Merge branch 'main' into D4CRIS-960

.github/workflows/label_merge_conflicts.yml

@@ -0,0 +1,25 @@
+# This workflow checks open PRs for merge conflicts and labels them when conflicts are found
+name: Check for merge conflicts
+
+# Run whenever the "main" branch is updated
+# NOTE: This means merge conflicts are only checked for when a PR is merged to main.
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  triage:
+    runs-on: ubuntu-latest
+    steps:
+      # See: https://github.com/mschilde/auto-label-merge-conflicts/
+      - name: Auto-label PRs with merge conflicts
+        uses: mschilde/auto-label-merge-conflicts@v2.0
+        # Add "merge conflict" label if a merge conflict is detected. Remove it when resolved.
+        # Note, the authentication token is created automatically
+        # See: https://docs.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token
+        with:
+          CONFLICT_LABEL_NAME: 'merge conflict'
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        # Ignore errors
+        continue-on-error: true

dspace-api/pom.xml

@@ -325,6 +325,14 @@
             <artifactId>apache-jena-libs</artifactId>
             <type>pom</type>
         </dependency>
+        <!-- Required to support PubMed API call in "PubmedImportMetadataSourceServiceImpl.GetRecord" -->
+        <!-- Makes runtime operations in Jersey Dependency Injection -->
+        <dependency>
+            <groupId>org.glassfish.jersey.inject</groupId>
+            <artifactId>jersey-hk2</artifactId>
+            <version>${jersey.version}</version>
+        </dependency>
+
         <dependency>
             <groupId>commons-cli</groupId>
             <artifactId>commons-cli</artifactId>

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExport.java

@@ -10,10 +10,14 @@
 import java.sql.SQLException;
 
 import org.apache.commons.cli.ParseException;
+import org.apache.commons.lang3.StringUtils;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataDSpaceCsvExportService;
 import org.dspace.core.Context;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
+import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.scripts.DSpaceRunnable;
 import org.dspace.utils.DSpace;
 
@@ -41,8 +45,7 @@ public class MetadataExport extends DSpaceRunnable<MetadataExportScriptConfigura
     public void internalRun() throws Exception {
 
         if (help) {
-            handler.logInfo("\nfull export: metadata-export -f filename");
-            handler.logInfo("partial export: metadata-export -i handle -f filename");
+            logHelpInfo();
             printHelp();
             return;
         }
@@ -61,6 +64,11 @@ public void internalRun() throws Exception {
         context.complete();
     }
 
+    protected void logHelpInfo() {
+        handler.logInfo("\nfull export: metadata-export");
+        handler.logInfo("partial export: metadata-export -i handle");
+    }
+
     @Override
     public MetadataExportScriptConfiguration getScriptConfiguration() {
         return new DSpace().getServiceManager().getServiceByName("metadata-export",
@@ -75,17 +83,32 @@ public void setup() throws ParseException {
             return;
         }
 
-        // Check a filename is given
-        if (!commandLine.hasOption('f')) {
-            throw new ParseException("Required parameter -f missing!");
+        if (!commandLine.hasOption('i')) {
+            exportAllItems = true;
         }
-        filename = commandLine.getOptionValue('f');
+        handle = commandLine.getOptionValue('i');
+        filename = getFileNameForExportFile();
 
         exportAllMetadata = commandLine.hasOption('a');
 
-        if (!commandLine.hasOption('i')) {
-            exportAllItems = true;
+    }
+
+    protected String getFileNameForExportFile() throws ParseException {
+        Context context = new Context();
+        try {
+            DSpaceObject dso = null;
+            if (StringUtils.isNotBlank(handle)) {
+                dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, handle);
+            } else {
+                dso = ContentServiceFactory.getInstance().getSiteService().findSite(context);
+            }
+            if (dso == null) {
+                throw new ParseException("A handle got given that wasn't able to be parsed to a DSpaceObject");
+            }
+            return dso.getID().toString() + ".csv";
+        } catch (SQLException e) {
+            handler.handleException("Something went wrong trying to retrieve DSO for handle: " + handle, e);
         }
-        handle = commandLine.getOptionValue('i');
+        return null;
     }
 }

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportCli.java

@@ -0,0 +1,33 @@
+/**
+ * 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.bulkedit;
+
+import org.apache.commons.cli.ParseException;
+
+public class MetadataExportCli extends MetadataExport {
+
+    @Override
+    protected String getFileNameForExportFile() {
+        return commandLine.getOptionValue('f');
+    }
+
+    @Override
+    public void setup() throws ParseException {
+        super.setup();
+        // Check a filename is given
+        if (!commandLine.hasOption('f')) {
+            throw new ParseException("Required parameter -f missing!");
+        }
+    }
+
+    @Override
+    protected void logHelpInfo() {
+        handler.logInfo("\nfull export: metadata-export -f filename");
+        handler.logInfo("partial export: metadata-export -i handle -f filename");
+    }
+}

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportCliScriptConfiguration.java

@@ -0,0 +1,26 @@
+/**
+ * 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.bulkedit;
+
+import java.io.OutputStream;
+
+import org.apache.commons.cli.Options;
+
+public class MetadataExportCliScriptConfiguration extends MetadataExportScriptConfiguration<MetadataExportCli> {
+
+
+    @Override
+    public Options getOptions() {
+        Options options = super.getOptions();
+        options.addOption("f", "file", true, "destination where you want file written");
+        options.getOption("f").setType(OutputStream .class);
+        options.getOption("f").setRequired(true);
+        super.options = options;
+        return options;
+    }
+}

