Fix identifer typo in code

Just in case code outside this project is referencing the old methods,
I created deprecated versions.

Author: bencomp

src/main/java/edu/harvard/iq/dataverse/DatasetVersionServiceBean.java

@@ -495,10 +495,24 @@ private DatasetVersion getDatasetVersionByQuery(String queryString){
          }
     } // end getDatasetVersionByQuery
 
-    
-    
-    
-    public DatasetVersion retrieveDatasetVersionByIdentiferClause(String identifierClause, String version){
+    /**
+     * @deprecated because of a typo; use {@link #retrieveDatasetVersionByIdentifierClause(String, String) retrieveDatasetVersionByIdentifierClause} instead
+     * @see #retrieveDatasetVersionByIdentifierClause(String, String)
+     * @param identifierClause
+     * @param version
+     * @return a DatasetVersion if found, or {@code null} otherwise
+     */
+    @Deprecated
+    public DatasetVersion retrieveDatasetVersionByIdentiferClause(String identifierClause, String version) {
+        return retrieveDatasetVersionByIdentifierClause(identifierClause, version);
+    }
+
+    /**
+     * @param identifierClause
+     * @param version
+     * @return a DatasetVersion if found, or {@code null} otherwise
+     */
+    public DatasetVersion retrieveDatasetVersionByIdentifierClause(String identifierClause, String version) {
 
         if (identifierClause == null){
             return null;
@@ -620,7 +634,7 @@ public RetrieveDatasetVersionResponse retrieveDatasetVersionByPersistentId(Strin
         identifierClause += " AND ds.identifier = '" + parsedId.getIdentifier() + "'"; 
 
 
-        DatasetVersion ds = retrieveDatasetVersionByIdentiferClause(identifierClause, version);
+        DatasetVersion ds = retrieveDatasetVersionByIdentifierClause(identifierClause, version);
 
         if (ds != null){
             msg("retrieved dataset: " + ds.getId() + " semantic: " + ds.getSemanticVersion());
@@ -718,7 +732,7 @@ public DatasetVersion getDatasetVersionById(Long datasetId, String version){
 
         String identifierClause = this.getIdClause(datasetId);
 
-        DatasetVersion ds = retrieveDatasetVersionByIdentiferClause(identifierClause, version);
+        DatasetVersion ds = retrieveDatasetVersionByIdentifierClause(identifierClause, version);
 
         return ds;
 

src/main/java/edu/harvard/iq/dataverse/Shib.java

@@ -24,6 +24,7 @@
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 import jakarta.ejb.EJB;
 import jakarta.ejb.EJBException;
@@ -62,7 +63,7 @@ public class Shib implements java.io.Serializable {
     HttpServletRequest request;
 
     private String userPersistentId;
-    private String internalUserIdentifer;
+    private String internalUserIdentifier;
     AuthenticatedUserDisplayInfo displayInfo;
     /**
      * @todo Remove this boolean some day? Now the mockups show a popup. Should
@@ -210,8 +211,8 @@ public void init() {
         }
 
         String usernameAssertion = getValueFromAssertion(ShibUtil.usernameAttribute);
-        internalUserIdentifer = ShibUtil.generateFriendlyLookingUserIdentifer(usernameAssertion, emailAddress);
-        logger.fine("friendly looking identifer (backend will enforce uniqueness):" + internalUserIdentifer);
+        internalUserIdentifier = ShibUtil.generateFriendlyLookingUserIdentifier(usernameAssertion, emailAddress);
+        logger.log(Level.FINE, "friendly looking identifier (backend will enforce uniqueness): {0}", internalUserIdentifier);
 
