Merge branch 'develop' into 3036-support-form-math-bug

doc/sphinx-guides/source/api/native-api.rst

@@ -169,6 +169,8 @@ Publishes the dataset whose id is passed. The new dataset version number is dete
 
     POST http://$SERVER/api/datasets/$id/actions/:publish?type=$type&key=$apiKey
 
+.. note:: POST should be used to publish a dataset. GET is supported for backward compatibility but is deprecated and may be removed: https://github.com/IQSS/dataverse/issues/2431
+
 Deletes the draft version of dataset ``$id``. Only the draft version can be deleted::
 
     DELETE http://$SERVER/api/datasets/$id/versions/:draft?key=$apiKey

doc/sphinx-guides/source/conf.py

@@ -425,3 +425,5 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'http://docs.python.org/': None}
+# Suppress "WARNING: unknown mimetype for ..." https://github.com/IQSS/dataverse/issues/3391
+suppress_warnings = ['epub.unknown_project_files']

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

@@ -345,6 +345,20 @@ Set ``GuidesBaseUrl`` to override the default value "http://guides.dataverse.org
 
 ``curl -X PUT -d http://dataverse.example.edu http://localhost:8080/api/admin/settings/:GuidesBaseUrl``
 
+:GuidesVersion
+++++++++++++++
+
+Set ``:GuidesVersion`` to override the version number in the URL of guides. For example, rather than http://guides.dataverse.org/en/4.6/user/account.html the version is overriden to http://guides.dataverse.org/en/1234-new-feature/user/account.html in the example below:
+
+``curl -X PUT -d 1234-new-feature http://localhost:8080/api/admin/settings/:GuidesVersion``
+
+:MetricsUrl
++++++++++++
+
+Make the metrics component on the root dataverse a clickable link to a website where you present metrics on your Dataverse installation. This could perhaps be an installation of https://github.com/IQSS/miniverse or any site.
+
+``curl -X PUT -d http://metrics.dataverse.example.edu http://localhost:8080/api/admin/settings/:MetricsUrl``
+
 :StatusMessageHeader
 ++++++++++++++++++++
 

src/main/java/Bundle.properties

@@ -1022,6 +1022,7 @@ dataset.exportBtn.itemLabel.ddi=DDI
 dataset.exportBtn.itemLabel.dublinCore=Dublin Core
 dataset.exportBtn.itemLabel.json=JSON
 metrics.title=Metrics
+metrics.title.tip=View more metrics information
 metrics.comingsoon=Coming soon...
 metrics.views=Views
 metrics.downloads={0, choice, 0#Downloads|1#Download|2#Downloads}

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

@@ -628,7 +628,7 @@ public String save() {
             if (editMode != null && editMode.equals(EditMode.FEATURED)) {
                 message = "The featured dataverses for this dataverse have been updated.";
             } else {
-                message = (create) ? BundleUtil.getStringFromBundle("dataverse.create.success", Arrays.asList(settingsWrapper.getGuidesBaseUrl(), systemConfig.getVersion())) : BundleUtil.getStringFromBundle("dataverse.update.success");
+                message = (create) ? BundleUtil.getStringFromBundle("dataverse.create.success", Arrays.asList(settingsWrapper.getGuidesBaseUrl(), systemConfig.getGuidesVersion())) : BundleUtil.getStringFromBundle("dataverse.update.success");
             }
             JsfHelper.addSuccessMessage(message);
 

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

@@ -8,6 +8,7 @@
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import edu.harvard.iq.dataverse.engine.command.impl.CreateGuestbookResponseCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.RequestAccessCommand;
+import edu.harvard.iq.dataverse.util.FileUtil;
 import java.io.IOException;
 import java.sql.Timestamp;
 import java.util.ArrayList;
@@ -295,7 +296,7 @@ public void downloadCitationXML(FileMetadata fileMetadata, Dataset dataset) {
             fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + ".xml";
         } else {
             // Datafile-level citation:
-            fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + "-" + fileMetadata.getLabel().replaceAll("\\.tab$", "-endnote.xml");
+            fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + "-" + FileUtil.getCiteDataFileFilename(fileMetadata, FileUtil.FileCitationExtension.ENDNOTE);
         }
         response.setHeader("Content-Disposition", fileNameString);
         try {
@@ -336,7 +337,7 @@ public void downloadCitationRIS(FileMetadata fileMetadata, Dataset dataset) {
             fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + ".ris";
         } else {
             // Datafile-level citation:
-            fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + "-" + fileMetadata.getLabel().replaceAll("\\.tab$", ".ris");
+            fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + "-" + FileUtil.getCiteDataFileFilename(fileMetadata, FileUtil.FileCitationExtension.RIS);
         }
         response.setHeader("Content-Disposition", fileNameString);
 
