Merged dspace-cris-2023_02_x into task/dspace-cris-2023_02_x/LM-46

4Science · Sep 20, 2024 · 020268d · 020268d
2 parents ee5b3d5 + 1cc8aed
commit 020268d
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -64,9 +64,9 @@ jobs:
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-maven-
 
-      - name: Install Grobid (only IT)
-        run:  ./dspace-api/src/test/data/dspaceFolder/bin/install_grobid.sh
-        if: matrix.type == 'Integration Tests'
+      #- name: Install Grobid (only IT)
+      #  run:  ./dspace-api/src/test/data/dspaceFolder/bin/install_grobid.sh
+      #  if: matrix.type == 'Integration Tests'
 
       # Run parallel Maven builds based on the above 'strategy.matrix'
       - name: Run Maven ${{ matrix.type }}

diff --git a/bitbucket-pipelines.yml b/bitbucket-pipelines.yml
@@ -45,7 +45,7 @@ definitions:
           - maven
         script:
           - export MAVEN_OPTS="-Xmx4096M"
-          - ./dspace-api/src/test/data/dspaceFolder/bin/install_grobid.sh
+          #- ./dspace-api/src/test/data/dspaceFolder/bin/install_grobid.sh
           - mvn clean install -DskipUnitTests=true -Pdspace-rest -DskipITs=true -DskipIntegrationTests=true -P !assembly -B -V
           - mvn test -pl dspace-iiif,dspace-oai,dspace-rdf,dspace-rest,dspace-server-webapp,dspace-services,dspace-sword,dspace-swordv2 -Dmaven.test.skip=false -DskipUnitTests=false -Pdspace-rest -DskipITs=false -Pdspace-rest -DskipIntegrationTests=false -B -V -Dsurefire.rerunFailingTestsCount=2 -Dtest.argLine=-Xmx4096M -DfailIfNoTests=false -Dtest=*IT,!Abstract*,!ItemImportIT,!GenericAuthorizationFeatureIT,!ItemRestRepositoryIT,!LeftTiltedRelationshipRestRepositoryIT,!RelationshipRestRepositoryIT,!StatisticsRestRepositoryIT,!WorkspaceItemRestRepositoryIT,!DiscoveryRestControllerIT,!PatchMetadataIT,!RightTiltedRelationshipRestRepositoryIT
         artifacts:
@@ -76,7 +76,7 @@ definitions:
           - maven
         script:
           - export MAVEN_OPTS="-Xmx4096M"
-          - ./dspace-api/src/test/data/dspaceFolder/bin/install_grobid.sh
+          #- ./dspace-api/src/test/data/dspaceFolder/bin/install_grobid.sh
           - mvn clean install -DskipUnitTests=true -Pdspace-rest -DskipITs=true -DskipIntegrationTests=true -P !assembly -B -V
           - mvn test -Dmaven.test.skip=false -DskipUnitTests=false -Pdspace-rest -DskipITs=false -Pdspace-rest -DskipIntegrationTests=false -B -V -Dsurefire.rerunFailingTestsCount=2 -Dtest.argLine=-Xmx4096M -DfailIfNoTests=false -Dtest=ItemImportIT,GenericAuthorizationFeatureIT,ItemRestRepositoryIT,LeftTiltedRelationshipRestRepositoryIT,RelationshipRestRepositoryIT,StatisticsRestRepositoryIT,WorkspaceItemRestRepositoryIT,DiscoveryRestControllerIT,PatchMetadataIT,RightTiltedRelationshipRestRepositoryIT
         artifacts:

diff --git a/dspace-api/src/main/java/org/dspace/administer/ProcessCleaner.java b/dspace-api/src/main/java/org/dspace/administer/ProcessCleaner.java
@@ -12,12 +12,15 @@
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
+import java.util.UUID;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang.time.DateUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.ProcessStatus;
 import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.scripts.DSpaceRunnable;
 import org.dspace.scripts.Process;
 import org.dspace.scripts.factory.ScriptServiceFactory;
@@ -78,12 +81,14 @@ public void internalRun() throws Exception {
         }
 
         Context context = new Context();
+        assignCurrentUserInContext(context);
+        assignSpecialGroupsInContext(context);
 
         try {
-            context.turnOffAuthorisationSystem();
+            handleAuthorizationSystem(context);
             performDeletion(context);
         } finally {
-            context.restoreAuthSystemState();
+            handleAuthorizationSystem(context);
             context.complete();
         }
 
