fixing epcfile reading (#21)

geosiris-technologies · Sep 21, 2023 · d8dd473 · d8dd473
1 parent 8e6e8d0
commit d8dd473
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Showing 7 changed files with 146 additions and 38 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>com.geosiris</groupId>
     <artifactId>energyml-utils</artifactId>
     <name>${project.groupId}:${project.artifactId}</name>
-    <version>1.0.7</version>
+    <version>1.0.8</version>
     <organization>
         <name>Geosiris</name>
         <url>http://www.geosiris.com</url>
@@ -102,6 +102,12 @@
             <version>1.0.4</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>com.geosiris</groupId>
+            <artifactId>energyml-resqml201</artifactId>
+            <version>1.0.4</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

diff --git a/src/main/java/com/geosiris/energyml/pkg/EPCFile.java b/src/main/java/com/geosiris/energyml/pkg/EPCFile.java
@@ -15,10 +15,7 @@
 */
 package com.geosiris.energyml.pkg;
 
-import com.geosiris.energyml.utils.EPCGenericManager;
-import com.geosiris.energyml.utils.ExportVersion;
-import com.geosiris.energyml.utils.ObjectController;
-import com.geosiris.energyml.utils.Utils;
+import com.geosiris.energyml.utils.*;
 import energyml.content_types.Default;
 import energyml.content_types.Override;
 import energyml.content_types.Types;
@@ -53,27 +50,38 @@ public class EPCFile {
     Map<String, InputStream> otherFiles;
     Map<Object, List<Relationship>> additionalRels;
 
+    // Key is (Uuid;ObjectVersion)
+//    Map<Pair<String, String>, List<Relationship>> readRels;
+
     ExportVersion version;
     CoreProperties coreProperties;
     EPCPackageManager pkgManager;
 
+    String filePath;
+
     public EPCFile(EPCPackageManager pkgManager, ExportVersion version, CoreProperties coreProperties, Map<String, List<Object>> energymlObjects, Map<String, InputStream> otherFiles, Map<Object, List<Relationship>> additionalRels ) {
         this.energymlObjects = energymlObjects;
         this.otherFiles = otherFiles;
         this.additionalRels = additionalRels;
         this.version = version;
         this.coreProperties = coreProperties;
         this.pkgManager = pkgManager;
+        this.filePath = null;
     }
 
-    public EPCFile(EPCPackageManager pkgManager, ExportVersion version,  CoreProperties coreProperties){
+    public EPCFile(EPCPackageManager pkgManager, ExportVersion version, CoreProperties coreProperties){
         this(pkgManager, version, coreProperties, new HashMap<>(), new HashMap<>(), new HashMap<>());
     }
 
     public EPCFile(EPCPackageManager pkgManager, ExportVersion version){
         this(pkgManager, version, new CoreProperties());
     }
 
+    public EPCFile(EPCPackageManager pkgManager, String filePath){
+        this(pkgManager);
+        this.filePath = filePath;
+    }
+
     public EPCFile(EPCPackageManager pkgManager){
         this(pkgManager, ExportVersion.EXPANDED);
         coreProperties.setVersion("1.0");
@@ -222,7 +230,7 @@ public List<String> getAllVersions(String uuid){
         return version;
     }
 
-    private Map<Object, Relationships> computeRelations(){
+    public Map<Object, Relationships> computeRelations(){
         Map<Object, Relationships> relations = new HashMap<>();
 
         Map<Object, List<Object>> sourceRels = new HashMap<>();
@@ -294,6 +302,12 @@ private Map<Object, Relationships> computeRelations(){
         return relations;
     }
 
