coar-notify-7 merge conflicts fixes, ldn configuration fixes

dspace-server-webapp/src/main/java/org/dspace/app/rest/WebApplication.java

@@ -70,11 +70,17 @@ public void generateSitemap() throws IOException, SQLException {
 
     @Scheduled(cron = "${ldn.queue.extractor.cron:-}")
     public void ldnExtractFromQueue() throws IOException, SQLException {
+        if (!configuration.getLdnEnabled()) {
+            return;
+        }
         LDNQueueExtractor.extractMessageFromQueue();
     }
 
     @Scheduled(cron = "${ldn.queue.timeout.checker.cron:-}")
     public void ldnQueueTimeoutCheck() throws IOException, SQLException {
+        if (!configuration.getLdnEnabled()) {
+            return;
+        }
         LDNQueueTimeoutChecker.checkQueueMessageTimeout();
     }
 

dspace-server-webapp/src/main/java/org/dspace/app/rest/model/step/DataUpload.java

@@ -9,6 +9,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.UUID;
 
 import com.fasterxml.jackson.annotation.JsonUnwrapped;
 
@@ -19,6 +20,11 @@
  */
 public class DataUpload implements SectionData {
 
+    /*
+     * primary bitstream uuid
+     */
+    private UUID primary;
+
     @JsonUnwrapped
     private List<UploadBitstreamRest> files;
 
@@ -32,4 +38,13 @@ public List<UploadBitstreamRest> getFiles() {
     public void setFiles(List<UploadBitstreamRest> files) {
         this.files = files;
     }
+
+    public UUID getPrimary() {
+        return primary;
+    }
+
+    public void setPrimary(UUID primary) {
+        this.primary = primary;
+    }
+
 }

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/DataProcessingStep.java

@@ -39,6 +39,7 @@ public interface DataProcessingStep extends RestProcessingStep {
     public static final String ACCESS_CONDITION_STEP_OPERATION_ENTRY = "discoverable";
     public static final String ACCESS_CONDITION_POLICY_STEP_OPERATION_ENTRY = "accessConditions";
     public static final String SHOW_IDENTIFIERS_ENTRY = "identifiers";
+    public static final String PRIMARY_FLAG_ENTRY = "primary";
 
     public static final String UPLOAD_STEP_METADATA_PATH = "metadata";
     public static final String COARNOTIFY_STEP_PATH = "coarnotify";

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/factory/impl/BitstreamMetadataValueAddPatchOperation.java

@@ -53,7 +53,7 @@ void add(Context context, HttpServletRequest currentRequest, InProgressSubmissio
         bitstreamMetadataValuePathUtils.validate(absolutePath);
         Item item = source.getItem();
         List<Bundle> bundle = itemService.getBundles(item, Constants.CONTENT_BUNDLE_NAME);
-        ;
+
         for (Bundle bb : bundle) {
             int idx = 0;
             for (Bitstream b : bb.getBitstreams()) {

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/factory/impl/PrimaryBitstreamAddPatchOperation.java

@@ -0,0 +1,87 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.rest.submit.factory.impl;
+
+import static org.dspace.core.Constants.CONTENT_BUNDLE_NAME;
+
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.UUID;
+import javax.servlet.http.HttpServletRequest;
+
+import org.dspace.app.rest.exception.UnprocessableEntityException;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.InProgressSubmission;
+import org.dspace.content.Item;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Submission "add" operation to set primary bitstream.
+ *
+ * @author Mykhaylo Boychuk ([email protected])
+ */
+public class PrimaryBitstreamAddPatchOperation extends AddPatchOperation<String> {
+
+    @Autowired
+    private ItemService itemService;
+
+    @Override
+    void add(Context context, HttpServletRequest currentRequest, InProgressSubmission source, String path, Object value)
+        throws Exception {
+        Item item = source.getItem();
+        UUID primaryUUID = parseValue(value);
+        List<Bundle> bundles = itemService.getBundles(item, CONTENT_BUNDLE_NAME);
+        Optional<Bundle> currentPrimaryBundle = bundles.stream()
+                                                       .filter(bundle -> Objects.nonNull(bundle.getPrimaryBitstream()))
+                                                       .findFirst();
+
+        Optional<Bitstream> primaryBitstreamToAdd = null;
+        for (Bundle bundle : bundles) {
+            primaryBitstreamToAdd = bundle.getBitstreams().stream()
+                                                          .filter(b -> b.getID().equals(primaryUUID))
+                                                          .findFirst();
+            if (primaryBitstreamToAdd.isPresent()) {
+                if (currentPrimaryBundle.isPresent()) {
+                    currentPrimaryBundle.get().setPrimaryBitstreamID(null);
+                }
+                bundle.setPrimaryBitstreamID(primaryBitstreamToAdd.get());
+                break;
+            }
+        }
+
+        if (primaryBitstreamToAdd.isEmpty()) {
+            throw new UnprocessableEntityException("The provided uuid: " + primaryUUID +
+                                                   " of bitstream to set as primary doesn't match any bitstream!");
+        }
+    }
+
+    private UUID parseValue(Object value) {
+        UUID primaryBitstreamUUID;
+        try {
+            primaryBitstreamUUID = UUID.fromString((String) value);
+        } catch (Exception e) {
+            throw new UnprocessableEntityException("The provided value is invalid!", e);
+        }
+        return primaryBitstreamUUID;
+    }
+
+    @Override
+    protected Class<String[]> getArrayClassForEvaluation() {
+        return null;
+    }
+
+    @Override
+    protected Class<String> getClassForEvaluation() {
+        return null;
+    }
+
+}

