- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] cdf938: PY3 fixes for galaxy.util.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cdf9380735878d44fee863c86b69a686ab0fd76f https://github.com/galaxyproject/galaxy/commit/cdf9380735878d44fee863c86b69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- PY3 fixes for galaxy.util. Commit: d9068a808994dee2b1c0ea873365846706e03d70 https://github.com/galaxyproject/galaxy/commit/d9068a808994dee2b1c0ea873365… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1359 from jmchilton/py3_0 PY3 fixes for galaxy.util. Compare: https://github.com/galaxyproject/galaxy/compare/f6557964b6b8...d9068a808994

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[galaxyproject/galaxy] b0deea: Fix change handler association
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: b0deead9c3260598f83d1ab2ec74b3c3e8974456 https://github.com/galaxyproject/galaxy/commit/b0deead9c3260598f83d1ab2ec74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Fix change handler association Commit: abd51e7f791c99a93062b9f2fee7827dea857c20 https://github.com/galaxyproject/galaxy/commit/abd51e7f791c99a93062b9f2fee7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1358 from guerler/fix_same_upload_000 [15.10] Fix change handler association Compare: https://github.com/galaxyproject/galaxy/compare/2d7c2019fba1...abd51e7f791c

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[galaxyproject/galaxy] b4683f: raise and show specific exception and warning when...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: b4683fbce4cf7c133fdd8af6c6fef58a5bf3c76d https://github.com/galaxyproject/galaxy/commit/b4683fbce4cf7c133fdd8af6c6fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- raise and show specific exception and warning when no files detected Commit: 2d7c2019fba1b3de89a5a5183c7bd147a309f958 https://github.com/galaxyproject/galaxy/commit/2d7c2019fba1b3de89a5a5183c7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1360 from martenson/raise-specific-exception [15.10] datalibs: raise and show specific exception and warning when no files detected Compare: https://github.com/galaxyproject/galaxy/compare/1b3ee81dbae9...2d7c2019fba1

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[galaxyproject/galaxy] 6f3852: Update documentation in migration 131 to not be co...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f3852188e35612800c6a5ab47b0dc800263778b https://github.com/galaxyproject/galaxy/commit/6f3852188e35612800c6a5ab47b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Update documentation in migration 131 to not be copypasta. Commit: f6557964b6b88b1752ea70e1132610596f6fa103 https://github.com/galaxyproject/galaxy/commit/f6557964b6b88b1752ea70e11326… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Merge pull request #1361 from dannon/oops_copypasta Update documentation in migration 131 Compare: https://github.com/galaxyproject/galaxy/compare/1562c74b2b93...f6557964b6b8

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[galaxyproject/galaxy]
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/py3_0 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy]
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/py3_0 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 66944b: Lint with Python 3 serveral modules.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66944ba7de178cc45ffa7a4aa9253ec4512cb6fd https://github.com/galaxyproject/galaxy/commit/66944ba7de178cc45ffa7a4aa925… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M tox.ini Log Message: ----------- Lint with Python 3 serveral modules. Namely the modules I'd like to be shared with planemo, pulsar, etc.... Commit: 1562c74b2b93aaea78c3fed62ed1de9a76ebe3e2 https://github.com/galaxyproject/galaxy/commit/1562c74b2b93aaea78c3fed62ed1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M tox.ini Log Message: ----------- Merge pull request #1354 from jmchilton/py3_0 Lint with Python 3 several modules. Compare: https://github.com/galaxyproject/galaxy/compare/41da9b0f8872...1562c74b2b93

