Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a80eaae7fa380b0f6d484307bcfde179809dac54 https://github.com/galaxyproject/galaxy/commit/a80eaae7fa380b0f6d484307bcfde... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py Log Message: ----------- Reduce duplication in galaxy.tools.parameters.wrapped. Commit: 6ddb2c2a6a44c2947e7e9b6edbaa4e11ad289595 https://github.com/galaxyproject/galaxy/commit/6ddb2c2a6a44c2947e7e9b6edbaa4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/special_tools.py A lib/galaxy/tools/unzip_collection.xml A lib/galaxy/tools/zip_collection.xml M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/twilltestcase.py Log Message: ----------- Implement framework for model tools. This special class of tools leverages the infrastructure for tool inputs, tool state tracking, tool module for workflows, tool API, etc... without actually producing command-line jobs. Instead these tools are provided the input model objects and are expected to produce output model objects directly. This provides an oppertunity to copy HDAs without copying the underlying datasets. The first driving use case for these tools are also included - namely tools that allow zipping and unzipping paired collections. These tools can be mapped over lists (e.g. list:paired to (list, list) or the inverse) using much of the existing infrastructure for tools. Test cases included that validate these work with mapping operations and in workflows. The most obvious advantage of these versus traditional tools that do the same thing is that the data isn't copied on disk - new HDAs are created directly from the source datasets. Testing: This PR includes various API test cases for functionality, these can be run with the following command: ``` ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_unzip_collection ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_zip_inputs ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_zip_list_inputs ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_zip_collections ``` Commit: ddeff4ec0cdb0c6a803ae09843d0c70e2a70556b https://github.com/galaxyproject/galaxy/commit/ddeff4ec0cdb0c6a803ae09843d0c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/special_tools.py M test/api/helpers.py M test/api/test_tools.py A test/functional/tools/exit_code_from_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- New model tool that filters failed datasets out of a collection. This differs from a traditional tool in that its inputs don't need to be in an 'ok' state and instead of creating new datasets and duplicating data on disk, new HDAs are created from the existing datasets. Commit: 68a72069433a029e690535f14c1b4c91d1603499 https://github.com/galaxyproject/galaxy/commit/68a72069433a029e690535f14c1b4... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/__init__.py A lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/special_tools.py Log Message: ----------- New model tool that flattens any collection into a list. Testing: ``` ./run_tests.sh -framework -id __FLATTEN__ ``` Commit: 8a0056530fec23d487f45e45dfa99ef6e61cc757 https://github.com/galaxyproject/galaxy/commit/8a0056530fec23d487f45e45dfa99... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Improve configuration and display of collection operation tools. Commit: a2578eb31a9a676355aab9c44b173b5d6f3a854c https://github.com/galaxyproject/galaxy/commit/a2578eb31a9a676355aab9c44b173... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/__init__.py M test/api/test_tools.py Log Message: ----------- Update unzip collection action to allow it to be mapped over. Commit: d9a108ab10277bc0f2c967285f0ffd42f1141192 https://github.com/galaxyproject/galaxy/commit/d9a108ab10277bc0f2c967285f0ff... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- fix few typos Commit: 80ac816af94d43d7214671582db127483baea2d3 https://github.com/galaxyproject/galaxy/commit/80ac816af94d43d7214671582db12... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- More general handling of what tool inputs are required in what state. Commit: d8ca09bcbe04ed665f4ebecbbd258b6c6e8494be https://github.com/galaxyproject/galaxy/commit/d8ca09bcbe04ed665f4ebecbbd258... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M test/api/test_tools.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Test and linting fixes for fewer_collection_opts branch. Commit: af5f3bbdb5dbb7e065bd9b0413da39ddaa37c7cd https://github.com/galaxyproject/galaxy/commit/af5f3bbdb5dbb7e065bd9b0413da3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Update "description" of filter_failed_collection to mention only lists. Should address some confusion caused by the tool and reference in this review (https://github.com/galaxyproject/galaxy/pull/2434#issuecomment-225682424). Commit: 0ed456ec47b10a4c9d3948e647c41d555e3b44e0 https://github.com/galaxyproject/galaxy/commit/0ed456ec47b10a4c9d3948e647c41... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M config/tool_conf.xml.sample M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/unzip_collection.xml A lib/galaxy/tools/zip_collection.xml M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/twilltestcase.py A test/functional/tools/exit_code_from_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #2434 from jmchilton/fewer_collection_opts Collection Operations (Limited) Compare: https://github.com/galaxyproject/galaxy/compare/20f035dce887...0ed456ec47b1