Abstracted the public methods out of DirectoryApi

In the future we may want to have a GraphQL extension of this class.

src/main/java/de/samply/directory_sync_service/Util.java

@@ -24,19 +24,6 @@ public static <K, V> Map<K, V> mapOf() {
   }
 
     /**
-     * Creates a new map with a single entry consisting of the specified key and value.
-     *
-     * @param key the key for the entry
-     * @param value the value associated with the key
-     * @return a new map containing the specified key-value pair
-     */
-  public static <K, V> Map<K, V> mapOf(K key, V value) {
-    HashMap<K, V> map = new HashMap<>();
-    map.put(key, value);
-    return map;
-  }
-
-  /**
   * Get a printable stack trace from an Exception object.
   * @param e
   * @return
@@ -48,21 +35,6 @@ public static String traceFromException(Exception e) {
        return sw.toString();
    }
 
-    /**
-     * Creates a list containing a single {@link OperationOutcome} that represents an error.
-     * <p>
-     * The generated {@code OperationOutcome} will have an issue with a severity level of
-     * {@code ERROR} and will include the provided diagnostic message.
-     *
-     * @param diagnostics A diagnostic message that provides details about the error.
-     * @return A list containing a single {@code OperationOutcome} object indicating an error.
-     */
-    public static List<OperationOutcome> createErrorOutcome(String diagnostics) {
-        OperationOutcome outcome = new OperationOutcome();
-        outcome.addIssue().setSeverity(ERROR).setDiagnostics(diagnostics);
-        return Collections.singletonList(outcome);
-    }
-
     /**
      * Extracts and concatenates error messages from an {@link OperationOutcome}.
      * <p>
@@ -86,27 +58,4 @@ public static String getErrorMessageFromOperationOutcome(OperationOutcome operat
         return errorMessage;
     }
 
-    /**
-     * Reports a list of {@link OperationOutcome} objects by logging any errors found.
-     * <p>
-     * This method iterates through the provided list of {@code OperationOutcome} objects,
-     * extracting and logging any error messages. If any errors are encountered, they are logged
-     * at the {@code ERROR} level and the method will return {@code false}.
-     * If no errors are found, the method returns {@code true}.
-     *
-     * @param operationOutcomes A list of {@code OperationOutcome} objects to be checked for errors.
-     * @return {@code true} if no errors were found in any of the {@code OperationOutcome} objects;
-     *         {@code false} if at least one error was found and logged.
-     */
-    public static boolean reportOperationOutcomes(List<OperationOutcome> operationOutcomes) {
-        boolean failed = false;
-        for (OperationOutcome operationOutcome : operationOutcomes) {
-            String errorMessage = Util.getErrorMessageFromOperationOutcome(operationOutcome);
-            if (errorMessage.length() > 0) {
-                logger.error(errorMessage);
-                failed = true;
-            }
-        }
-        return !failed;
-    }
 }

src/main/java/de/samply/directory_sync_service/directory/DirectoryApiRest.java

@@ -23,14 +23,9 @@
  * and performing various validation and correction operations.
  * It supports a mock mode for testing purposes, where no real Directory interactions are performed.
  */
-public class DirectoryApiRest {
-  private static final Logger logger = LoggerFactory.getLogger(DirectoryApiRest.class);
+public class DirectoryApiRest extends DirectoryApi {
   private DirectoryRestCalls directoryRestCalls;
 
-  // Setting this variable to true will prevent any contact being made to the Directory.
-  // All public methods will return feasible fake results.
-  private boolean mockDirectory = false;
-
   /**
    * Constructs a new DirectoryApiRest instance.
    * If we are not in mocking mode, log in to the Directory.
@@ -41,7 +36,7 @@ public class DirectoryApiRest {
    * @param password The password for authenticating with the Directory.
    */
   public DirectoryApiRest(String baseUrl, boolean mockDirectory, String username, String password) {
-    this.mockDirectory = mockDirectory;
+    super(baseUrl, mockDirectory, username, password);
     this.directoryRestCalls = new DirectoryRestCalls(baseUrl, username, password);
   }
 
