Added option that just logs into Directory without further actions

For testing purposes only.

Also removed a logging statement that caused problems in mock mode.

README.md

@@ -53,6 +53,7 @@ First, you will need to set up the environment variables for this:
 | DS_DIRECTORY_MAX_FACTS             | Max number of star model hypercubes to be generated                                                                                                                  |                                        |
 | DS_DIRECTORY_ALLOW_STAR_MODEL      | Set to 'True' to send star model info to Directory                                                                                                                   | False                                  |
 | DS_DIRECTORY_MOCK                  | Set to 'True' mock a Directory. In this mode, directory-sync will not contact the Directory. All Directory-related methods will simply return plausible fake values. | False                                  |
+| DS_DIRECTORY_ONLY_LOGIN            | Set to 'True' to log in to the Directory, without carrying out any further actions.                                                                                  | False                                  |
 | DS_FHIR_STORE_URL                  | URL for FHIR store                                                                                                                                                   | http://bridgehead-bbmri-blaze:8080     |
 | DS_TIMER_CRON                      | Execution interval for Directory sync, cron format                                                                                                                   |                                        |
 | DS_RETRY_MAX                       | Maximum number of retries when sync fails                                                                                                                            | 10                                     |

pom.xml

@@ -10,7 +10,7 @@
     </parent>
     <groupId>de.samply</groupId>
     <artifactId>directory_sync_service</artifactId>
-    <version>1.4.6</version>
+    <version>1.4.7</version>
     <name>directory_sync_service</name>
     <description>Directory sync</description>
     <url>https://github.com/samply/directory_sync_service</url>

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

@@ -43,22 +43,15 @@ public class DirectoryApi {
   public DirectoryApi(String baseUrl, boolean mockDirectory, String username, String password) {
     this.mockDirectory = mockDirectory;
     this.directoryRest = new DirectoryRest(baseUrl, username, password);
-    if (!mockDirectory)
-      // Log in if we are not in mock mode
-      this.directoryRest.login();
+    relogin();
   }
 
   /**
    * Log back in to the Directory. This is typically used in situations where there has
-   * been a long pause since the last API call to the Directory. It returns a fresh
-   * DirectoryApi object, which you should use to replace the existing one.
-   * <p>
-   * Returns null if something goes wrong.
-   *
-   * @return new DirectoryApi object.
+   * been a long pause since the last API call to the Directory.
    */
   public void relogin() {
-    logger.info("login: logging back in");
+    logger.info("login: logging  in");
 
     if (mockDirectory)
       // Don't try logging in if we are mocking

src/main/java/de/samply/directory_sync_service/fhir/FhirApi.java

@@ -97,7 +97,6 @@ public static Optional<BbmriEricId> bbmriEricId(Organization collection) {
    */
   public OperationOutcome updateResource(IBaseResource resource) {
     logger.info("updateResource: @@@@@@@@@@ entered");
-    logger.info("updateResource: @@@@@@@@@@ theResource: " + ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource));
 
     // Remove the version ID, so that no If-Match header gets added to the request
     // If you don't do this, Blaze will throw an exception like this:

src/main/java/de/samply/directory_sync_service/service/Configuration.java

@@ -40,7 +40,11 @@ public class Configuration {
 
     @Value("${ds.directory.max_facts}")
     private String directoryMaxFacts;
-
+    
     @Value("${ds.directory.mock}")
     private String directoryMock;
+
+    @Value("${ds.directory.only_login}")
+    private String directoryOnlyLogin;
+
 }

src/main/java/de/samply/directory_sync_service/service/DirectorySyncJob.java

@@ -52,8 +52,9 @@ public void execute(Configuration configuration) {
         int directoryMinDonors = Integer.parseInt(configuration.getDirectoryMinDonors());
         int directoryMaxFacts = Integer.parseInt(configuration.getDirectoryMaxFacts());
         boolean directoryMock = Boolean.parseBoolean(configuration.getDirectoryMock());
+        boolean directoryOnlyLogin = Boolean.parseBoolean(configuration.getDirectoryOnlyLogin());
 
-        Sync.syncWithDirectoryFailover(retryMax, retryInterval, fhirStoreUrl, directoryUrl, directoryUserName, directoryUserPass, directoryDefaultCollectionId, directoryAllowStarModel, directoryMinDonors, directoryMaxFacts, directoryMock);
+        Sync.syncWithDirectoryFailover(retryMax, retryInterval, fhirStoreUrl, directoryUrl, directoryUserName, directoryUserPass, directoryDefaultCollectionId, directoryAllowStarModel, directoryMinDonors, directoryMaxFacts, directoryMock, directoryOnlyLogin);
     }
 
