Pass kinshipValidation setting through job XML

Author: bbimber

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java

@@ -40,6 +40,7 @@
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.pipeline.RecordedAction;
 import org.labkey.api.pipeline.RecordedActionSet;
 import org.labkey.api.pipeline.file.FileAnalysisJobSupport;
@@ -153,7 +154,9 @@ public RecordedActionSet run() throws PipelineJobException
             processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
             processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
 
-            if (GeneticCalculationsJob.isKinshipValidation())
+            // NOTE: pass this through XML in case the job runs on a remote server:
+            boolean kinshipValidation = Boolean.parseBoolean(getJob().getParameters().getOrDefault("kinshipValidation", "false"));
+            if (kinshipValidation)
             {
                 validateKinship();
             }
@@ -521,6 +524,11 @@ private boolean validateKinship()
         PipelineJob job = getJob();
         job.getLogger().info("Validate kinship");
 
+        if (PipelineJobService.get().getLocationType() != PipelineJobService.LocationType.WebServer)
+        {
+            throw new IllegalStateException("Kinship validation must be run on the webserver. This task is set to execute on: " + PipelineJobService.get().getLocationType());
+        }
+
         UserSchema ehrSchema = QueryService.get().getUserSchema(job.getUser(), job.getContainer(), "ehr");
         if (ehrSchema == null)
         {

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java

@@ -86,6 +86,7 @@ private void startCalculation(User u, Container c, boolean allowRunningDuringDay
             String xml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
                 "<bioml>\n" +
                     "\t<note label=\"allowRunningDuringDay\" type=\"input\">" + allowRunningDuringDay + "</note>" +
+                    "\t<note label=\"kinshipValidation\" type=\"input\">" + GeneticCalculationsJob.isKinshipValidation() + "</note>" +
                 "</bioml>";
 
             AbstractFileAnalysisProtocol<?> protocol = factory.createProtocolInstance(protocolName, "", xml);