Merge pull request #10026 from bencomp/7138-identifer

Replace "identifer" with "identifier" in docs and code

doc/sphinx-guides/source/developers/s3-direct-upload-api.rst

@@ -116,7 +116,7 @@ The allowed checksum algorithms are defined by the edu.harvard.iq.dataverse.Data
   curl -X POST -H "X-Dataverse-key: $API_TOKEN" "$SERVER_URL/api/datasets/:persistentId/add?persistentId=$PERSISTENT_IDENTIFIER" -F "jsonData=$JSON_DATA"
   
 Note that this API call can be used independently of the others, e.g. supporting use cases in which the file already exists in S3/has been uploaded via some out-of-band method. Enabling out-of-band uploads is described at :ref:`file-storage` in the Configuration Guide.
-With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifer must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
+With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifier must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
 
 To add multiple Uploaded Files to the Dataset
 ---------------------------------------------
@@ -147,7 +147,7 @@ The allowed checksum algorithms are defined by the edu.harvard.iq.dataverse.Data
   curl -X POST -H "X-Dataverse-key: $API_TOKEN" "$SERVER_URL/api/datasets/:persistentId/addFiles?persistentId=$PERSISTENT_IDENTIFIER" -F "jsonData=$JSON_DATA"
 
 Note that this API call can be used independently of the others, e.g. supporting use cases in which the files already exists in S3/has been uploaded via some out-of-band method. Enabling out-of-band uploads is described at :ref:`file-storage` in the Configuration Guide.
-With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifer must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
+With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifier must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
 
 
 Replacing an existing file in the Dataset
@@ -177,7 +177,7 @@ Note that the API call does not validate that the file matches the hash value su
   curl -X POST -H "X-Dataverse-key: $API_TOKEN" "$SERVER_URL/api/files/$FILE_IDENTIFIER/replace" -F "jsonData=$JSON_DATA"
   
 Note that this API call can be used independently of the others, e.g. supporting use cases in which the file already exists in S3/has been uploaded via some out-of-band method. Enabling out-of-band uploads is described at :ref:`file-storage` in the Configuration Guide.
-With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifer must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
+With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifier must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
 
 Replacing multiple existing files in the Dataset
 ------------------------------------------------
@@ -275,4 +275,4 @@ The JSON object returned as a response from this API call includes a "data" that
 
 
 Note that this API call can be used independently of the others, e.g. supporting use cases in which the files already exists in S3/has been uploaded via some out-of-band method. Enabling out-of-band uploads is described at :ref:`file-storage` in the Configuration Guide.
-With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifer must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.
+With current S3 stores the object identifier must be in the correct bucket for the store, include the PID authority/identifier of the parent dataset, and be guaranteed unique, and the supplied storage identifier must be prefaced with the store identifier used in the Dataverse installation, as with the internally generated examples above.

doc/sphinx-guides/source/user/dataset-management.rst

@@ -783,7 +783,7 @@ The "Compute" button on dataset and file pages will allow you to compute on a si
 Cloud Storage Access
 --------------------
 
-If you need to access a dataset in a more flexible way than the Compute button provides, then you can use the Cloud Storage Access box on the dataset page to copy the dataset's container name. This unique identifer can then be used to allow direct access to the dataset.
+If you need to access a dataset in a more flexible way than the Compute button provides, then you can use the Cloud Storage Access box on the dataset page to copy the dataset's container name. This unique identifier can then be used to allow direct access to the dataset.
 
 .. _deaccession:
 

doc/sphinx-guides/source/user/find-use-data.rst

@@ -71,7 +71,7 @@ View Files
 
 Files in a Dataverse installation each have their own landing page that can be reached through the search results or through the Files table on their parent dataset's page. The dataset page and file page offer much the same functionality in terms of viewing and editing files, with a few small exceptions. 
 
-- In installations that have enabled support for persistent identifers (PIDs) at the file level, the file page includes the file's DOI or handle, which can be found in the file citation and also under the Metadata tab.
+- In installations that have enabled support for persistent identifiers (PIDs) at the file level, the file page includes the file's DOI or handle, which can be found in the file citation and also under the Metadata tab.
 - Previewers for several common file types are available and can be added by installation administrators.
 - The file page's Versions tab gives you a version history that is more focused on the individual file rather than the dataset as a whole. 
 

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)) {