Merge branch 'develop' into 11387-fix-inputLevel-api

sekmiller · sekmiller · commit 079c26f61de4 · 2025-09-05T13:35:47.000-04:00
diff --git a/doc/release-notes/11703-notifications-and-templates-api-fixes.md b/doc/release-notes/11703-notifications-and-templates-api-fixes.md
@@ -0,0 +1,13 @@
+# Release Notes
+
+## Templates API fixes
+- Added the missing `isDefault` field to the **Get Dataset Templates** API response.
+- Added the missing `fileAccessRequest` field of terms of use and access to the **Get Dataset Templates** API response.
+- Added the missing `contactForAccess` field of terms of use and access to the **Get Dataset Templates** API response.
+- Resolved an API **500 error** that occurred when working with templates containing custom license terms.
+- Updated API behavior so templates are **no longer returned from parent dataverses** when the "Include Templates from Root" option is unchecked in the UI.
+
+## Notifications API fixes
+- Fixed API errors caused by NullPointerException when retrieving notifications without a requestor.
+
+See #11704
diff --git a/doc/sphinx-guides/source/installation/config.rst b/doc/sphinx-guides/source/installation/config.rst
@@ -3797,6 +3797,9 @@ please find all known feature flags below. Any of these flags can be activated u
     * - shibboleth-use-localhost
       - A Shibboleth-using Dataverse instance needs to make network calls to the locally-running ``shibd`` service. The default behavior is to use the address configured via the ``siteUrl`` setting. There are however situations (firewalls, etc.) where localhost would be preferable.
       - ``Off``
+    * - add-local-contexts-permission-check
+      - Adds a permission check to ensure that the user calling the /api/localcontexts/datasets/{id} API can edit the dataset with that id. This is currently the only use case - see https://github.com/gdcc/dataverse-external-vocab-support/tree/main/packages/local_contexts. The flag adds additional security to stop other uses, but would currently have to be used in conjunction with the api-session-auth feature flag (the security implications of which have not been fully investigated) to still allow adding Local Contexts metadata to a dataset.
+      - ``Off``
 
 **Note:** Feature flags can be set via any `supported MicroProfile Config API source`_, e.g. the environment variable
 ``DATAVERSE_FEATURE_XXX`` (e.g. ``DATAVERSE_FEATURE_API_SESSION_AUTH=1``). These environment variables can be set in your shell before starting Payara. If you are using :doc:`Docker for development </container/dev-usage>`, you can set them in the `docker compose <https://docs.docker.com/compose/environment-variables/set-environment-variables/>`_ file.
diff --git a/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java b/src/main/java/edu/harvard/iq/dataverse/CustomizationFilesServlet.java
@@ -22,6 +22,7 @@
 import jakarta.servlet.http.HttpServletRequest;
 import jakarta.servlet.http.HttpServletResponse;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
+import edu.harvard.iq.dataverse.util.FileUtil;
 import jakarta.ejb.EJB;
 import org.apache.commons.io.IOUtils;
 import org.apache.tika.Tika;
@@ -60,13 +61,11 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
         try {
             File fileIn = physicalPath.toFile();
             if (fileIn != null) {
-                Tika tika = new Tika();
-                try {
-                    String mimeType = tika.detect(fileIn);
-                    response.setContentType(mimeType);
-                } catch (Exception e) {
-                    logger.info("Error getting MIME Type for " + filePath + " : " + e.getMessage());
-                }
+                String filename = physicalPath.getFileName().toString();
+                int dotIndex = filename.lastIndexOf('.');
+                String ext = dotIndex >= 0 ? filename.substring(dotIndex) : "";
+                String mimeType = FileUtil.lookupFileTypeByExtension(ext);
+                response.setContentType(mimeType);
                 inputStream = new FileInputStream(fileIn);
 