@@ -383,7 +384,7 @@ public void downloadCitationBibtex(FileMetadata fileMetadata, Dataset dataset) {
             fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + ".bib";
         } else {
             // Datafile-level citation:
-            fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + "-" + fileMetadata.getLabel().replaceAll("\\.tab$", ".bib");
+            fileNameString = "attachment;filename=" + getFileNameDOI(workingVersion) + "-" + FileUtil.getCiteDataFileFilename(fileMetadata, FileUtil.FileCitationExtension.BIBTEX);
         }
         response.setHeader("Content-Disposition", fileNameString);
 

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

@@ -364,7 +364,7 @@ private String getMessageTextBasedOnNotification(UserNotification userNotificati
                         parentDataverseDisplayName,
                         parentDataverseUrl,
                         systemConfig.getGuidesBaseUrl(),
-                        systemConfig.getVersion()));
+                        systemConfig.getGuidesVersion()));
                 logger.fine(dataverseCreatedMessage);
                 return messageText += dataverseCreatedMessage;
             case REQUESTFILEACCESS:
@@ -393,7 +393,7 @@ private String getMessageTextBasedOnNotification(UserNotification userNotificati
                         version.getDataset().getOwner().getDisplayName(),
                         getDataverseLink(version.getDataset().getOwner()),
                         systemConfig.getGuidesBaseUrl(),
-                        systemConfig.getVersion()
+                        systemConfig.getGuidesVersion()
                 ));
                 logger.fine(datasetCreatedMessage);
                 return messageText += datasetCreatedMessage;
@@ -427,7 +427,7 @@ private String getMessageTextBasedOnNotification(UserNotification userNotificati
             case CREATEACC:
                 String accountCreatedMessage = BundleUtil.getStringFromBundle("notification.email.welcome", Arrays.asList(
                         systemConfig.getGuidesBaseUrl(),
-                        systemConfig.getVersion()
+                        systemConfig.getGuidesVersion()
                 ));
                 String optionalConfirmEmailAddon = confirmEmailService.optionalConfirmEmailAddonMsg(userNotification.getUser());
                 accountCreatedMessage += optionalConfirmEmailAddon;

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

@@ -68,7 +68,7 @@
 @Path("datasets")
 public class Datasets extends AbstractApiBean {
 
-    private static final Logger LOGGER = Logger.getLogger(Datasets.class.getName());
+    private static final Logger logger = Logger.getLogger(Datasets.class.getCanonicalName());
 
     private static final String PERSISTENT_ID_KEY=":persistentId";
 
@@ -148,7 +148,7 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @
             // (the way Access API streams its output). 
             // -- L.A., 4.5
 
-            LOGGER.fine("xml to return: " + xml);
+            logger.fine("xml to return: " + xml);
             String mediaType = MediaType.TEXT_PLAIN;
             if (instance.isXMLFormat(exporter)){
                 mediaType = MediaType.APPLICATION_XML;
@@ -334,7 +334,7 @@ public Response updateDraftVersion( String jsonBody, @PathParam("id") String id,
             return ok( json(managedVersion) );
 
         } catch (JsonParseException ex) {
-            LOGGER.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex);
+            logger.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex);
             return error( Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage() );
 
         } catch (WrappedResponse ex) {
@@ -343,36 +343,45 @@ public Response updateDraftVersion( String jsonBody, @PathParam("id") String id,
         }
     }
 