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[galaxyproject/galaxy] d41caa: Database migration enabling subworkflow and input ...
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d41caa53cf24aca29bb90e32b420558558461d9c https://github.com/galaxyproject/galaxy/commit/d41caa53cf24aca29bb90e32b420… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Database migration enabling subworkflow and input parameter modules. Commit: 45962f32344a00162f5d04b94096c8a570f2adf1 https://github.com/galaxyproject/galaxy/commit/45962f32344a00162f5d04b94096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Input parameter workflow module (experimental). - Implement a input parameter module that mirrors data and collection input modules but has a type that can currently be one of text, integer, float, color, and boolean. - Allow connections between these and tool step inputs. - Extend model to support this. - Add new input types for format 2 workflow definitions for various types that all map to this kind of step. Typed inputs such as this match well with CWL workflow inputs. Someday I imagine these will be superior to just marking a tool input "Specify at Runtime" for all the same reasons input steps are superior to leaving inputs unattached. Commit: 157939aa8f46b7599f48011d9f1e2c40c9f6cd47 https://github.com/galaxyproject/galaxy/commit/157939aa8f46b7599f48011d9f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.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.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/unit/test_galaxy_mapping.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 test/unit/workflows/workflow_support.py Log Message: ----------- Implement nested workflows. Details: - Add a new workflow module describing subworkflows. - Add workflow list to editor side panel - with options to link in a subworkflow module or copy the target workflow into the workflow being editted node for node. - Update workflow, workflow step, and workflow invocation models to track subworkflow connections and execution. - Extend workflow outputs with concepts of labels (and UUIDs while I'm there) to match workflow inputs. This allow us to have something to label outputs with in the workflow editor and to reference in the format 2 workflow description language. - Extend workflow editor UI to allow labeling workflow outputs (and enforce that these are unique across a workflow). - Extend workflow invocation and progress tracking to allow invoking a subworkflow as part of another workflow invocation. - Extend workflow import and export code to allow a nested representation of workflows. - Update format 2 workflow description to allow testing nested workflows. Most relevant new and modified test cases can be run using the following commands: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_run_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_outputs nosetests test/unit/test_galaxy_mapping.py nosetests test/unit/workflows/test_workflow_progress.py ``` Commit: f88ad8d4e35b51a5f88b0d29b71755f576fc1f7a https://github.com/galaxyproject/galaxy/commit/f88ad8d4e35b51a5f88b0d29b717… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map 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/mvc/tool/tool-form-workflow.js Log Message: ----------- Fix Change type label in editor form Commit: 48eec81f48f92d7b5e7a42a9cf4be453f9f14fa5 https://github.com/galaxyproject/galaxy/commit/48eec81f48f92d7b5e7a42a9cf4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow specifying workflow outputs on subworkflow nodes. Commit: f10b968075e37b650f46811f6f83286c6aaefccd https://github.com/galaxyproject/galaxy/commit/f10b968075e37b650f46811f6f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Build section dom in js Commit: b4bfde4089a5f1893ddd839fa4a2c34c71378ae2 https://github.com/galaxyproject/galaxy/commit/b4bfde4089a5f1893ddd839fa4a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix attribute Commit: 530ceb13befdc0850efb9db47c5389c3218338b3 https://github.com/galaxyproject/galaxy/commit/530ceb13befdc0850efb9db47c53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix for failing qunit test. Commit: 12014cc2252d710b617953dbfcc804fc9b3f0a67 https://github.com/galaxyproject/galaxy/commit/12014cc2252d710b617953dbfcc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Show correct subworkflow name Commit: 2ff3bf0c0c66946557f21f0bafa55768b7a8cd63 https://github.com/galaxyproject/galaxy/commit/2ff3bf0c0c66946557f21f0bafa5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix label change handling Commit: c9016f9553784b3a83f448c787fa8b90e11a2599 https://github.com/galaxyproject/galaxy/commit/c9016f9553784b3a83f448c787fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #15 from guerler/fix_subworkflows_005 Fix subworkflows 005 Commit: 41da9b0f88727759d1d2453a90b548858d10ffa7 https://github.com/galaxyproject/galaxy/commit/41da9b0f88727759d1d2453a90b5… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map 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/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.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.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/test_galaxy_mapping.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 test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #1306 from common-workflow-language/subworkflows New Workflow Modules - Input Parameters and Subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/1ec67c864b3a...41da9b0f8872

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[galaxyproject/galaxy] 83f57c: Refactor is_multi_byte out of galaxy.util.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83f57c56c183f38b6a8915d506dbf6d00c634c65 https://github.com/galaxyproject/galaxy/commit/83f57c56c183f38b6a8915d506db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/multi_byte.py M tools/data_source/upload.py Log Message: ----------- Refactor is_multi_byte out of galaxy.util. It introduces a fairly esoteric dependency in galaxy.util for just a couple uses in Galaxy. Separating it out like this will allow reuse of the entire galaxy.util with only one external dependency (docutils, which planemo for instance already depends on). Commit: 1ec67c864b3af590c337d86c2f2a6b52ae96fd0e https://github.com/galaxyproject/galaxy/commit/1ec67c864b3af590c337d86c2f2a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/multi_byte.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #1352 from jmchilton/multibyte_refactor Refactor is_multi_byte out of top-level galaxy.util. Compare: https://github.com/galaxyproject/galaxy/compare/8e0b6af87658...1ec67c864b3a

