Added a GUI example test for running workflows
- RandomLinesGuiExampleTest: added a new unit test for the "random lines" GUI example that focuses on the run workflow functionality.
- BaseGuiExample: added the waitForWorkflowToFinish parameter to the runWorkflow method.
Expanded the test for GalaxyWorkflowEngine.runWorkflow
- GalaxyWorkflowEngineTest: added second scenario for testing the GalaxyWorkflowEngine.runWorkflow method.
- GalaxyWorkflowEngine: changed visibility of FILE_TYPE_TABULAR and FILE_TYPE_TEXT to public.
* to fix later: a FindBugs bug.
Expanded the test for GalaxyWorkflowEngine.runWorkflow - 2
- GalaxyWorkflowEngineTest: added mock data to test uploading of input files.
Minor changes to Maven pom.xml
- pom.xml: removed PowerMock dependency, use slf4j version 1.7.7, cleanup.
Removed old PowerMock dependent test
- GalaxyWorkflowEngineTest: removed old PowerMock dependent unit test.
Pass history ID to Galaxy workflow engine
- pom.xml: small changes.
Fixed a Checkstyle issue
Temporarily switched to Belgian server
- temporarily switched to biominavm-galaxy.biomina.be/galaxy instead of usegalaxy.org.
- used the GALAXY_INSTANCE_URL constant everywhere.
Fixed Checkstyle and FindBugs issues
Moved Checkstyle configuration files
- moved checkstyle.xml and checkstyle-suppressions.xml to the new src/configuration directory.
Moved developer documentation
- moved DevelopersInformation.md to the new src/documentation directory.
- ignoring the DefaultWorkflowEngineFactoryTest and WorkflowEngineTest unit tests for the moment.
Moved log directory
- moved the log directory to the new src/log directory.
Moved WorkflowRunner-runWorkflow.txt to tmp directory
- moved the default Galaxy workflow engine output file to the tmp directory (see GalaxyWorkflowEngine.OUTPUT_FILE_PATH).
Create directories for download files
- HistoryUtils: make sure all necessary directories are created when downloading a Galaxy dataset tot a local file in the downloadFileFromUrl method.
Restored main Galaxy server as default
- GalaxyWorkflowEngine: added todo because Galaxy workflows cannot specify which version of a tool should be used.
Added dummy file to tmp directory
- The tmp directory is used by some of the unit tests. So although this directory is in the .gitignore file, we do need it to exist.
Removed ignore annotation for two unit tests
- These unit tests were failing when the main Galaxy server (usegalaxy.org) was not available.
Fixed issue with downloading files
- only create output directory for download file if this directory does not exist already.
Added debugging support
- GalaxyConfiguration: added support for switching debugging information on.
- pom.xml: use blend4j 0.1.1 (with debugging support).
- .travis.yml: print the log file to Travis after a failure.
Added debugging support
- .travis.yml: modified the location of the log file in Travis.
- BaseWorkflowTest: show current directory (to determine paths in Travis).