Version 1.3.1.

julielab-concept-creation-bioportal/pom.xml

@@ -4,7 +4,8 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-concept-db-manager</artifactId>
-        <version>1.3.0</version>
+        <version>1.3.1</version>
+        <relativePath>../pom.xml</relativePath>
     </parent>
     <artifactId>julielab-concept-creation-bioportal</artifactId>
     <name>JULIE Lab Concept Creation for BioPortal</name>

julielab-concept-creation-famplex/pom.xml

@@ -5,7 +5,8 @@
     <parent>
         <artifactId>julielab-concept-db-manager</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.3.0</version>
+        <version>1.3.1</version>
+        <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <name>JULIE Lab Concept Creation for FamPlex</name>

julielab-concept-creation-hgnc-groups/pom.xml

@@ -5,7 +5,8 @@
     <parent>
         <artifactId>julielab-concept-db-manager</artifactId>
         <groupId>de.julielab</groupId>
-        <version>1.3.0</version>
+        <version>1.3.1</version>
+        <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <name>JULIE Lab Concept Creation HGNC Groups</name>

julielab-concept-creation-mesh/pom.xml

@@ -4,7 +4,8 @@
 	<parent>
 		<groupId>de.julielab</groupId>
 		<artifactId>julielab-concept-db-manager</artifactId>
-		<version>1.3.0</version>
+		<version>1.3.1</version>
+		<relativePath>../pom.xml</relativePath>
 	</parent>
 	<artifactId>julielab-concept-creation-mesh</artifactId>
 	<name>JULIE Lab Concept Creation Provider MeSH</name>
@@ -13,7 +14,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>julielab-concept-db-manager-core</artifactId>
-            <version>1.3.0</version>
+            <version>1.3.1</version>
         </dependency>
         <dependency>
             <groupId>org.assertj</groupId>

julielab-concept-creation-ncbi-gene/pom.xml

@@ -4,7 +4,8 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-concept-db-manager</artifactId>
-        <version>1.3.0</version>
+        <version>1.3.1</version>
+        <relativePath>../pom.xml</relativePath>
     </parent>
     <artifactId>julielab-concept-creation-ncbi-gene</artifactId>
     <name>JULIE Lab Concept Creation for NCBI Gene</name>

julielab-concept-db-application/pom.xml

@@ -4,7 +4,8 @@
 	<parent>
 		<groupId>de.julielab</groupId>
 		<artifactId>julielab-concept-db-manager</artifactId>
-		<version>1.3.0</version>
+		<version>1.3.1</version>
+		<relativePath>../pom.xml</relativePath>
 	</parent>
 	<artifactId>julielab-concept-db-application</artifactId>
 	<name>JULIE Lab Concept DB Manager Application</name>

julielab-concept-db-manager-core/pom.xml

@@ -4,7 +4,8 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-concept-db-manager</artifactId>
-        <version>1.3.0</version>
+        <version>1.3.1</version>
+        <relativePath>../pom.xml</relativePath>
     </parent>
     <artifactId>julielab-concept-db-manager-core</artifactId>
     <name>JULIE Lab Concept Database Manager Core</name>

julielab-concept-db-manager-core/src/main/java/de/julielab/concepts/db/core/FileDatabaseConceptInserter.java

@@ -24,6 +24,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -68,6 +69,9 @@ public void insertConcepts(HierarchicalConfiguration<ImmutableNode> importConfig
             try {
                 log.debug("Inserting the concepts of facet {} (customId: {}) into the Neo4j database", facet.getName(),
                         facet.getCustomId());
+                // The JULIE Lab Neo4j plugins cannot handle parents in merging mode
+                if (concepts.getImportOptions().merge)
+                    concepts.setConcepts(concepts.getConcepts().map(c -> {c.parentCoordinates = Collections.emptyList(); return c;}));
                 Map<String, Object> response = new HashMap<>();
                 ConceptInsertion.insertConcepts(graphDb, ciLog, concepts, response);
                 log.debug("Successfully inserted the given concepts: {}", response);

julielab-concept-db-manager-core/src/main/java/de/julielab/concepts/db/core/RestConceptInserter.java

@@ -33,6 +33,7 @@
 import java.io.PipedInputStream;
 import java.io.PipedOutputStream;
 import java.io.UnsupportedEncodingException;
+import java.util.Collections;
 import java.util.stream.Stream;
 
 import static de.julielab.concepts.db.core.ConfigurationConstants.*;
@@ -83,6 +84,9 @@ public void insertConcepts(HierarchicalConfiguration<ImmutableNode> importConfig
                     g.writeFieldName(NAME_CONCEPTS);
                     g.writeStartArray();
                     for (ImportConcept concept : (Iterable<ImportConcept>) importConcepts::iterator) {
+                        // The JULIE Lab Neo4j plugins cannot handle parents in merging mode
+                        if (concepts.getImportOptions().merge)
+                            concept.parentCoordinates = Collections.emptyList();
                         g.writeObject(concept);
                         progressBar.incrementDone(true);
                     }

julielab-concept-db-manager-core/src/main/java/de/julielab/concepts/db/core/spi/ConceptInserter.java

