add deprecation notices to Java code for rsync #8985

IQSS · Jun 7, 2024 · 44b43f8 · 44b43f8
1 parent ace254b
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diff --git a/doc/release-notes/8985-deprecate-rsync.md b/doc/release-notes/8985-deprecate-rsync.md
@@ -1 +1,9 @@
 Support for rsync has been deprecated. Information has been removed from the guides for rsync and related software such as Data Capture Module (DCM) and Repository Storage Abstraction Layer (RSAL). You can still find this information in [older versions](https://guides.dataverse.org/en/6.2/developers/big-data-support.html#data-capture-module-dcm) of the guides.
+
+The following related database settings have been deprecated as well:
+
+- :DataCaptureModuleUrl
+- :DownloadMethods
+- :LocalDataAccessPath
+- :PublicInstall
+- :RepositoryStorageAbstractionLayerUrl
diff --git a/src/main/java/edu/harvard/iq/dataverse/FilePage.java b/src/main/java/edu/harvard/iq/dataverse/FilePage.java
@@ -1546,6 +1546,7 @@ public String getIngestMessage() {
     }
 
     //Determines whether this File uses a public store and therefore doesn't support embargoed or restricted files
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isHasPublicStore() {
         return settingsWrapper.isTrueForKey(SettingsServiceBean.Key.PublicInstall, StorageIO.isPublicStore(DataAccess.getStorageDriverFromIdentifier(file.getStorageIdentifier())));
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java b/src/main/java/edu/harvard/iq/dataverse/SettingsWrapper.java
@@ -299,20 +299,23 @@ public Long getZipDownloadLimit(){
         return zipDownloadLimit;
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isPublicInstall(){
         if (publicInstall == null) {
             publicInstall = systemConfig.isPublicInstall();
         }
         return publicInstall; 
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isRsyncUpload() {
         if (rsyncUpload == null) {
             rsyncUpload = getUploadMethodAvailable(SystemConfig.FileUploadMethods.RSYNC.toString());
         }
         return rsyncUpload; 
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isRsyncDownload() {
         if (rsyncDownload == null) {
             rsyncDownload = systemConfig.isRsyncDownload();
@@ -379,7 +382,8 @@ public boolean isWebloaderUpload() {
         }
         return webloaderUpload;
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isRsyncOnly() {
         if (rsyncOnly == null) {
             String downloadMethods = getValueForKey(SettingsServiceBean.Key.DownloadMethods);
@@ -398,7 +402,7 @@ public boolean isRsyncOnly() {
         }
         return rsyncOnly;
     }
-    
+
     public boolean isHTTPUpload(){
         if (httpUpload == null) {
             httpUpload = getUploadMethodAvailable(SystemConfig.FileUploadMethods.NATIVE.toString());

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
@@ -2297,6 +2297,7 @@ public Response removeDatasetLogo(@Context ContainerRequestContext crc, @PathPar
         }
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     @GET
     @AuthRequired
     @Path("{identifier}/dataCaptureModule/rsync")

diff --git a/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleException.java b/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleException.java
@@ -1,7 +1,9 @@
 package edu.harvard.iq.dataverse.datacapturemodule;
 
+@Deprecated(forRemoval = true, since = "2024-07-07")
 public class DataCaptureModuleException extends Exception {
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public DataCaptureModuleException(String message, Throwable cause) {
         super(message, cause);
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleUtil.java b/src/main/java/edu/harvard/iq/dataverse/datacapturemodule/DataCaptureModuleUtil.java
@@ -12,10 +12,12 @@
 import jakarta.json.JsonObject;
 import jakarta.json.JsonObjectBuilder;
 
+@Deprecated(forRemoval = true, since = "2024-07-07")
 public class DataCaptureModuleUtil {
 