                 in = new BufferedReader(new InputStreamReader(inputStream));
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/dto/NewTemplateDTO.java b/src/main/java/edu/harvard/iq/dataverse/api/dto/NewTemplateDTO.java
@@ -38,6 +38,7 @@ public Template toTemplate() {
         template.updateInstructions();
         template.setCreateTime(new Timestamp(new Date().getTime()));
         template.setUsageCount(0L);
+        template.setIsDefaultForDataverse(isDefault);
 
         return template;
     }
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateTemplateCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateTemplateCommand.java
@@ -48,7 +48,14 @@ public Template execute(CommandContext ctxt) throws CommandException {
             DatasetFieldUtil.tidyUpFields(template.getDatasetFields(), false);
         }
 
-        return ctxt.templates().save(template);
+        Template createdTemplate = ctxt.templates().save(template);
+
+        if (initialize && template.isIsDefaultForDataverse()) {
+            dataverse.setDefaultTemplate(createdTemplate);
+            ctxt.em().merge(dataverse);
+        }
+
+        return template;
     }
 
     private static void updateTermsOfUseAndAccess(CommandContext ctxt, Template template) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ListDataverseTemplatesCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/ListDataverseTemplatesCommand.java
@@ -26,14 +26,22 @@ public ListDataverseTemplatesCommand(DataverseRequest request, Dataverse dataver
 
     @Override
     public List<Template> execute(CommandContext ctxt) throws CommandException {
-        List<Template> templates = new ArrayList<>();
+        List<Template> availableTemplates = new ArrayList<>(dataverse.getTemplates());
 
-        if (dataverse.getOwner() != null) {
-            templates.addAll(dataverse.getParentTemplates());
+        if (!dataverse.isTemplateRoot() && dataverse.getOwner() != null) {
+            availableTemplates.addAll(dataverse.getParentTemplates());
         }
 
-        templates.addAll(dataverse.getTemplates());
+        setDefaultTemplate(availableTemplates);
 
-        return templates;
+        return availableTemplates;
+    }
+
+    private void setDefaultTemplate(List<Template> availableTemplates) {
+        Optional.ofNullable(dataverse.getDefaultTemplate())
+                .map(Template::getId).flatMap(defaultTemplateId -> availableTemplates.stream()
+                        .filter(template -> template.getId().equals(defaultTemplateId))
+                        .findFirst())
+                .ifPresent(template -> template.setIsDefaultForDataverse(true));
     }
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java
@@ -598,7 +598,10 @@ public static String determineFileTypeByNameAndExtension(final String fileName)
         return lookupFileTypeByExtension(fileName);
     }
 
-    private static String lookupFileTypeByExtension(final String fileName) {
+    /** determineFileTypeByNameAndExtension should be used instead for any user supplied content. 
+     *
+     */
+    public static String lookupFileTypeByExtension(final String fileName) {
         final String mimetypesFileTypeMapResult = MIME_TYPE_MAP.getContentType(fileName);
         logger.fine("MimetypesFileTypeMap type by extension, for " + fileName + ": " + mimetypesFileTypeMapResult);
         if (mimetypesFileTypeMapResult == null) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/InAppNotificationsJsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/InAppNotificationsJsonPrinter.java
@@ -195,9 +195,11 @@ private void addDatasetCreatedFields(final NullSafeJsonBuilder notificationJson,
     }
 
     private void addRequestorFields(final NullSafeJsonBuilder notificationJson, final AuthenticatedUser requestor) {
-        notificationJson.add(KEY_REQUESTOR_FIRST_NAME, requestor.getFirstName());
-        notificationJson.add(KEY_REQUESTOR_LAST_NAME, requestor.getLastName());
-        notificationJson.add(KEY_REQUESTOR_EMAIL, requestor.getEmail());
+        if (requestor != null) {
+            notificationJson.add(KEY_REQUESTOR_FIRST_NAME, requestor.getFirstName());
+            notificationJson.add(KEY_REQUESTOR_LAST_NAME, requestor.getLastName());
+            notificationJson.add(KEY_REQUESTOR_EMAIL, requestor.getEmail());
+        }
     }
 
