bugfix for closed polylines (#30)

bugfix for closed polylines
geosiris-technologies · Dec 12, 2024 · 5dfb9e6 · 5dfb9e6
1 parent ccbc011
commit 5dfb9e6
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Showing 6 changed files with 61 additions and 25 deletions.
diff --git a/.gitignore b/.gitignore
@@ -15,4 +15,6 @@ target/*
 pom-test.xml
 rc/*log4j2.properties
 logs
-src/test/manip*
+src/test/manip*
+
+src/main/java/sample
diff --git a/src/main/java/com/geosiris/energyml/data/Mesh.java b/src/main/java/com/geosiris/energyml/data/Mesh.java
@@ -56,7 +56,11 @@ public static String meshNameMapping(String arrayTypeName) {
 
     public static List<AbstractMesh> readMeshObject(Object energymlObject, EnergymlWorkspace workspace) throws InvocationTargetException, IllegalAccessException {
         if (energymlObject instanceof List) {
-            return (List<AbstractMesh>) energymlObject;
+            List<AbstractMesh> meshes = new ArrayList<>();
+            for(var m: (List<?>) energymlObject){
+                meshes.addAll(readMeshObject(m, workspace));
+            }
+            return meshes;
         }
         String arrayTypeName = meshNameMapping(energymlObject.getClass().getSimpleName());
 
@@ -219,13 +223,14 @@ public static List<PolylineSetMesh> readPolylineRepresentation(Object energymlOb
                     for (Long nbNode : nodeCountsList) {
                         pointIndices.add(IntStream.range((int) idx, (int) idx + nbNode.intValue())
                                 .boxed().map(Long::valueOf).collect(Collectors.toList()));
-                        if (closePoly != null && closePoly.size() > polyIdx && closePoly.get(polyIdx) != null) {
+                        if (closePoly != null && closePoly.size() > polyIdx && closePoly.get(polyIdx) != null && ((boolean)closePoly.get(polyIdx))) {
                             pointIndices.get(pointIndices.size() - 1).add(idx);
                         }
                         idx += nbNode;
                         polyIdx++;
                     }
-                } catch (IndexOutOfBoundsException ignore) {
+                } catch (IndexOutOfBoundsException err) {
+                    logger.error(err);
                 }
 
                 if(isZReversed(crs)){

diff --git a/src/main/java/com/geosiris/energyml/pkg/EPCPackage.java b/src/main/java/com/geosiris/energyml/pkg/EPCPackage.java
@@ -166,7 +166,7 @@ public JAXBElement<?> parseXmlContent(String xmlContent, boolean alternateDevVer
             logger.debug("Success reading with '" + this.packagePath + "' object class : "
                     + result.getValue().getClass().getName());
         } else {
-            logger.error("error reading with package " + this.packagePath);
+            logger.error("error reading with package " + this.packagePath);  // + " --> " + xmlContent);
         }
 
         long ticEnd = System.currentTimeMillis();

diff --git a/src/main/java/com/geosiris/energyml/pkg/EpcHdf5FileManager.java b/src/main/java/com/geosiris/energyml/pkg/EpcHdf5FileManager.java
@@ -28,6 +28,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
@@ -38,7 +39,7 @@
 public class EpcHdf5FileManager implements EnergymlWorkspace {
     public static Logger logger = LogManager.getLogger(EpcHdf5FileManager.class);
 
-    private EPCFile epcFile = null;
+    private final EPCFile epcFile;
 
     private EpcHdf5FileManager(EPCFile epc){
         super();
@@ -127,7 +128,8 @@ public static List<String> getHdf5PathFromExternalPath(
             Object rootObj,
             EPCFile epc
     ) {
-        if (externalPathObj instanceof String) {
+        logger.debug("{} {}", externalPathObj, pathInRoot);
+        if (externalPathObj instanceof String && pathInRoot != null) {
             // externalPathObj is maybe an attribute of an ExternalDataArrayPart, now search upper in the object
             String upperPath = pathInRoot.substring(0, pathInRoot.lastIndexOf("."));
             return getHdf5PathFromExternalPath(
@@ -145,6 +147,7 @@ public static List<String> getHdf5PathFromExternalPath(
         } else {
             List<Object> hdfProxyLst = searchAttributeMatchingName(externalPathObj, "HdfProxy");
             List<Object> extFileProxyLst = searchAttributeMatchingName(externalPathObj, "ExternalFileProxy");
+            List<Object> extDataArrayPart = searchAttributeMatchingName(externalPathObj, "ExternalDataArrayPart");
 
             // resqml 2.0.1
             if (!hdfProxyLst.isEmpty()) {
@@ -175,9 +178,28 @@ public static List<String> getHdf5PathFromExternalPath(
                 );
                 return getH5PathPossibilities((String) ObjectController.getObjectAttributeValue(extPartRefObj, "Filename"), epc);
             }
+
+            // resqml 2.2
+            if(!extDataArrayPart.isEmpty()){
+                logger.debug(extDataArrayPart);
+                List<String> result = new ArrayList<>();
+                for(var edap: extDataArrayPart){
+                    result.addAll(getHdf5PathFromExternalPath(
+                            edap,
+                            null,
+                            rootObj,
+                            epc
+                    ));
+                }
+                return result;
+            }
+
+            // Nothing found here, try with epc name
+            String epcPath = epc.getFilePath();
+            return List.of(epcPath.substring(0, epcPath.length()-4) + ".h5");
         }
 