@@ -136,16 +131,22 @@ public DirectoryCollectionGet fetchCollectionGetOutcomes(String countryCode, Lis
    * @param directoryCollectionPut Summary information about one or more collections
    * @return an outcome, either successful or null
    */
-  public OperationOutcome updateEntities(DirectoryCollectionPut directoryCollectionPut) {
-    if (mockDirectory)
+  public boolean updateEntities(DirectoryCollectionPut directoryCollectionPut) {
+    if (mockDirectory) {
       // Dummy return if we're in mock mode
-      return DirectoryUtils.success("DirectoryApiRest.updateEntities: in mock mode, skip update");
+      logger.info("DirectoryApiRest.updateEntities: in mock mode, skip update");
+      return true;
+    }
 
     String response = directoryRestCalls.put(DirectoryRestEndpoints.getCollectionEndpoint(directoryCollectionPut.getCountryCode()), directoryCollectionPut);
-    if (response == null)
-      return DirectoryUtils.error("entity update, PUT problem");
+    if (response == null) {
+      logger.warn("entity update, PUT problem");
+      return false;
+    }
 
-    return DirectoryUtils.success("DirectoryApiRest.updateEntities: successfully put " + directoryCollectionPut.size() + " collections to the Directory");
+    logger.info("DirectoryApiRest.updateEntities: successfully put " + directoryCollectionPut.size() + " collections to the Directory");
+
+    return true;
   }
 
   /**

src/main/java/de/samply/directory_sync_service/sync/BiobanksUpdater.java

@@ -1,7 +1,7 @@
 package de.samply.directory_sync_service.sync;
 
 import de.samply.directory_sync_service.Util;
-import de.samply.directory_sync_service.directory.DirectoryApiRest;
+import de.samply.directory_sync_service.directory.DirectoryApi;
 import de.samply.directory_sync_service.directory.model.Biobank;
 import de.samply.directory_sync_service.fhir.FhirApi;
 import de.samply.directory_sync_service.model.BbmriEricId;
@@ -29,7 +29,7 @@ public class BiobanksUpdater {
      *
      * @return the individual {@link OperationOutcome}s from each update
      */
-    public static boolean updateBiobanksInFhirStore(FhirApi fhirApi, DirectoryApiRest directoryApiRest) {
+    public static boolean updateBiobanksInFhirStore(FhirApi fhirApi, DirectoryApi directoryApi) {
         // Retrieve the list of all biobanks
         List<Organization> organizations = fhirApi.listAllBiobanks();
 
@@ -42,7 +42,7 @@ public static boolean updateBiobanksInFhirStore(FhirApi fhirApi, DirectoryApiRes
             // If successful, process each biobank and update it on the FHIR server if necessary
             for (Organization organization : organizations) {
                 // Update each biobank and report any errors
-                if (!updateBiobankInFhirStore(fhirApi, directoryApiRest, organization)) {
+                if (!updateBiobankInFhirStore(fhirApi, directoryApi, organization)) {
                     logger.warn("updateBiobankOnFhirServerIfNecessary: problem updating: " + organization.getIdElement().getValue());
                     succeeded = false;
                 }
@@ -58,7 +58,7 @@ public static boolean updateBiobanksInFhirStore(FhirApi fhirApi, DirectoryApiRes
      * @param fhirBiobank the biobank to update.
      * @return the {@link OperationOutcome} from the FHIR server update
      */
-    private static boolean updateBiobankInFhirStore(FhirApi fhirApi, DirectoryApiRest directoryApiRest, Organization fhirBiobank) {
+    private static boolean updateBiobankInFhirStore(FhirApi fhirApi, DirectoryApi directoryApi, Organization fhirBiobank) {
         logger.info("updateBiobankOnFhirServerIfNecessary: entered");
 
         // Retrieve the biobank's BBMRI-ERIC identifier from the FHIR organization
@@ -76,7 +76,7 @@ private static boolean updateBiobankInFhirStore(FhirApi fhirApi, DirectoryApiRes
         logger.info("updateBiobankOnFhirServerIfNecessary: bbmriEricId: " + bbmriEricId);
 