     private static final Logger logger = Logger.getLogger(DataCaptureModuleUtil.class.getCanonicalName());
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static boolean rsyncSupportEnabled(String uploadMethodsSettings) {
         logger.fine("uploadMethodsSettings: " + uploadMethodsSettings);; 
         if (uploadMethodsSettings==null){
@@ -28,6 +30,7 @@ public static boolean rsyncSupportEnabled(String uploadMethodsSettings) {
     /**
      * generate JSON to send to DCM
      */
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static JsonObject generateJsonForUploadRequest(AuthenticatedUser user, Dataset dataset) {
         JsonObjectBuilder jab = Json.createObjectBuilder();
         // The general rule should be to always pass the user id and dataset identifier to the DCM.
@@ -39,6 +42,7 @@ public static JsonObject generateJsonForUploadRequest(AuthenticatedUser user, Da
     /**
      * transfer script from DCM
      */
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static ScriptRequestResponse getScriptFromRequest(HttpResponse<JsonNode> uploadRequest) {
         int status = uploadRequest.getStatus();
         JsonNode body = uploadRequest.getBody();
@@ -54,13 +58,15 @@ public static ScriptRequestResponse getScriptFromRequest(HttpResponse<JsonNode>
         return scriptRequestResponse;
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     static UploadRequestResponse makeUploadRequest(HttpResponse<String> uploadRequest) {
         int status = uploadRequest.getStatus();
         String body = uploadRequest.getBody();
         logger.fine("Got " + status + " with body: " + body);
         return new UploadRequestResponse(uploadRequest.getStatus(), body);
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static String getMessageFromException(DataCaptureModuleException ex) {
         if (ex == null) {
             return "DataCaptureModuleException was null!";
@@ -76,6 +82,7 @@ public static String getMessageFromException(DataCaptureModuleException ex) {
         return message + " was caused by " + cause.getMessage();
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static String getScriptName(DatasetVersion datasetVersion) {
         return "upload-" + datasetVersion.getDataset().getIdentifier().replace("/", "_") + ".bash";
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RequestRsyncScriptCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/RequestRsyncScriptCommand.java
@@ -27,6 +27,7 @@
  * "actiontype" in the actionlogrecord rather than "InternalError" if you throw
  * a CommandExecutionException.
  */
+@Deprecated(forRemoval = true, since = "2024-07-07")
 @RequiredPermissions(Permission.EditDataset)
 public class RequestRsyncScriptCommand extends AbstractCommand<ScriptRequestResponse> {
 

diff --git a/...iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerPage.java b/...iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerPage.java
@@ -11,6 +11,7 @@
 import jakarta.inject.Named;
 import jakarta.json.JsonArray;
 
+@Deprecated(forRemoval = true, since = "2024-07-07")
 @Stateless
 @Named
 public class RepositoryStorageAbstractionLayerPage {
@@ -22,17 +23,20 @@ public class RepositoryStorageAbstractionLayerPage {
     @EJB
     StorageSiteServiceBean storageSiteServiceBean;
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public String getLocalDataAccessDirectory(DatasetVersion datasetVersion) {
         String localDataAccessParentDir = settingsService.getValueForKey(SettingsServiceBean.Key.LocalDataAccessPath);
         return RepositoryStorageAbstractionLayerUtil.getLocalDataAccessDirectory(localDataAccessParentDir, datasetVersion.getDataset());
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public List<RsyncSite> getRsyncSites(DatasetVersion datasetVersion) {
         List<StorageSite> storageSites = storageSiteServiceBean.findAll();
         JsonArray storageSitesAsJson = RepositoryStorageAbstractionLayerUtil.getStorageSitesAsJson(storageSites);
         return RepositoryStorageAbstractionLayerUtil.getRsyncSites(datasetVersion.getDataset(), storageSitesAsJson);
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public String getVerifyDataCommand(DatasetVersion datasetVersion) {
         return RepositoryStorageAbstractionLayerUtil.getVerifyDataCommand(datasetVersion.getDataset());
     }

diff --git a/...iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerUtil.java b/...iq/dataverse/repositorystorageabstractionlayer/RepositoryStorageAbstractionLayerUtil.java
@@ -13,10 +13,12 @@
 import jakarta.json.JsonArrayBuilder;
 import jakarta.json.JsonObject;
 
+@Deprecated(forRemoval = true, since = "2024-07-07")
 public class RepositoryStorageAbstractionLayerUtil {
 
     private static final Logger logger = Logger.getLogger(RepositoryStorageAbstractionLayerUtil.class.getCanonicalName());
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static List<RsyncSite> getRsyncSites(Dataset dataset, JsonArray rsalSitesAsJson) {
         List<RsyncSite> rsalSites = new ArrayList<>();
         boolean leafDirectoryOnly = false;
@@ -30,6 +32,7 @@ public static List<RsyncSite> getRsyncSites(Dataset dataset, JsonArray rsalSites
         return rsalSites;
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     static String getLocalDataAccessDirectory(String localDataAccessParentDir, Dataset dataset) {
         if (localDataAccessParentDir == null) {
             localDataAccessParentDir = File.separator + "UNCONFIGURED ( " + SettingsServiceBean.Key.LocalDataAccessPath + " )";
@@ -38,6 +41,7 @@ static String getLocalDataAccessDirectory(String localDataAccessParentDir, Datas
         return localDataAccessParentDir + File.separator + getDirectoryContainingTheData(dataset, leafDirectoryOnly);
     }
 
