Issue #1980 - changes per PR review

Signed-off-by: John T.E. Timm <johntimm@us.ibm.com>

docs/src/pages/guides/FHIRServerUsersGuide.md

@@ -2054,7 +2054,6 @@ This section contains reference information about each of the configuration prop
 |`fhirServer/core/checkReferenceTypes`|true|
 |`fhirServer/core/serverRegistryResourceProviderEnabled`|false|
 |`fhirServer/core/graphTermServiceProvider/enabled`|false|
-|`fhirServer/core/graphTermServiceProvider/configuration`|null|
 |`fhirServer/core/conditionalDeleteMaxNumber`|10|
 |`fhirServer/core/capabilityStatementCacheTimeout`|60|
 |`fhirServer/core/extendedCodeableConceptValidation`|true|

fhir-parent/pom.xml

@@ -438,6 +438,36 @@
                 <artifactId>commons-text</artifactId>
                 <version>1.9</version>
             </dependency>
+            <dependency>
+                <groupId>org.janusgraph</groupId>
+                <artifactId>janusgraph-core</artifactId>
+                <version>0.5.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.janusgraph</groupId>
+                <artifactId>janusgraph-berkeleyje</artifactId>
+                <version>0.5.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.janusgraph</groupId>
+                <artifactId>janusgraph-cql</artifactId>
+                <version>0.5.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.janusgraph</groupId>
+                <artifactId>janusgraph-lucene</artifactId>
+                <version>0.5.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.janusgraph</groupId>
+                <artifactId>janusgraph-es</artifactId>
+                <version>0.5.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.tinkerpop</groupId>
+                <artifactId>gremlin-driver</artifactId>
+                <version>3.4.6</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 

fhir-term-graph/pom.xml

@@ -18,32 +18,26 @@
         <dependency>
             <groupId>org.janusgraph</groupId>
             <artifactId>janusgraph-core</artifactId>
-            <version>0.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.janusgraph</groupId>
             <artifactId>janusgraph-berkeleyje</artifactId>
-            <version>0.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.janusgraph</groupId>
             <artifactId>janusgraph-cql</artifactId>
-            <version>0.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.janusgraph</groupId>
             <artifactId>janusgraph-lucene</artifactId>
-            <version>0.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.janusgraph</groupId>
             <artifactId>janusgraph-es</artifactId>
-            <version>0.5.3</version>
         </dependency>
         <dependency>
             <groupId>org.apache.tinkerpop</groupId>
             <artifactId>gremlin-driver</artifactId>
-            <version>3.4.6</version>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/FHIRTermGraph.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/factory/FHIRTermGraphFactory.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -12,9 +12,20 @@
 import com.ibm.fhir.term.graph.FHIRTermGraph;
 import com.ibm.fhir.term.graph.impl.FHIRTermGraphImpl;
 
+/*
+ * Factory class used to create FHIRTermGraph instances
+ */
 public final class FHIRTermGraphFactory {
     private FHIRTermGraphFactory() { }
 
+    /**
+     * Create a {@link FHIRTermGraph} instance using the given configuration properties file
+     *
+     * @param propFileName
+     *     the configuration properties file
+     * @return
+     *     the {@link FHIRTermGraph} instance
+     */
     public static FHIRTermGraph open(String propFileName) {
         try {
             return open(new PropertiesConfiguration(propFileName));
@@ -23,6 +34,14 @@ public static FHIRTermGraph open(String propFileName) {
         }
     }
 
+    /**
+     * Create a {@link FHIRTermGraph} instance using the given configuration object
+     *
+     * @param configuration
+     *     the configuration object
+     * @return
+     *     the {@link FHIRTermGraph} instance
+     */
     public static FHIRTermGraph open(Configuration configuration) {
         return new FHIRTermGraphImpl(configuration);
     }

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/factory/FHIRTermGraphLoaderFactory.java

@@ -14,7 +14,20 @@
 import com.ibm.fhir.term.graph.loader.impl.SnomedTermGraphLoader;
 import com.ibm.fhir.term.graph.loader.impl.UMLSTermGraphLoader;
 
+/*
+ * Factory class used to create FHIRTermGraphLoader instances
+ */
 public class FHIRTermGraphLoaderFactory {
+    /**
+     * Create {@link FHIRTermGraphLoader} instance using the provided type and options map
+     *
+     * @param type
+     *     the type
+     * @param options
+     *     the options map
+     * @return
+     *     a {@link FHIRTermGraphLoader} instance
+     */
     public static FHIRTermGraphLoader create(Type type, Map<String, String> options) {
         switch (type) {
         case CODESYSTEM:

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/CodeSystemTermGraphLoader.java

@@ -214,7 +214,6 @@ public static void main(String[] args) throws Exception {
             HelpFormatter formatter = new HelpFormatter();
             formatter.printHelp("CodeSystemTermGraphLoader", options);
         } catch (Exception e) {
-            e.printStackTrace();
             System.out.println("An error occurred: " + e.getMessage());
         } finally {
             if (loader != null) {

