mvc/dataset/dataset-choice.js.map R static/maps/mvc/dataset/dataset-edit-attributes.js.map R static/maps/mvc/dataset/dataset-error.js.map R static/maps/mvc/dataset/dataset-li-edit.js.map R static/maps/mvc/dataset/dataset-li.js.map R static/maps/mvc/dataset/dataset-list.js.map R static/maps/mvc/dataset/dataset-model.js.map R static/maps/mvc/dataset/states.js.map R static/maps/mvc/form/form-data.js.map R static/maps/mvc/form/form-input.js.map R static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-repeat.js.map R static/maps/mvc/form/form-section.js.map R static/maps/mvc/form/form-view.js.map R static/maps/mvc/form/form-wrapper.js.map R static/maps/mvc/grid/grid-model.js.map R static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/grid/grid-template.js.map R static/maps/mvc/grid/grid-view.js.map R static/maps/mvc/groups/group-detail-view.js.map R static/maps/mvc/groups/group-groupdetail-view.js.map R static/maps/mvc/groups/group-grouprow-view.js.map R static/maps/mvc/groups/group-list-view.js.map R static/maps/mvc/groups/group-listrow-view.js.map R static/maps/mvc/groups/group-model.js.map R static/maps/mvc/groups/group.model.js.map R static/maps/mvc/history/copy-dialog.js.map R static/maps/mvc/history/hda-li-edit.js.map R static/maps/mvc/history/hda-li.js.map R static/maps/mvc/history/hda-model.js.map R static/maps/mvc/history/hdca-li-edit.js.map R static/maps/mvc/history/hdca-li.js.map R static/maps/mvc/history/hdca-model.js.map R static/maps/mvc/history/history-content-model.js.map R static/maps/mvc/history/history-contents.js.map R static/maps/mvc/history/history-item-li.js.map R static/maps/mvc/history/history-list.js.map R static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-preferences.js.map R static/maps/mvc/history/history-structure-view.js.map R static/maps/mvc/history/history-view-annotated.js.map R static/maps/mvc/history/history-view-edit-current.js.map R static/maps/mvc/history/history-view-edit.js.map R static/maps/mvc/history/history-view.js.map R static/maps/mvc/history/job-dag.js.map R static/maps/mvc/history/multi-panel.js.map R static/maps/mvc/job/job-li.js.map R static/maps/mvc/job/job-model.js.map R static/maps/mvc/job/job-params.js.map R static/maps/mvc/lazy/lazy-limited.js.map R static/maps/mvc/library/library-dataset-view.js.map R static/maps/mvc/library/library-folder-view.js.map R static/maps/mvc/library/library-folderrow-view.js.map R static/maps/mvc/library/library-library-view.js.map R static/maps/mvc/library/library-librarylist-view.js.map R static/maps/mvc/library/library-librarytoolbar-view.js.map R static/maps/mvc/library/library-model.js.map R static/maps/mvc/library/library-util.js.map R static/maps/mvc/list/list-item.js.map R static/maps/mvc/list/list-panel.js.map R static/maps/mvc/list/list-view.js.map R static/maps/mvc/page/page-list.js.map R static/maps/mvc/tag.js.map R static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form.js.map R static/maps/mvc/tool/tool-genomespace.js.map R static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tool-webhooks.js.map R static/maps/mvc/tool/tools.js.map R static/maps/mvc/toolshed/categories-view.js.map R static/maps/mvc/toolshed/repo-queue-view.js.map R static/maps/mvc/toolshed/repo-status-view.js.map R static/maps/mvc/toolshed/repositories-view.js.map R static/maps/mvc/toolshed/repository-queue-view.js.map R static/maps/mvc/toolshed/repository-view.js.map R static/maps/mvc/toolshed/shed-category-view.js.map R static/maps/mvc/toolshed/shed-list-view.js.map R static/maps/mvc/toolshed/shed-repo-details-view.js.map R static/maps/mvc/toolshed/shed-repo-list-view.js.map R static/maps/mvc/toolshed/sheds-list-view.js.map R static/maps/mvc/toolshed/toolshed-model.js.map R static/maps/mvc/toolshed/util.js.map R static/maps/mvc/toolshed/workflows-view.js.map R static/maps/mvc/tours.js.map R static/maps/mvc/ui/error-modal.js.map R static/maps/mvc/ui/icon-button.js.map R