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[galaxyproject/galaxy] c8e611: Remove unused lrucache.py file in galaxy.util.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8e61140e7b297356f1830d46761660a85d7b79d https://github.com/galaxyproject/galaxy/commit/c8e61140e7b297356f1830d46761… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: R lib/galaxy/util/lrucache.py Log Message: ----------- Remove unused lrucache.py file in galaxy.util. Added without context in https://github.com/galaxyproject/galaxy/commit/88164c123d3faafe04bf38193e60…. Commit: 869b1a4ef0ec647cca1420e6c0f82023c5ffbad0 https://github.com/galaxyproject/galaxy/commit/869b1a4ef0ec647cca1420e6c0f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/util/hash_util.py Log Message: ----------- Remove Python 2.4- from hash_util.py. Commit: 73dce68376df898d01cc8fcf843d363914a39adf https://github.com/galaxyproject/galaxy/commit/73dce68376df898d01cc8fcf843d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: R lib/galaxy/util/debugging.py Log Message: ----------- Remove seemingly unused debugging.py. Add in https://github.com/galaxyproject/galaxy/commit/017a3c356b8742dd09e65f1c6ce8…. Commit: 8e0b6af87658cd2a014a16cdf35349db6e61a84d https://github.com/galaxyproject/galaxy/commit/8e0b6af87658cd2a014a16cdf353… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: R lib/galaxy/util/debugging.py M lib/galaxy/util/hash_util.py R lib/galaxy/util/lrucache.py Log Message: ----------- Merge pull request #1351 from jmchilton/util_clean_0 Remove some unused stuff from galaxy.util. Compare: https://github.com/galaxyproject/galaxy/compare/58ce52a0bae5...8e0b6af87658

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[galaxyproject/galaxy] 984ceb: Move Dictifiable out of model package into util.
by GitHub 17 Dec '15

17 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 984ceb104d91cdd23daf8a1b6c2382d1eacd1e90 https://github.com/galaxyproject/galaxy/commit/984ceb104d91cdd23daf8a1b6c23… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/dictifiable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Move Dictifiable out of model package into util. Many objects that aren't model objects are Dictifiable at this point so there is no reason to have this in model. This changes eliminates Dictifiable's dependency on sqlalchemy (by using a more pythonic type check). Now that Dictifiable has no external dependencies, it is much easier to reuse it (and more important objects that extend it) in other projects such as planemo. Commit: 58ce52a0bae5971670a99bf41502867b02ebb1f3 https://github.com/galaxyproject/galaxy/commit/58ce52a0bae5971670a99bf41502… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/dictifiable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #1350 from jmchilton/dictifiable_refactor Move Dictifiable out of model package into util. Compare: https://github.com/galaxyproject/galaxy/compare/e52cc6614769...58ce52a0bae5

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[galaxyproject/galaxy] fc8585: Separate abstractions for parsing discovered datas...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc85857a71a270172e8390c1846daad86f547b14 https://github.com/galaxyproject/galaxy/commit/fc85857a71a270172e8390c1846d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py A lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Separate abstractions for parsing discovered datasets and discovering. This is part of a long effort to build a galaxy.tools.parser module that has no dependencies outside of say galaxy.util - so I can add it to the code shared with planemo and pulsar. This would allow planemo (and by extension Tool Shed 2.0) to reason about tools in an abstract way without the billion dependencies of galxaxy.tools.Tool. Commit: 586ab24970856f12112714759f1ead088bc48a04 https://github.com/galaxyproject/galaxy/commit/586ab24970856f12112714759f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py R lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parser/interface.py A lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Move galaxy.tools.parameters.outputs into galaxy.tools.paraser.output_actions. This module has not external dependencies so it is prefect for the parser module. There still remains work to be done to separate it from XML. Commit: e52cc6614769c0b332c32a1068db816917a5708c https://github.com/galaxyproject/galaxy/commit/e52cc6614769c0b332c32a1068db… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py R lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py A lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #1349 from jmchilton/planemo_refactor_0 Refactor tool parsing handling toward reuse outside Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/14d25e9d426e...e52cc6614769

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[galaxyproject/usegalaxy-playbook] e2e3db: update test to 14d25e9d426ef6fb329c0a04f0c0fdf0bea...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e2e3dba47c943790c1397cea89e5d1c1b794828c https://github.com/galaxyproject/usegalaxy-playbook/commit/e2e3dba47c943790… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test to 14d25e9d426ef6fb329c0a04f0c0fdf0beabe9bf