@@ -137,4 +142,18 @@ public ProcessCleanerConfiguration<ProcessCleaner> getScriptConfiguration() {
             .getServiceByName("process-cleaner", ProcessCleanerConfiguration.class);
     }
 
+    private void assignCurrentUserInContext(Context context) throws SQLException {
+        UUID uuid = getEpersonIdentifier();
+        if (uuid != null) {
+            EPerson ePerson = EPersonServiceFactory.getInstance().getEPersonService().find(context, uuid);
+            context.setCurrentUser(ePerson);
+        }
+    }
+
+    private void assignSpecialGroupsInContext(Context context) throws SQLException {
+        for (UUID uuid : handler.getSpecialGroups()) {
+            context.setSpecialGroup(uuid);
+        }
+    }
+
 }
diff --git a/dspace-api/src/main/java/org/dspace/app/bulkedit/CollectionExport.java b/dspace-api/src/main/java/org/dspace/app/bulkedit/CollectionExport.java
@@ -62,7 +62,7 @@ public void internalRun() throws Exception {
         assignCurrentUserInContext();
         assignSpecialGroupsInContext();
 
-        context.turnOffAuthorisationSystem();
+        handleAuthorizationSystem(context);
 
         Collection collection = getCollection();
         if (collection == null) {
@@ -76,7 +76,7 @@ public void internalRun() throws Exception {
         try {
             performExport(collection);
             context.complete();
-            context.restoreAuthSystemState();
+            handleAuthorizationSystem(context);
         } catch (Exception e) {
             handler.handleException(e);
             context.abort();

diff --git a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExport.java b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExport.java
@@ -7,6 +7,7 @@
  */
 package org.dspace.app.bulkedit;
 
+import java.io.InputStream;
 import java.sql.SQLException;
 import java.util.UUID;
 
@@ -18,6 +19,7 @@
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataDSpaceCsvExportService;
 import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.handle.factory.HandleServiceFactory;
@@ -54,19 +56,31 @@ public void internalRun() throws Exception {
             printHelp();
             return;
         }
+
         Context context = new Context();
-        context.turnOffAuthorisationSystem();
         try {
-            context.setCurrentUser(ePersonService.find(context, this.getEpersonIdentifier()));
+            assignCurrentUserInContext(context);
+            assignSpecialGroupsInContext(context);
         } catch (SQLException e) {
             handler.handleException(e);
         }
-        DSpaceCSV dSpaceCSV = metadataDSpaceCsvExportService
-            .handleExport(context, exportAllItems, exportAllMetadata, identifier,
-                          handler);
-        handler.writeFilestream(context, filename, dSpaceCSV.getInputStream(), EXPORT_CSV);
-        context.restoreAuthSystemState();
-        context.complete();
+
+        handleAuthorizationSystem(context);
+        try {
+            DSpaceCSV dSpaceCSV =
+                metadataDSpaceCsvExportService.handleExport(
+                    context, exportAllItems, exportAllMetadata, identifier, handler
+                );
+            try (InputStream is = dSpaceCSV.getInputStream()) {
+                handler.writeFilestream(context, filename, is, EXPORT_CSV);
+            }
+
+            handleAuthorizationSystem(context);
+            context.complete();
+        } catch (Exception e) {
+            handler.handleException(e);
+            context.abort();
+        }
     }
 
     protected void logHelpInfo() {
@@ -119,4 +133,18 @@ protected String getFileNameForExportFile() throws ParseException {
         }
         return null;
     }
+
+    private void assignCurrentUserInContext(Context context) throws SQLException {
+        UUID uuid = getEpersonIdentifier();
+        if (uuid != null) {
+            EPerson ePerson = EPersonServiceFactory.getInstance().getEPersonService().find(context, uuid);
+            context.setCurrentUser(ePerson);
+        }
+    }
+
+    private void assignSpecialGroupsInContext(Context context) throws SQLException {
+        for (UUID uuid : handler.getSpecialGroups()) {
+            context.setSpecialGroup(uuid);
+        }
+    }
 }
diff --git a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportScriptConfiguration.java b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportScriptConfiguration.java
@@ -7,7 +7,12 @@
  */
 package org.dspace.app.bulkedit;
 
