Scottx611x/workflow launching and monitoring #1949
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…_collection_creation
…w_launching_and_monitoring
…ad diff, and isn't crucial
…saturated with Workflow-based Tool specific methods
Codecov Report
@@ Coverage Diff @@
## develop #1949 +/- ##
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+ Coverage 42.78% 44.1% +1.31%
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Files 414 415 +1
Lines 26988 28087 +1099
Branches 1321 1322 +1
==========================================
+ Hits 11548 12388 +840
- Misses 15440 15699 +259
Continue to review full report at Codecov.
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| ).delete() | ||
| galaxy_workflow_taskset.delete() | ||
| analysis.galaxy_cleanup() | ||
| return |
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Why these blank returns throughout analysis monitoring code?
| @@ -352,13 +347,58 @@ def _get_analysis_config(self): | |||
| } | |||
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| def launch(self): | |||
| if self.get_tool_type() == ToolDefinition.VISUALIZATION: | |||
| return self._launch_visualization() | |||
| raise NotImplementedError(Tool.LAUNCH_WARNING) | |||
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Look at AbstractBaseClass decorators: @abstractmethod
https://docs.python.org/2/library/abc.html
refinery/tool_manager/models.py
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| 'src': 'hda' | ||
| } | ||
| for item in self.get_file_relationships_galaxy() | ||
| ] |
refinery/tool_manager/models.py
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| 'name': "{} File: {}".format(self.name, item), | ||
| 'src': 'hda' | ||
| } | ||
| for item in self.get_file_relationships_galaxy() |
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rename item to something better
refinery/tool_manager/models.py
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| structure=structure | ||
| ) | ||
| except RuntimeError: | ||
| return structure[:-1] |
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This line on 559 and no runtimeException handling
refinery/tool_manager/models.py
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| inputs=self.create_workflow_inputs() | ||
| ) | ||
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| def _get_nesting_string(self, nesting=None, structure=""): |
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flatten structure into array and do list/paired concat. from that DS
refinery/tool_manager/models.py
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| tool_launch_config[self.FILE_RELATIONSHIPS_GALAXY] = ( | ||
| tool_launch_config[self.FILE_RELATIONSHIPS] | ||
| ) | ||
| if tool_launch_config.get(self.FILE_RELATIONSHIPS_GALAXY) is None: |
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Set this in create_tool()
refinery/tool_manager/utils.py
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| if tool_type == ToolDefinition.WORKFLOW: | ||
| tool_launch_configuration[WorkflowTool.GALAXY_DATA] = {} | ||
| tool = WorkflowToolFactory( | ||
| name=tool_name, |
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| user_tools = get_objects_for_user( | ||
| self.request.user, | ||
| "tool_manager.read_tool" | ||
| user_tools.extend( |
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is there a better way?
…tionships_nesting`
ToolPolymorphism (there are nowWorkflowTool&VisualizationTool)RefineryImport,GalaxyImport,GalaxyAnalysisstages forWorkflowToollaunches<DatasetCollection:list>, InvokeWorkflowToolswith saidDatasetCollection, and have the GalaxyAnalysis stage successfully complete.analysis_manager.tasks._check_galaxy_history_statefor easier testing