Fix replace bug

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

@@ -1873,7 +1873,8 @@ private void handleReplaceFileUpload(FacesEvent event, InputStream inputStream,
 
         if (fileReplacePageHelper.handleNativeFileUpload(inputStream,null,
                                     fileName,
-                                    contentType
+                                    contentType, 
+                                    null
                                 )){
             saveEnabled = true;
 
@@ -1932,11 +1933,13 @@ the uploadFinished() method, triggered next, after the upload event
 
     private void handleReplaceFileUpload(String fullStorageLocation, 
     		String fileName, 
-    		String contentType){
+    		String contentType, 
+    		String checkSum){
 
     	fileReplacePageHelper.resetReplaceFileHelper();
     	saveEnabled = false;
-    	if (fileReplacePageHelper.handleNativeFileUpload(null, fullStorageLocation, fileName, contentType)){
+    	String storageIdentifier = DataAccess.getStorarageIdFromLocation(fullStorageLocation);
+    	if (fileReplacePageHelper.handleNativeFileUpload(null, storageIdentifier, fileName, contentType, checkSum)){
     		saveEnabled = true;
 
     		/**
@@ -2069,6 +2072,16 @@ public void handleExternalUpload() {
     		//get file size
     		long fileSize = sio.getSize();
 
+			if(StringUtils.isEmpty(contentType)) {
+				contentType = FileUtil.MIME_TYPE_UNDETERMINED_DEFAULT;
+			}
+
+			if(DataFile.ChecksumType.fromString(checksumType) != DataFile.ChecksumType.MD5 ) {
+				String warningMessage = "Non-MD5 checksums not yet supported in external uploads";
+				localWarningMessage = warningMessage;
+				//ToDo - methods like handleReplaceFileUpload and classes like OptionalFileParams will need to track the algorithm in addition to the value to enable this
+			}
+
     		/* ----------------------------
                 Check file size
                 - Max size NOT specified in db: default is unlimited
@@ -2083,7 +2096,7 @@ public void handleExternalUpload() {
     			// Is this a FileReplaceOperation?  If so, then diverge!
     			// -----------------------------------------------------------
     			if (this.isFileReplaceOperation()){
-    				this.handleReplaceFileUpload(storageLocation, fileName, FileUtil.MIME_TYPE_UNDETERMINED_DEFAULT);
+    				this.handleReplaceFileUpload(storageLocation, fileName, contentType, checksumValue);
     				this.setFileMetadataSelectedForTagsPopup(fileReplacePageHelper.getNewFileMetadatasBeforeSave().get(0));
     				return;
     			}
@@ -2099,13 +2112,8 @@ public void handleExternalUpload() {
     				// for example, multiple files can be extracted from an uncompressed
     				// zip file.
     				//datafiles = ingestService.createDataFiles(workingVersion, dropBoxStream, fileName, "application/octet-stream");
-    				if(StringUtils.isEmpty(contentType)) {
-    					contentType = "application/octet-stream";
-    				}
-    				if(DataFile.ChecksumType.fromString(checksumType) != DataFile.ChecksumType.MD5 ) {
-    					String warningMessage = "Non-MD5 checksums not yet supported in external uploads";
-    					localWarningMessage = warningMessage;
-    				}
+
+
     				datafiles = FileUtil.createDataFiles(workingVersion, null, fileName, contentType, fullStorageIdentifier, checksumValue, systemConfig);
     			} catch (IOException ex) {
     				logger.log(Level.SEVERE, "Error during ingest of file {0}", new Object[]{fileName});

src/main/java/edu/harvard/iq/dataverse/dataaccess/DataAccess.java

@@ -122,6 +122,11 @@ public static String[] getDriverIdAndStorageLocation(String storageLocation) {
     }
 