@@ -31,8 +31,8 @@ public interface ConceptInserter extends DatabaseConnected {
 	 */
 	default ImportOptions setGlobalOptions(HierarchicalConfiguration<ImmutableNode> importConfiguration, @Nullable ImportOptions optionsFromConceptCreator) {
 		ImportOptions retOptions = optionsFromConceptCreator != null ? optionsFromConceptCreator : new ImportOptions();
-		final Boolean merge = importConfiguration.getBoolean(slash(IMPORT_OPTIONS, MERGE));
-		final Boolean overridePreferredName = importConfiguration.getBoolean(slash(IMPORT_OPTIONS, OVERRIDE_PREFERRED_NAME));
+		final Boolean merge = importConfiguration.getBoolean(slash(IMPORT_OPTIONS, MERGE), null);
+		final Boolean overridePreferredName = importConfiguration.getBoolean(slash(IMPORT_OPTIONS, OVERRIDE_PREFERRED_NAME), null);
 
 		if (merge != null)
 			retOptions.merge = merge;

julielab-concept-db-manager-core/src/main/resources/conceptdb-1.2.0.xsd → julielab-concept-db-manager-core/src/main/resources/conceptdb-1.2.1.xsd

@@ -98,6 +98,7 @@
         <xs:complexType>
             <xs:sequence>
                 <xs:element ref="rest" minOccurs="0"/>
+                <xs:element ref="importoptions" minOccurs="0"/>
                 <xs:element ref="concepts" minOccurs="0"/>
                 <xs:element ref="facet" minOccurs="0"/>
                 <xs:element ref="mappings" minOccurs="0"/>

julielab-concept-db-manager-core/src/main/resources/methodcallbase-1.1.0.xsd

@@ -26,6 +26,15 @@
         </xs:complexType>
     </xs:element>
 
+    <xs:element name="importoptions">
+        <xs:complexType>
+            <xs:sequence>
+                <xs:element name="merge" type="xs:boolean"/>
+                <xs:element name="overridepreferredname" type="xs:boolean"/>
+            </xs:sequence>
+        </xs:complexType>
+    </xs:element>
+
     <xs:element name="parameter">
         <xs:annotation>
             <xs:documentation xml:lang="en">

julielab-concept-db-manager-core/src/test/java/de/julielab/concepts/db/core/ITTestsSetup.java

@@ -25,7 +25,7 @@ public class ITTestsSetup {
     public static GenericContainer neo4j = new GenericContainer(
             new ImageFromDockerfile("cdbm-1.2.0-test", true)
                     .withFileFromClasspath("Dockerfile", "dockercontext/Dockerfile")
-                    .withFileFromClasspath("julielab-neo4j-plugins-concepts-3.1.0-assembly.jar", "dockercontext/julielab-neo4j-plugins-concepts-3.1.0-assembly.jar")
+                    .withFileFromClasspath("julielab-neo4j-plugins-concepts-3.2.1-assembly.jar", "dockercontext/julielab-neo4j-plugins-concepts-3.2.1-assembly.jar")
                     .withFileFromClasspath("neo4j.conf", "dockercontext/neo4j.conf"))
             .withExposedPorts(7474, 7687)
             .withEnv("NEO4J_AUTH", "none");

julielab-concept-db-manager-core/src/test/resources/dockercontext/Dockerfile

@@ -1,3 +1,3 @@
 FROM neo4j:4.4.2
-COPY julielab-neo4j-plugins-concepts-3.1.0-assembly.jar /var/lib/neo4j/plugins
+COPY julielab-neo4j-plugins-concepts-3.2.1-assembly.jar /var/lib/neo4j/plugins
 COPY neo4j.conf /var/lib/neo4j/conf/neo4j.conf

pom.xml

@@ -19,7 +19,7 @@
         <version>2.5.0</version>
     </parent>
     <artifactId>julielab-concept-db-manager</artifactId>
-    <version>1.3.1-SNAPSHOT</version>
+    <version>1.3.1</version>
     <name>JULIE Lab Concept Database Manager</name>
     <description>This project is a collection of tools with the goal to import ontological concepts into a graph
         database. The graph database then allows to traverse the imported data with a graph-specific query language. In
@@ -59,7 +59,7 @@
         </dependencies>
     </dependencyManagement>
     <properties>
-        <julielab-neo4j-plugins-version>3.2.1-SNAPSHOT</julielab-neo4j-plugins-version>
+        <julielab-neo4j-plugins-version>3.2.1</julielab-neo4j-plugins-version>
         <neo4j-version>4.4.2</neo4j-version>
     </properties>
 </project>