No Longer Use Class Globals When Exporting

docker/swarm/README_zeke_stack_on_linux.md

@@ -11,7 +11,7 @@
    2. 
        ```bash
        pushd ../build
-       ./build.sh --skip-maven --skip-singularity --skip-sudo all localhost:5000/virtualcell dev_zeke
+       ./build.sh --skip-maven --skip-sudo all localhost:5000/virtualcell dev_zeke
        popd
       ```
 

vcell-core/src/main/java/cbit/vcell/export/server/ExportServiceImpl.java

@@ -53,12 +53,6 @@ public class ExportServiceImpl implements ExportConstants, ExportService {
 
 	private Hashtable<Long, User> jobRequestIDs = new Hashtable<Long, User>();
 	private Hashtable<ExportSpecs, JobRequest> completedExportRequests = new Hashtable<ExportSpecs, JobRequest>();
-
-	private ASCIIExporter asciiExporter = new ASCIIExporter(this);
-	private IMGExporter imgExporter = new IMGExporter(this);
-	private RasterExporter rrExporter = new RasterExporter(this);
-
-	private N5Exporter n5Exporter = new N5Exporter(this);
 
 
 /**
@@ -268,6 +262,10 @@ public ExportEvent makeRemoteFile(OutputContext outputContext,User user, DataSer
 		FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
 		try{
 			ExportOutput[] exportOutputs = null;
+			RasterExporter rrExporter = new RasterExporter(this);
+			IMGExporter imgExporter = new IMGExporter(this);
+			ASCIIExporter asciiExporter = new ASCIIExporter(this);
+
 			switch (exportSpecs.getFormat()) {
 				case CSV:
 				case HDF5:
@@ -313,9 +311,9 @@ public ExportEvent makeRemoteFile(OutputContext outputContext,User user, DataSer
 					exportOutputs = rrExporter.makeVTKUnstructuredData(outputContext,newExportJob, user, dataServerImpl, exportSpecs,fileDataContainerManager);
 					return saveResultsToRemoteFile(fileFormat, exportBaseDir, exportBaseURL, exportOutputs, exportSpecs, newExportJob,fileDataContainerManager);
 				case N5:
-					n5Exporter.initalizeDataControllers(user, dataServerImpl,  (VCSimulationDataIdentifier) exportSpecs.getVCDataIdentifier());
+					N5Exporter n5Exporter = new N5Exporter(this, user, dataServerImpl,  (VCSimulationDataIdentifier) exportSpecs.getVCDataIdentifier());
 					ExportOutput exportOutput = n5Exporter.makeN5Data(outputContext, newExportJob, exportSpecs, fileDataContainerManager);
-					return makeRemoteN5File(fileFormat, n5Exporter.getN5FileNameHash(), exportOutput, exportSpecs, newExportJob);
+					return makeRemoteN5File(fileFormat, n5Exporter.getN5FileNameHash(), exportOutput, exportSpecs, newExportJob, n5Exporter.getN5FilePathSuffix());
 				default:
 					throw new DataAccessException("Unknown export format requested");
 			}
@@ -475,11 +473,11 @@ private ExportEvent makeRemoteFile_Unzipped(String fileFormat, String exportBase
 }
 
 
-private ExportEvent makeRemoteN5File(String fileFormat, String fileName, ExportOutput exportOutput, ExportSpecs exportSpecs, JobRequest newExportJob) throws DataFormatException, IOException{
+private ExportEvent makeRemoteN5File(String fileFormat, String fileName, ExportOutput exportOutput, ExportSpecs exportSpecs, JobRequest newExportJob, String pathSuffix) throws DataFormatException, IOException{
 	if (exportOutput.isValid()) {
 		completedExportRequests.put(exportSpecs, newExportJob);
 		String url = PropertyLoader.getRequiredProperty(PropertyLoader.s3ExportBaseURLProperty);
-		url += "/" + n5Exporter.getN5FilePathSuffix();
+		url += "/" + pathSuffix;
 		N5Specs n5Specs = (N5Specs) exportSpecs.getFormatSpecificSpecs();
 		url += "?dataSetName=" + newExportJob.getExportJobID();
 		if (lg.isTraceEnabled()) lg.trace("ExportServiceImpl.makeRemoteFile(): Successfully exported to file: " + fileName);

vcell-core/src/main/java/cbit/vcell/export/server/N5Exporter.java

@@ -64,9 +64,9 @@ public class N5Exporter implements ExportConstants {
 	));
 
 
-	public N5Exporter(ExportServiceImpl exportServiceImpl) {
-	this.exportServiceImpl = exportServiceImpl;
-}
+	public N5Exporter(ExportServiceImpl exportServiceImpl, User user, DataServerImpl dataServer, VCSimulationDataIdentifier vcSimulationDataIdentifier) {
+		this.exportServiceImpl = exportServiceImpl;
+	}
 
 	private ExportOutput exportToN5(OutputContext outputContext, long jobID, N5Specs n5Specs, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
 		VCUnitDefinition lengthUnit = ModelUnitSystem.createDefaultVCModelUnitSystem().getLengthUnit();
@@ -139,10 +139,12 @@ private ExportOutput exportToN5(OutputContext outputContext, long jobID, N5Specs
 
 		int timeLoops = 1;
 		double progress = 0;
+
 		for (int variableIndex=0; variableIndex < (numVariables -1); variableIndex++){
 			for (int timeIndex=timeSpecs.getBeginTimeIndex(); timeIndex <= timeSpecs.getEndTimeIndex(); timeIndex++){
 				int normalizedTimeIndex = timeIndex - timeSpecs.getBeginTimeIndex();
 
+				System.out.print("Writing with VCid: " + vcDataID + ".");
 				double[] data = this.dataServer.getSimDataBlock(outputContext, user, this.vcDataID, variableNames[variableIndex], allTimes[timeIndex]).getData();
 				data = containsPostProcessed ? data : MeshToImage.convertMeshIntoImage(data, mesh).data();
 				for (int z=0; z < sizeZ; z++){
@@ -195,12 +197,6 @@ private boolean containsPostProcessedVariable(String[] variableNames, OutputCont
 		return false;
 	}
 
-	public void initalizeDataControllers(User user, DataServerImpl dataServer, VCSimulationDataIdentifier vcSimulationDataIdentifier) throws IOException, DataAccessException {
-		this.user = user;
-		this.vcDataID = vcSimulationDataIdentifier;
-		this.dataServer = dataServer;
-	}
-
 
 	public VCSimulationDataIdentifier getVcDataID(){return vcDataID;}