Renamed stepId to stepNumber
Use stepNumber for the setParameter method: a one-based index derived from the ordered Galaxy step IDs.
- Workflow, BaseWorkflow, DemonstrationWorkflowEngineTest, and HistogramExample, RandomLinesExample: renamed stepId to stepNumber.
Added create unique file path method
- FileUtils: added check for rubout character (127) and added new createUniqueFilePath method.
- FileUtilsTest: extended testCleanFileName test and added new testCreateUniqueFilePath test.
- GalaxyWorkflowEngine - downloadOutputFile method: use new FileUtils.createUniqueFilePath method and changed prefix to baseName.
Removed downloadDataset.useDatasetName parameter
- HistoryUtils, HistoryUtilsTest, GalaxyWorkflowEngine, GalaxyWorkflowEngineTest: removed the useDatasetName parameter from the downloadDataset method (was always false).
- GalaxyWorkflowEngine: added some todo items.
Added RNA-Seq edgeR DGE workflow example
- added RnaSeqDgeExample and RNA-Seq-edgeR-DGE.ga: an example of the RNA-Seq edgeR DGE workflow (in progress).
- Constants: added constants for the SURFsara CTMM TraIT Galaxy server and for the RNA-Seq edgeR DGE workflow.
- GalaxyWorkflowEngine: added todo for separate check and/or better error message when the server is not available, working on appropriate extensions for downloaded files (in progress).
Fixed some Checkstyle issues
- RnaSeqDgeExample: variable for magic number 7.
- GalaxyWorkflowEngine: constants for file types and extension, variable for period.
Added Coveralls support
- added the first version of Coveralls support to the project, using JaCoCo and Travis CI.
Added Coveralls support
- added the Coveralls badge (coverage status) to the README.md.
Added Coveralls support - 3/n
- put the jacoco.exec file directly in the target directory.
Added Coveralls support - 4/4
- upgraded the JaCoCo Maven plugin to version 0.7.1.201405082137.
- moved the Coveralls Maven plugin version to the right section.
Unit tests and disabled examples
- ConcatenateExampleTest: added tests for no output and for invalid output.
- RandomLinesExampleTest: added tests for no output and for invalid output.
- GalaxyWorkflowEngineTest: added simple test of the downloadOutputFile method with invalid input (test method: testDownloadOutputFile).
- disabled the RemoveTopAndLeftExample and RnaSeqDgeExample example classes because they are not working yet.
Extended GalaxyWorkflowEngine.runWorkflow test
- extended the testRunWorkflowV2 method to test retrieving the workflow name, all available workflows & workflow details, handling input files & parameters, and retrieving the workflow steps.
Test downloading of datasets
- GalaxyWorkflowEngineTest: added checks for the GalaxyWorkflowEngine.checkWorkflowResults code, commented out the testRunWorkflow and getHiddenStaticField methods.
- DefaultWorkflowEngineFactory, WorkflowEngineFactory, GalaxyWorkflowEngine, and DummyWorkflowEngineFactory: added a historyUtils parameter to the WorkflowEngineFactory.getWorkflowEngine methods.
- FileUtils: added the createFile method, moved the createOutputFile method here (from the DemonstrationWorkflowEngine class).
Resolved some Checkstyle issues
Fixed downloadFileFromUrl and unit tests
- HistoryUtils: the downloadFileFromUrl method now returns false when the response code is not equal to HTTP_OK and the unexpected response code is logged.
- HistoryUtilsTest: test the downloadFileFromUrl method with a valid and with an invalid URL.
- FileUtils: refactored the methods to create (temporary) files.
- FileUtilsTest: added some more cases to the testCleanFileName method and removed the local createFile method.
Added testCreateFileInvalidPath unit test
-also removed the code coverage todo from the README.md file.
Merge branch 'master' of https://github.com/CTMM-TraIT/trait_workflow_runner