     /**

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

@@ -26,7 +26,7 @@ public class DiagnosisCorrections {
      * * Retrieves diagnoses from the FHIR store for specimens with identifiable collections and their associated patients.
      * * Converts raw ICD-10 codes into MIRIAM-compatible codes.
      * * Collects corrected diagnosis codes from the Directory API based on the MIRIAM-compatible codes.
-     *
+     * <p>
      * @param fhirApi
      * @param directoryApi
      * @param defaultCollectionId Default collection ID. May be null.

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

@@ -37,7 +37,7 @@ public class Sync {
      *
      * @throws IOException
      */
-    public static void syncWithDirectoryFailover(String retryMax, String retryInterval, String fhirStoreUrl, String directoryUrl, String directoryUserName, String directoryUserPass, String directoryDefaultCollectionId, boolean directoryAllowStarModel, int directoryMinDonors, int directoryMaxFacts, boolean directoryMock) {
+    public static void syncWithDirectoryFailover(String retryMax, String retryInterval, String fhirStoreUrl, String directoryUrl, String directoryUserName, String directoryUserPass, String directoryDefaultCollectionId, boolean directoryAllowStarModel, int directoryMinDonors, int directoryMaxFacts, boolean directoryMock, boolean directoryOnlyLogin) {
         for (int retryNum = 0; retryNum < Integer.parseInt(retryMax); retryNum++) {
             if (retryNum > 0) {
                 try {
@@ -47,17 +47,23 @@ public static void syncWithDirectoryFailover(String retryMax, String retryInterv
                 }
                 logger.info("syncWithDirectoryFailover: retrying sync, attempt " + retryNum + " of " + retryMax);
             }
-            if (syncWithDirectory(retryMax, retryInterval, fhirStoreUrl, directoryUrl, directoryUserName, directoryUserPass, directoryDefaultCollectionId, directoryAllowStarModel, directoryMinDonors, directoryMaxFacts, directoryMock))
+            if (syncWithDirectory(fhirStoreUrl, directoryUrl, directoryUserName, directoryUserPass, directoryDefaultCollectionId, directoryAllowStarModel, directoryMinDonors, directoryMaxFacts, directoryMock, directoryOnlyLogin))
                 break;
         }
     }
 
-    private static boolean syncWithDirectory(String retryMax, String retryInterval, String fhirStoreUrl, String directoryUrl, String directoryUserName, String directoryUserPass, String directoryDefaultCollectionId, boolean directoryAllowStarModel, int directoryMinDonors, int directoryMaxFacts, boolean directoryMock) {
+    private static boolean syncWithDirectory(String fhirStoreUrl, String directoryUrl, String directoryUserName, String directoryUserPass, String directoryDefaultCollectionId, boolean directoryAllowStarModel, int directoryMinDonors, int directoryMaxFacts, boolean directoryMock, boolean directoryOnlyLogin) {
         Map<String, String> correctedDiagnoses = null;
         // Re-initialize helper classes every time this method gets called
         FhirApi fhirApi = new FhirApi(fhirStoreUrl);
         DirectoryApi directoryApi = new DirectoryApi(directoryUrl, directoryMock, directoryUserName, directoryUserPass);
 
+        // Login test. Don't perform any further actions on the Directory.
+        if (directoryOnlyLogin) {
+            logger.info(">>>>>>>>>>>>>>> syncWithDirectory: login was successful, now quitting because onlyLogin was set to true");
+            return true;
+        }
+
         correctedDiagnoses = DiagnosisCorrections.generateDiagnosisCorrections(fhirApi, directoryApi, directoryDefaultCollectionId);
         if (correctedDiagnoses == null) {
             logger.warn("syncWithDirectory: there was a problem during diagnosis corrections");
@@ -78,7 +84,7 @@ private static boolean syncWithDirectory(String retryMax, String retryInterval,
             return false;
         }
 
-        logger.info("__________ syncWithDirectory: all synchronization tasks finished");
+        logger.info(">>>>>>>>>>>>>>> syncWithDirectory: all synchronization tasks finished");
         return true;
     }
 }

src/main/resources/application.yml

@@ -17,5 +17,4 @@ ds:
     min_donors: "10"
     max_facts: "-1"
     mock: "False"
-
-
+    only_login: "False"