Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9904bf595c3815c4827bb0852004d036600936e https://github.com/galaxyproject/galaxy/commit/d9904bf595c3815c4827bb0852004... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message: ----------- Fix for split columns rule definition.
Commit: 8af243c176fd9c261277327750aaa71806add4ef https://github.com/galaxyproject/galaxy/commit/8af243c176fd9c261277327750aaa... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.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-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/tool_conf.xml.main M lib/galaxy/app.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/rules_dsl_spec.yml A test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py
Log Message: ----------- Allow rule based operations on existing collections.
Allow the rules DSL & GUI component to operate on existing collections to allow filtering, sorting, modifying identifiers and general re-organization of existing collections (e.g. the outputs of tools). Implementing this as a collection operation tool so that it should be executable interactively in the tool form and in a batch fashion as part of workflow executions.
For this to be tracked properly as a tool execution and to work properly in the tool form, I've implemented a new tool framework and tool form parameter type called "rules".
This can thought of as a more GUI friendly alternative to my proposed collection operations that consumed JavaScript expressions.
This includes API tests for both tool and workflow execution of the new tool as well as Selenium tests for tool form execution, workflow editor interactions, and workflow running.
Commit: c225c5dbd651b048b3354e97a8821d8148b559fe https://github.com/galaxyproject/galaxy/commit/c225c5dbd651b048b3354e97a8821... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M lib/galaxy/tools/apply_rules.xml
Log Message: ----------- Add simple help for apply rules tool.
Commit: d2b8ad9105e5c06c8ab3685672c1a6dc64b31406 https://github.com/galaxyproject/galaxy/commit/d2b8ad9105e5c06c8ab3685672c1a... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- RuleBuilder tool param fix for to_dict.
An exception in generating a "text representation" of a None value was preventing the rest of to_dict from running properly for that parameter value. This restores the rule preview table in the tool form.
Commit: a6d052a6819d2bc277744b3e2633785c31c844fb https://github.com/galaxyproject/galaxy/commit/a6d052a6819d2bc277744b3e26337... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js
Log Message: ----------- Fix modal title for apply_rules branch changes.
Commit: 383eb0d2736269d24d595ed5b8aa730908812be3 https://github.com/galaxyproject/galaxy/commit/383eb0d2736269d24d595ed5b8aa7... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M config/tool_conf.xml.sample
Log Message: ----------- Add apply rules tool to standard tool xml sample
Commit: f4eda4fd173b64d782a39da97d7a2b224a7637c3 https://github.com/galaxyproject/galaxy/commit/f4eda4fd173b64d782a39da97d7a2... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M lib/galaxy/tools/apply_rules.xml
Log Message: ----------- Fix up help language in apply_rules tool.
Commit: cf2f6d7dcf2dba76dc02f1fe6ab0abd360584ef4 https://github.com/galaxyproject/galaxy/commit/cf2f6d7dcf2dba76dc02f1fe6ab0a... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py
Log Message: ----------- Fix selenium tests failing because APPLY_RULES appears twice in panel.
Commit: dbd86642d514badcc0fedf3f822f19d7b4dd9d15 https://github.com/galaxyproject/galaxy/commit/dbd86642d514badcc0fedf3f822f1... Author: John Chilton jmchilton@gmail.com Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message: ----------- Merge other recent rule PRs into apply_rules branch.
Commit: e7158658d026b7559adb173cea1ac0a26852bca8 https://github.com/galaxyproject/galaxy/commit/e7158658d026b7559adb173cea1ac... Author: Martin Cech marten@bx.psu.edu Date: 2018-04-25 (Wed, 25 Apr 2018)
Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.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-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/rules_dsl_spec.yml A test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py
Log Message: ----------- Merge pull request #5819 from jmchilton/apply_rules
Allow rule based operations on existing collections.
Compare: https://github.com/galaxyproject/galaxy/compare/8f8dc08a4cbe...e7158658d026