Fix merge conflicts with "main"

UNC-Libraries · Jan 2, 2024 · 4da2b5d · 4da2b5d
2 parents 96113ec + 2aaa757
commit 4da2b5d
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Showing 41 changed files with 1,051 additions and 761 deletions.
diff --git a/auth-api/src/main/java/edu/unc/lib/boxc/auth/api/services/DatastreamPermissionUtil.java b/auth-api/src/main/java/edu/unc/lib/boxc/auth/api/services/DatastreamPermissionUtil.java
@@ -30,8 +30,8 @@ public class DatastreamPermissionUtil {
         DS_PERMISSION_MAP.put(DatastreamType.ORIGINAL_FILE, Permission.viewOriginal);
         DS_PERMISSION_MAP.put(DatastreamType.TECHNICAL_METADATA, Permission.viewHidden);
         DS_PERMISSION_MAP.put(DatastreamType.TECHNICAL_METADATA_HISTORY, Permission.viewHidden);
-        DS_PERMISSION_MAP.put(DatastreamType.THUMBNAIL_SMALL, Permission.viewMetadata);
-        DS_PERMISSION_MAP.put(DatastreamType.THUMBNAIL_LARGE, Permission.viewMetadata);
+        DS_PERMISSION_MAP.put(DatastreamType.THUMBNAIL_SMALL, Permission.viewAccessCopies);
+        DS_PERMISSION_MAP.put(DatastreamType.THUMBNAIL_LARGE, Permission.viewAccessCopies);
     }
 
     private DatastreamPermissionUtil() {

diff --git a/deposit-app/src/main/java/edu/unc/lib/boxc/deposit/validate/VirusScanJob.java b/deposit-app/src/main/java/edu/unc/lib/boxc/deposit/validate/VirusScanJob.java
@@ -42,6 +42,7 @@ public class VirusScanJob extends AbstractConcurrentDepositJob {
             .getLogger(VirusScanJob.class);
 
     private static final int MAX_RETRIES = 5;
+    private long maxStreamSize;
 
     private ClamAVClient clamClient;
 
@@ -97,18 +98,20 @@ public void runJob() {
                     Path file = Paths.get(fileURI);
 
                     ScanResult result;
-                    // Clamd is unable to find files with unicode characters in their path
-                    if (charactersInBoundsForClam(file)) {
-                        result = clamClient.scanWithResult(file);
-                    } else {
-                        // Scan files with unicode in their paths via streaming
-                        try {
+                    try {
+                        if (shouldScanByPath(file)) {
+                            // Scan entire file by path
+                            log.debug("Scanning file {} by path", file);
+                            result = clamClient.scanWithResult(file);
+                        } else {
+                            // Scanning via InputStream up to the max number of bytes
+                            log.debug("Scanning file {} by stream", file);
                             result = clamClient.scanWithResult(Files.newInputStream(file));
-                        } catch (IOException e) {
-                            failures.put(fileURI.toString(), "Failed to scan file");
-                            log.error("Unable to scan file {}", file, e);
-                            return;
                         }
+                    } catch (IOException e) {
+                        failures.put(fileURI.toString(), "Failed to scan file");
+                        log.error("Unable to scan file {}", file, e);
+                        return;
                     }
 
                     switch (result.getStatus()) {
@@ -180,8 +183,23 @@ private boolean charactersInBoundsForClam(Path path) {
         return CharMatcher.ascii().matchesAllOf(path.toString());
     }
 
+    /**
+     * Determines if we should scan a file by its file path or use streaming. Files larger than the scanning
+     * limit or with characters in their path that clamd can't handle will return false.
+     * @param path
+     * @return
+     * @throws IOException
+     */
+    private boolean shouldScanByPath(Path path) throws IOException {
+        return Files.size(path) < this.maxStreamSize && charactersInBoundsForClam(path);
+    }
+
     // unused, no results to flush
     @Override
     protected void registrationAction() {
     }
-}
+
+    public void setMaxStreamSize(long maxStreamSize) {
+        this.maxStreamSize = maxStreamSize;
+    }
+}
diff --git a/deposit-app/src/main/webapp/WEB-INF/deposit-jobs-context.xml b/deposit-app/src/main/webapp/WEB-INF/deposit-jobs-context.xml
@@ -191,6 +191,7 @@
         <property name="clamClient" ref="clamClient" />
         <property name="maxQueuedJobs" value="${job.fileValidation.maxQueuedJobs:5}" />
         <property name="executorService" ref="fileValidationExecutor" />
+        <property name="maxStreamSize" value="${clamd.maxStreamSize:64000000}" />
     </bean>
 