+    public static EPCFile read(String filePath, EPCPackageManager pkgManager) throws FileNotFoundException {
+        EPCFile file = read(new FileInputStream(filePath), pkgManager);
+        file.filePath = filePath;
+        return file;
+    }
+
     public static EPCFile read(InputStream input, EPCPackageManager pkgManager){
         EPCFile epc = new EPCFile(pkgManager);
         byte[] buffer = new byte[2048];
@@ -335,7 +349,7 @@ public static EPCFile read(InputStream input, EPCPackageManager pkgManager){
                     }else if (entry.getName().endsWith("." + OPCRelsPackage.getRelsExtension())){
                         Relationships rels = (Relationships) OPCRelsPackage.unmarshal(new ByteArrayInputStream(entryBOS.toByteArray()));
                         String objPath = entry.getName()
-                                .substring(0, entry.getName().length() - 4)
+                                .substring(0, entry.getName().lastIndexOf(".")) // removing rels extension
                                 .replace(OPCRelsPackage.genRelsFolderPath(epc.version) + "/", "")
                                 .replace(OPCRelsPackage.genRelsFolderPath(epc.version) + "\\", "");
                         mapPathToRelationships.put(objPath, rels);
@@ -346,10 +360,23 @@ public static EPCFile read(InputStream input, EPCPackageManager pkgManager){
             throw new RuntimeException(e);
         }
 
+//        if(epc.readRels == null){
+//            epc.readRels = new HashMap<>();
+//        }else {
+//            epc.readRels.clear();
+//        }
+
         for(Map.Entry<String, Relationships> rels: mapPathToRelationships.entrySet()) {
             if (mapPathToObject.containsKey(rels.getKey())){
                 Object target = mapPathToObject.get(rels.getKey());
 
+                Pair<String, String> obj_pair = new Pair<>((String) ObjectController.getObjectAttributeValue(target, "uuid"),
+                                (String) ObjectController.getObjectAttributeValue(target, "ObjectVersion"));
+//                if(!epc.readRels.containsKey(obj_pair)){
+//                    epc.readRels.put(obj_pair, new ArrayList<>());
+//                }
+//                epc.readRels.get(obj_pair).addAll(rels.getValue().getRelationship());
+
                 for(Relationship r: rels.getValue().getRelationship()){
                     if(EPCRelsRelationshipType.DestinationObject.getType() .compareToIgnoreCase(r.getType()) != 0
                             && EPCRelsRelationshipType.SourceObject.getType().compareToIgnoreCase(r.getType()) != 0){
@@ -361,11 +388,62 @@ public static EPCFile read(InputStream input, EPCPackageManager pkgManager){
                 }
             }else{
                 logger.error("Object " + rels.getKey() + " not found for rels");
+                    for(String k: mapPathToObject.keySet()){
+                        logger.info("\t" + k + " ==> " + mapPathToObject.containsKey(rels.getKey()) + "--" + mapPathToObject.get(rels.getKey()));
+                    }
             }
         }
-        logger.info("EPC " + epc.energymlObjects.size());
+        logger.debug("EPC " + epc.energymlObjects.size());
 
         epc.version = foundNamespaceFolder ? ExportVersion.EXPANDED : ExportVersion.CLASSIC;
         return epc;
     }
+
+//    public String findNumericalDataLocation(String uuid, String objectVersion){
+//        Object related = getObject(uuid, objectVersion);
+//        if(related != null){
+//            Relationships rels = computeRelations().get(related);
+//            for(Relationship rel : rels.getRelationship()){
+//                if(rel.getType().compareToIgnoreCase(EPCRelsRelationshipType.ExternalResource.label) == 0){
+//                    if(rel.getTarget().toLowerCase().endsWith(".h5") || rel.getTarget().toLowerCase().endsWith(".hdf5")){
+//                        return rel.getTarget();
+//                    }
+//                }
+//            }
+//            List<Object> references = new ArrayList<>();
+//            references.addAll(ObjectController.findAllAttributesFromName(related, "EpcExternalPartReference", true, false));
+//            references.addAll(ObjectController.findAllAttributesFromName(related, "HdfProxy", true, false));
+//
+//            for(Object ref: references){
+//
+//            }
+//        }
+//        return null;
+//    }
+
+    /* --------------------------------------------------- */
+
+    public Map<String, List<Object>> getEnergymlObjects() {
+        return energymlObjects;
+    }
+
+    public Map<String, InputStream> getOtherFiles() {
+        return otherFiles;
+    }
+
+    public Map<Object, List<Relationship>> getAdditionalRels() {
+        return additionalRels;
+    }
+
+//    public Map<Pair<String, String>, List<Relationship>> getReadRels() {
+//        return readRels;
+//    }
+
+    public ExportVersion getVersion() {
+        return version;
+    }
+
+    public CoreProperties getCoreProperties() {
+        return coreProperties;
+    }
 }
diff --git a/src/main/java/com/geosiris/energyml/pkg/EPCPackage.java b/src/main/java/com/geosiris/energyml/pkg/EPCPackage.java
@@ -34,6 +34,7 @@
 import java.lang.reflect.Method;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 import java.util.regex.Matcher;
@@ -102,7 +103,12 @@ public boolean isReleaseVersion(){
     }
 
