4.1 years ago by
Blend4j is always lagging behind bioblend - it just doesn't have as many people actively using it. So the newest version of blend4j in Maven central has an incredibly limited ability to run tools - like it cannot even specify input files I don't think.
I have created a branch of blend4j with some improvements that allow a simple example of running a tool such as randomlines to work. If you want to checkout, compile, and install that branch a simple example call would be something like:
final History history = TestHelpers.createTestHistoryObject(instance, "randomlineshistorytest");
final String inputId = TestHelpers.populateTestDataset(instance, history.getId(), "1\n2\n3\n");
final Map<String, Object> parameters = new HashMap<String, Object>();
final Map<String, String> inputDict = new HashMap<String, String>();
final ToolInputs toolInputs = new ToolInputs("random_lines1", parameters);
It is pretty low-level to use and doesn't produce parsed result data structures, etc... so I am not sure it is terribly useful yet even with the changes in that branch. I have created an issue on Github to address these short-comings.
Sorry I don't have better news.