     <bean id="FixityCheckJob" class="edu.unc.lib.boxc.deposit.validate.FixityCheckJob"

diff --git a/deposit-app/src/test/java/edu/unc/lib/boxc/deposit/validate/VirusScanJobTest.java b/deposit-app/src/test/java/edu/unc/lib/boxc/deposit/validate/VirusScanJobTest.java
@@ -1,44 +1,10 @@
 package edu.unc.lib.boxc.deposit.validate;
 
-import static edu.unc.lib.boxc.common.test.TestHelpers.setField;
-import static org.junit.jupiter.api.Assertions.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyBoolean;
-import static org.mockito.Matchers.anyInt;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Matchers.eq;
-import static org.mockito.Mockito.doReturn;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.never;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
-
-import java.io.File;
-import java.io.InputStream;
-import java.nio.file.Path;
-import java.util.UUID;
-import java.util.concurrent.ExecutorService;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.jena.rdf.model.Bag;
-import org.apache.jena.rdf.model.Model;
-import org.apache.jena.rdf.model.Resource;
-import org.apache.jena.vocabulary.RDF;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import org.mockito.Mock;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-
 import com.google.common.util.concurrent.MoreExecutors;
-
 import edu.unc.lib.boxc.common.util.URIUtil;
 import edu.unc.lib.boxc.deposit.api.RedisWorkerConstants.DepositState;
 import edu.unc.lib.boxc.deposit.fcrepo4.AbstractDepositJobTest;
 import edu.unc.lib.boxc.deposit.impl.model.DepositModelHelpers;
-import edu.unc.lib.boxc.deposit.validate.VirusScanJob;
 import edu.unc.lib.boxc.deposit.work.JobFailedException;
 import edu.unc.lib.boxc.deposit.work.JobInterruptedException;
 import edu.unc.lib.boxc.model.api.exceptions.RepositoryException;
@@ -51,6 +17,37 @@
 import fi.solita.clamav.ClamAVClient;
 import fi.solita.clamav.ScanResult;
 import fi.solita.clamav.ScanResult.Status;
+import org.apache.commons.io.FileUtils;
+import org.apache.jena.rdf.model.Bag;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.vocabulary.RDF;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.mockito.Mock;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+
+import java.io.File;
+import java.io.InputStream;
+import java.nio.file.Path;
+import java.util.UUID;
+import java.util.concurrent.ExecutorService;
+
+import static edu.unc.lib.boxc.common.test.TestHelpers.setField;
+import static org.junit.jupiter.api.Assertions.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyBoolean;
+import static org.mockito.Matchers.anyInt;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.never;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 /**
  *
@@ -92,6 +89,7 @@ public PID answer(InvocationOnMock invocation) throws Throwable {
         });
 
         when(clamClient.scanWithResult(any(Path.class))).thenReturn(scanResult);
+        when(clamClient.scanWithResult(any(InputStream.class))).thenReturn(scanResult);
 
         File examplesFile = new File("src/test/resources/examples");
         FileUtils.copyDirectory(examplesFile, depositDir);
@@ -104,6 +102,7 @@ private void initializeJob() {
         job.setJobUUID(jobUUID);
         job.setDepositUUID(depositUUID);
         job.setDepositDirectory(depositDir);
+        job.setMaxStreamSize(300l);
         setField(job, "pidMinter", pidMinter);
         job.setClamClient(clamClient);
         job.setPremisLoggerFactory(premisLoggerFactory);
@@ -142,7 +141,8 @@ public void passScanTest() throws Exception {
 
         job.run();
 