     public List<Class<?>> getRootsElementsClasses() {
-        return pkgClasses.stream().filter(EPCGenericManager::isRootClass).collect(Collectors.toList());
+        // return pkgClasses.stream().filter(EPCGenericManager::isRootClass).collect(Collectors.toList()); OLD Way, but it includes types with no "createMY_TYPE_NAME(MY_TYPE value) -> JaxbElement" functions
+        Object objFactory = getObjectFactory();
+        return Arrays.stream(objFactory.getClass().getMethods())
+                .filter(m -> m.getReturnType() == JAXBElement.class && m.getParameterCount() == 1)
+                .map(m->m.getParameters()[0].getType())
+                .collect(Collectors.toList());
     }
 
     public Object createInstance(String className) {
@@ -295,9 +301,11 @@ public static JAXBElement<?> wrap(Object energymlObject, Object factory) throws
         methodPotentialName.add("create" + typename);
         methodPotentialName.add(typename.substring(0, 1).toLowerCase() + typename.substring(1));
         for (String prefixToRemove : listOfPotentialRemovablePrefix) {
-            String noPrefix = typename.substring(prefixToRemove.length());
-            methodPotentialName.add("create" + noPrefix);
-            methodPotentialName.add(noPrefix.substring(0, 1).toLowerCase() + noPrefix.substring(1));
+            if(typename.startsWith(prefixToRemove)) {
+                String noPrefix = typename.substring(prefixToRemove.length());
+                methodPotentialName.add("create" + noPrefix);
+                methodPotentialName.add(noPrefix.substring(0, 1).toLowerCase() + noPrefix.substring(1));
+            }
         }
 
         for(String m_name : methodPotentialName){

diff --git a/src/main/java/com/geosiris/energyml/pkg/EPCPackageManager.java b/src/main/java/com/geosiris/energyml/pkg/EPCPackageManager.java
@@ -600,7 +600,7 @@ public HashMap<String, String> getClassesComment() {
 
         for (EPCPackage pkg : PKG_LIST) {
             try {
-                logger.info("@getClassesComment " + pkg);
+                logger.debug("@getClassesComment " + pkg);
                 result.putAll(Utils.readJsonFileOrRessource(xsdCommentsFolderPath + pkg.getPackageName() + ".json",
                         HashMap.class));
             } catch (Exception ignore) {

diff --git a/src/main/java/com/geosiris/energyml/utils/Pair.java b/src/main/java/com/geosiris/energyml/utils/Pair.java
@@ -31,4 +31,15 @@ public TL l() {
 	public TR r() {
 		return _r;
 	}
+
+	@Override
+	public boolean equals(Object b){
+		return b instanceof Pair
+				&& ((this._l == null && ((Pair<?, ?>)b)._l == null)
+					|| ((this._l != null && ((Pair<?, ?>)b)._l != null && this._l.equals(((Pair<?, ?>)b)._l)))
+				)
+				&& ((this._r == null && ((Pair<?, ?>)b)._r == null)
+					|| ((this._r != null && ((Pair<?, ?>)b)._r != null && this._r.equals(((Pair<?, ?>)b)._r)))
+				);
+	}
 }
diff --git a/src/test/java/com/geosiris/energyml/utils/test/EPCGenericManagerTest.java b/src/test/java/com/geosiris/energyml/utils/test/EPCGenericManagerTest.java
@@ -15,16 +15,20 @@
 */
 package com.geosiris.energyml.utils.test;
 
