December 2015 - galaxy-commits - lists.galaxyproject.org

[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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