-        verify(clamClient, times(3)).scanWithResult(any(Path.class));
+        verify(clamClient, times(1)).scanWithResult(any(InputStream.class));
+        verify(clamClient, times(2)).scanWithResult(any(Path.class));
 
         verify(jobStatusFactory).setTotalCompletion(eq(jobUUID), eq(3));
         verify(jobStatusFactory, times(3)).incrCompletion(eq(jobUUID), eq(1));
@@ -189,9 +189,8 @@ public void failOneScanTest() throws Exception {
         when(result2.getStatus()).thenReturn(Status.FOUND);
         File pdfFile = new File(depositDir, "pdf.pdf");
         File textFile = new File(depositDir, "text.txt");
-        when(clamClient.scanWithResult(any(Path.class)))
-                .thenReturn(scanResult)
-                .thenReturn(result2);
+        when(clamClient.scanWithResult(any(InputStream.class))).thenReturn(scanResult);
+        when(clamClient.scanWithResult(any(Path.class))).thenReturn(result2);
 
         Model model = job.getWritableModel();
         Bag depBag = model.createBag(depositPid.getRepositoryPath());

diff --git a/...xing-solr/src/main/java/edu/unc/lib/boxc/indexing/solr/filter/SetContentStatusFilter.java b/...xing-solr/src/main/java/edu/unc/lib/boxc/indexing/solr/filter/SetContentStatusFilter.java
@@ -54,7 +54,7 @@ private List<String> determineContentStatus(DocumentIndexingPackage dip)
                 status.add(FacetConstants.IS_PRIMARY_OBJECT);
             }
             if (parentResc.hasProperty(Cdr.useAsThumbnail, resc)) {
-                status.add(FacetConstants.IS_ASSIGNED_THUMBNAIL);
+                status.add(FacetConstants.ASSIGNED_AS_THUMBNAIL);
             }
         }
 
@@ -75,7 +75,7 @@ private void addWorkObjectStatuses(List<String> status, Resource resource) {
         }
 
         if (resource.hasProperty(Cdr.useAsThumbnail)) {
-            status.add(FacetConstants.THUMBNAIL_ASSIGNED);
+            status.add(FacetConstants.HAS_THUMBNAIL_ASSIGNED);
         } else {
             status.add(FacetConstants.NO_THUMBNAIL_ASSIGNED);
         }

diff --git a/...-solr/src/test/java/edu/unc/lib/boxc/indexing/solr/filter/SetContentStatusFilterTest.java b/...-solr/src/test/java/edu/unc/lib/boxc/indexing/solr/filter/SetContentStatusFilterTest.java
@@ -190,7 +190,7 @@ public void testWorkWithAssignedThumbnail() throws Exception {
         filter.filter(dip);
 
         verify(idb).setContentStatus(listCaptor.capture());
-        assertTrue(listCaptor.getValue().contains(FacetConstants.THUMBNAIL_ASSIGNED));
+        assertTrue(listCaptor.getValue().contains(FacetConstants.HAS_THUMBNAIL_ASSIGNED));
         assertFalse(listCaptor.getValue().contains(FacetConstants.NO_THUMBNAIL_ASSIGNED));
     }
 
@@ -216,6 +216,6 @@ public void testIsAssignedThumbnail() throws Exception {
         filter.filter(dip);
 
         verify(idb).setContentStatus(listCaptor.capture());
-        assertTrue(listCaptor.getValue().contains(FacetConstants.IS_ASSIGNED_THUMBNAIL));
+        assertTrue(listCaptor.getValue().contains(FacetConstants.ASSIGNED_AS_THUMBNAIL));
     }
 }
diff --git a/pom.xml b/pom.xml
@@ -104,7 +104,8 @@
         <commons-fileupload.version>1.5</commons-fileupload.version>
         <abdera.version>1.1.3</abdera.version>
 
-        <activemq.version>5.16.3</activemq.version>
+        <activemq.version>5.17.6</activemq.version>
+        <activemq-camel.version>5.16.7</activemq-camel.version>
         <activemq-protobuf.version>1.1</activemq-protobuf.version>
 
