Expand test cases for cross-workbook jobs and remove many warnings

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java

@@ -221,7 +221,7 @@ private int createTestVcf(int genomeId, File vcf)
                 writer.add(vcb.make());
             }
 
-            ExpData d = createExpData(vcf);
+            ExpData d = createExpData(vcf, _project);
             Map<String, Object> params = new CaseInsensitiveHashMap<>();
             params.put("name", "TestVcf");
             params.put("description", "Description");

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -1924,7 +1924,7 @@ else if (o.has("relPath") || o.has("fileName"))
 
                     if (f == null || !f.exists())
                     {
-                        throw new PipelineValidationException("Unknown file: " + o.getString("relPath") + " / " + o.getString("fileName"));
+                        throw new PipelineValidationException("Unknown file: " + o.optString("relPath") + " / " + o.optString("fileName"));
                     }
 
                     ret.add(f.toNioPathForRead().toFile());