         String shibAffiliationAttribute = settingsService.getValueForKey(SettingsServiceBean.Key.ShibAffiliationAttribute);
         String affiliation = (StringUtils.isNotBlank(shibAffiliationAttribute))
@@ -326,7 +327,7 @@ public String confirmAndCreateAccount() {
         AuthenticatedUser au = null;
         try {
             au = authSvc.createAuthenticatedUser(
-                    new UserRecordIdentifier(shibAuthProvider.getId(), lookupStringPerAuthProvider), internalUserIdentifer, displayInfo, true);
+                    new UserRecordIdentifier(shibAuthProvider.getId(), lookupStringPerAuthProvider), internalUserIdentifier, displayInfo, true);
         } catch (EJBException ex) {
             /**
              * @todo Show the ConstraintViolationException, if any.
@@ -354,7 +355,7 @@ public String confirmAndConvertAccount() {
         visibleTermsOfUse = false;
         ShibAuthenticationProvider shibAuthProvider = new ShibAuthenticationProvider();
         String lookupStringPerAuthProvider = userPersistentId;
-        UserIdentifier userIdentifier = new UserIdentifier(lookupStringPerAuthProvider, internalUserIdentifer);
+        UserIdentifier userIdentifier = new UserIdentifier(lookupStringPerAuthProvider, internalUserIdentifier);
         logger.fine("builtin username: " + builtinUsername);
         AuthenticatedUser builtInUserToConvert = authSvc.canLogInAsBuiltinUser(builtinUsername, builtinPassword);
         if (builtInUserToConvert != null) {

src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionListManagerImpl.java

@@ -94,7 +94,7 @@ public Feed listCollectionContents(IRI iri, AuthCredentials authCredentials, Swo
                 throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Could not find dataverse: " + dvAlias);
             }
         } else {
-            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't determine target type or identifer from URL: " + iri);
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Couldn't determine target type or identifier from URL: " + iri);
         }
     }
 

src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java

@@ -219,7 +219,7 @@ public void deleteMediaResource(String uri, AuthCredentials authCredentials, Swo
                 throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unsupported file type found in URL: " + uri);
             }
         } else {
-            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target or identifer not specified in URL: " + uri);
+            throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Target or identifier not specified in URL: " + uri);
         }
     }
 

src/main/java/edu/harvard/iq/dataverse/authorization/AuthenticationServiceBean.java

@@ -580,7 +580,7 @@ public boolean updateProvider( AuthenticatedUser authenticatedUser, String authe
      * {@code userDisplayInfo}, a lookup entry for them based
      * UserIdentifier.getLookupStringPerAuthProvider (within the supplied
      * authentication provider), and internal user identifier (used for role
-     * assignments, etc.) based on UserIdentifier.getInternalUserIdentifer.
+     * assignments, etc.) based on UserIdentifier.getInternalUserIdentifier.
      *
      * @param userRecordId
      * @param proposedAuthenticatedUserIdentifier
@@ -605,20 +605,20 @@ public AuthenticatedUser createAuthenticatedUser(UserRecordIdentifier userRecord
             proposedAuthenticatedUserIdentifier = proposedAuthenticatedUserIdentifier.trim();
         }
         // we now select a username for the generated AuthenticatedUser, or give up
-        String internalUserIdentifer = proposedAuthenticatedUserIdentifier;
+        String internalUserIdentifier = proposedAuthenticatedUserIdentifier;
         // TODO should lock table authenticated users for write here
-        if ( identifierExists(internalUserIdentifer) ) {
+        if ( identifierExists(internalUserIdentifier) ) {
             if ( ! generateUniqueIdentifier ) {
                 return null;
             }
             int i=1;
-            String identifier = internalUserIdentifer + i;
+            String identifier = internalUserIdentifier + i;
             while ( identifierExists(identifier) ) {
                 i += 1;
             }
             authenticatedUser.setUserIdentifier(identifier);
         } else {
-            authenticatedUser.setUserIdentifier(internalUserIdentifer);
+            authenticatedUser.setUserIdentifier(internalUserIdentifier);
         }
         authenticatedUser = save( authenticatedUser );
         // TODO should unlock table authenticated users for write here

src/main/java/edu/harvard/iq/dataverse/authorization/UserIdentifier.java

@@ -25,18 +25,31 @@ public class UserIdentifier {
     /**
      * The String used in the permission system to assign roles, for example.
      */
-    String internalUserIdentifer;
+    String internalUserIdentifier;
 