+import com.geosiris.energyml.pkg.EPCFile;
 import com.geosiris.energyml.pkg.EPCPackageManager;
-import com.geosiris.energyml.utils.EPCGenericManager;
-import com.geosiris.energyml.utils.ExportVersion;
-import com.geosiris.energyml.utils.ObjectController;
-import com.geosiris.energyml.utils.Utils;
-import energyml.common2_2.DataObjectReference;
+import com.geosiris.energyml.utils.*;
 import energyml.common2_3.Citation;
+import energyml.relationships.Relationship;
+import energyml.relationships.Relationships;
 import energyml.resqml2_2.TriangulatedSetRepresentation;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.jupiter.api.Test;
 
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.util.Map;
 import java.util.Objects;
 import java.util.UUID;
 import java.util.regex.Matcher;
@@ -315,23 +319,4 @@ public static energyml.resqml_dev3x_2_2.TriangulatedSetRepresentation createTest
 
         return tr;
     }
-
-    public static void main(String[] argv){
-//        System.out.println(EPCGenericManager.getObjectQualifiedType(cName_tsr22dev3, true));
-//        Matcher m_tsr201 = EPCGenericManager.PATTERN_QUALIFIED_TYPE.matcher(EPCGenericManager.getObjectQualifiedType(cName_tsr201, true));
-//        m_tsr201.find();
-//        System.out.println(m_tsr201.group("domain"));
-//        System.out.println(m_tsr201.group("domainVersion"));
-//        System.out.println(m_tsr201.group("type"));
-//        EPCPackageManager manager = new EPCPackageManager("energyml", "", "", "");
-//        String tr0 = Utils.readFileOrRessource("C:/Users/Cryptaro/Downloads/TriangulatedSetRepresentation_616f910c-b3f2-4910-978b-146c21762d12.xml");
-//        System.out.println(tr0);
-//        manager.getClasses().stream().filter(cl -> cl != null && !Modifier.isAbstract(cl.getModifiers())).collect(Collectors.toList()).forEach(x -> System.out.println(x));
-
-
-        String graphical = "<?xml version=\"1.0\" encoding=\"utf-8\"?><GraphicalInformationSet xmlns=\"http://www.energistics.org/energyml/data/commonv2\" xmlns:ns2=\"http://www.energistics.org/energyml/data/resqmlv2\" uuid=\"5e3206c9-b3fa-4506-9ac0-1c76fdf72fbc\" schemaVersion=\"2.3\"><Citation><Title>GRAPHICAL INFORMATION SET 1</Title><Originator>Geosiris user</Originator><Creation>2023-05-24T09:15:46.016Z</Creation><Format>Geosiris WebStudio</Format><LastUpdate>2023-05-25T20:27:34.990Z</LastUpdate></Citation><GraphicalInformation xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:type=\"ns2:ColorInformation\"><TargetObject><Uuid>d1966850-6b1e-4dd7-abda-3c5b7b975712</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F3_2011</Title></TargetObject><TargetObject><Uuid>8e329639-4097-4467-9e0e-a04e645c9035</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F20_2013_update</Title></TargetObject><TargetObject><Uuid>38bf3283-9514-43ab-81e3-17080dc5826f</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F20_2011_New2</Title></TargetObject><TargetObject><Uuid>7908100a-68c1-4c07-a2f9-1c6f76af3a43</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F52_2011</Title></TargetObject><TargetObject><Uuid>052ec11a-e9f9-4faa-8512-ba0ef589952e</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F28_2011</Title></TargetObject><TargetObject><Uuid>3229af74-8dcd-4df5-8148-9b4f54d0c381</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F11_2011</Title></TargetObject><TargetObject><Uuid>4e23ee3e-54a7-427a-83f9-1473de6c56a4</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F27_2011</Title></TargetObject><TargetObject><Uuid>303bed39-6290-4ea7-b9f1-917438833fd5</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F8_2013_update</Title></TargetObject><TargetObject><Uuid>203ebec9-df29-4a6b-b621-ba1b8378c7fa</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F10