     public static String getStorarageIdFromLocation(String location) {
+    	if(location.contains("://")) {
+    		//It's a full location with a driverId, so strip and reapply the driver id
+    		//NOte that this will strip the bucketname out (which s3 uses) but the S3IOStorage class knows to look at re-insert it
+    		return location.substring(0,location.indexOf("://") +3) + location.substring(location.lastIndexOf('/')+1); 
+    	}
     	return location.substring(location.lastIndexOf('/')+1);
     }
 

src/main/java/edu/harvard/iq/dataverse/dataaccess/S3AccessIO.java

@@ -165,7 +165,36 @@ public void open(DataAccessOption... options) throws IOException {
             if (storageIdentifier == null || "".equals(storageIdentifier)) {
                 throw new FileNotFoundException("Data Access: No local storage identifier defined for this datafile.");
             }
+
+
+            //Fix new DataFiles: DataFiles that have not yet been saved may use this method when they don't have their storageidentifier in the final <driverId>://<bucketname>:<id> form
+            // So we fix it up here. ToDo: refactor so that storageidentifier is generated by the appropriate StorageIO class and is final from the start.
+            String newStorageIdentifier = null;
+            if (storageIdentifier.startsWith(this.driverId + "://")) {
+            	if(!storageIdentifier.substring((this.driverId + "://").length()).contains(":")) {
+            		//Driver id but no bucket
+            		if(bucketName!=null) {
+            			newStorageIdentifier=this.driverId + "://" + bucketName + ":" + storageIdentifier.substring((this.driverId + "://").length()); 
+            		} else {
+            			throw new IOException("S3AccessIO: DataFile (storage identifier " + storageIdentifier + ") is not associated with a bucket.");
+            		}
+            	} // else we're OK (assumes bucket name in storageidentifier matches the driver's bucketname)
+            } else {
+            	if(!storageIdentifier.substring((this.driverId + "://").length()).contains(":")) {
+            		//No driver id or bucket 
+            		newStorageIdentifier= this.driverId + "://" + bucketName + ":" + storageIdentifier;
+            	} else {
+            		//Just the bucketname
+            		newStorageIdentifier= this.driverId + "://" + storageIdentifier;
+            	}
+            }
+            if(newStorageIdentifier != null) {
+        		//Fixup needed:
+        		storageIdentifier = newStorageIdentifier;
+        		dvObject.setStorageIdentifier(newStorageIdentifier);
+        	}
 
+
             if (isReadAccess) {
                 key = getMainFileKey();
                 ObjectMetadata objectMetadata = null; 
@@ -189,14 +218,7 @@ public void open(DataAccessOption... options) throws IOException {
 
             } else if (isWriteAccess) {
                 key = dataFile.getOwner().getAuthorityForFileStorage() + "/" + this.getDataFile().getOwner().getIdentifierForFileStorage();
-
-                if (storageIdentifier.startsWith(this.driverId + "://")) {
-                    key += "/" + storageIdentifier.substring(storageIdentifier.lastIndexOf(":") + 1);
-                } else {
-                    key += "/" + storageIdentifier;
-                    dvObject.setStorageIdentifier(this.driverId + "://" + bucketName + ":" + storageIdentifier);
-                }
-
+                key += "/" + storageIdentifier.substring(storageIdentifier.lastIndexOf(":") + 1);
             }
 
             this.setMimeType(dataFile.getContentType());
@@ -784,7 +806,7 @@ String getMainFileKey() throws IOException {
 
             if (storageIdentifier.startsWith(this.driverId + "://")) {
                 bucketName = storageIdentifier.substring((this.driverId + "://").length(), storageIdentifier.lastIndexOf(":"));
-                key = baseKey + "/" + storageIdentifier.substring(storageIdentifier.lastIndexOf(":") + 1);
+            	key = baseKey + "/" + storageIdentifier.substring(storageIdentifier.lastIndexOf(":") + 1);	
             } else {
                 throw new IOException("S3AccessIO: DataFile (storage identifier " + storageIdentifier + ") does not appear to be an S3 object.");
             }

src/main/java/edu/harvard/iq/dataverse/datasetutility/AddReplaceFileHelper.java

@@ -502,10 +502,12 @@ private boolean runAddReplacePhase1(Dataset dataset,
             return false;
 