         <slf4j.version>1.7.25</slf4j.version>

diff --git a/search-api/src/main/java/edu/unc/lib/boxc/search/api/FacetConstants.java b/search-api/src/main/java/edu/unc/lib/boxc/search/api/FacetConstants.java
@@ -23,8 +23,8 @@ public abstract class FacetConstants {
     public static final String STAFF_ONLY_ACCESS = "Staff-Only Access";
     public static final String MEMBERS_ARE_ORDERED = "Members Are Ordered";
     public static final String MEMBERS_ARE_UNORDERED = "Members Are Unordered";
-    public static final String THUMBNAIL_ASSIGNED = "Has Assigned Thumbnail";
+    public static final String HAS_THUMBNAIL_ASSIGNED = "Has Assigned Thumbnail";
     public static final String NO_THUMBNAIL_ASSIGNED = "No Assigned Thumbnail";
-    public static final String IS_ASSIGNED_THUMBNAIL = "Is Assigned Thumbnail";
+    public static final String ASSIGNED_AS_THUMBNAIL = "Assigned As Thumbnail";
 
 }
diff --git a/services-camel-app/pom.xml b/services-camel-app/pom.xml
@@ -56,7 +56,7 @@
     <dependency>
         <groupId>org.apache.activemq</groupId>
         <artifactId>activemq-camel</artifactId>
-        <version>${activemq.version}</version>
+        <version>${activemq-camel.version}</version>
     </dependency>
     <dependency>
         <groupId>org.apache.activemq</groupId>

diff --git a/...p/src/main/java/edu/unc/lib/boxc/services/camel/thumbnails/ThumbnailRequestProcessor.java b/...p/src/main/java/edu/unc/lib/boxc/services/camel/thumbnails/ThumbnailRequestProcessor.java
@@ -3,6 +3,7 @@
 import edu.unc.lib.boxc.auth.api.Permission;
 import edu.unc.lib.boxc.auth.api.services.AccessControlService;
 import edu.unc.lib.boxc.model.api.objects.RepositoryObjectLoader;
+import edu.unc.lib.boxc.model.api.objects.WorkObject;
 import edu.unc.lib.boxc.model.api.rdf.Cdr;
 import edu.unc.lib.boxc.model.api.services.RepositoryObjectFactory;
 import edu.unc.lib.boxc.model.fcrepo.ids.PIDs;
@@ -39,17 +40,26 @@ public void process(Exchange exchange) throws IOException {
                 pid, agent.getPrincipals(), Permission.editDescription);
 
         var file = repositoryObjectLoader.getFileObject(pid);
-        var work = file.getParent();
+        var work = (WorkObject) file.getParent();
 
         if (Objects.equals(action, ThumbnailRequest.ASSIGN)) {
+            // Capture the old thumbnail id before it gets cleared
+            var oldThumbnailFile = work.getThumbnailObject();
             repositoryObjectFactory.createExclusiveRelationship(work, Cdr.useAsThumbnail, file.getResource());
+            // reindex old thumbnail object
+            if (oldThumbnailFile != null) {
+                indexingMessageSender.sendIndexingOperation(
+                        agent.getUsername(), oldThumbnailFile.getPid(), IndexingActionType.UPDATE_DATASTREAMS);
+            }
         } else if ( Objects.equals(action, ThumbnailRequest.DELETE)) {
             repositoryObjectFactory.deleteProperty(work, Cdr.useAsThumbnail);
         }
 
         // send message to update solr
         indexingMessageSender.sendIndexingOperation(
                 agent.getUsername(), work.getPid(), IndexingActionType.UPDATE_DATASTREAMS);
+        indexingMessageSender.sendIndexingOperation(
+                agent.getUsername(), file.getPid(), IndexingActionType.UPDATE_DATASTREAMS);
     }
 
     public void setRepositoryObjectLoader(RepositoryObjectLoader repositoryObjectLoader) {

diff --git a/...-app/src/test/java/edu/unc/lib/boxc/services/camel/thumbnails/ThumbnailProcessorTest.java b/...-app/src/test/java/edu/unc/lib/boxc/services/camel/thumbnails/ThumbnailProcessorTest.java
@@ -87,14 +87,37 @@ void closeService() throws Exception {
     }
 