     private void addDatasetFields(final NullSafeJsonBuilder notificationJson, final UserNotification userNotification) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
@@ -1592,6 +1592,7 @@ public static JsonObjectBuilder jsonTemplate(Template template) {
         return jsonObjectBuilder()
                 .add("id", template.getId())
                 .add("name", template.getName())
+                .add("isDefault", template.isIsDefaultForDataverse())
                 .add("usageCount", template.getUsageCount())
                 .add("createTime", template.getCreateTime().toString())
                 .add("createDate", template.getCreateDate())
@@ -1602,9 +1603,10 @@ public static JsonObjectBuilder jsonTemplate(Template template) {
     }
 
     public static JsonObjectBuilder jsonTermsOfUseAndAccess(TermsOfUseAndAccess termsOfUseAndAccess) {
+        License license = termsOfUseAndAccess.getLicense();
         return jsonObjectBuilder()
                 .add("id", termsOfUseAndAccess.getId())
-                .add("license", json(termsOfUseAndAccess.getLicense()))
+                .add("license", license != null ? json(license) : null)
                 .add("termsOfUse", termsOfUseAndAccess.getTermsOfUse())
                 .add("termsOfAccess", termsOfUseAndAccess.getTermsOfAccess())
                 .add("confidentialityDeclaration", termsOfUseAndAccess.getConfidentialityDeclaration())
@@ -1618,7 +1620,9 @@ public static JsonObjectBuilder jsonTermsOfUseAndAccess(TermsOfUseAndAccess term
                 .add("originalArchive", termsOfUseAndAccess.getOriginalArchive())
                 .add("availabilityStatus", termsOfUseAndAccess.getAvailabilityStatus())
                 .add("sizeOfCollection", termsOfUseAndAccess.getSizeOfCollection())
-                .add("studyCompletion", termsOfUseAndAccess.getStudyCompletion());
+                .add("studyCompletion", termsOfUseAndAccess.getStudyCompletion())
+                .add("contactForAccess", termsOfUseAndAccess.getContactForAccess())
+                .add("fileAccessRequest", termsOfUseAndAccess.isFileAccessRequest());
     }
 
     public static JsonArrayBuilder jsonTemplateInstructions(Map<String, String> templateInstructions) {
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java
@@ -2412,6 +2412,7 @@ public void testCreateAndGetTemplates() {
         );
         createTemplateResponse.then().assertThat().statusCode(OK.getStatusCode())
                 .body("data.name", equalTo("Dataverse template"))
+                .body("data.isDefault", equalTo(true))
                 .body("data.usageCount", equalTo(0))
                 .body("data.termsOfUseAndAccess.license.name", equalTo("CC0 1.0"))
                 .body("data.datasetFields.citation.fields.size()", equalTo(1))
@@ -2435,6 +2436,7 @@ public void testCreateAndGetTemplates() {
         getTemplateResponse.then().assertThat().statusCode(OK.getStatusCode())
                 .body("data.size()", equalTo(1))
                 .body("data[0].name", equalTo("Dataverse template"))
+                .body("data[0].isDefault", equalTo(true))
                 .body("data[0].usageCount", equalTo(0))
                 .body("data[0].termsOfUseAndAccess.license.name", equalTo("CC0 1.0"))
                 .body("data[0].datasetFields.citation.fields.size()", equalTo(1))
diff --git a/src/test/java/edu/harvard/iq/dataverse/engine/command/impl/ListDataverseTemplatesCommandTest.java b/src/test/java/edu/harvard/iq/dataverse/engine/command/impl/ListDataverseTemplatesCommandTest.java
@@ -5,14 +5,18 @@
 import edu.harvard.iq.dataverse.engine.command.CommandContext;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
+import edu.harvard.iq.dataverse.util.template.TemplateBuilder;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.mockito.Mockito;
 