         }
-
-        if(optionalFileParams.hasCheckSum()) {
-        	newCheckSum = optionalFileParams.getCheckSum();
+        if(optionalFileParams != null) {
+        	if(optionalFileParams.hasCheckSum()) {
+        		newCheckSum = optionalFileParams.getCheckSum();
+        	}
         }
+
         msgt("step_030_createNewFilesViaIngest");
         if (!this.step_030_createNewFilesViaIngest()){
             return false;
@@ -950,9 +952,7 @@ private boolean step_020_loadNewFile(String fileName, String fileContentType, St
 			if (storageIdentifier == null) {
 				this.addErrorSevere(getBundleErr("file_upload_failed"));
 				return false;
-			} else { 
-				newStorageIdentifier = storageIdentifier;
-			}	
+			} 
 		} 
 
         newFileName = fileName;

src/main/java/edu/harvard/iq/dataverse/datasetutility/FileReplacePageHelper.java

@@ -94,9 +94,10 @@ public boolean resetReplaceFileHelper(){
 
     /**
      * Handle native file replace
+     * @param checkSum 
      * @param event 
      */
-    public boolean handleNativeFileUpload(InputStream inputStream, String fullStorageId, String fileName, String fileContentType) {
+    public boolean handleNativeFileUpload(InputStream inputStream, String fullStorageId, String fileName, String fileContentType, String checkSum) {
 
         phase1Success = false;
 
@@ -111,15 +112,25 @@ public boolean handleNativeFileUpload(InputStream inputStream, String fullStorag
         if (fileContentType == null){
             throw new NullPointerException("fileContentType cannot be null");
         }
-
+
+        OptionalFileParams ofp = null;
+        if(checkSum != null) {
+        	try {
+				ofp = new OptionalFileParams(null);
+			} catch (DataFileTagException e) {
+				//Shouldn't happen with null input
+				e.printStackTrace();
+			}
+        	ofp.setCheckSum(checkSum);
+        }
         // Run 1st phase of replace
         //
         replaceFileHelper.runReplaceFromUI_Phase1(fileToReplace.getId(),
                 fileName,
                 fileContentType,
                 inputStream,
                 fullStorageId,
-                null
+                ofp
         );
 
         // Did it work?

src/main/java/edu/harvard/iq/dataverse/datasetutility/OptionalFileParams.java

@@ -217,6 +217,10 @@ public String getMimeType() {
 		return mimeType;
 	}
 
+	public void setCheckSum(String checkSum) {
+		this.checkSum = checkSum;
+	}
+
 	public boolean hasCheckSum() {
 		return ((checkSum!=null)&&(!checkSum.isEmpty()));
 	}

src/main/webapp/resources/js/fileupload.js

@@ -24,12 +24,14 @@ function setupDirectUpload(enabled, theDatasetId) {
     $('.ui-fileupload-cancel').hide();
     //Catch files entered via upload dialog box. Since this 'select' widget is replaced by PF, we need to add a listener again when it is replaced
     var fileInput=document.getElementById('datasetForm:fileUpload_input');
-    fileInput.addEventListener('change', function(event) {
+    if(fileInput !==null) {
+      fileInput.addEventListener('change', function(event) {
         fileList=[];
         for(var i=0;i<fileInput.files.length;i++) {
           queueFileForDirectUpload(fileInput.files[i], datasetId);
         }
       }, {once:false});
+    }  
     //Add support for drag and drop. Since the fileUploadForm is not replaced by PF, catching changes with a mutationobserver isn't needed
     var fileDropWidget=document.getElementById('datasetForm:fileUpload');
     fileDropWidget.addEventListener('drop', function(event) {