Selective downloading of output files
- Workflow: added automatic download getter and setter.
- BaseWorkflow: added automaticDownload field (with getter and setter).
- GalaxyWorkflow: added reference to workflow engine and overridden version of the getOutput method for delayed downloading.
- GalaxyWorkflowEngine: store history ID in field (saves lots of parameters), added the outputNameToIdsMap field and getOutputIdForOutputName method, created separate downloadOutputFile method, handle automatic downloading.
- GalaxyWorkflowTest and GalaxyWorkflowEngineTest: pass workflow engine to Galaxy workflow constructor.
- ConcatenateExample, HistogramExample, and RandomLinesExample: use the workflow.getOutput() method instead of the workflow.getOutputMap().get() methods.
Fixed tests and replaced DummyWorkflow by BaseWorkflow
- fixed some failing unit tests.
- eliminated the DummyWorkflow class by using the BaseWorkflow class directly instead.
- BaseWorkflow: renamed inputs and outputs fields to inputsFiles and outputsFiles (used in GalaxyWorkflow too).
- ConcatenateExample: added OUTPUT_NAME field and used it in ConcatenateExampleTest.
- HistogramExample: added OUTPUT_NAME field and used it in HistogramExampleTest.
- TestGuiceModule, DummyWorkflowEngineFactory and DummyWorkflowEngine: added Javadocs and copyright/license information.
Fixed several Checkstyle issues
Added exception to log statement
- added the exception to the log statement in the catch part of the exception handler in the isWorkflowOnServer method.
- also added comments with an example of error message confusion.
Fixed invalid file name characters
- FileUtils: added the cleanFileName method.
- FileUtilsTest: added a simple unit test for the cleanFileName method.
- GalaxyWorkflowEngine: use the new cleanFileName method in the downloadOutputFile method.
- HistoryUtils: use the new cleanFileName method in the downloadDataset method.
- DefaultWorkflowEngineFactory: constructor is public (in case you want to use it without dependency injection).
- pom.xml: small textual changes.
Merge branch 'master' of https://github.com/CTMM-TraIT/trait_workflow_runner