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/SnomedTermGraphLoader.java

@@ -308,7 +308,6 @@ public static void main(String[] args) throws Exception {
             HelpFormatter formatter = new HelpFormatter();
             formatter.printHelp("SnomedTermGraphLoader", options);
         } catch (Exception e) {
-            e.printStackTrace();
             System.out.println("An error occurred: " + e.getMessage());
         } finally {
             if (loader != null) {

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/impl/UMLSTermGraphLoader.java

@@ -17,11 +17,9 @@
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Properties;
-import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.logging.Level;
@@ -58,9 +56,6 @@ public class UMLSTermGraphLoader extends AbstractTermGraphLoader {
     // Map of code system name to preferred label, configured in properties file
     private Properties codeSystemMap = new Properties();
 
-    // Set of code systems which are case sensitive, configured in properties file
-    private Set<String> caseSensitiveCodeSystems = new HashSet<>();
-
     // Map of code system id to corresponding vertex
     private Map<String, Vertex> codeSystemVertices = new ConcurrentHashMap<>();
 
@@ -104,7 +99,6 @@ public UMLSTermGraphLoader(Map<String, String> options) {
     public void load() {
         try {
             loadSourceAttributes();
-            loadCaseSensitiveCodeSystems();
             loadConcepts();
             loadRelations();
         } catch (Exception e) {
@@ -121,12 +115,7 @@ public void load() {
     private final Vertex createCodeSystemVertex(String sab) {
         String version = sabToVersion.get(sab);
         String url = (String) codeSystemMap.getOrDefault(sab, sab);
-
-        boolean caseSensitive = false;
-        if (caseSensitiveCodeSystems.contains(sab)) {
-            caseSensitive = true;
-        }
-        Vertex csv = g.addV("CodeSystem").property("url", url).property("version", version).property("caseSensitive", caseSensitive).next();
+        Vertex csv = g.addV("CodeSystem").property("url", url).property("version", version).next();
         g.tx().commit();
         return csv;
 
@@ -307,20 +296,6 @@ private void loadSourceAttributes() throws IOException {
         }
     }
 
-    /**
-     * Loads configuration of code systems noted to be case sensitive
-     *
-     * @throws IOException
-     */
-    private void loadCaseSensitiveCodeSystems() throws IOException {
-        try (BufferedReader reader = new BufferedReader(new InputStreamReader(getClass().getClassLoader().getResourceAsStream("conf/umlsSourceCaseSensitivity.txt")))) {
-            String line = reader.readLine().trim();
-            if (!line.isEmpty()) {
-                caseSensitiveCodeSystems.add(reader.readLine());
-            }
-        }
-    }
-
     /**
      * Load UMLS data using properties provided in arguments
      *

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/loader/main/FHIRTermGraphLoaderMain.java

@@ -47,7 +47,6 @@ public static void main(String[] args) throws Exception {
             HelpFormatter formatter = new HelpFormatter();
             formatter.printHelp(String.format("FHIRTermGraphLoaderMain %s <loader-specific-options>", type.toString()), options);
         } catch (Exception e) {
-            e.printStackTrace();
             System.out.println("An error occurred: " + e.getMessage());
         } finally {
             if (loader != null) {

fhir-term-graph/src/main/java/com/ibm/fhir/term/graph/util/FHIRTermGraphUtil.java

@@ -32,6 +32,14 @@
 public class FHIRTermGraphUtil {
     private FHIRTermGraphUtil() { }
 
+    /**
+     * Convert the given element value to an object value that is compatible with the graph schema
+     *
+     * @param value
+     *     the element value
+     * @return
+     *     an object value that is compatible with the graph schema
+     */
     public static Object toObject(Element value) {
         if (value.is(FHIR_BOOLEAN)) {
             return value.as(FHIR_BOOLEAN).getValue();
@@ -54,18 +62,40 @@ public static Object toObject(Element value) {
         throw new IllegalArgumentException();
     }
 
+    /**
+     * Normalize the string by making it case and accent insensitive
+     *
+     * @param value
+     *     the string value to normalized
+     * @return
+     *     the normalized string value
+     */
     public static String normalize(String value) {
         if (value != null) {
             return Normalizer.normalize(value, Form.NFD).replaceAll("\\p{InCombiningDiacriticalMarks}+", "").toLowerCase();
         }
         return null;
     }
 
+    /**
+     * Sets the root logger level for the logback classic root logger
+     *
+     * @param level
+     *     the level
+     */
     public static void setRootLoggerLevel(Level level) {
         Logger rootLogger = (Logger) LoggerFactory.getLogger(Logger.ROOT_LOGGER_NAME);
         rootLogger.setLevel(level);
     }
 
+    /**
+     * Convert the {@link DateTime} value to a Long value that is compatible with the graph schema
+     *
+     * @param dateTime
+     *     the dateTime value
+     * @return
+     *     the Long equivalent value (milliseconds from the epoch)
+     */
     public static Long toLong(DateTime dateTime) {
         TemporalAccessor value = dateTime.getValue();
         if (value instanceof ZonedDateTime) {