         // Fetch the corresponding biobank from the Directory API
-        Biobank directoryBiobank = directoryApiRest.fetchBiobank(bbmriEricId);
+        Biobank directoryBiobank = directoryApi.fetchBiobank(bbmriEricId);
 
         logger.info("updateBiobankOnFhirServerIfNecessary: directoryBiobank: " + directoryBiobank);
 

src/main/java/de/samply/directory_sync_service/sync/CollectionUpdater.java

@@ -2,14 +2,13 @@
 
 import de.samply.directory_sync_service.Util;
 import de.samply.directory_sync_service.converter.FhirCollectionToDirectoryCollectionPutConverter;
-import de.samply.directory_sync_service.directory.DirectoryApiRest;
+import de.samply.directory_sync_service.directory.DirectoryApi;
 import de.samply.directory_sync_service.directory.MergeDirectoryCollectionGetToDirectoryCollectionPut;
 import de.samply.directory_sync_service.directory.model.DirectoryCollectionGet;
 import de.samply.directory_sync_service.directory.model.DirectoryCollectionPut;
 import de.samply.directory_sync_service.fhir.FhirApi;
 import de.samply.directory_sync_service.fhir.model.FhirCollection;
 import de.samply.directory_sync_service.model.BbmriEricId;
-import org.hl7.fhir.r4.model.OperationOutcome;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -40,7 +39,7 @@ public class CollectionUpdater {
      * @param defaultCollectionId The default collection ID to use for fetching collections from the FHIR store.
      * @return A list of OperationOutcome objects indicating the outcome of the update operation.
      */
-    public static boolean sendUpdatesToDirectory(FhirApi fhirApi, DirectoryApiRest directoryApiRest, Map<String, String> correctedDiagnoses, String defaultCollectionId) {
+    public static boolean sendUpdatesToDirectory(FhirApi fhirApi, DirectoryApi directoryApi, Map<String, String> correctedDiagnoses, String defaultCollectionId) {
         try {
             BbmriEricId defaultBbmriEricCollectionId = BbmriEricId
                     .valueOf(defaultCollectionId)
@@ -62,8 +61,8 @@ public static boolean sendUpdatesToDirectory(FhirApi fhirApi, DirectoryApiRest d
 
             List<String> collectionIds = directoryCollectionPut.getCollectionIds();
             String countryCode = directoryCollectionPut.getCountryCode();
-            directoryApiRest.login();
-            DirectoryCollectionGet directoryCollectionGet = directoryApiRest.fetchCollectionGetOutcomes(countryCode, collectionIds);
+            directoryApi.login();
+            DirectoryCollectionGet directoryCollectionGet = directoryApi.fetchCollectionGetOutcomes(countryCode, collectionIds);
             if (directoryCollectionGet == null) {
                 logger.warn("Problem getting collections from Directory");
                 return false;
@@ -81,12 +80,10 @@ public static boolean sendUpdatesToDirectory(FhirApi fhirApi, DirectoryApiRest d
             directoryCollectionPut.applyDiagnosisCorrections(correctedDiagnoses);
             logger.info("__________ sendUpdatesToDirectory: 2 directoryCollectionPut.getCollectionIds().size()): " + directoryCollectionPut.getCollectionIds().size());
 
-            directoryApiRest.login();
-            OperationOutcome updateOutcome = directoryApiRest.updateEntities(directoryCollectionPut);
-            String errorMessage = Util.getErrorMessageFromOperationOutcome(updateOutcome);
+            directoryApi.login();
 