+import java.sql.SQLException;
+import java.util.List;
+
 import org.apache.commons.cli.Options;
+import org.dspace.core.Context;
+import org.dspace.scripts.DSpaceCommandLineParameter;
 import org.dspace.scripts.configuration.ScriptConfiguration;
 
 /**
@@ -17,6 +22,16 @@ public class MetadataExportScriptConfiguration<T extends MetadataExport> extends
 
     private Class<T> dspaceRunnableClass;
 
+    public boolean isAllowedToExecute(Context context, List<DSpaceCommandLineParameter> commandLineParameters) {
+        try {
+            return authorizeService.isAdmin(context) || authorizeService.isComColAdmin(context) ||
+                authorizeService.isItemAdmin(context);
+        } catch (SQLException e) {
+            throw new RuntimeException(
+                "SQLException occurred when checking if the current user is eligible to run the script", e);
+        }
+    }
+
     @Override
     public Class<T> getDspaceRunnableClass() {
         return dspaceRunnableClass;

diff --git a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportSearch.java b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExportSearch.java
@@ -8,6 +8,7 @@
 
 package org.dspace.app.bulkedit;
 
+import java.io.InputStream;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -32,6 +33,7 @@
 import org.dspace.discovery.indexobject.IndexableCommunity;
 import org.dspace.discovery.utils.DiscoverQueryBuilder;
 import org.dspace.discovery.utils.parameter.QueryBuilderSearchFilter;
+import org.dspace.eperson.EPerson;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.scripts.DSpaceRunnable;
@@ -113,7 +115,8 @@ public void internalRun() throws Exception {
 
         IndexableObject dso = null;
         Context context = new Context();
-        context.setCurrentUser(ePersonService.find(context, this.getEpersonIdentifier()));
+        assignCurrentUserInContext(context);
+        assignSpecialGroupsInContext(context);
 
         if (hasScope) {
             dso = resolveScope(context, identifier);
@@ -135,20 +138,28 @@ public void internalRun() throws Exception {
                 queryBuilderSearchFilters.add(queryBuilderSearchFilter);
             }
         }
-        handler.logDebug("building query");
-        DiscoverQuery discoverQuery =
-            queryBuilder.buildQuery(context, dso, discoveryConfiguration, query, queryBuilderSearchFilters,
-            "Item", 10, Long.getLong("0"), null, SortOption.DESCENDING);
-        handler.logDebug("creating iterator");
-
-        Iterator<Item> itemIterator = searchService.iteratorSearch(context, dso, discoverQuery);
-        handler.logDebug("creating dspacecsv");
-        DSpaceCSV dSpaceCSV = metadataDSpaceCsvExportService.export(context, itemIterator, true);
-        handler.logDebug("writing to file " + getFileNameOrExportFile());
-        handler.writeFilestream(context, getFileNameOrExportFile(), dSpaceCSV.getInputStream(), EXPORT_CSV);
-        context.restoreAuthSystemState();
-        context.complete();
+        try {
+            handler.logDebug("building query");
+            DiscoverQuery discoverQuery =
+                queryBuilder.buildQuery(context, dso, discoveryConfiguration, query, queryBuilderSearchFilters,
+                "Item", 10, Long.getLong("0"), null, SortOption.DESCENDING);
+
+            handler.logDebug("creating iterator");
+            Iterator<Item> itemIterator = searchService.iteratorSearch(context, dso, discoverQuery);
+            handler.logDebug("creating dspacecsv");
+            DSpaceCSV dSpaceCSV = metadataDSpaceCsvExportService.export(context, itemIterator, true);
+
+            try (InputStream is = dSpaceCSV.getInputStream()) {
+                handler.logDebug("writing to file " + getFileNameOrExportFile());
+                handler.writeFilestream(context, getFileNameOrExportFile(), is, EXPORT_CSV);
+            }
 
+            handleAuthorizationSystem(context);
+            context.complete();
+        } catch (Exception e) {
+            handler.handleException(e);
+            context.abort();
+        }
     }
 
     protected void loghelpinfo() {
@@ -159,6 +170,21 @@ protected String getFileNameOrExportFile() {
         return "metadataExportSearch.csv";
     }
 
