Version 1.1.1.

julielab-concept-creation-bioportal/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-concept-db-manager</artifactId>
-        <version>1.1.0</version>
+        <version>1.1.1</version>
     </parent>
     <artifactId>julielab-concept-creation-bioportal</artifactId>
     <name>JULIE Lab Concept Creation for BioPortal</name>

julielab-concept-creation-mesh/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>de.julielab</groupId>
 		<artifactId>julielab-concept-db-manager</artifactId>
-		<version>1.1.0</version>
+		<version>1.1.1</version>
 	</parent>
 	<artifactId>julielab-concept-creation-mesh</artifactId>
 	<name>JULIE Lab Concept Creation Provider MeSH</name>
@@ -13,7 +13,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>julielab-concept-db-manager-core</artifactId>
-            <version>1.1.0</version>
+            <version>1.1.1</version>
         </dependency>
         <dependency>
             <groupId>org.assertj</groupId>

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

@@ -4,7 +4,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-concept-db-manager</artifactId>
-        <version>1.1.0</version>
+        <version>1.1.1</version>
     </parent>
     <artifactId>julielab-concept-creation-ncbi-gene</artifactId>
     <name>JULIE Lab Concept Creation for NCBI Gene</name>

julielab-concept-creation-ncbi-gene/src/main/java/de/julielab/concepts/db/creators/NCBIGeneConceptCreator.java

@@ -375,12 +375,15 @@ protected Stream<ImportConcept> convertGeneInfoToTerms(File geneInfo, Set<String
         Iterator<String> it = bw.lines().filter(record -> !record.startsWith("#")).iterator();
         Iterator<ImportConcept> geneIterator = new Iterator<>() {
 
+            private boolean closed = false;
+
             @Override
             public boolean hasNext() {
-                boolean hasNext = it.hasNext();
+                boolean hasNext = closed ? false : it.hasNext();
                 if (!hasNext) {
                     try {
                         bw.close();
+                        closed = true;
                     } catch (IOException e) {
                         throw new IllegalStateException(e);
                     }
@@ -585,6 +588,7 @@ public Stream<ImportConcepts> createConcepts(HierarchicalConfiguration<Immutable
             options.doNotCreateHollowParents = false;
             ImportConcepts importConcepts = new ImportConcepts(conceptStream, facet);
             importConcepts.setNumConcepts(totalGeneIds.size() + homologeneAggregateCounter + orthologAggregateCounter + topHomologyAggregateCounter);
+            log.info("Created a total of {} concepts.", importConcepts.getNumConcepts());
             importConcepts.setImportOptions(options);
             return Stream.of(importConcepts);
         } catch (IOException e) {

julielab-concept-db-application/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>de.julielab</groupId>
 		<artifactId>julielab-concept-db-manager</artifactId>
-		<version>1.1.0</version>
+		<version>1.1.1</version>
 	</parent>
 	<artifactId>julielab-concept-db-application</artifactId>
 	<name>JULIE Lab Concept DB Manager Application</name>

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

@@ -4,7 +4,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-concept-db-manager</artifactId>
-        <version>1.1.0</version>
+        <version>1.1.1</version>
     </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/RestConceptInserter.java

@@ -72,6 +72,7 @@ public void insertConcepts(HierarchicalConfiguration<ImmutableNode> importConfig
             g.writeStartObject();
             g.writeObjectField(NAME_FACET, concepts.getFacet());
             g.writeObjectField(NAME_IMPORT_OPTIONS, concepts.getImportOptions());
+            g.writeNumberField(NAME_NUM_CONCEPTS, concepts.getNumConcepts());
 
             Thread concept2json = new Thread(() -> {
                 try {
@@ -87,7 +88,8 @@ public void insertConcepts(HierarchicalConfiguration<ImmutableNode> importConfig
                     g.writeEndObject();
                     g.close();
                 } catch (IOException e) {
-                    e.printStackTrace();
+                    log.error("An error occurred while writing concepts into the output stream.", e);
+                    throw new IllegalStateException(new ConceptInsertionException(e));
                 }
             });
             concept2json.start();

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

@@ -54,7 +54,7 @@ public void exportData(HierarchicalConfiguration<ImmutableNode> exportConfig) th
                     File outputFile = new File(outputPath);
                     response = callNeo4jRestEndpoint(connectionConfiguration, exportConfig, "GET");
                     log.info("Writing file {}", outputFile);
-                    HierarchicalConfiguration<ImmutableNode> decodingConfiguration = exportConfig.configurationAt(DECODING);
+                    HierarchicalConfiguration<ImmutableNode> decodingConfiguration = exportConfig.configurationsAt(DECODING).size() > 0 ? exportConfig.configurationAt(DECODING) : null;
                     InputStream decodedResponse = decodingConfiguration != null ? decode(response, decodingConfiguration) : response;
                     writeData(outputFile, getResourceHeader(connectionConfiguration),decodedResponse);
                     log.info("Done.");

pom.xml

@@ -16,10 +16,10 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>julielab-parent</artifactId>
-        <version>2.4.1</version>
+        <version>2.5.0</version>
     </parent>
     <artifactId>julielab-concept-db-manager</artifactId>
-    <version>1.1.0</version>
+    <version>1.1.1</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