WIP: MAINT: refactor retrieve properties (move backend-logic to backend)

src/main/java/org/caosdb/server/database/DatabaseUtils.java

@@ -40,9 +40,6 @@ import org.caosdb.server.database.proto.VerySparseEntity;
 import org.caosdb.server.datatype.AbstractCollectionDatatype;
 import org.caosdb.server.datatype.CollectionValue;
 import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
 import org.caosdb.server.entity.EntityID;
 import org.caosdb.server.entity.EntityInterface;
 import org.caosdb.server.entity.Message;
@@ -55,6 +52,9 @@ import org.caosdb.server.entity.wrapper.Property;
 
 public class DatabaseUtils {
 
+  private static final String DELETED_REFERENCE_IN_PREVIOUS_VERSION =
+      "DELETED_REFERENCE_IN_PREVIOUS_VERSION";
+
   public static final String bytes2UTF8(final byte[] bytes) {
     if (bytes == null) {
       return null;
@@ -265,100 +265,6 @@ public class DatabaseUtils {
     }
   }
 
-  private static void replace(
-      final Property p, final Map<EntityID, Property> domainMap, final boolean isHead) {
-    // ... find the corresponding domain and replace it
-    ReferenceValue ref;
-    try {
-      ref = ReferenceValue.parseReference(p.getValue());
-    } catch (final Message e) {
-      throw new RuntimeException("This should never happen.");
-    }
-    final EntityInterface replacement = domainMap.get(ref.getId());
-    if (replacement == null) {
-      if (isHead) {
-        throw new NullPointerException("Replacement was null");
-      }
-      // entity has been deleted (we are processing properties of an old entity version)
-      p.setValue(null);
-      p.addWarning(
-          new Message(
-              "The referenced entity has been deleted in the mean time and is not longer available."));
-      return;
-    }
-    if (replacement.isDescOverride()) {
-      p.setDescOverride(true);
-      p.setDescription(replacement.getDescription());
-    }
-    if (replacement.isNameOverride()) {
-      p.setNameOverride(true);
-      p.setName(replacement.getName());
-    }
-    if (replacement.isDatatypeOverride()) {
-      p.setDatatypeOverride(true);
-      p.setDatatype(replacement.getDatatype());
-    }
-    p.setProperties(replacement.getProperties());
-    p.setStatementStatus(replacement.getStatementStatus());
-    p.setValue(replacement.getValue());
-  }
-
-  public static void transformToDeepPropertyTree(
-      final EntityInterface e, final List<Property> protoProperties) {
-    // here we will store every domain we can find and we will index it by
-    // its id.
-    final Map<EntityID, Property> domainMap = new HashMap<>();
-
-    // loop over all properties and collect the domains
-    for (final Property p : protoProperties) {
-      // if this is a domain it represents a deeper branch of the property
-      // tree.
-      if (p.getRole() == Role.Domain) {
-        if (domainMap.containsKey(p.getId())) {
-          // aggregate the multiple values.
-          final Property domain = domainMap.get(p.getId());
-          if (!(domain.getValue() instanceof CollectionValue)) {
-            final SingleValue singleValue = (SingleValue) domain.getValue();
-            final CollectionValue vals = new CollectionValue();
-            final IndexedSingleValue iSingleValue =
-                new IndexedSingleValue(domain.getPIdx(), singleValue);
-            vals.add(iSingleValue);
-            domain.setValue(vals);
-          }
-          ((CollectionValue) domain.getValue()).add(p.getPIdx(), p.getValue());
-        } else {
-          domainMap.put(p.getId(), p);
-        }
-      }
-    }
-
-    // loop over all properties
-    final boolean isHead =
-        e.getVersion().getSuccessors() == null || e.getVersion().getSuccessors().isEmpty();
-    for (final Property p : protoProperties) {
-
-      // if this is a replacement
-      if (p.getStatementStatus() == StatementStatus.REPLACEMENT) {
-        replace(p, domainMap, isHead);
-      }
-
-      for (final Property subP : p.getProperties()) {
-        if (subP.getStatementStatus() == StatementStatus.REPLACEMENT) {
-          replace(subP, domainMap, isHead);
-        }
-      }
-
-      if (p.getId().equals(e.getId())) {
-        // this is the value of an abstract property.
-        e.setValue(p.getValue());
-      } else if (p.getRole() != Role.Domain) {
-        // if this is not a domain it is to be added to the properties
-        // of e.
-        e.addProperty(p);
-      }
-    }
-  }
-
   public static ArrayList<Property> parseFromProtoProperties(
       EntityInterface entity, List<ProtoProperty> protos) {
     final ArrayList<Property> ret = new ArrayList<Property>();
@@ -380,24 +286,23 @@ public class DatabaseUtils {
         }
 
       } else {
+        Message warning = null;
+        if (pp.status == DELETED_REFERENCE_IN_PREVIOUS_VERSION) {
+          pp.status = StatementStatus.FIX.name();
+          warning =
+              new Message(
+                  "The referenced entity has been deleted in the mean time and is not longer available.");
+        }
         final Property property = parseFlatProperty(pp);
-        // parseFromFlatProperties(property.getProperties(), pp.subProperties);
+        if (warning != null) {
+          property.addWarning(warning);
+        }
         ret.add(property);
       }
     }
     return ret;
   }
 