-            if (!errorMessage.isEmpty()) {
-                logger.warn("sendUpdatesToDirectory: Problem during star model update");
+            if (!directoryApi.updateEntities(directoryCollectionPut)) {
+                logger.warn("sendUpdatesToDirectory: Problem during collection update");
                 return false;
             }
 

src/main/java/de/samply/directory_sync_service/sync/DiagnosisCorrections.java

@@ -2,7 +2,7 @@
 
 import de.samply.directory_sync_service.Util;
 import de.samply.directory_sync_service.converter.FhirToDirectoryAttributeConverter;
-import de.samply.directory_sync_service.directory.DirectoryApiRest;
+import de.samply.directory_sync_service.directory.DirectoryApi;
 import de.samply.directory_sync_service.fhir.FhirApi;
 import de.samply.directory_sync_service.model.BbmriEricId;
 import org.slf4j.Logger;
@@ -28,12 +28,12 @@ public class DiagnosisCorrections {
      * * Collects corrected diagnosis codes from the Directory API based on the MIRIAM-compatible codes.
      * <p>
      * @param fhirApi
-     * @param directoryApiRest
+     * @param directoryApi
      * @param defaultCollectionId Default collection ID. May be null.
      * @return A list containing diagnosis corrections.
      *         If any errors occur during the process, null is returned.
      */
-    public static Map<String, String> generateDiagnosisCorrections(FhirApi fhirApi, DirectoryApiRest directoryApiRest, String defaultCollectionId) {
+    public static Map<String, String> generateDiagnosisCorrections(FhirApi fhirApi, DirectoryApi directoryApi, String defaultCollectionId) {
         try {
             Map<String, String> correctedDiagnoses = new HashMap<String, String>();
             // Convert string version of collection ID into a BBMRI ERIC ID.
@@ -59,7 +59,7 @@ public static Map<String, String> generateDiagnosisCorrections(FhirApi fhirApi,
             logger.info("__________ generateDiagnosisCorrections: 1 correctedDiagnoses.size(): " + correctedDiagnoses.size());
 
             // Get corrected diagnosis codes from the Directory
-            directoryApiRest.collectDiagnosisCorrections(correctedDiagnoses);
+            directoryApi.collectDiagnosisCorrections(correctedDiagnoses);
             logger.info("__________ generateDiagnosisCorrections: 2 correctedDiagnoses.size(): " + correctedDiagnoses.size());
 
             return correctedDiagnoses;

src/main/java/de/samply/directory_sync_service/sync/StarModelUpdater.java

@@ -2,7 +2,7 @@
 
 import de.samply.directory_sync_service.Util;
 import de.samply.directory_sync_service.directory.CreateFactTablesFromStarModelInputData;
-import de.samply.directory_sync_service.directory.DirectoryApiRest;
+import de.samply.directory_sync_service.directory.DirectoryApi;
 import de.samply.directory_sync_service.fhir.FhirApi;
 import de.samply.directory_sync_service.fhir.PopulateStarModelInputData;
 import de.samply.directory_sync_service.model.BbmriEricId;
@@ -27,7 +27,7 @@ public class StarModelUpdater {
      * The method handles errors by returning a list of OperationOutcome objects describing the issues.
      * </p>
      * @param fhirApi
-     * @param directoryApiRest
+     * @param directoryApi
      * @param correctedDiagnoses
      * @param defaultCollectionId The default BBMRI-ERIC collection ID for fetching data from the FHIR store.
      * @param minDonors The minimum number of donors required for a fact to be included in the star model output.
@@ -36,7 +36,7 @@ public class StarModelUpdater {
      *
      * @throws IllegalArgumentException if the defaultCollectionId is not a valid BbmriEricId.
      */
-    public static boolean sendStarModelUpdatesToDirectory(FhirApi fhirApi, DirectoryApiRest directoryApiRest, Map<String, String> correctedDiagnoses, String defaultCollectionId, int minDonors, int maxFacts) {
+    public static boolean sendStarModelUpdatesToDirectory(FhirApi fhirApi, DirectoryApi directoryApi, Map<String, String> correctedDiagnoses, String defaultCollectionId, int minDonors, int maxFacts) {
         logger.info("__________ sendStarModelUpdatesToDirectory: minDonors: " + minDonors);
         try {
             BbmriEricId defaultBbmriEricCollectionId = BbmriEricId
@@ -52,7 +52,7 @@ public static boolean sendStarModelUpdatesToDirectory(FhirApi fhirApi, Directory
             }
             logger.info("__________ sendStarModelUpdatesToDirectory: number of collection IDs: " + starModelInputData.getInputCollectionIds().size());
 
-            directoryApiRest.login();
+            directoryApi.login();
 