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class ListDataverseTemplatesCommandTest {
@@ -28,52 +32,138 @@ public void setUp() {
 
     @Test
     public void execute_shouldReturnTemplates_noParent() throws CommandException {
+        // Arrange
         Dataverse dataverseMock = Mockito.mock(Dataverse.class);
-
         Mockito.when(dataverseMock.getTemplates()).thenReturn(Collections.singletonList(testTemplate));
 
         ListDataverseTemplatesCommand sut = new ListDataverseTemplatesCommand(dataverseRequestStub, dataverseMock);
 
+        // Act
         List<Template> result = sut.execute(Mockito.mock(CommandContext.class));
 
+        // Assert
         assertEquals(1, result.size());
         assertEquals(testTemplate, result.get(0));
     }
 
     @Test
     public void execute_shouldReturnTemplates_parentHasTemplates() throws CommandException {
+        // Arrange
         Template parentTemplate = new Template();
-
         Dataverse dataverseMock = Mockito.mock(Dataverse.class);
         Dataverse parentDataverseMock = Mockito.mock(Dataverse.class);
-
         Mockito.when(dataverseMock.getTemplates()).thenReturn(Collections.singletonList(testTemplate));
         Mockito.when(dataverseMock.getParentTemplates()).thenReturn(Collections.singletonList(parentTemplate));
         Mockito.when(dataverseMock.getOwner()).thenReturn(parentDataverseMock);
 
         ListDataverseTemplatesCommand sut = new ListDataverseTemplatesCommand(dataverseRequestStub, dataverseMock);
 
+        // Act
         List<Template> result = sut.execute(Mockito.mock(CommandContext.class));
 
+        // Assert
         assertEquals(2, result.size());
         assertTrue(result.contains(testTemplate));
         assertTrue(result.contains(parentTemplate));
     }
 
+    @Test
+    public void execute_shouldNotIncludeParentTemplates_whenDataverseIsRoot() throws CommandException {
+        // Arrange
+        String parentTemplateName = "parentTemplate";
+        Template parentTemplate = TemplateBuilder.aTemplate().withName(parentTemplateName).build();
+        String childTemplateName = "childTemplateName";
+        Template childTemplate = TemplateBuilder.aTemplate().withName(childTemplateName).build();
+        Dataverse dataverseMock = Mockito.mock(Dataverse.class);
+        Dataverse parentDataverseMock = Mockito.mock(Dataverse.class);
+        Mockito.when(dataverseMock.getTemplates()).thenReturn(Collections.singletonList(childTemplate));
+        Mockito.when(dataverseMock.getParentTemplates()).thenReturn(Collections.singletonList(parentTemplate));
+        Mockito.when(dataverseMock.getOwner()).thenReturn(parentDataverseMock);
+        Mockito.when(dataverseMock.isTemplateRoot()).thenReturn(true);
+
+        ListDataverseTemplatesCommand sut = new ListDataverseTemplatesCommand(dataverseRequestStub, dataverseMock);
+
+        // Act
+        List<Template> result = sut.execute(Mockito.mock(CommandContext.class));
+
+        // Assert
+        assertEquals(1, result.size());
+        assertTrue(result.get(0).getName().equals(childTemplateName));
+    }
+
+
     @Test
     public void execute_shouldReturnTemplates_parentHasNoTemplates() throws CommandException {
+        // Arrange
         Dataverse dataverseMock = Mockito.mock(Dataverse.class);
         Dataverse parentDataverseStub = Mockito.mock(Dataverse.class);
-
         Mockito.when(dataverseMock.getTemplates()).thenReturn(Collections.singletonList(testTemplate));
         Mockito.when(dataverseMock.getOwner()).thenReturn(parentDataverseStub);
         Mockito.when(dataverseMock.getParentTemplates()).thenReturn(Collections.emptyList());
 
         ListDataverseTemplatesCommand sut = new ListDataverseTemplatesCommand(dataverseRequestStub, dataverseMock);
 