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     static String getVerifyDataCommand(Dataset dataset) {
         boolean leafDirectoryOnly = true;
         // TODO: if "files.sha" is defined somewhere, use it.
@@ -51,6 +55,7 @@ static String getVerifyDataCommand(Dataset dataset) {
      * leafDirectoryOnly. See also
      * http://www.gnu.org/software/coreutils/manual/html_node/basename-invocation.html
      */
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public static String getDirectoryContainingTheData(Dataset dataset, boolean leafDirectoryOnly) {
         /**
          * FIXME: What if there is more than one package in the dataset?
@@ -81,6 +86,7 @@ public static String getDirectoryContainingTheData(Dataset dataset, boolean leaf
      * RSAL or some other "big data" component live for a list of remotes sites
      * to which a particular dataset is replicated to.
      */
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     static JsonArray getStorageSitesAsJson(List<StorageSite> storageSites) {
         JsonArrayBuilder arraybuilder = Json.createArrayBuilder();
         if (storageSites == null || storageSites.isEmpty()) {

diff --git a/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java
@@ -55,7 +55,10 @@ public enum Key {
         CustomDatasetSummaryFields,
         /**
          * Defines a public installation -- all datafiles are unrestricted
+         *
+         * This was added for rsync, which is now deprecated.
          */
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         PublicInstall,
         /**
          * Sets the name of your cloud computing environment.
@@ -75,9 +78,12 @@ public enum Key {
         /**
          * For example, https://datacapture.example.org
          */
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         DataCaptureModuleUrl,
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         RepositoryStorageAbstractionLayerUrl,
         UploadMethods,
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         DownloadMethods,
         /**
          * If the data replicated around the world using RSAL (Repository
@@ -87,6 +93,7 @@ public enum Key {
          * TODO: Think about if it makes sense to make this a column in the
          * StorageSite database table.
          */
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         LocalDataAccessPath,
         /**
          * The algorithm used to generate PIDs, randomString (default) or

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java b/src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java
@@ -752,6 +752,7 @@ public enum FileUploadMethods {
          * DCM stands for Data Capture Module. Right now it supports upload over
          * rsync+ssh but DCM may support additional methods in the future.
          */
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         RSYNC("dcm/rsync+ssh"),
         /**
          * Traditional Dataverse file handling, which tends to involve users
@@ -809,6 +810,7 @@ public enum FileDownloadMethods {
          * RSAL stands for Repository Storage Abstraction Layer. Downloads don't
          * go through Glassfish.
          */
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         RSYNC("rsal/rsync"),
         NATIVE("native/http"),
         GLOBUS("globus")
@@ -862,6 +864,7 @@ public String toString() {
      */
     public enum TransferProtocols {
 
+        @Deprecated(forRemoval = true, since = "2024-07-07")
         RSYNC("rsync"),
         /**
          * POSIX includes NFS. This is related to Key.LocalDataAccessPath in
@@ -893,12 +896,14 @@ public String toString() {
         }
 
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isPublicInstall(){
         boolean saneDefault = false;
         return settingsService.isTrueForKey(SettingsServiceBean.Key.PublicInstall, saneDefault);
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isRsyncUpload(){
         return getMethodAvailable(SystemConfig.FileUploadMethods.RSYNC.toString(), true);
     }
@@ -915,7 +920,8 @@ public boolean isWebloaderUpload(){
     public boolean isHTTPUpload(){       
         return getMethodAvailable(SystemConfig.FileUploadMethods.NATIVE.toString(), true);
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isRsyncOnly(){
         String downloadMethods = settingsService.getValueForKey(SettingsServiceBean.Key.DownloadMethods);
         if(downloadMethods == null){
@@ -931,11 +937,12 @@ public boolean isRsyncOnly(){
            return  Arrays.asList(uploadMethods.toLowerCase().split("\\s*,\\s*")).size() == 1 && uploadMethods.toLowerCase().equals(SystemConfig.FileUploadMethods.RSYNC.toString());
         }
     }
-
+
+    @Deprecated(forRemoval = true, since = "2024-07-07")
     public boolean isRsyncDownload() {
         return getMethodAvailable(SystemConfig.FileUploadMethods.RSYNC.toString(), false);
     }
-    
+
     public boolean isHTTPDownload() {
         return getMethodAvailable(SystemConfig.FileUploadMethods.NATIVE.toString(), false);
     }