3443 exclude email

doc/sphinx-guides/source/installation/config.rst

@@ -409,6 +409,13 @@ Specify a URL where users can read your API Terms of Use.
 
 ``curl -X PUT -d http://best-practices.dataverse.org/harvard-policies/harvard-api-tou.html http://localhost:8080/api/admin/settings/:ApiTermsOfUse``
 
+:ExcludeEmailFromExport
++++++++++++++++++++++++
+
+Set ``:ExcludeEmailFromExport`` to prevent email addresses for dataset contacts from being exposed in XML or JSON representations of dataset metadata. For a list exported formats such as DDI, see the :doc:`/admin/metadataexport` section of the Admin Guide.
+
+``curl -X PUT -d true http://localhost:8080/api/admin/settings/:ExcludeEmailFromExport``
+
 :GuidesBaseUrl
 ++++++++++++++
 
@@ -607,7 +614,7 @@ The default checksum algorithm used is MD5 and should be sufficient for establis
 :ShibPassiveLoginEnabled
 ++++++++++++++++++++++++
 
-Set ``ShibPassiveLoginEnabled`` to true to enable passive login for Shibboleth. When this feature is enabled, an additional Javascript file (isPassive.js) will be loaded for every page. It will generate a passive login request to your Shibboleth SP when an anonymous user navigates to the site. A cookie named "_check_is_passive_dv" will be created to keep track of whether or not a passive login request has already been made for the user.
+Set ``:ShibPassiveLoginEnabled`` to true to enable passive login for Shibboleth. When this feature is enabled, an additional Javascript file (isPassive.js) will be loaded for every page. It will generate a passive login request to your Shibboleth SP when an anonymous user navigates to the site. A cookie named "_check_is_passive_dv" will be created to keep track of whether or not a passive login request has already been made for the user.
 
 This implementation follows the example on the Shibboleth wiki documentation page for the isPassive feature: https://wiki.shibboleth.net/confluence/display/SHIB2/isPassive
 

src/main/java/edu/harvard/iq/dataverse/DatasetPage.java

@@ -339,10 +339,6 @@ public boolean isUnlimitedUploadFileSize(){
         return false;
     }
 
-    public boolean isMetadataExportEnabled() {
-        return metadataExportEnabled;
-    }
-
     public String getDataverseSiteUrl() {
         return this.dataverseSiteUrl;
     }
@@ -1003,7 +999,6 @@ public void setDisplayFileMetadata(List<FileMetadata> displayFileMetadata) {
     }
 
     private boolean readOnly = true; 
-    private boolean metadataExportEnabled;
     private String originalSourceUrl = null;
 
     public String getOriginalSourceUrl() {
@@ -1027,11 +1022,6 @@ private String init(boolean initFull) {
 
         this.maxFileUploadSizeInBytes = systemConfig.getMaxFileUploadSize();
         setDataverseSiteUrl(systemConfig.getDataverseSiteUrl());
-        /**
-         * For now having DDI export enabled is a proxy for having any metadata
-         * export enabled (JSON, Dublin Core, etc.).
-         */
-        metadataExportEnabled = systemConfig.isDdiExportEnabled();
 
         guestbookResponse = new GuestbookResponse();
 
@@ -2586,28 +2576,16 @@ public String getTabularDataFileURL(Long fileid) {
         return dataURL;
     }
 
-    public String getMetadataAsJsonUrl() {
-        if (dataset != null) {
-            Long datasetId = dataset.getId();
-            if (datasetId != null) {
-                String myHostURL = getDataverseSiteUrl();
-                String metadataAsJsonUrl = myHostURL + "/api/datasets/" + datasetId;
-                return metadataAsJsonUrl;
-            }
-        }
-        return null;
-    }
-
     public List< String[]> getExporters(){
         List<String[]> retList = new ArrayList();
         String myHostURL = getDataverseSiteUrl();
-        for (String [] provider : ExportService.getInstance().getExportersLabels() ){
+        for (String [] provider : ExportService.getInstance(settingsService).getExportersLabels() ){
             String formatName = provider[1];
             String formatDisplayName = provider[0];
 