+    /**
+     * @deprecated This was shipped as a GET but should have been a POST, see https://github.com/IQSS/dataverse/issues/2431
+     */
     @GET
-    @Path("{id}/actions/:publish") 
-    public Response publishDataset( @PathParam("id") String id, @QueryParam("type") String type ) {
+    @Path("{id}/actions/:publish")
+    @Deprecated
+    public Response publishDataseUsingGetDeprecated( @PathParam("id") String id, @QueryParam("type") String type ) {
+        logger.info("publishDataseUsingGetDeprecated called on id " + id + ". Encourage use of POST rather than GET, which is deprecated.");
+        return publishDataset(id, type);
+    }
+
+    @POST
+    @Path("{id}/actions/:publish")
+    public Response publishDataset(@PathParam("id") String id, @QueryParam("type") String type) {
         try {
-            if ( type == null ) {
-                return error( Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major' or 'minor').");
+            if (type == null) {
+                return error(Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major' or 'minor').");
             }
-            
+
             type = type.toLowerCase();
             boolean isMinor;
-            switch ( type ) {
-                case "minor": isMinor = true; break;
-                case "major": isMinor = false; break;
-                default: return error( Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major' or 'minor'.");
+            switch (type) {
+                case "minor":
+                    isMinor = true;
+                    break;
+                case "major":
+                    isMinor = false;
+                    break;
+                default:
+                    return error(Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major' or 'minor'.");
             }
-            long dsId;
-            try {
-                dsId = Long.parseLong(id);
-            } catch ( NumberFormatException nfe ) {
-                return error( Response.Status.BAD_REQUEST, "Bad dataset id. Please provide a number.");
-            }
-
-            Dataset ds = datasetService.find(dsId);
-
-            return ( ds == null ) ? notFound("Can't find dataset with id '" + id + "'")
-                                  : ok( json(execCommand(new PublishDatasetCommand(ds, 
-                                                                            createDataverseRequest(findAuthenticatedUserOrDie()),
-                                                                            isMinor))) );
-
-        }  catch (WrappedResponse ex) {
+
+            Dataset ds = findDatasetOrDie(id);
+
+            return ok(json(execCommand(new PublishDatasetCommand(ds,
+                    createDataverseRequest(findAuthenticatedUserOrDie()),
+                    isMinor))));
+
+        } catch (WrappedResponse ex) {
             return ex.getResponse();
         }
     }
@@ -420,7 +429,7 @@ public Response getDdi(@QueryParam("id") long id, @QueryParam("persistentId") St
                 return error(Response.Status.FORBIDDEN, "Not a superuser");
             }
 
-            LOGGER.fine("looking up " + persistentId);
+            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.");
@@ -439,7 +448,7 @@ public Response getDdi(@QueryParam("id") long id, @QueryParam("persistentId") St
                 ddiExportService.exportDataset(dataset.getId(), outputStream, null, null);
                 xml = outputStream.toString();
             }
-            LOGGER.fine("xml to return: " + xml);
+            logger.fine("xml to return: " + xml);
 
             return Response.ok()
                     .entity(xml)
@@ -473,7 +482,7 @@ public Response createAssignment(String userOrGroup, @PathParam("identifier") St
             return ok(
                     json(execCommand(new AssignRoleCommand(assignee, theRole, dataset, createDataverseRequest(findUserOrDie()), privateUrlToken))));
         } catch (WrappedResponse ex) {
-            LOGGER.log(Level.WARNING, "Can''t create assignment: {0}", ex.getMessage());
+            logger.log(Level.WARNING, "Can''t create assignment: {0}", ex.getMessage());
             return ex.getResponse();
         }
     }

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

@@ -77,6 +77,11 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
             throw new IllegalCommandException("Latest version of dataset " + theDataset.getIdentifier() + " is already released. Only draft versions can be released.", this);
         }
 
+        // prevent publishing of 0.1 version
+        if (minorRelease && theDataset.getVersions().size() == 1 && theDataset.getLatestVersion().isDraft()) {
+            throw new IllegalCommandException("Cannot publish as minor version. Re-try as major release.", this);
+        }
+
         if (minorRelease && !theDataset.getLatestVersion().isMinorUpdate()) {
             throw new IllegalCommandException("Cannot release as minor version. Re-try as major release.", this);
         }