     @Test
-    public void testUpdateThumbnail() throws Exception {
+    public void testAssignThumbnail() throws Exception {
         var exchange = createRequestExchange(ThumbnailRequest.ASSIGN);
 
         processor.process(exchange);
         verify(repositoryObjectFactory).createExclusiveRelationship(eq(parentWork), eq(Cdr.useAsThumbnail), fileResourceCaptor.capture());
         // check to see the right file was related to the work
         assertEquals(resource, fileResourceCaptor.getValue());
-        assertIndexingMessageSent();
+        assertIndexingMessageSent(workPid);
+        assertIndexingMessageSent(filePid);
+    }
+
+    // test for when the work already has an assigned thumbnail and a new one is chosen
+    @Test
+    public void testAssignNewThumbnail() throws Exception {
+        // set up pre-existing assigned thumbnail
+        var oldThumbnailPid = ProcessorTestHelper.makePid();
+        var oldThumbnailFile = mock(FileObject.class);
+        var oldResource = mock(Resource.class);
+        when(oldThumbnailFile.getResource()).thenReturn(oldResource);
+        when(oldThumbnailFile.getPid()).thenReturn(oldThumbnailPid);
+        when(parentWork.getThumbnailObject()).thenReturn(oldThumbnailFile);
+
+        var exchange = createRequestExchange(ThumbnailRequest.ASSIGN);
+
+        processor.process(exchange);
+        verify(repositoryObjectFactory).createExclusiveRelationship(eq(parentWork), eq(Cdr.useAsThumbnail), fileResourceCaptor.capture());
+        // check to see the right file was related to the work
+        assertEquals(resource, fileResourceCaptor.getValue());
+        assertIndexingMessageSent(workPid);
+        assertIndexingMessageSent(filePid);
+        assertIndexingMessageSent(oldThumbnailPid);
     }
 
     @Test
@@ -114,11 +137,11 @@ public void testDeleteAssignedThumbnail() throws IOException {
 
         processor.process(exchange);
         verify(repositoryObjectFactory).deleteProperty(eq(parentWork), eq(Cdr.useAsThumbnail));
-        assertIndexingMessageSent();
+        assertIndexingMessageSent(workPid);
     }
 
-    private void assertIndexingMessageSent() {
-        verify(indexingMessageSender).sendIndexingOperation(agent.getUsername(), workPid,
+    private void assertIndexingMessageSent(PID pid) {
+        verify(indexingMessageSender).sendIndexingOperation(agent.getUsername(), pid,
                 IndexingActionType.UPDATE_DATASTREAMS);
     }
 

diff --git a/static/js/admin/src/ResultObject.js b/static/js/admin/src/ResultObject.js
@@ -31,7 +31,7 @@ define('ResultObject', [ 'jquery', 'jquery-ui', 'underscore', 'ModalLoadingOverl
 
 		if (tags.length > 0) {
 			this.metadata.tags = tags.filter(function(d) {
-				return !/^(has|not|no.primary|public.access|members.are.unordered)/i.test(d);
+				return !/^(has|not|no.primary|public.access|members.are.unordered|no.assigned.thumbnail)/i.test(d);
 			}).map(function(d) {
 				var tagValue;
 
@@ -85,7 +85,7 @@ define('ResultObject', [ 'jquery', 'jquery-ui', 'underscore', 'ModalLoadingOverl
 			case 'patron-settings':
 				helpText = 'Patron access settings for this object have been added';
 				break;
-			case 'primary-object':
+			case 'is-primary-object':
 				helpText = 'This file is the representative object for the work which contains it';
 				break;
 			case 'staff-only':
@@ -94,6 +94,9 @@ define('ResultObject', [ 'jquery', 'jquery-ui', 'underscore', 'ModalLoadingOverl
 			case 'inherited-settings':
 				helpText = 'Object is inheriting patron access settings which have been modified (typically they are more restrictive)';
 				break;
+			case 'assigned-as-thumbnail':
+				helpText = 'This file is the assigned thumbnail for the work which contains it';
+				break;
 			default:
 				helpText = '';
 		}