_2011</Title></TargetObject><TargetObject><Uuid>27cf5a6d-6869-45e8-a061-555236f1546c</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F17_2011</Title></TargetObject><TargetObject><Uuid>162b0fd8-6dad-43ce-af6c-4b6370af767a</Uuid><QualifiedType>resqml22.PolylineSetRepresentation</QualifiedType><Title>depthVolve_F7_2011</Title></TargetObject><ns2:UseLogarithmicMapping>false</ns2:UseLogarithmicMapping><ns2:UseReverseMapping>false</ns2:UseReverseMapping><ns2:ValueVectorIndex>2</ns2:ValueVectorIndex><ns2:ColorMap><Uuid>44920872-7f80-4fd9-992e-cd941f45c2e4</Uuid><QualifiedType>resqml22.DiscreteColorMap</QualifiedType><Title>DISCRETE COLOR MAP 0</Title></ns2:ColorMap></GraphicalInformation><GraphicalInformation xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:type=\"ns2:ColorInformation\"><TargetObject><Uuid>349ecd25-5db0-40c1-b179-b5316fbc754f</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F27_2011_MBA</Title></TargetObject><TargetObject><Uuid>c2f53ce1-1b2d-4819-b397-f174bc8c23e0</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F11_2011_MBA</Title></TargetObject><TargetObject><Uuid>5db39032-4998-4b75-9156-ea104a8649d2</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F17_2011_MBA</Title></TargetObject><TargetObject><Uuid>fa4e80d0-d30f-48d3-aa70-41d06b837c2b</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F3_2011_MBA</Title></TargetObject><TargetObject><Uuid>bc1fbf7f-1495-4f1f-9c30-8be4b19a5475</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F7_2011_MBA</Title></TargetObject><TargetObject><Uuid>79f43d6a-77e1-46b7-b161-127b395a64be</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F28_2011_MBA</Title></TargetObject><TargetObject><Uuid>cdd9c2cd-6673-44b0-8d6d-812319daacaa</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F20_2013_update_MBA</Title></TargetObject><TargetObject><Uuid>13f6b289-3b0a-4ec3-b060-347c1efd6e5e</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F10_2011_MBA</Title></TargetObject><TargetObject><Uuid>5755aa3a-87b3-4a5d-bdf1-b8a6c1ebdf36</Uuid><QualifiedType>resqml22.TriangulatedSetRepresentation</QualifiedType><Title>depthVolve_F52_2011_MBA</Title></TargetObject><ns2:UseLogarithmicMapping>false</ns2:UseLogarithmicMapping><ns2:UseReverseMapping>false</ns2:UseReverseMapping><ns2:ValueVectorIndex>5</ns2:ValueVectorIndex><ns2:ColorMap><Uuid>44920872-7f80-4fd9-992e-cd941f45c2e4</Uuid><QualifiedType>resqml22.DiscreteColorMap</QualifiedType><Title>DISCRETE COLOR MAP 0</Title></ns2:ColorMap></GraphicalInformation></GraphicalInformationSet>";
-
-        EPCPackageManager manager = new EPCPackageManager("energyml");
-        System.out.println(manager.unmarshal(graphical).getValue());
-    }
 }
diff --git a/src/test/java/com/geosiris/energyml/utils/test/PairTest.java b/src/test/java/com/geosiris/energyml/utils/test/PairTest.java
@@ -0,0 +1,20 @@
+package com.geosiris.energyml.utils.test;
+
+import com.geosiris.energyml.utils.Pair;
+import org.junit.jupiter.api.Test;
+
+public class PairTest {
+
+    @Test
+    void test_equality(){
+        assert new Pair<>("abdc", "COUCOU").equals(new Pair<>("abdc", "COUCOU"));
+        assert new Pair<>("abdc", "COUCOU").equals(new Pair<>("abdc", "COUCOU"));
+        assert new Pair<>(1, "COUCOU").equals(new Pair<>(1, "COUCOU"));
+        assert new Pair<>(1, 2.3).equals(new Pair<>(1, 2.3));
+        assert ! new Pair<>("a", "COUCOU").equals(new Pair<>("abdc", "COUCOU"));
+        assert ! new Pair<>("abdc", "C").equals(new Pair<>("abdc", "COUCOU"));
+        assert new Pair<>("abdc", null).equals(new Pair<>("abdc", null));
+        assert ! new Pair<>("abdc", (Object) "a").equals(new Pair<>("abdc", null));
+        assert ! new Pair<>("abdc", null).equals(new Pair<>("abdc", (Object) "a"));
+    }
+}