+    private void assignCurrentUserInContext(Context context) throws SQLException {
+        UUID uuid = getEpersonIdentifier();
+        if (uuid != null) {
+            EPerson ePerson = EPersonServiceFactory.getInstance().getEPersonService().find(context, uuid);
+            context.setCurrentUser(ePerson);
+        }
+    }
+
+    private void assignSpecialGroupsInContext(Context context) throws SQLException {
+        for (UUID uuid : handler.getSpecialGroups()) {
+            context.setSpecialGroup(uuid);
+        }
+    }
+
+
     public IndexableObject resolveScope(Context context, String id) throws SQLException {
         UUID uuid = UUID.fromString(id);
         IndexableObject scopeObj = new IndexableCommunity(communityService.find(context, uuid));

diff --git a/...ce-api/src/main/java/org/dspace/app/bulkedit/MetadataExportSearchScriptConfiguration.java b/...ce-api/src/main/java/org/dspace/app/bulkedit/MetadataExportSearchScriptConfiguration.java
@@ -8,7 +8,12 @@
 
 package org.dspace.app.bulkedit;
 
+import java.sql.SQLException;
+import java.util.List;
+
 import org.apache.commons.cli.Options;
+import org.dspace.core.Context;
+import org.dspace.scripts.DSpaceCommandLineParameter;
 import org.dspace.scripts.configuration.ScriptConfiguration;
 
 /**
@@ -18,6 +23,17 @@ public class MetadataExportSearchScriptConfiguration<T extends MetadataExportSea
 
     private Class<T> dspaceRunnableclass;
 
+    @Override
+    public boolean isAllowedToExecute(Context context, List<DSpaceCommandLineParameter> commandLineParameters) {
+        try {
+            return authorizeService.isAdmin(context) || authorizeService.isComColAdmin(context) ||
+                authorizeService.isItemAdmin(context);
+        } catch (SQLException e) {
+            throw new RuntimeException(
+                "SQLException occurred when checking if the current user is eligible to run the script", e);
+        }
+    }
+
     @Override
     public Class<T> getDspaceRunnableClass() {
         return dspaceRunnableclass;

diff --git a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
@@ -182,10 +182,10 @@ public void internalRun() throws Exception {
         // Create a context
         Context c = null;
         c = new Context();
-        c.turnOffAuthorisationSystem();
 
         // Find the EPerson, assign to context
         assignCurrentUserInContext(c);
+        assignSpecialGroupsInContext(c);
 
         // Read commandLines from the CSV file
         try {
@@ -207,6 +207,7 @@ public void internalRun() throws Exception {
         initMetadataImport(csv);
         List<BulkEditChange> changes;
 
+        handleAuthorizationSystem(c);
         if (!commandLine.hasOption('s') || validateOnly) {
             // See what has changed
             try {
@@ -250,7 +251,7 @@ public void internalRun() throws Exception {
             }
 
             // Finsh off and tidy up
-            c.restoreAuthSystemState();
+            handleAuthorizationSystem(c);
             c.complete();
         } catch (Exception e) {
             c.abort();
@@ -272,6 +273,12 @@ protected void assignCurrentUserInContext(Context context) throws ParseException
         }
     }
 
+    private void assignSpecialGroupsInContext(Context context) throws SQLException {
+        for (UUID uuid : handler.getSpecialGroups()) {
+            context.setSpecialGroup(uuid);
+        }
+    }
+
     /**
      * 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

diff --git a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportScriptConfiguration.java b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportScriptConfiguration.java
@@ -8,8 +8,12 @@
 package org.dspace.app.bulkedit;
 
 import java.io.InputStream;
+import java.sql.SQLException;
+import java.util.List;
 
 import org.apache.commons.cli.Options;
+import org.dspace.core.Context;
+import org.dspace.scripts.DSpaceCommandLineParameter;
 import org.dspace.scripts.configuration.ScriptConfiguration;
 
 /**
@@ -19,6 +23,17 @@ public class MetadataImportScriptConfiguration<T extends MetadataImport> extends
 
     private Class<T> dspaceRunnableClass;
 
+    @Override
+    public boolean isAllowedToExecute(Context context, List<DSpaceCommandLineParameter> commandLineParameters) {
+        try {
+            return authorizeService.isAdmin(context) || authorizeService.isComColAdmin(context) ||
+                authorizeService.isItemAdmin(context);
+        } catch (SQLException e) {
+            throw new RuntimeException(
+                "SQLException occurred when checking if the current user is eligible to run the script", e);
+        }
+    }
+
     @Override
     public Class<T> getDspaceRunnableClass() {
         return dspaceRunnableClass;