             Exporter exporter = null; 
             try {
-                exporter = ExportService.getInstance().getExporter(formatName);
+                exporter = ExportService.getInstance(settingsService).getExporter(formatName);
             } catch (ExportException ex) {
                 exporter = null;
             }

src/main/java/edu/harvard/iq/dataverse/FilePage.java

@@ -200,13 +200,13 @@ public void setVersion(String version) {
     public List< String[]> getExporters(){
         List<String[]> retList = new ArrayList();
         String myHostURL = systemConfig.getDataverseSiteUrl();
-        for (String [] provider : ExportService.getInstance().getExportersLabels() ){
+        for (String [] provider : ExportService.getInstance(settingsService).getExportersLabels() ){
             String formatName = provider[1];
             String formatDisplayName = provider[0];
 
             Exporter exporter = null; 
             try {
-                exporter = ExportService.getInstance().getExporter(formatName);
+                exporter = ExportService.getInstance(settingsService).getExporter(formatName);
             } catch (ExportException ex) {
                 exporter = null;
             }

src/main/java/edu/harvard/iq/dataverse/api/Datasets.java

@@ -167,7 +167,7 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @
                 return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found.");
             }
 
-            ExportService instance = ExportService.getInstance();
+            ExportService instance = ExportService.getInstance(settingsSvc);
 
             String xml = instance.getExportAsString(dataset, exporter);
             // I'm wondering if this going to become a performance problem 
@@ -290,7 +290,7 @@ public Response getVersionMetadataBlock( @PathParam("id") String datasetId,
             Map<MetadataBlock, List<DatasetField>> fieldsByBlock = DatasetField.groupByBlock(dsv.getDatasetFields());
             for ( Map.Entry<MetadataBlock, List<DatasetField>> p : fieldsByBlock.entrySet() ) {
                 if ( p.getKey().getName().equals(blockName) ) {
-                    return ok( json(p.getKey(), p.getValue()) );
+                    return ok(json(p.getKey(), p.getValue()));
                 }
             }
             return notFound("metadata block named " + blockName + " not found");
@@ -441,55 +441,6 @@ public Response getLinks(@PathParam("id") String idSupplied ) {
         }
     }
 
-    /**
-     * @todo Implement this for real as part of
-     * https://github.com/IQSS/dataverse/issues/2579
-     */
-    @GET
-    @Path("ddi")
-    @Produces({"application/xml", "application/json"})
-    @Deprecated
-    public Response getDdi(@QueryParam("id") long id, @QueryParam("persistentId") String persistentId, @QueryParam("dto") boolean dto) {
-        boolean ddiExportEnabled = systemConfig.isDdiExportEnabled();
-        if (!ddiExportEnabled) {
-            return error(Response.Status.FORBIDDEN, "Disabled");
-        }
-        try {
-            User u = findUserOrDie();
-            if (!u.isSuperuser()) {
-                return error(Response.Status.FORBIDDEN, "Not a superuser");
-            }
-
-            logger.fine("looking up " + persistentId);
-            Dataset dataset = datasetService.findByGlobalId(persistentId);
-            if (dataset == null) {
-                return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found.");
-            }
-
-            String xml = "<codeBook>XML_BEING_COOKED</codeBook>";
-            if (dto) {
-                /**
-                 * @todo We can only assume that this should not be hard-coded
-                 * to getLatestVersion
-                 */
-                final JsonObjectBuilder datasetAsJson = jsonAsDatasetDto(dataset.getLatestVersion());
-                xml = DdiExportUtil.datasetDtoAsJson2ddi(datasetAsJson.toString());
-            } else {
-                OutputStream outputStream = new ByteArrayOutputStream();
-                ddiExportService.exportDataset(dataset.getId(), outputStream, null, null);
-                xml = outputStream.toString();
-            }
-            logger.fine("xml to return: " + xml);
-
-            return Response.ok()
-                    .entity(xml)
-                    .type(MediaType.APPLICATION_XML).
-                    build();
-        } catch (WrappedResponse wr) {
-            return wr.getResponse();
-        }
-    }
-
     /**
      * @todo Make this real. Currently only used for API testing. Copied from
      * the equivalent API endpoint for dataverses and simplified with values