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

@@ -152,7 +152,14 @@ public enum Key {
         TwoRavensUrl,
         /** Optionally override http://guides.dataverse.org . */
         GuidesBaseUrl,
+        /**
+         * A link to an installation of https://github.com/IQSS/miniverse or
+         * some other metrics app.
+         */
+        MetricsUrl,
         /* zip download size limit */
+        /** Optionally override version number in guides. */
+        GuidesVersion,
         ZipDownloadLimit,
         /* zip upload number of files limit */
         ZipUploadFilesLimit,

src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java

@@ -1153,7 +1153,34 @@ private static void createIngestReport (DataFile dataFile, int status, String me
                 dataFile.setIngestReport(errorReport);
         }
     }
-
-
-
+
+    public enum FileCitationExtension {
+
+        ENDNOTE("-endnote.xml"),
+        RIS(".ris"),
+        BIBTEX(".bib");
+
+        private final String text;
+
+        private FileCitationExtension(final String text) {
+            this.text = text;
+        }
+    }
+
+    public static String getCiteDataFileFilename(FileMetadata fileMetadata, FileCitationExtension fileCitationExtension) {
+        if (fileMetadata == null) {
+            logger.info("In getCitationBibtex but FileMetadata is null!");
+            return null;
+        }
+        if (fileCitationExtension == null) {
+            logger.info("In getCitationBibtex but fileCitationExtension is null!");
+            return null;
+        }
+        if (fileMetadata.getLabel().endsWith("tab")) {
+            return fileMetadata.getLabel().replaceAll("\\.tab$", fileCitationExtension.text);
+        } else {
+            return fileMetadata.getLabel() + fileCitationExtension.text;
+        }
+    }
+
 }

src/main/java/edu/harvard/iq/dataverse/util/SystemConfig.java

@@ -310,6 +310,21 @@ private String getGuidesLanguage() {
         return saneDefault;
     }
 
+    public String getGuidesVersion() {
+        String saneDefault = getVersion();
+        String guidesVersion = settingsService.getValueForKey(SettingsServiceBean.Key.GuidesVersion, saneDefault);
+        if (guidesVersion != null) {
+            return guidesVersion;
+        }
+        return saneDefault;
+    }
+
+    public String getMetricsUrl() {
+        String saneDefault = null;
+        String metricsUrl = settingsService.getValueForKey(SettingsServiceBean.Key.MetricsUrl, saneDefault);
+        return metricsUrl;
+    }
+
     /**
      * Download-as-zip size limit.
      * returns 0 if not specified; 

src/main/webapp/dashboard.xhtml

@@ -94,7 +94,7 @@
                                                 <span class="glyphicon glyphicon-info-sign"/>
                                                 <h:outputFormat value=" #{bundle['dashboard.card.metadataexport.message']}" escape="false">
                                                     <f:param value="#{dataverseServiceBean.findRootDataverse().displayName}"/>
-                                                    <f:param value="&lt;a href=&#34;#{systemConfig.guidesBaseUrl}/#{systemConfig.version}/api&#34; target=&#34;_blank&#34;&gt;"/>
+                                                    <f:param value="&lt;a href=&#34;#{systemConfig.guidesBaseUrl}/#{systemConfig.guidesVersion}/api&#34; target=&#34;_blank&#34;&gt;"/>
                                                     <f:param value="&lt;/a&gt;"/>
                                                 </h:outputFormat>
                                             </p>

src/main/webapp/dataset-widgets.xhtml

@@ -35,14 +35,14 @@
                             <li>
                                 <h:outputFormat value="#{bundle['dataset.widgets.notPublished.how.tip3']}" escape="false">
                                     <f:param value="#{systemConfig.guidesBaseUrl}"/>
-                                    <f:param value="#{systemConfig.version}"/>
+                                    <f:param value="#{systemConfig.guidesVersion}"/>
                                 </h:outputFormat>
                             </li>
                         </ul>
                         <p>
                             <h:outputFormat value="#{bundle['dataset.widgets.notPublished.getStarted']}" escape="false">
                                 <f:param value="#{systemConfig.guidesBaseUrl}"/>
-                                <f:param value="#{systemConfig.version}"/>
+                                <f:param value="#{systemConfig.guidesVersion}"/>
                             </h:outputFormat>
                         </p>
                     </div>
@@ -52,7 +52,7 @@
                     <p class="help-block"><span class="glyphicon glyphicon-info-sign"/> 
                         <h:outputFormat value=" #{bundle['dataset.widgets.tip']}" escape="false">
                             <f:param value="#{systemConfig.guidesBaseUrl}"/>
-                            <f:param value="#{systemConfig.version}"/>
+                            <f:param value="#{systemConfig.guidesVersion}"/>
                         </h:outputFormat>
                     </p>
                     <div>