             // Hypercubes containing less than the minimum number of donors will not be
             // included in the star model output.
@@ -69,8 +69,8 @@ public static boolean sendStarModelUpdatesToDirectory(FhirApi fhirApi, Directory
             logger.info("__________ sendStarModelUpdatesToDirectory: 2 starModelInputData.getFactCount(): " + starModelInputData.getFactCount());
 
             // Send fact tables to Direcory.
-            directoryApiRest.login();
-            OperationOutcome updateOutcome = directoryApiRest.updateStarModel(starModelInputData);
+            directoryApi.login();
+            OperationOutcome updateOutcome = directoryApi.updateStarModel(starModelInputData);
             String errorMessage = Util.getErrorMessageFromOperationOutcome(updateOutcome);
 
             if (!errorMessage.isEmpty()) {

src/main/java/de/samply/directory_sync_service/sync/Sync.java

@@ -1,5 +1,6 @@
 package de.samply.directory_sync_service.sync;
 
+import de.samply.directory_sync_service.directory.DirectoryApi;
 import de.samply.directory_sync_service.directory.DirectoryApiRest;
 import de.samply.directory_sync_service.fhir.FhirApi;
 
@@ -56,14 +57,14 @@ private static boolean syncWithDirectory(String fhirStoreUrl, String directoryUr
         Map<String, String> correctedDiagnoses = null;
         // Re-initialize helper classes every time this method gets called
         FhirApi fhirApi = new FhirApi(fhirStoreUrl);
-        DirectoryApiRest directoryApiRest = new DirectoryApiRest(directoryUrl, directoryMock, directoryUserName, directoryUserPass);
+        DirectoryApi directoryApi = new DirectoryApiRest(directoryUrl, directoryMock, directoryUserName, directoryUserPass);
 
-        if (!directoryApiRest.isAvailable()) {
+        if (!directoryApi.isAvailable()) {
             logger.warn("syncWithDirectory: Directory REST API is not available");
             return false;
         }
 
-        if (!directoryApiRest.login()) {
+        if (!directoryApi.login()) {
             logger.warn("syncWithDirectory: there was a problem during login to Directory");
             return false;
         }
@@ -74,22 +75,22 @@ private static boolean syncWithDirectory(String fhirStoreUrl, String directoryUr
             return true;
         }
 
-        correctedDiagnoses = DiagnosisCorrections.generateDiagnosisCorrections(fhirApi, directoryApiRest, directoryDefaultCollectionId);
+        correctedDiagnoses = DiagnosisCorrections.generateDiagnosisCorrections(fhirApi, directoryApi, directoryDefaultCollectionId);
         if (correctedDiagnoses == null) {
             logger.warn("syncWithDirectory: there was a problem during diagnosis corrections");
             return false;
         }
         if (directoryAllowStarModel)
-            if (!StarModelUpdater.sendStarModelUpdatesToDirectory(fhirApi, directoryApiRest, correctedDiagnoses, directoryDefaultCollectionId, directoryMinDonors, directoryMaxFacts)) {
+            if (!StarModelUpdater.sendStarModelUpdatesToDirectory(fhirApi, directoryApi, correctedDiagnoses, directoryDefaultCollectionId, directoryMinDonors, directoryMaxFacts)) {
                 logger.warn("syncWithDirectory: there was a problem during star model update to Directory");
                 return false;
             }
-        if (!CollectionUpdater.sendUpdatesToDirectory(fhirApi, directoryApiRest, correctedDiagnoses, directoryDefaultCollectionId)) {
+        if (!CollectionUpdater.sendUpdatesToDirectory(fhirApi, directoryApi, correctedDiagnoses, directoryDefaultCollectionId)) {
             logger.warn("syncWithDirectory: there was a problem during sync to Directory");
             return false;
         }
 
-        if (!BiobanksUpdater.updateBiobanksInFhirStore(fhirApi, directoryApiRest)) {
+        if (!BiobanksUpdater.updateBiobanksInFhirStore(fhirApi, directoryApi)) {
             logger.warn("syncWithDirectory: there was a problem during sync from Directory");
             return false;
         }