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[galaxyproject/galaxy] 87ce6c: Fix for loading workflows that have tool verions /...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87ce6c778ffc9087d589914a5eec640da067c231 https://github.com/galaxyproject/galaxy/commit/87ce6c778ffc9087d589914a5eec… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix for loading workflows that have tool verions / step upgrade messages. Commit: 14d25e9d426ef6fb329c0a04f0c0fdf0beabe9bf https://github.com/galaxyproject/galaxy/commit/14d25e9d426ef6fb329c0a04f0c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1348 from blankenberg/workflow_fix Fix for loading workflows that have tool version / step upgrade messages. Compare: https://github.com/galaxyproject/galaxy/compare/f51ee306b1e8...14d25e9d426e

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[galaxyproject/galaxy] e38e44: If GALAXY_SLOTS is defined in the environment, use...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e38e4449cddc0a6b31ca6f19d849cae1796e22df https://github.com/galaxyproject/galaxy/commit/e38e4449cddc0a6b31ca6f19d849… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- If GALAXY_SLOTS is defined in the environment, use it for the local runner when job destinations haven't been configured. Commit: f51ee306b1e88001f76fd818e495cdbd9db2e10c https://github.com/galaxyproject/galaxy/commit/f51ee306b1e88001f76fd818e495… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Merge pull request #1346 from dannon/local_slots If GALAXY_SLOTS is defined in the environment, use it for the local r… Compare: https://github.com/galaxyproject/galaxy/compare/191f75407ed9...f51ee306b1e8

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[galaxyproject/usegalaxy-playbook] a597ab: update Test
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a597ab44eb195565f35b4d51bc47e3b886761491 https://github.com/galaxyproject/usegalaxy-playbook/commit/a597ab44eb195565… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test

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[galaxyproject/galaxy] f54138: Fix optional parameters
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f54138237dcba721d61af5f692b3195e812a6939 https://github.com/galaxyproject/galaxy/commit/f54138237dcba721d61af5f692b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix optional parameters Commit: 191f75407ed955b3b0836b7503616f664f0d0a73 https://github.com/galaxyproject/galaxy/commit/191f75407ed955b3b0836b750361… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1343 from guerler/fix_validation_000 Fix optional parameters Compare: https://github.com/galaxyproject/galaxy/compare/8480f9187e8c...191f75407ed9

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[galaxyproject/galaxy] 952eb3: Upgrade Paste to 2.0.2
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 952eb34f447772918f8af7f66779c5dfa734424a https://github.com/galaxyproject/galaxy/commit/952eb34f447772918f8af7f66779… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Upgrade Paste to 2.0.2 Commit: 8480f9187e8cae34fc4822ae1d2d8971f3504f5a https://github.com/galaxyproject/galaxy/commit/8480f9187e8cae34fc4822ae1d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1344 from natefoo/paste2 Upgrade Paste to 2.0.2 Compare: https://github.com/galaxyproject/galaxy/compare/b9cba364982a...8480f9187e8c

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[galaxyproject/galaxy] 9b30b1: Reduce code duplication by reusing get_installed_r...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 9b30b134d6ab93c2a84a856352f32a6713dd49cd https://github.com/galaxyproject/galaxy/commit/9b30b134d6ab93c2a84a856352f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Commit: 11eca70db129173ea20aac0040c9645049af189c https://github.com/galaxyproject/galaxy/commit/11eca70db129173ea20aac0040c9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Commit: 1b3ee81dbae9375443ea396280c1e418cae84876 https://github.com/galaxyproject/galaxy/commit/1b3ee81dbae9375443ea396280c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1314 from nsoranzo/release_15.10_tool_load_fixes [15.10] When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Compare: https://github.com/galaxyproject/galaxy/compare/a23e644a9cd7...1b3ee81dbae9

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[galaxyproject/galaxy] 41b77d: Use local versions of node modules instead of syst...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41b77d0c1352e569d861ed327fd523dd12efffae https://github.com/galaxyproject/galaxy/commit/41b77d0c1352e569d861ed327fd5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M Makefile M client/README.md Log Message: ----------- Use local versions of node modules instead of system-installed, add a 'build-it-all' target for building the whole client. Fix two old typos. Commit: b9cba364982a9fa77fc2952fb803da75ee8d26e2 https://github.com/galaxyproject/galaxy/commit/b9cba364982a9fa77fc2952fb803… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M Makefile M client/README.md Log Message: ----------- Merge pull request #1337 from dannon/makefile_singletarget Simpler build-it-all rule in Makefile Compare: https://github.com/galaxyproject/galaxy/compare/8cc10c98ec45...b9cba364982a