+        // Act
         List<Template> result = sut.execute(Mockito.mock(CommandContext.class));
 
+        // Assert
         assertEquals(1, result.size());
         assertTrue(result.contains(testTemplate));
     }
+
+
+    @Test
+    public void execute_shouldSetDefaultTemplate_whenDefaultIsPresent() throws CommandException {
+        // Arrange
+        String defaultTplName = "defaultTplName";
+        String otherTplName = "otherTplName";
+
+        Template defaultTpl = TemplateBuilder.aTemplate().withName(defaultTplName).isDefault(true).build();
+        Template otherTpl = TemplateBuilder.aTemplate().withName(otherTplName).isDefault(false).build();
+
+        Dataverse dataverseMock = Mockito.mock(Dataverse.class);
+        Mockito.when(dataverseMock.getTemplates()).thenReturn(Arrays.asList(defaultTpl, otherTpl));
+        Mockito.when(dataverseMock.getDefaultTemplate()).thenReturn(defaultTpl);
+
+        ListDataverseTemplatesCommand sut = new ListDataverseTemplatesCommand(dataverseRequestStub, dataverseMock);
+
+        // Act
+        List<Template> result = sut.execute(Mockito.mock(CommandContext.class));
+
+        // Assert
+        assertEquals(2, result.size());
+
+        Template resultDefault = findTemplateByName(result, defaultTplName);
+        assertNotNull(resultDefault, "Default template should be in the list");
+        assertTrue(resultDefault.isIsDefaultForDataverse(), "The template with name " + defaultTplName + " should be marked as default");
+
+        Template resultOther = findTemplateByName(result, otherTplName);
+        assertNotNull(resultOther, "Other template should be in the list");
+        assertFalse(resultOther.isIsDefaultForDataverse(), "The template with name " + otherTplName + " should NOT be marked as default");
+    }
+
+    @Test
+    public void execute_shouldNotSetDefault_whenNoDefaultTemplateExists() throws CommandException {
+        // Arrange
+        testTemplate = TemplateBuilder.aTemplate().isDefault(false).build();
+        Dataverse dataverseMock = Mockito.mock(Dataverse.class);
+        Mockito.when(dataverseMock.getTemplates()).thenReturn(Collections.singletonList(testTemplate));
+        Mockito.when(dataverseMock.getDefaultTemplate()).thenReturn(null);
+
+        ListDataverseTemplatesCommand sut = new ListDataverseTemplatesCommand(dataverseRequestStub, dataverseMock);
+
+        // Act
+        List<Template> result = sut.execute(Mockito.mock(CommandContext.class));
+
+        // Assert
+        assertEquals(1, result.size());
+        assertFalse(result.get(0).isIsDefaultForDataverse(), "No template should be marked as default");
+    }
+
+    private Template findTemplateByName(List<Template> templates, String name) {
+        return templates.stream()
+                .filter(t -> name.equals(t.getName()))
+                .findFirst()
+                .orElse(null);
+    }
 }
diff --git a/src/test/java/edu/harvard/iq/dataverse/util/json/InAppNotificationsJsonPrinterTest.java b/src/test/java/edu/harvard/iq/dataverse/util/json/InAppNotificationsJsonPrinterTest.java
@@ -229,6 +229,26 @@ public void testAddFieldsByType_requestFileAccess() {
         verify(notificationJson).add(KEY_DATAFILE_DISPLAY_NAME, "Test File");
     }
 
