Merge pull request #1371 from virtualcell/jhdf5-migration

use pure-java io.jhdf library for nonspatial HDF5 file writing while executing omex archives.

pom.xml

@@ -106,7 +106,7 @@
 		<commons-configuration2.version>2.9.0</commons-configuration2.version>
 		<commons-csv.version>1.10.0</commons-csv.version>
 		<commons-discovery.version>0.5</commons-discovery.version>
-		<commons-io.version>2.4</commons-io.version>
+		<commons-io.version>2.7</commons-io.version>
 		<commons-lang.version>2.6</commons-lang.version>
 		<commons-lang3.version>3.13.0</commons-lang3.version>
 		<commons-math3.version>3.6.1</commons-math3.version>
@@ -133,7 +133,8 @@
 		<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>0.7.0-alpha</jhdf5.version>
+		<jgrapht.version>1.3.0</jgrapht.version>
+		<jhdf.version>0.8.4</jhdf.version>
 		<jhdf5-2-10.version>2.9</jhdf5-2-10.version>
 		<jmatio.version>1.0</jmatio.version>
 		<joda-time.version>2.12.2</joda-time.version>
@@ -158,6 +159,7 @@
 		<netcdf.version>4.3.22</netcdf.version>
 		<nitrite.version>2.1.1</nitrite.version>
 		<ojdbc-bom.version>23.3.0.23.09</ojdbc-bom.version>
+		<ome-common.version>6.0.22</ome-common.version>
 		<opencsv.version>5.7.1</opencsv.version>
 		<picocli.version>4.6.3</picocli.version>
 		<postgresql.version>42.6.0</postgresql.version>
@@ -169,6 +171,7 @@
 		<sesame-rio-n3.version>2.9.0</sesame-rio-n3.version>
 		<slf4j-api.version>2.0.9</slf4j-api.version>
 		<sshj.version>0.35.0</sshj.version>
+		<thrift.version>0.18.0</thrift.version>
 		<xercesImpl.version>2.8.1</xercesImpl.version>
 		<xstream.version>1.4.20</xstream.version>
 		<xalan.version>2.7.3</xalan.version>

vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java

@@ -21,7 +21,7 @@
 import java.util.List;
 import java.util.Map;
 
-import static org.vcell.cli.run.hdf5.BiosimulationsHdf5Writer.BiosimulationsHdfWriterException;
+import org.vcell.cli.run.hdf5.BiosimulationsHdfWriterException;
 
 public class ExecuteImpl {
 

vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java

@@ -15,7 +15,7 @@
 import java.nio.file.Paths;
 import java.util.List;
 
-import static org.vcell.cli.run.hdf5.BiosimulationsHdf5Writer.BiosimulationsHdfWriterException;
+import org.vcell.cli.run.hdf5.BiosimulationsHdfWriterException;
 
 /**
  * Contains the code necessary to execute an Omex archive in VCell

vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java

@@ -128,11 +128,12 @@ public List<String> getSedmlLocationsRelative(){
 
         // Test corner cases
         if (sedmlMap.get(MASTER).isEmpty()){
-            if (masterCount > 0)
-                throw new RuntimeException("No SED-MLs are intended to be executed (non SED-ML file is set to be master)");
-            if (sedmlMap.get(REGULAR).isEmpty())
+            if (sedmlMap.get(REGULAR).isEmpty()) {
                 throw new RuntimeException("There are no SED-MLs in the archive to execute");
-
+            }
+            if (masterCount > 0) {
+                logger.warn("No SED-MLs are marked as master, so will run them all");
+            }
             return sedmlMap.get(REGULAR).stream().map(ArchiveEntry::getFilePath).toList();
         }