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[galaxyproject/galaxy] f1c364: Don't bother querying on unencoded IDs
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f1c36485c1ecef33667f3c35bad44899233d04f5 https://github.com/galaxyproject/galaxy/commit/f1c36485c1ecef33667f3c35bad4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Don't bother querying on unencoded IDs Commit: 8cc10c98ec4569ccfe1226d4c28a8526abbf3f44 https://github.com/galaxyproject/galaxy/commit/8cc10c98ec4569ccfe1226d4c28a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1340 from erasche/id_decoding Don't bother querying on unencoded IDs for error form Compare: https://github.com/galaxyproject/galaxy/compare/ea785ea59837...8cc10c98ec45

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[galaxyproject/galaxy] 99f9d7: Use the datetime object instead of a string for pr...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99f9d7724c53326330a41fa6a1b1c36624fef02d https://github.com/galaxyproject/galaxy/commit/99f9d7724c53326330a41fa6a1b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Use the datetime object instead of a string for pretty interval formatting. Commit: ea785ea598371f7aef0b37df59996e892d82f281 https://github.com/galaxyproject/galaxy/commit/ea785ea598371f7aef0b37df5999… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #1339 from dannon/library_datetime_tweak Use the datetime object instead of a string for pretty interval formatting. Compare: https://github.com/galaxyproject/galaxy/compare/0c8df84685c5...ea785ea59837

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[galaxyproject/galaxy] 54b54b: UI, Users: when an first logging out, anon users m...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54b54b1f11a30bad0b2e15802c44b30e745ca4a6 https://github.com/galaxyproject/galaxy/commit/54b54b1f11a30bad0b2e15802c44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- UI, Users: when an first logging out, anon users may not have a history when they're serialized, return 0 usage from the user serilializer when this is the case Commit: 0c8df84685c587322f6c3b83ea45c0b20819d3ab https://github.com/galaxyproject/galaxy/commit/0c8df84685c587322f6c3b83ea45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #1328 from carlfeberhard/fix.quotameter UI, Users: when an first logging out, anon users may not have a histo… Compare: https://github.com/galaxyproject/galaxy/compare/cf5d209e0f01...0c8df84685c5