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeaccessionDatasetVersionCommand.java

@@ -73,7 +73,7 @@ public DatasetVersion execute(CommandContext ctxt) throws CommandException {
         // if there is still another released version of this dataset, 
         // we want to re-export it : 
 
-        ExportService instance = ExportService.getInstance();
+        ExportService instance = ExportService.getInstance(ctxt.settings());
 
         if (managed.getDataset().getReleasedVersion() != null) {
             try {

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/PublishDatasetCommand.java

@@ -226,7 +226,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
         */
 
         try {
-            ExportService instance = ExportService.getInstance();
+            ExportService instance = ExportService.getInstance(ctxt.settings());
             instance.exportAllFormats(theDataset);
 
         } catch (ExportException ex) {

src/main/java/edu/harvard/iq/dataverse/export/ExportService.java

@@ -4,15 +4,14 @@
 import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.DatasetVersion;
 import edu.harvard.iq.dataverse.export.spi.Exporter;
-import edu.harvard.iq.dataverse.util.SystemConfig;
-import static edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonAsDatasetDto;
+import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
+import edu.harvard.iq.dataverse.util.json.JsonPrinter;
 import java.io.BufferedReader;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.io.OutputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -23,9 +22,6 @@
 import java.util.List;
 import java.util.ServiceConfigurationError;
 import java.util.ServiceLoader;
-import javax.ejb.EJB;
-import javax.ejb.TransactionAttribute;
-import static javax.ejb.TransactionAttributeType.REQUIRES_NEW;
 import javax.json.JsonObject;
 import javax.json.JsonObjectBuilder;
 
@@ -37,12 +33,22 @@ public class ExportService {
 
     private static ExportService service;
     private ServiceLoader<Exporter> loader;
+    static SettingsServiceBean settingsService;
 
     private ExportService() {
         loader = ServiceLoader.load(Exporter.class);        
     }
 
+    /**
+     * TODO: Audit all calls to this getInstance method that doesn't take a
+     * SettingsServiceBean as an argument to make sure nothing broke.
+     */
     public static synchronized ExportService getInstance() {
+        return getInstance(null);
+    }
+
+    public static synchronized ExportService getInstance(SettingsServiceBean settingsService) {
+        ExportService.settingsService = settingsService;
         if (service == null) {
             service = new ExportService();
         } else{
@@ -127,7 +133,8 @@ public void exportAllFormats (Dataset dataset) throws ExportException {
             if (releasedVersion == null) {
                 throw new ExportException("No released version for dataset "+dataset.getGlobalId());
             }
-            final JsonObjectBuilder datasetAsJsonBuilder = jsonAsDatasetDto(releasedVersion);
+            JsonPrinter jsonPrinter = new JsonPrinter(settingsService);
+            final JsonObjectBuilder datasetAsJsonBuilder = jsonPrinter.jsonAsDatasetDto(releasedVersion);
             JsonObject datasetAsJson = datasetAsJsonBuilder.build();
 