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/factory/impl/PrimaryBitstreamRemovePatchOperation.java

@@ -0,0 +1,50 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.rest.submit.factory.impl;
+
+import static org.dspace.core.Constants.CONTENT_BUNDLE_NAME;
+
+import java.util.List;
+import javax.servlet.http.HttpServletRequest;
+
+import org.dspace.content.Bundle;
+import org.dspace.content.InProgressSubmission;
+import org.dspace.content.Item;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Submission "remove" operation to remove primary bitstream.
+ *
+ * @author Mykhaylo Boychuk ([email protected])
+ */
+public class PrimaryBitstreamRemovePatchOperation extends RemovePatchOperation<String> {
+
+    @Autowired
+    private ItemService itemService;
+
+    @Override
+    void remove(Context context, HttpServletRequest request, InProgressSubmission source, String path, Object value)
+         throws Exception {
+        Item item = source.getItem();
+        List<Bundle> bundles = itemService.getBundles(item, CONTENT_BUNDLE_NAME);
+        bundles.forEach(b -> b.setPrimaryBitstreamID(null));
+    }
+
+    @Override
+    protected Class<String[]> getArrayClassForEvaluation() {
+        return null;
+    }
+
+    @Override
+    protected Class<String> getClassForEvaluation() {
+        return null;
+    }
+
+}

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/factory/impl/PrimaryBitstreamReplacePatchOperation.java

@@ -0,0 +1,88 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.rest.submit.factory.impl;
+
+import static org.dspace.core.Constants.CONTENT_BUNDLE_NAME;
+
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.UUID;
+import javax.servlet.http.HttpServletRequest;
+
+import org.dspace.app.rest.exception.UnprocessableEntityException;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.InProgressSubmission;
+import org.dspace.content.Item;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Submission "replace" operation to replace primary bitstream.
+ *
+ * @author Mykhaylo Boychuk ([email protected])
+ */
+public class PrimaryBitstreamReplacePatchOperation extends ReplacePatchOperation<String> {
+
+    private final String EX_MESSAGE = "It is impossible to replace primary bitstrem if it wasn't set!";
+
+    @Autowired
+    private ItemService itemService;
+
+    @Override
+    void replace(Context context, HttpServletRequest request, InProgressSubmission source, String path, Object value)
+         throws Exception {
+        Item item = source.getItem();
+        UUID primaryUUID = parseValue(value);
+        List<Bundle> bundles = itemService.getBundles(item, CONTENT_BUNDLE_NAME);
+        Bundle currentPrimaryBundle = bundles.stream()
+                                             .filter(bundle -> Objects.nonNull(bundle.getPrimaryBitstream()))
+                                             .findFirst()
+                                             .orElseThrow(() -> new UnprocessableEntityException(EX_MESSAGE));
+
+        Optional<Bitstream> primaryBitstream = null;
+        for (Bundle bundle : bundles) {
+            primaryBitstream = bundle.getBitstreams().stream()
+                                                     .filter(b -> b.getID().equals(primaryUUID))
+                                                     .findFirst();
+            if (primaryBitstream.isPresent()) {
+                currentPrimaryBundle.setPrimaryBitstreamID(null);
+                bundle.setPrimaryBitstreamID(primaryBitstream.get());
+                break;
+            }
+        }
+
+        if (primaryBitstream.isEmpty()) {
+            throw new UnprocessableEntityException("The provided uuid: " + primaryUUID +
+                                                   " of bitstream to set as primary doesn't match any bitstream!");
+        }
+    }
+
+    private UUID parseValue(Object value) {
+        UUID primaryBitstreamUUID;
+        try {
+            primaryBitstreamUUID = UUID.fromString((String) value);
+        } catch (Exception e) {
+            throw new UnprocessableEntityException("The provided value is invalid!", e);
+        }
+        return primaryBitstreamUUID;
+    }
+
+    @Override
+    protected Class<String[]> getArrayClassForEvaluation() {
+        return null;
+    }
+
+    @Override
+    protected Class<String> getClassForEvaluation() {
+        return null;
+    }
+
+}