static/maps/mvc/ui/popup-menu.js.map R static/maps/mvc/ui/ui-buttons.js.map R static/maps/mvc/ui/ui-color-picker.js.map R static/maps/mvc/ui/ui-drilldown.js.map R static/maps/mvc/ui/ui-frames.js.map R static/maps/mvc/ui/ui-list.js.map R static/maps/mvc/ui/ui-misc.js.map R static/maps/mvc/ui/ui-modal.js.map R static/maps/mvc/ui/ui-options.js.map R static/maps/mvc/ui/ui-popover.js.map R static/maps/mvc/ui/ui-portlet.js.map R static/maps/mvc/ui/ui-select-content.js.map R static/maps/mvc/ui/ui-select-default.js.map R static/maps/mvc/ui/ui-select-ftp.js.map R static/maps/mvc/ui/ui-select-genomespace.js.map R static/maps/mvc/ui/ui-select-library.js.map R static/maps/mvc/ui/ui-select.js.map R static/maps/mvc/ui/ui-slider.js.map R static/maps/mvc/ui/ui-table.js.map R static/maps/mvc/ui/ui-tabs.js.map R static/maps/mvc/ui/ui-thumbnails.js.map R static/maps/mvc/upload/collection/collection-row.js.map R static/maps/mvc/upload/collection/collection-view.js.map R static/maps/mvc/upload/composite/composite-row.js.map R static/maps/mvc/upload/composite/composite-view.js.map R static/maps/mvc/upload/default/default-row.js.map R static/maps/mvc/upload/default/default-view.js.map R static/maps/mvc/upload/upload-button.js.map R static/maps/mvc/upload/upload-extension.js.map R static/maps/mvc/upload/upload-ftp.js.map R static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-settings.js.map R static/maps/mvc/upload/upload-view.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/extra-information.js.map R static/maps/mvc/user/manage-user-information.js.map R static/maps/mvc/user/user-custom-builds.js.map R static/maps/mvc/user/user-model.js.map R static/maps/mvc/user/user-preferences.js.map R static/maps/mvc/user/user-quotameter.js.map R static/maps/mvc/visualization/visualization-model.js.map R static/maps/mvc/webhooks.js.map R static/maps/mvc/workflow/workflow-canvas.js.map R static/maps/mvc/workflow/workflow-configure-menu.js.map R static/maps/mvc/workflow/workflow-connector.js.map R static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow-icons.js.map R static/maps/mvc/workflow/workflow-manager.js.map R static/maps/mvc/workflow/workflow-model.js.map R static/maps/mvc/workflow/workflow-node.js.map R static/maps/mvc/workflow/workflow-terminals.js.map R static/maps/mvc/workflow/workflow-view-data.js.map R static/maps/mvc/workflow/workflow-view-node.js.map R static/maps/mvc/workflow/workflow-view-terminals.js.map R static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map R static/maps/nls/de/locale.js.map R static/maps/nls/es/locale.js.map R static/maps/nls/fr/locale.js.map R static/maps/nls/ja/locale.js.map R static/maps/nls/locale.js.map R static/maps/nls/zh/locale.js.map R static/maps/onload.js.map R static/maps/polyfills.js.map R static/maps/reports_webapp/run_stats.js.map R static/maps/templates/compiled/panel_section.js.map R static/maps/templates/compiled/tool_form.js.map R static/maps/templates/compiled/tool_link.js.map R static/maps/templates/compiled/tool_search.js.map R static/maps/toolshed.groups.js.map R static/maps/ui/autocom_tagging.js.map R static/maps/ui/editable-text.js.map R static/maps/ui/fa-icon-button.js.map R static/maps/ui/filter-control.js.map R static/maps/ui/hoverhighlight.js.map R static/maps/ui/loading-indicator.js.map R static/maps/ui/mode-button.js.map R static/maps/ui/pagination.js.map R static/maps/ui/peek-column-selector.js.map R static/maps/ui/popupmenu.js.map R static/maps/ui/scroll-panel.js.map R static/maps/ui/search-input.js.map R static/maps/utils/add-logging.js.map R static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.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/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-import.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/library/library-util.