-    public UserIdentifier(String lookupStringPerAuthProvider, String internalUserIdentifer) {
+    public UserIdentifier(String lookupStringPerAuthProvider, String internalUserIdentifier) {
         this.lookupStringPerAuthProvider = lookupStringPerAuthProvider;
-        this.internalUserIdentifer = internalUserIdentifer;
+        this.internalUserIdentifier = internalUserIdentifier;
     }
 
     public String getLookupStringPerAuthProvider() {
         return lookupStringPerAuthProvider;
     }
 
+    /**
+     * @deprecated because of a typo; use {@link #getInternalUserIdentifier()} instead
+     * @see #getInternalUserIdentifier()
+     * @return the internal user identifier
+     */
+    @Deprecated
     public String getInternalUserIdentifer() {
-        return internalUserIdentifer;
+        return getInternalUserIdentifier();
+    }
+
+    /**
+     * @return the internal user identifier
+     */
+    public String getInternalUserIdentifier() {
+        return internalUserIdentifier;
     }
 }

src/main/java/edu/harvard/iq/dataverse/authorization/providers/shib/ShibUtil.java

@@ -133,7 +133,24 @@ public static String findSingleValue(String mayHaveMultipleValues) {
         return singleValue;
     }
 
+    /**
+     * @deprecated because of a typo; use {@link #generateFriendlyLookingUserIdentifier(String, String)} instead
+     * @see #generateFriendlyLookingUserIdentifier(String, String)
+     * @param usernameAssertion
+     * @param email
+     * @return a friendly-looking user identifier based on the asserted username or email, or a UUID as fallback
+     */
+    @Deprecated
     public static String generateFriendlyLookingUserIdentifer(String usernameAssertion, String email) {
+        return generateFriendlyLookingUserIdentifier(usernameAssertion, email);
+    }
+
+    /**
+     * @param usernameAssertion
+     * @param email
+     * @return a friendly-looking user identifier based on the asserted username or email, or a UUID as fallback
+     */
+    public static String generateFriendlyLookingUserIdentifier(String usernameAssertion, String email) {
         if (usernameAssertion != null && !usernameAssertion.isEmpty()) {
             return usernameAssertion;
         }

src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordJobListener.java

@@ -450,7 +450,7 @@ private void loadChecksumManifest() {
         // We probably want package files to be able to use specific stores instead.
         // More importantly perhaps, the approach above does not take into account
         // if the dataset may have an AlternativePersistentIdentifier, that may be 
-        // designated isStorageLocationDesignator() - i.e., if a different identifer
+        // designated isStorageLocationDesignator() - i.e., if a different identifier
         // needs to be used to name the storage directory, instead of the main/current
         // persistent identifier above. 
         getJobLogger().log(Level.INFO, "Reading checksum manifest: " + manifestAbsolutePath);

src/main/java/edu/harvard/iq/dataverse/batch/jobs/importer/filesystem/FileRecordReader.java

@@ -109,7 +109,7 @@ public void open(Serializable checkpoint) throws Exception {
         // We probably want package files to be able to use specific stores instead.
         // More importantly perhaps, the approach above does not take into account
         // if the dataset may have an AlternativePersistentIdentifier, that may be 
-        // designated isStorageLocationDesignator() - i.e., if a different identifer
+        // designated isStorageLocationDesignator() - i.e., if a different identifier
         // needs to be used to name the storage directory, instead of the main/current
         // persistent identifier above. 
         getJobLogger().log(Level.INFO, "Reading dataset directory: " + directory.getAbsolutePath() 

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ImportFromFileSystemCommand.java

@@ -83,7 +83,7 @@ public JsonObject execute(CommandContext ctxt) throws CommandException {
             //       We probably want package files to be able to use specific stores instead.
             //       More importantly perhaps, the approach above does not take into account
             //       if the dataset may have an AlternativePersistentIdentifier, that may be
-            //       designated isStorageLocationDesignator() - i.e., if a different identifer
+            //       designated isStorageLocationDesignator() - i.e., if a different identifier
             //       needs to be used to name the storage directory, instead of the main/current
             //       persistent identifier above.
             if (!isValidDirectory(directory)) {