-        return null;
+        return new ArrayList<>();
     }
 
     public EPCFile getEpcFile() {
@@ -203,13 +225,13 @@ public Object getObjectByUUID(String uuid) {
     public List<?> readExternalArray(Object energyml_array, Object energymlObject, String pathInHDF) throws ObjectNotFoundNotError {
         List<String> h5filePaths;
         try {
-            h5filePaths = getHdf5PathFromExternalPath(energymlObject, null, energymlObject, this.epcFile);
+            h5filePaths = getHdf5PathFromExternalPath(energyml_array, null, energymlObject, this.epcFile);
         }catch (Exception e){
             logger.error(e);
             throw e;
         }
         String pathInExternal = getHdfReference(energyml_array).get(0);
-
+        logger.debug(h5filePaths);
         List<?> resultArray = null;
         assert h5filePaths != null;
         for(String hdf5Path: h5filePaths) {

diff --git a/src/main/java/com/geosiris/energyml/utils/EnergymlWorkspaceHelper.java b/src/main/java/com/geosiris/energyml/utils/EnergymlWorkspaceHelper.java
@@ -284,23 +284,30 @@ public static List<?> readPoint3dZValueArray(Object energymlArray, Object rootOb
                     workspace
             );
             Object zvalues = ObjectController.getObjectAttributeValue(energymlArray, "ZValues");
-            List<?> zvaluesArray = readArray(
-                    zvalues,
-                    rootObj,
-                    pathInRoot + ".ZValues",
-                    workspace
-            );
+            List<?> zvaluesArray = new ArrayList<>();
 
-            List<Double> zvalueFlat = null;
-            if(zvaluesArray.get(0) instanceof Collection){
-                zvalueFlat = ((List<List<?>>)zvaluesArray).stream().flatMap(List::stream).map(z-> z instanceof String ? Double.parseDouble((String) z) : ((Number)z).doubleValue()).collect(Collectors.toList());
-            }else{
-                zvalueFlat = zvaluesArray.stream().map(z-> z instanceof String ? Double.parseDouble((String) z) : ((Number)z).doubleValue()).collect(Collectors.toList());
+            try {
+                zvaluesArray = readArray(
+                        zvalues,
+                        rootObj,
+                        pathInRoot + ".ZValues",
+                        workspace
+                );
+            }catch (InvocationTargetException e){
+                logger.error("Failed to read Z values for {}", energymlArray);
             }
-//            logger.info("supGeomArray : {}", (((List<?>)supGeomArray.get(0)).get(0)));
-//            logger.info("zvaluesArrayNotFlat");
 
             if(!zvaluesArray.isEmpty()) {
+                List<Double> zvalueFlat = null;
+                if(zvaluesArray.get(0) instanceof Collection){
+                    zvalueFlat = ((List<List<?>>)zvaluesArray).stream().flatMap(List::stream).map(z-> z instanceof String ? Double.parseDouble((String) z) : ((Number)z).doubleValue()).collect(Collectors.toList());
+                }else{
+                    zvalueFlat = zvaluesArray.stream().map(z-> z instanceof String ? Double.parseDouble((String) z) : ((Number)z).doubleValue()).collect(Collectors.toList());
+                }
+    //            logger.info("supGeomArray : {}", (((List<?>)supGeomArray.get(0)).get(0)));
+    //            logger.info("zvaluesArrayNotFlat");
+
+
                 if(supGeomArray.get(0) instanceof Collection && !(((List<?>)supGeomArray.get(0)).get(0) instanceof Collection)){
                     // supGeom is List<List<Double>>, a list of points
 //                    final int colSize = ((List<List<?>>)supGeomArray).get(0).size();
@@ -484,7 +491,7 @@ public static List<List<List<Double>>> readPoint3dLatticeArray(
         }catch (Exception e){
             logger.error(e);
         }
-        logger.error(result);
+        logger.debug(result);
 
         return result;
     }

diff --git a/src/test/java/com/geosiris/energyml/utils/test/EPCPackageTest.java b/src/test/java/com/geosiris/energyml/utils/test/EPCPackageTest.java
@@ -21,13 +21,13 @@
 import org.apache.logging.log4j.Logger;
 import org.junit.jupiter.api.Test;
 
+
 public class EPCPackageTest {
     public static Logger logger = LogManager.getLogger(EPCPackage.class);
 
     @Test
     void testPkgInformation() throws EPCPackageInitializationException {
         EPCPackage pkg22 = new EPCPackage("energyml.resqml2_2", "");
-
         assert pkg22.getDomainVersion().compareTo("2.2") == 0;
         assert pkg22.getVersionNum().compareTo("2.2") == 0;
         assert pkg22.getPackagePath().compareTo("energyml.resqml2_2") == 0;