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: 78508e200ab1ce2b6a665e0076eebabd1db4a14f https://github.com/galaxyproject/galaxy/commit/78508e200ab1ce2b6a665e0076ee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py R static/maps/galaxy.library.js.map R static/maps/layout/panel.js.map R static/maps/mvc/citation/citation-model.js.map R static/maps/mvc/citation/citation-view.js.map R static/maps/mvc/citations.js.map R static/maps/mvc/history/options-menu.js.map R static/maps/mvc/library/library-folderlist-view.js.map R static/maps/mvc/library/library-foldertoolbar-view.js.map R static/maps/mvc/library/library-libraryrow-view.js.map R static/maps/mvc/tool/tool-form-base.js.map R static/maps/mvc/user/user_api_keys.js.map M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/library.bundled.js.map R static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js R static/scripts/bundled/login.bundled.js.map M static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/masthead.bundled.js.map R static/scripts/bundled/viz.bundled.js.map M static/scripts/bundled/workflow.bundled.js R static/scripts/bundled/workflow.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/tag.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M test/selenium_tests/test_workflow_editor.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: f58ef136168999c3dc86468b3cf9d1220b4cf59a https://github.com/galaxyproject/galaxy/commit/f58ef136168999c3dc86468b3cf9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Fix import by url for history archive import tool Commit: 3c3b47e8ef2b5b2c4072f3e9d92dd6dadd72646e https://github.com/galaxyproject/galaxy/commit/3c3b47e8ef2b5b2c4072f3e9d92d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: A client/galaxy/scripts/components/history-import.vue M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Restore history vue component Commit: 1785f6314d0e3fc2d2b189839f6e031448781dca 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lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/commit_util.py R manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main A scripts/get_uwsgi_args.py R scripts/manage_tools.py M test/base/driver_util.py M test/base/integration_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_mules_as_job_handlers.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'dev' into replace_history_import Commit: 9800013ec2cd7433db329ad9db9114e57af37e07 https://github.com/galaxyproject/galaxy/commit/9800013ec2cd7433db329ad9db91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Switch to transparent readmode for history tarfiles Commit: 081cbc4bb0cdbe202cf24b394beba4eb50125d0f https://github.com/galaxyproject/galaxy/commit/081cbc4bb0cdbe202cf24b394beb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Add quotes Commit: 75a6d434ee00b51d66ea5bf40b0ddd19601d35e3 https://github.com/galaxyproject/galaxy/commit/75a6d434ee00b51d66ea5bf40b0d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/history-import.vue M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js A static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/history/options-menu.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4993 from guerler/replace_history_import Replace history import form Compare: https://github.com/galaxyproject/galaxy/compare/8d7f344140d7...75a6d434ee00

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[galaxyproject/infrastructure-playbook] 84239f: Add status.galaxyproject.org to the inventory
by GitHub 29 Nov '17

29 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 84239ffd6793dda8b8ab46bf18a1e0908a637d11 https://github.com/galaxyproject/infrastructure-playbook/commit/84239ffd679… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M common_env/secret_group_vars/sslwebservers.yml A galaxyenv/files/ssl/status.galaxyproject.org_cert.pem A galaxyenv/host_vars/status.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/templates/nginx/status.j2 Log Message: ----------- Add status.galaxyproject.org to the inventory

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