Merge pull request #1182 from virtualcell/1170-local-sim-M2-mac

local sims fail on m2 mac due to hdf5 native libs
virtualcell · Mar 11, 2024 · 5af5a1e · 5af5a1e
2 parents 20678d5 + 55f2994
commit 5af5a1e
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Showing 17 changed files with 1,315 additions and 720 deletions.
diff --git a/pom.xml b/pom.xml
@@ -109,9 +109,10 @@
 		<commons-discovery.version>0.5</commons-discovery.version>
 		<commons-io.version>2.4</commons-io.version>
 		<commons-lang.version>2.6</commons-lang.version>
-		<commons-lang3.version>3.12.0</commons-lang3.version>
+		<commons-lang3.version>3.13.0</commons-lang3.version>
 		<commons-math3.version>3.6.1</commons-math3.version>
 		<commons-pool2.version>2.5.0</commons-pool2.version>
+		<commons-text.version>1.11.0</commons-text.version>
 		<gson.version>2.9.1</gson.version>
 		<guava.version>33.0.0-jre</guava.version>
 		<guice.version>7.0.0</guice.version>
@@ -133,7 +134,7 @@
 		<jdom-contrib.version>1.1.3</jdom-contrib.version>
 		<jetty.version>9.4.29.v20200521</jetty.version>
 		<jfreechart.version>1.5.0</jfreechart.version>
-		<jhdf5.version>0.6.8</jhdf5.version>
+		<jhdf5.version>0.7.0-alpha</jhdf5.version>
 		<jhdf5-2-10.version>2.9</jhdf5-2-10.version>
 		<jmatio.version>1.0</jmatio.version>
 		<joda-time.version>2.3</joda-time.version>

diff --git a/vcell-cli/pom.xml b/vcell-cli/pom.xml
@@ -88,17 +88,6 @@
             <artifactId>log4j-core</artifactId>
             <version>${log4j-core.version}</version>
         </dependency>
-        <dependency>
-            <groupId>io.jhdf</groupId>
-            <artifactId>jhdf</artifactId>
-            <version>${jhdf5.version}</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>slf4j-api</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j2-impl</artifactId>

diff --git a/vcell-client/src/main/java/cbit/vcell/client/data/PDEDataViewerPostProcess.java b/vcell-client/src/main/java/cbit/vcell/client/data/PDEDataViewerPostProcess.java
@@ -374,16 +374,16 @@ public void run(Hashtable<String, Object> hashTable) throws Exception {
 				if(getClientTaskStatusSupport() != null){
 					getClientTaskStatusSupport().setMessage("Getting Simulation status...");
 				}
-				SimulationStatus simStatus =
-						PDEDataViewerPostProcess.this.getDataViewerManager().getRequestManager().getServerSimulationStatus(PDEDataViewerPostProcess.this.getSimulation().getSimulationInfo());
-				if(simStatus == null){
-					hashTable.put(SPATIAL_ERROR_KEY, "PostProcessing Image, no simulation status");
-					return;
-				}else if(!simStatus.isCompleted()){
-					//sim still busy, no postprocessing data
-					hashTable.put(SPATIAL_ERROR_KEY, "PostProcessing Image, waiting for completed simulation: "+simStatus.toString());
-					return;
-				}
+//				SimulationStatus simStatus =
+//						PDEDataViewerPostProcess.this.getDataViewerManager().getRequestManager().getServerSimulationStatus(PDEDataViewerPostProcess.this.getSimulation().getSimulationInfo());
+//				if(simStatus == null){
+//					hashTable.put(SPATIAL_ERROR_KEY, "PostProcessing Image, no simulation status");
+//					return;
+//				}else if(!simStatus.isCompleted()){
+//					//sim still busy, no postprocessing data
+//					hashTable.put(SPATIAL_ERROR_KEY, "PostProcessing Image, waiting for completed simulation: "+simStatus.toString());
+//					return;
+//				}
 				if(getClientTaskStatusSupport() != null){
 					getClientTaskStatusSupport().setMessage("Getting Post Process Info...");
 				}

diff --git a/vcell-core/pom.xml b/vcell-core/pom.xml
@@ -232,6 +232,21 @@
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-configuration2</artifactId>
 			<version>${commons-configuration2.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.apache.commons</groupId>
+					<artifactId>commons-lang3</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.apache.commons</groupId>
+					<artifactId>commons-text</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-text</artifactId>
+			<version>${commons-text.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-beanutils</groupId>
@@ -243,6 +258,21 @@
 		    <artifactId>commons-pool2</artifactId>
 		    <version>${commons-pool2.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>io.jhdf</groupId>
+			<artifactId>jhdf</artifactId>
+			<version>${jhdf5.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-api</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.apache.commons</groupId>
+					<artifactId>commons-lang3</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
 		<dependency>
 			<groupId>org.scala-saddle</groupId>
 			<artifactId>jhdf5_2.10</artifactId>

diff --git a/vcell-core/src/main/java/cbit/vcell/microscopy/FRAPOptData.java b/vcell-core/src/main/java/cbit/vcell/microscopy/FRAPOptData.java
@@ -13,6 +13,7 @@
 import java.io.File;
 import java.util.Arrays;
 