+    @Test
+    public void testAddFieldsByType_requestFileAccess_nullRequestor() {
+        userNotification.setType(UserNotification.Type.REQUESTFILEACCESS);
+        userNotification.setObjectId(1L);
+        userNotification.setRequestor(null);
+
+        DataFile dataFile = mock(DataFile.class);
+        when(dataFile.getId()).thenReturn(1L);
+        when(dataFile.getDisplayName()).thenReturn("Test File");
+        when(dataFileService.find(1L)).thenReturn(dataFile);
+
+        sut.addFieldsByType(notificationJson, authenticatedUser, userNotification);
+
+        verify(notificationJson, never()).add(eq(KEY_REQUESTOR_FIRST_NAME), anyString());
+        verify(notificationJson, never()).add(eq(KEY_REQUESTOR_LAST_NAME), anyString());
+        verify(notificationJson, never()).add(eq(KEY_REQUESTOR_EMAIL), anyString());
+        verify(notificationJson).add(KEY_DATAFILE_ID, Long.valueOf("1"));
+        verify(notificationJson).add(KEY_DATAFILE_DISPLAY_NAME, "Test File");
+    }
+
     @Test
     public void testAddFieldsByType_grantFileAccess() {
         userNotification.setType(UserNotification.Type.GRANTFILEACCESS);
diff --git a/src/test/java/edu/harvard/iq/dataverse/util/json/JsonPrinterTest.java b/src/test/java/edu/harvard/iq/dataverse/util/json/JsonPrinterTest.java
diff --git a/src/test/java/edu/harvard/iq/dataverse/util/template/TemplateBuilder.java b/src/test/java/edu/harvard/iq/dataverse/util/template/TemplateBuilder.java

Original file line number	Diff line number	Diff line change
`@@ -38,6 +38,7 @@ public Template toTemplate() {`
`38`	`38`	`template.updateInstructions();`
`39`	`39`	`template.setCreateTime(new Timestamp(new Date().getTime()));`
`40`	`40`	`template.setUsageCount(0L);`
	`41`	`+ template.setIsDefaultForDataverse(isDefault);`
`41`	`42`
`42`	`43`	`return template;`
`43`	`44`	`}`
Original file line number	Diff line number	Diff line change
`@@ -48,7 +48,14 @@ public Template execute(CommandContext ctxt) throws CommandException {`
`48`	`48`	`DatasetFieldUtil.tidyUpFields(template.getDatasetFields(), false);`
`49`	`49`	`}`
`50`	`50`
`51`		`- return ctxt.templates().save(template);`
	`51`	`+ Template createdTemplate = ctxt.templates().save(template);`
	`52`	`+`
	`53`	`+ if (initialize && template.isIsDefaultForDataverse()) {`
	`54`	`+ dataverse.setDefaultTemplate(createdTemplate);`
	`55`	`+ ctxt.em().merge(dataverse);`
	`56`	`+ }`
	`57`	`+`
	`58`	`+ return template;`
`52`	`59`	`}`
`53`	`60`
`54`	`61`	`private static void updateTermsOfUseAndAccess(CommandContext ctxt, Template template) {`
Original file line number	Diff line number	Diff line change
`@@ -195,9 +195,11 @@ private void addDatasetCreatedFields(final NullSafeJsonBuilder notificationJson,`
`195`	`195`	`}`
`196`	`196`
`197`	`197`	`private void addRequestorFields(final NullSafeJsonBuilder notificationJson, final AuthenticatedUser requestor) {`
`198`		`- notificationJson.add(KEY_REQUESTOR_FIRST_NAME, requestor.getFirstName());`
`199`		`- notificationJson.add(KEY_REQUESTOR_LAST_NAME, requestor.getLastName());`
`200`		`- notificationJson.add(KEY_REQUESTOR_EMAIL, requestor.getEmail());`
	`198`	`+ if (requestor != null) {`
	`199`	`+ notificationJson.add(KEY_REQUESTOR_FIRST_NAME, requestor.getFirstName());`
	`200`	`+ notificationJson.add(KEY_REQUESTOR_LAST_NAME, requestor.getLastName());`
	`201`	`+ notificationJson.add(KEY_REQUESTOR_EMAIL, requestor.getEmail());`
	`202`	`+ }`
`201`	`203`	`}`
`202`	`204`
`203`	`205`	`private void addDatasetFields(final NullSafeJsonBuilder notificationJson, final UserNotification userNotification) {`