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TESTING_PROFILE=workflow-integration-tests

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Fix WDL import issues (#2941)


#2941 

There were two problems:

In WDLHandler.processImports, there is map of files that have been processed so that we don't process the same file more than once. The map key was just the filename, so if the same filename exists in more than one directory, the code would only process the first instance of the filename.

Once getting past that, there were issues resolving imports, particularly if a WDL file imported from a sub-directory relatively imported more WDL from the same sub-directory.

For the first issue, the key of the map is now the absolute path, so all files will get processed. The CWL code still works/expects a map with just the filename, so I changed the LanguageHandlerInterface.getContentto take a Set<SourceFile> instead of the Map<String, String>; that way each language implementation can internally construct their own Map for their needs.

For the second issue, MapResolver now has a string to resolve imports relative to.

Other notes

*  I committed the files from the workflow directly to the repo. It's a big one, but it might be good for other tests, and it simplifies the testing.
*  One test started to fail with these changes, DAGWorkflowTestIT.testComplexImportWdlWorkflow. However, running WOMTool validate standalone against the workflow also fails, so I think this is the correct behavior, and I updated the test to expect a failure.
* There is a circular dependency with the CLI. Some tests are using the CLI which uses WDLBridge, which is in this project. Had to leave some old method signatures in there for the tests to run.
* Needed to make SoruceCodeRepoInterface.getCommitId protected in
order to have an implementation in the tests.
* Also removed BridgeHelper.java, which isn't being used
anywhere.
* Removal of BridgeHelper means commons-validator
no longer needed
* Builds often failing on WDLHandlerTest or
NFLParseTest; separate them out into their
block of tests.
* U... (continued)

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Source Files on job 10080.5 (TESTING_PROFILE=workflow-integration-tests)