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportScriptConfiguration.java

@@ -7,7 +7,6 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.OutputStream;
 import java.sql.SQLException;
 
 import org.apache.commons.cli.Options;
@@ -56,9 +55,6 @@ public Options getOptions() {
 
             options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
             options.getOption("i").setType(String.class);
-            options.addOption("f", "file", true, "destination where you want file written");
-            options.getOption("f").setType(OutputStream.class);
-            options.getOption("f").setRequired(true);
             options.addOption("a", "all", false,
                               "include all metadata fields that are not normally changed (e.g. provenance)");
             options.getOption("a").setType(boolean.class);

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java

@@ -182,24 +182,7 @@ public void internalRun() throws Exception {
         c.turnOffAuthorisationSystem();
 
         // Find the EPerson, assign to context
-        try {
-            if (commandLine.hasOption('e')) {
-                EPerson eperson;
-                String e = commandLine.getOptionValue('e');
-                if (e.indexOf('@') != -1) {
-                    eperson = EPersonServiceFactory.getInstance().getEPersonService().findByEmail(c, e);
-                } else {
-                    eperson = EPersonServiceFactory.getInstance().getEPersonService().find(c, UUID.fromString(e));
-                }
-
-                if (eperson == null) {
-                    throw new ParseException("Error, eperson cannot be found: " + e);
-                }
-                c.setCurrentUser(eperson);
-            }
-        } catch (Exception e) {
-            throw new ParseException("Unable to find DSpace user: " + e.getMessage());
-        }
+        assignCurrentUserInContext(c);
 
         if (authorityControlled == null) {
             setAuthorizedMetadataFields();
@@ -277,6 +260,18 @@ public void internalRun() throws Exception {
 
     }
 
+    protected void assignCurrentUserInContext(Context context) throws ParseException {
+        UUID uuid = getEpersonIdentifier();
+        if (uuid != null) {
+            try {
+                EPerson ePerson = EPersonServiceFactory.getInstance().getEPersonService().find(context, uuid);
+                context.setCurrentUser(ePerson);
+            } catch (SQLException e) {
+                log.error("Something went wrong trying to fetch the eperson for uuid: " + uuid, e);
+            }
+        }
+    }
+
     /**
      * This method determines whether the changes should be applied or not. This is default set to true for the REST
      * script as we don't want to interact with the caller. This will be overwritten in the CLI script to ask for
@@ -312,9 +307,6 @@ public void setup() throws ParseException {
             throw new ParseException("Required parameter -f missing!");
         }
         filename = commandLine.getOptionValue('f');
-        if (!commandLine.hasOption('e')) {
-            throw new ParseException("Required parameter -e missing!");
-        }
 
         // Option to apply template to new items
         if (commandLine.hasOption('t')) {

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportCLI.java

@@ -10,7 +10,12 @@
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.util.UUID;
 
+import org.apache.commons.cli.ParseException;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.scripts.handler.DSpaceRunnableHandler;
 
 /**
@@ -30,4 +35,34 @@ protected boolean determineChange(DSpaceRunnableHandler handler) throws IOExcept
             return false;
         }
     }
+
+    @Override
+    protected void assignCurrentUserInContext(Context context) throws ParseException {
+        try {
+            if (commandLine.hasOption('e')) {
+                EPerson eperson;
+                String e = commandLine.getOptionValue('e');
+                if (e.indexOf('@') != -1) {
+                    eperson = EPersonServiceFactory.getInstance().getEPersonService().findByEmail(context, e);
+                } else {
+                    eperson = EPersonServiceFactory.getInstance().getEPersonService().find(context, UUID.fromString(e));
+                }
+
+                if (eperson == null) {
+                    throw new ParseException("Error, eperson cannot be found: " + e);
+                }
+                context.setCurrentUser(eperson);
+            }
+        } catch (Exception e) {
+            throw new ParseException("Unable to find DSpace user: " + e.getMessage());
+        }
+    }
+
+    @Override
+    public void setup() throws ParseException {
+        super.setup();
+        if (!commandLine.hasOption('e')) {
+            throw new ParseException("Required parameter -e missing!");
+        }
+    }
 }

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportCliScriptConfiguration.java

@@ -7,10 +7,21 @@
  */
 package org.dspace.app.bulkedit;
 
+import org.apache.commons.cli.Options;
 import org.dspace.scripts.configuration.ScriptConfiguration;
 
 /**
  * The {@link ScriptConfiguration} for the {@link org.dspace.app.bulkedit.MetadataImportCLI} CLI script
  */
 public class MetadataImportCliScriptConfiguration extends MetadataImportScriptConfiguration<MetadataImportCLI> {
+
+    @Override
+    public Options getOptions() {
+        Options options = super.getOptions();
+        options.addOption("e", "email", true, "email address or user id of user (required if adding new items)");
+        options.getOption("e").setType(String.class);
+        options.getOption("e").setRequired(true);
+        super.options = options;
+        return options;
+    }
 }

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportScriptConfiguration.java

@@ -57,9 +57,6 @@ public Options getOptions() {
             options.addOption("f", "file", true, "source file");
             options.getOption("f").setType(InputStream.class);
             options.getOption("f").setRequired(true);
-            options.addOption("e", "email", true, "email address or user id of user (required if adding new items)");
-            options.getOption("e").setType(String.class);
-            options.getOption("e").setRequired(true);
             options.addOption("s", "silent", false,
                               "silent operation - doesn't request confirmation of changes USE WITH CAUTION");
             options.getOption("s").setType(boolean.class);