+import cbit.vcell.simdata.*;
 import org.vcell.optimization.ProfileData;
 import org.vcell.optimization.ProfileDataElement;
 import org.vcell.util.ClientTaskStatusSupport;
@@ -27,12 +28,8 @@
 import cbit.vcell.field.io.FieldDataFileOperationSpec;
 import cbit.vcell.opt.Parameter;
 import cbit.vcell.opt.SimpleReferenceData;
-import cbit.vcell.simdata.DataOperation;
 import cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP.DataIndexHelper;
 import cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP.TimePointHelper;
-import cbit.vcell.simdata.DataOperationResults;
-import cbit.vcell.simdata.DataSetControllerImpl;
-import cbit.vcell.simdata.SimDataConstants;
 import cbit.vcell.solver.DefaultOutputTimeSpec;
 import cbit.vcell.solver.Simulation;
 import cbit.vcell.solver.TimeBounds;
@@ -196,11 +193,12 @@ public void refreshDimensionReducedRefData(final ClientTaskStatusSupport progres
 		//read results from netCDF file
 		File hdf5File = new File(getLocalWorkspace().getDefaultSimDataDirectory(), vcSimDataID.getID()+SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
 		//get dataprocessing output
+		Hdf5DataProcessingReaderPure hdf5DataProcessingReaderPure = new Hdf5DataProcessingReaderPure();
 		DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo =
-				(DataOperationResults.DataProcessingOutputInfo)DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(null/*no vcDataIdentifier OK*/,false,null), hdf5File);
+                hdf5DataProcessingReaderPure.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(null/*no vcDataIdentifier OK*/,false,null), hdf5File);
 		DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues =
-				(DataOperationResults.DataProcessingOutputDataValues)DataSetControllerImpl.getDataProcessingOutput(
-					new DataOperation.DataProcessingOutputDataValuesOP(null/*no vcDataIdentifier OK*/,FRAPStudy.ROI_EXTDATA_NAME,TimePointHelper.createAllTimeTimePointHelper(),DataIndexHelper.createSliceDataIndexHelper(0),null,null), hdf5File);
+                hdf5DataProcessingReaderPure.getDataProcessingOutput(
+                    new DataOperation.DataProcessingOutputDataValuesOP(null/*no vcDataIdentifier OK*/,FRAPStudy.ROI_EXTDATA_NAME,TimePointHelper.createAllTimeTimePointHelper(),DataIndexHelper.createSliceDataIndexHelper(0),null,null), hdf5File);
 
 //		DataProcessingOutput dataProcessingOutput = getRawReferenceDataFromHDF5(hdf5File);
 		//get ref sim time points

diff --git a/vcell-core/src/main/java/cbit/vcell/microscopy/server/FrapDataUtils.java b/vcell-core/src/main/java/cbit/vcell/microscopy/server/FrapDataUtils.java
@@ -7,6 +7,7 @@
 import java.util.BitSet;
 import java.util.Random;
 
+import cbit.vcell.simdata.*;
 import org.vcell.util.ClientTaskStatusSupport;
 import org.vcell.util.Extent;
 import org.vcell.util.ISize;
@@ -37,13 +38,8 @@
 import cbit.vcell.microscopy.FRAPData;
 import cbit.vcell.microscopy.FRAPOptimizationUtils;
 import cbit.vcell.microscopy.LocalWorkspace;
-import cbit.vcell.simdata.Cachetable;
-import cbit.vcell.simdata.DataIdentifier;
-import cbit.vcell.simdata.DataOperation;
 import cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP.DataIndexHelper;
 import cbit.vcell.simdata.DataOperation.DataProcessingOutputDataValuesOP.TimePointHelper;
-import cbit.vcell.simdata.DataOperationResults;
-import cbit.vcell.simdata.DataSetControllerImpl;
 import cbit.vcell.solver.VCSimulationDataIdentifier;
 import cbit.vcell.solver.VCSimulationIdentifier;
 import cbit.vcell.solvers.CartesianMesh;
@@ -261,12 +257,13 @@ public void dataJobMessage(DataJobEvent event) {
 	public static FRAPData importFRAPDataFromHDF5Data(File inputHDF5File, Double maxIntensity, ClientTaskStatusSupport progressListener) throws Exception{
 		if(progressListener != null){
 			progressListener.setMessage("Loading HDF5 file " + inputHDF5File.getAbsolutePath() + "...");
-		}		
+		}
+		Hdf5DataProcessingReaderPure hdf5DataProcessingReaderPure = new Hdf5DataProcessingReaderPure();
 		DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo =
-			(DataOperationResults.DataProcessingOutputInfo)DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(null/*no vcDataIdentifier OK*/,false,null), inputHDF5File);
+                hdf5DataProcessingReaderPure.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(null/*no vcDataIdentifier OK*/,false,null), inputHDF5File);
 		DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues =
-			(DataOperationResults.DataProcessingOutputDataValues)DataSetControllerImpl.getDataProcessingOutput(
-				new DataOperation.DataProcessingOutputDataValuesOP(null/*no vcDataIdentifier OK*/, SimulationContext.FLUOR_DATA_NAME,TimePointHelper.createAllTimeTimePointHelper(),DataIndexHelper.createSliceDataIndexHelper(0),null,null), inputHDF5File);
+                hdf5DataProcessingReaderPure.getDataProcessingOutput(
+                    new DataOperation.DataProcessingOutputDataValuesOP(null/*no vcDataIdentifier OK*/, SimulationContext.FLUOR_DATA_NAME,TimePointHelper.createAllTimeTimePointHelper(),DataIndexHelper.createSliceDataIndexHelper(0),null,null), inputHDF5File);
 		ArrayList<SourceDataInfo> sdiArr =
 			dataProcessingOutputDataValues.createSourceDataInfos(
 				dataProcessingOutputInfo.getVariableISize(SimulationContext.FLUOR_DATA_NAME),