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[galaxyproject/galaxy] 784274: UI, History: refactor the history copy dialog, use...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78427438adcb794af630ebb3b9b77b3628c2c5bb https://github.com/galaxyproject/galaxy/commit/78427438adcb794af630ebb3b9b7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/ui-modal.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/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/ui/ui-modal.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- UI, History: refactor the history copy dialog, use it from the options menu (instead of history/copy), pass ui-modal closing_callback a flag whether it was a cancellation or not Commit: e391fa4975800fd1d21e1e7d03183d146728f1c8 https://github.com/galaxyproject/galaxy/commit/e391fa4975800fd1d21e1e7d0318… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, History: allow copy dialog to have default of copy-all-datasets passed in as option; Replace import link with copy dialog in published histories Commit: 7187eddd2fdec95093c765b838814435c9f6b92d https://github.com/galaxyproject/galaxy/commit/7187eddd2fdec95093c765b83881… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M templates/display_base.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako Log Message: ----------- UI, published items: fix css bleeding of trackster.css into other published item displays Commit: 941109dda860325938960b93f66e50d314b67e4a https://github.com/galaxyproject/galaxy/commit/941109dda860325938960b93f66e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.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/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M templates/grid_base.mako M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, History: use copy dialog as import dialog in published history pages, refactor copy-dialog Commit: 253ca7ec4940188d11157448d73be09e762e65f8 https://github.com/galaxyproject/galaxy/commit/253ca7ec4940188d11157448d73b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/popup-menu.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/history/copy-dialog.js M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, History: insert/use copy dialog in the 'Saved Histories' grid Commit: 09cb673a9b13f6f9faae21b48c317e485afb8eb1 https://github.com/galaxyproject/galaxy/commit/09cb673a9b13f6f9faae21b48c31… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.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/history/copy-dialog.js M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- UI, History: use copy dialog for shared history popupmenus, use custom templates for both saved and shared history lists/grids. refactor custom grid code for insertion of copy dialog Commit: cb23e010d7750b533be7690e72c92500ddc8e2f1 https://github.com/galaxyproject/galaxy/commit/cb23e010d7750b533be7690e72c9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M static/maps/mvc/history/copy-dialog.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/copy-dialog.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, History: use copy dialog in history/view for import, minor fixes Commit: d72b913c1d25bf9e2ee2c9e7320bff4f52b366e3 https://github.com/galaxyproject/galaxy/commit/d72b913c1d25bf9e2ee2c9e7320b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/utils/ajax-queue.js M static/maps/utils/ajax-queue.js.map M static/scripts/utils/ajax-queue.js M templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- UI, History: hack multiple copy by API into the 'histories shared with me' mako grid Commit: 9e512f52465c158855c2a0750d8a7d794316940e https://github.com/galaxyproject/galaxy/commit/9e512f52465c158855c2a0750d8a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/model/__init__.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/tool/tools-form-base.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/copy-dialog.js M static/scripts/mvc/tool/tools-form-base.js M static/scripts/utils/ajax-queue.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, History: use copy dialog in the embedded histories in Pages, add autoClose option to copy dialog Commit: 324af9caeda230bfe35ce79cf3e6f84a3ca27ee5 https://github.com/galaxyproject/galaxy/commit/324af9caeda230bfe35ce79cf3e6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, History: remove copy and imp methods from controllers/history.py, remove history copy template Commit: 32be886f0f51103a648003997c7d06cd12ba08d9 https://github.com/galaxyproject/galaxy/commit/32be886f0f51103a648003997c7d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.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/copy-dialog.js Log Message: ----------- API, Histories: allow api/histories/create to be used as anon user; UI, Histories: minor fixes Commit: 84f3b72e1ad829e6f2f46049ff4af42f27429a5b https://github.com/galaxyproject/galaxy/commit/84f3b72e1ad829e6f2f46049ff4a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/less/ui.less M doc/source/dev/faq.rst M lib/galaxy/datatypes/text.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/style/blue/base.css R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/base/interactor.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/functional/test_1460_data_managers.py M test/unit/managers/test_UserManager.py M test/unit/workflows/test_modules.py Log Message: ----------- (merge dev); Testing, histories: update tests to reflect allowing anon to create/copy histories via the API Commit: cf5d209e0f01b7fb13e06f013f2a3693f194ebb4 https://github.com/galaxyproject/galaxy/commit/cf5d209e0f01b7fb13e06f013f2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/ajax-queue.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/utils/ajax-queue.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/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/utils/ajax-queue.js M templates/display_base.mako M templates/grid_base.mako R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Manual merge of #1303 to resolve build artifact conflicts. Compare: https://github.com/galaxyproject/galaxy/compare/d1fd23a2f4e5...cf5d209e0f01

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[galaxyproject/galaxy] e505a4: Add the CSG Viewer visualization plugin
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e505a4f6123f119577955459cda1846b5f67f0b8 https://github.com/galaxyproject/galaxy/commit/e505a4f6123f119577955459cda1… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako Log Message: ----------- Add the CSG Viewer visualization plugin based on conversations here: https://github.com/galaxyproject/galaxy/issues/1191#issuecomment-162553926 Commit: 80bd59dd90722afb837c01a26b78eebe04dd277b https://github.com/galaxyproject/galaxy/commit/80bd59dd90722afb837c01a26b78… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_UserManager.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 946438ceba25151706ba2ca62e5c488e358c4f55 https://github.com/galaxyproject/galaxy/commit/946438ceba25151706ba2ca62e5c… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M config/reports.ini.sample M config/tool_shed.ini.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py A static/maps/galaxy-app-base.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.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/citation/citation-model.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/paired-collection-creator.js M static/scripts/mvc/dataset/dataset-li-edit.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-select-content.js M static/scripts/mvc/form/form-view.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py M test/unit/tools/test_tool_deps.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: d1fd23a2f4e5c5408f469ee5560f526833f5f682 https://github.com/galaxyproject/galaxy/commit/d1fd23a2f4e5c5408f469ee5560f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako Log Message: ----------- Merge pull request #1254 from gregvonkuster/dev Add the CSG Viewer visualization plugin Compare: https://github.com/galaxyproject/galaxy/compare/7b11ebc52e30...d1fd23a2f4e5

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