             Iterator<Exporter> exporters = loader.iterator();
@@ -175,7 +182,8 @@ public void exportFormat(Dataset dataset, String formatName) throws ExportExcept
                     if (releasedVersion == null) {
                         throw new IllegalStateException("No Released Version");
                     }
-                    final JsonObjectBuilder datasetAsJsonBuilder = jsonAsDatasetDto(releasedVersion);
+                    JsonPrinter jsonPrinter = new JsonPrinter(settingsService);
+                    final JsonObjectBuilder datasetAsJsonBuilder = jsonPrinter.jsonAsDatasetDto(releasedVersion);
                     cacheExport(releasedVersion, formatName, datasetAsJsonBuilder.build(), e);
                 }
             }

src/main/java/edu/harvard/iq/dataverse/export/ddi/DdiExportUtil.java

@@ -3,16 +3,13 @@
 import com.google.gson.Gson;
 import edu.harvard.iq.dataverse.DataFile;
 import edu.harvard.iq.dataverse.DataTable;
-import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.DatasetFieldConstant;
 import edu.harvard.iq.dataverse.DatasetVersion;
 import edu.harvard.iq.dataverse.FileMetadata;
-import edu.harvard.iq.dataverse.api.dto.DataVariableDTO;
 import edu.harvard.iq.dataverse.api.dto.DatasetDTO;
 import edu.harvard.iq.dataverse.api.dto.DatasetVersionDTO;
 import edu.harvard.iq.dataverse.api.dto.FieldDTO;
 import edu.harvard.iq.dataverse.api.dto.FileDTO;
-import edu.harvard.iq.dataverse.api.dto.FileMetadataDTO;
 import edu.harvard.iq.dataverse.api.dto.MetadataBlockDTO;
 import edu.harvard.iq.dataverse.datavariable.DataVariable;
 import edu.harvard.iq.dataverse.datavariable.SummaryStatistic;
@@ -29,13 +26,11 @@
 import edu.harvard.iq.dataverse.util.xml.XmlPrinter;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.OutputStream;
 import java.net.InetAddress;
 import java.net.UnknownHostException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
-import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
@@ -586,9 +581,10 @@ private static void writeContactsElement(XMLStreamWriter xmlw, DatasetVersionDTO
                                     datasetContactAffiliation =  next.getSinglePrimitive();
                                 }
                                 if (DatasetFieldConstant.datasetContactEmail.equals(next.getTypeName())) {
-                                    datasetContactEmail =  next.getSinglePrimitive();
+                                    datasetContactEmail = next.getSinglePrimitive();
                                 }
                             }
+                            // TODO: Since datasetContactEmail is a required field but datasetContactName is not consider not checking if datasetContactName is empty so we can write out datasetContactEmail.
                             if (!datasetContactName.isEmpty()){
                                 xmlw.writeStartElement("contact"); 
                                 if(!datasetContactAffiliation.isEmpty()){

src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java

@@ -129,11 +129,11 @@ private Context createContext() {
     }
 
     private void addSupportedMetadataFormats(Context context) {
-        for (String[] provider : ExportService.getInstance().getExportersLabels()) {
+        for (String[] provider : ExportService.getInstance(settingsService).getExportersLabels()) {
             String formatName = provider[1];
             Exporter exporter;
             try {
-                exporter = ExportService.getInstance().getExporter(formatName);
+                exporter = ExportService.getInstance(settingsService).getExporter(formatName);
             } catch (ExportException ex) {
                 exporter = null;
             }

src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java

@@ -128,10 +128,6 @@ public enum Key {
         SolrHostColonPort,
         /** Key for limiting the number of bytes uploaded via the Data Deposit API, UI (web site and . */
         MaxFileUploadSizeInBytes,
-        /**
-         * Experimental: Key for if DDI export is enabled or disabled.
-         */
-        DdiExportEnabled,
         /** Key for if ScrubMigrationData is enabled or disabled. */
         ScrubMigrationData,
         /** Key for the url to send users who want to sign up to. */
@@ -241,7 +237,11 @@ Whether Harvesting (OAI) service is enabled
         /**
         * Whether Shibboleth passive authentication mode is enabled
         */
-       ShibPassiveLoginEnabled;
+        ShibPassiveLoginEnabled,
+        /**
+         * Whether Export should exclude FieldType.EMAIL
+         */
+        ExcludeEmailFromExport;
 
         @Override
         public String toString() {