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/step/UploadStep.java

@@ -10,8 +10,10 @@
 import java.io.BufferedInputStream;
 import java.io.InputStream;
 import java.util.List;
+import java.util.Objects;
 import javax.servlet.http.HttpServletRequest;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.ErrorRest;
@@ -56,8 +58,12 @@ public DataUpload getData(SubmissionService submissionService, InProgressSubmiss
         List<Bundle> bundles = itemService.getBundles(obj.getItem(), Constants.CONTENT_BUNDLE_NAME);
         for (Bundle bundle : bundles) {
             for (Bitstream source : bundle.getBitstreams()) {
+                Bitstream primaryBitstream = bundle.getPrimaryBitstream();
                 UploadBitstreamRest b = submissionService.buildUploadBitstream(configurationService, source);
                 result.getFiles().add(b);
+                if (Objects.nonNull(primaryBitstream)) {
+                    result.setPrimary(primaryBitstream.getID());
+                }
             }
         }
         return result;
@@ -73,6 +79,8 @@ public void doPatchProcessing(Context context, HttpServletRequest currentRequest
                 instance = UPLOAD_STEP_METADATA_OPERATION_ENTRY;
             } else if (op.getPath().contains(UPLOAD_STEP_ACCESSCONDITIONS_OPERATION_ENTRY)) {
                 instance = stepConf.getType() + "." + UPLOAD_STEP_ACCESSCONDITIONS_OPERATION_ENTRY;
+            } else if (op.getPath().contains(PRIMARY_FLAG_ENTRY)) {
+                instance = PRIMARY_FLAG_ENTRY;
             } else {
                 instance = UPLOAD_STEP_REMOVE_OPERATION_ENTRY;
             }
@@ -87,9 +95,11 @@ public void doPatchProcessing(Context context, HttpServletRequest currentRequest
                 instance = stepConf.getType() + "." + UPLOAD_STEP_ACCESSCONDITIONS_OPERATION_ENTRY;
             } else if (op.getPath().contains(UPLOAD_STEP_METADATA_PATH)) {
                 instance = UPLOAD_STEP_METADATA_OPERATION_ENTRY;
+            } else if (op.getPath().contains(PRIMARY_FLAG_ENTRY)) {
+                instance = PRIMARY_FLAG_ENTRY;
             }
         }
-        if (instance == null) {
+        if (StringUtils.isBlank(instance)) {
             throw new UnprocessableEntityException("The path " + op.getPath() + " is not supported by the operation "
                                                                               + op.getOp());
         }

dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/ApplicationConfig.java

@@ -72,6 +72,10 @@ public class ApplicationConfig {
     @Value("${dspace.ui.url:http://localhost:4000}")
     private String uiURL;
 
+    // LDN enable status
+    @Value("ldn.enabled")
+    private boolean ldnEnabled;
+
     /**
      * Return the array of allowed origins (client URLs) for the CORS "Access-Control-Allow-Origin" header
      * Used by Application class
@@ -130,6 +134,14 @@ public boolean getCorsAllowCredentials() {
         return corsAllowCredentials;
     }
 
+    /**
+     * Return the ldn.enabled value
+     * @return true or false
+     */
+    public boolean getLdnEnabled() {
+        return this.ldnEnabled;
+    }
+
     /**
      * Return whether to allow credentials (cookies) on IIIF requests. This is used to set the
      * CORS "Access-Control-Allow-Credentials" header in Application class. Defaults to false.