-  private static void parseFromFlatProperties(
-      final List<Property> properties, final List<ProtoProperty> props) {
-    if (props != null)
-      for (final ProtoProperty fp : props) {
-        final Property property = parseFlatProperty(fp);
-        parseFromFlatProperties(properties, fp.subProperties);
-        properties.add(property);
-      }
-  }
-
   private static Property parseFlatProperty(final ProtoProperty fp) {
     final Property property = new Property(new RetrieveEntity());
     property.parseProtoProperty(fp);
@@ -406,7 +311,7 @@ public class DatabaseUtils {
 
   @SuppressWarnings("unchecked")
   public static LinkedList<ProtoProperty> transformToDeepPropertyTree(
-      List<ProtoProperty> properties) {
+      List<ProtoProperty> properties, boolean isHead) {
     LinkedList<ProtoProperty> result = new LinkedList<>();
     Map<String, ProtoProperty> replacements = new HashMap<>();
     for (ProtoProperty pp : properties) {
@@ -436,7 +341,7 @@ public class DatabaseUtils {
     }
     for (ProtoProperty pp : properties) {
       if (pp.status.equals(StatementStatus.REPLACEMENT.toString())) {
-        replace(pp, replacements.get(pp.value));
+        replace(pp, replacements.get(pp.value), isHead);
       }
       if (pp.collValues != null) {
         // sort
@@ -455,16 +360,15 @@ public class DatabaseUtils {
     return result;
   }
 
-  private static void replace(ProtoProperty pp, ProtoProperty replacement) {
+  private static void replace(ProtoProperty pp, ProtoProperty replacement, boolean isHead) {
     if (replacement == null) {
-      throw new NullPointerException("Replacement was null");
-      //		    // entity has been deleted (we are processing properties of an old entity version)
-      //		    p.setValue(null);
-      //		    p.addWarning(
-      //		        new Message(
-      //		            "The referenced entity has been deleted in the mean time and is not longer
-      // available."));
-      //		    return;
+      if (isHead) {
+        throw new NullPointerException("Replacement was null");
+      }
+      // entity has been deleted (we are processing properties of an old entity version)
+      pp.value = null;
+      pp.status = DELETED_REFERENCE_IN_PREVIOUS_VERSION;
+      return;
     }
     pp.desc = replacement.desc;
     pp.name = replacement.name;

src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java

@@ -44,11 +44,10 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
 
   private static final String stmtStr = "call retrieveEntityProperties(?,?,?)";
   private static final String stmtStr2 = "call retrieveOverrides(?,?,?)";
-  private static final String isCollectionStmt = "call isCollection(?,?)";
 
   @Override
-  public LinkedList<ProtoProperty> execute(final EntityID entity, final String version)
-      throws TransactionException {
+  public LinkedList<ProtoProperty> execute(
+      final EntityID entity, final String version, boolean isHead) throws TransactionException {
     try {
       final PreparedStatement prepareStatement = prepareStatement(stmtStr);
 
@@ -60,7 +59,7 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
         p.subProperties =
             retrieveFlatPropertiesStage1(entity.toInteger(), p.id, version, prepareStatement);
       }
-      return DatabaseUtils.transformToDeepPropertyTree(propsStage1);
+      return DatabaseUtils.transformToDeepPropertyTree(propsStage1, isHead);
     } catch (final SQLException e) {
       throw new TransactionException(e);
     } catch (final ConnectionException e) {
@@ -99,14 +98,12 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
 
       retrieveOverrides(domain, entity, version, retrieveOverrides, props);
 
-      PreparedStatement isCollectionStatement = prepareStatement(isCollectionStmt);
-
-      return handleCollectionValues(props, isCollectionStatement);
+      return handleCollectionValues(props);
     }
   }
 
-  public List<ProtoProperty> handleCollectionValues(
-      List<FlatProperty> props, PreparedStatement isCollectionStatement) throws SQLException {
+  @Deprecated
+  public List<ProtoProperty> handleCollectionValues(List<FlatProperty> props) throws SQLException {
 
     List<ProtoProperty> result = new LinkedList<>();
     for (FlatProperty fp : props) {

src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java

@@ -29,5 +29,6 @@ import org.caosdb.server.entity.EntityID;
 
 public interface RetrievePropertiesImpl extends BackendTransactionImpl {
 
-  public LinkedList<ProtoProperty> execute(EntityID id, String version) throws TransactionException;
+  public LinkedList<ProtoProperty> execute(EntityID id, String version, boolean isHead)
+      throws TransactionException;
 }

src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java

@@ -64,7 +64,8 @@ public class RetrieveProperties
   @Override
   public LinkedList<ProtoProperty> executeNoCache() throws TransactionException {
     final RetrievePropertiesImpl t = getImplementation(RetrievePropertiesImpl.class);
-    return t.execute(this.entity.getId(), this.entity.getVersion().getId());
+    return t.execute(
+        this.entity.getId(), this.entity.getVersion().getId(), this.entity.getVersion().isHead());
   }
 
   @Override