Merge branch 'develop' of https://github.com/IQSS/dataverse into develop

doc/sphinx-guides/source/admin/dataverses-datasets.rst

@@ -103,5 +103,5 @@ As a superuser, click "Update Current Version" when publishing. (This option is
 Diagnose Constraint Violations Issues in Datasets
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-To identifiy invalid data values in specific datasets (if, for example, an attempt to edit a dataset results in a ConstraintViolationException in the server log), or to check all the datasets in the Dataverse for constraint violations, see :ref:`Dataset Validation <dataset-validation-api>` in the :doc:`/api/native-api` section of the User Guide.
+To identify invalid data values in specific datasets (if, for example, an attempt to edit a dataset results in a ConstraintViolationException in the server log), or to check all the datasets in the Dataverse for constraint violations, see :ref:`Dataset Validation <dataset-validation-api>` in the :doc:`/api/native-api` section of the User Guide.
 

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

@@ -100,9 +100,18 @@ It returns a zipped bundle that contains the data in the following formats:
 * Data (Variable) metadata record, in DDI XML;
 * File citation, in Endnote and RIS formats. 
 
+
 Parameters: 
 ~~~~~~~~~~~
-none.
+
+``fileMetadataId``
+
+==============  ===========
+Value           Description
+==============  ===========
+ID              Exports file with specific file metadata ``ID``.
+==============  ===========
+
 
 Data Variable Metadata Access
 -----------------------------
@@ -177,6 +186,19 @@ Example:
       </dataDscr>
    </codeBook>
 
+
+Parameters: 
+~~~~~~~~~~~
+
+``fileMetadataId``
+
+==============  ===========
+Value           Description
+==============  ===========
+ID              Exports file with specific file metadata ``ID``. For example for data file with id 6 and file metadata id 2: ``curl 'http://localhost:8080/api/access/datafile/6/metadata/ddi?fileMetadataId=2'``
+==============  ===========
+
+
 More information on DDI is available in the :doc:`/user/tabulardataingest/ingestprocess` section of the User Guide.
 
 Advanced options/Parameters: 

doc/sphinx-guides/source/developers/making-releases.rst

@@ -5,7 +5,7 @@ Making Releases
 .. contents:: |toctitle|
 	:local:
 
-Use the number of the milestone with a "v" in front for the relase tag. For example: ``v4.6.2``.
+Use the number of the milestone with a "v" in front for the release tag. For example: ``v4.6.2``.
 
 Create the release GitHub issue and branch 
 ------------------------------------------
@@ -32,18 +32,7 @@ Add the version being released to the lists in the following two files:
 
 Here's an example commit where three of the four files above were updated at once: https://github.com/IQSS/dataverse/commit/99e23f96ec362ac2f524cb5cd80ca375fa13f196
 
-2. Save the EJB Database Create Script
-======================================
-
-Save the script ``domains/domain1/generated/ejb/dataverse/dataverse_VDCNet-ejbPU_createDDL.jdbc`` created by EJB during the deployment of the release candidate. **Important:** add semicolons to the ends of the SQL commands in the EJB-generated file (see below)! Save the resulting file as ``scripts/database/create/create_v{VERSION_TAG}.sql`` using the version number tag for the release. For example: 
-
-.. code-block:: none
-
-	sed 's/$/;/' dataverse_VDCNet-ejbPU_createDDL.jdbc > scripts/database/create/create_v4.10.sql
-
-(We are saving the script above to support the new experimental process for updating the database across multiple versions; see ``scripts/database/README_upgrade_across_versions.txt`` for more information.)
-
-3. Check in the Changes Above... 
+2. Check in the Changes Above...
 ================================
 
 ... into the release branch, make a pull request and merge the release branch into develop. 

src/main/java/ValidationMessages.properties

@@ -3,7 +3,7 @@ user.lastName=Please enter your last name.
 user.invalidEmail=Please enter a valid email address.
 user.enterUsername=Please enter a username.
 user.usernameLength=Username must be between 2 and 60 characters.
-user.illegalCharacters=Found an illegal character(s). Valid characters are a-Z, 0-9, '_', '-', and '.'."
+user.illegalCharacters=Found an illegal character(s). Valid characters are a-Z, 0-9, '_', '-', and '.'.
 
 user.enterNickname=Please enter a nickname.
 user.nicknameLength=Nickname must be at most 30 characters.
@@ -46,4 +46,4 @@ password.retype=The new password is blank: re-type it again.
 password.current=Please enter your current password.
 password.validate=Password reset page default email message.
 
-guestbook.name=Enter a name for the guestbook
+guestbook.name=Enter a name for the guestbook

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

@@ -39,6 +39,7 @@ public class ConfigureFragmentBean implements java.io.Serializable{
     private Long fileId = null;
     private ExternalToolHandler toolHandler = null;
     private String messageApi = "";
+    private Long fileMetadataId = null;
 
     @EJB
     DataFileServiceBean datafileService;
@@ -95,7 +96,7 @@ public ExternalToolHandler getConfigurePopupToolHandler() {
         }
 
 
-        toolHandler = new ExternalToolHandler(tool, datafileService.find(fileId), apiToken);
+        toolHandler = new ExternalToolHandler(tool, datafileService.find(fileId), apiToken, datafileService.findFileMetadata(fileMetadataId));
 
         return toolHandler;
     }
@@ -116,8 +117,10 @@ public void  generateApiToken() {
 
     }
 
-    public void setConfigureFileId(Long setFileId) {
+    public void setConfigureIds(Long setFileId, Long setFileMetadataId) {
+
         fileId = setFileId;
+        fileMetadataId = setFileMetadataId;
     }
 
     public String getMessageApi() {

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

@@ -1853,7 +1853,7 @@ public String getJsonLd() {
                 } else {
                     if (FileUtil.isPubliclyDownloadable(fileMetadata)) {
                         String nullDownloadType = null;
-                        fileObject.add("contentUrl", dataverseSiteUrl + FileUtil.getFileDownloadUrlPath(nullDownloadType, fileMetadata.getDataFile().getId(), false));
+                        fileObject.add("contentUrl", dataverseSiteUrl + FileUtil.getFileDownloadUrlPath(nullDownloadType, fileMetadata.getDataFile().getId(), false, fileMetadata.getId()));
                     }
                 }
                 fileArray.add(fileObject);

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

@@ -109,7 +109,7 @@ public void writeGuestbookAndStartBatchDownload(GuestbookResponse guestbookRespo
                 writeGuestbookResponseRecord(guestbookResponse);
             }
 
-            redirectToDownloadAPI(guestbookResponse.getFileFormat(), fileId, true);
+            redirectToDownloadAPI(guestbookResponse.getFileFormat(), fileId, true, null);
             return;
         }
 
@@ -138,7 +138,7 @@ public void writeGuestbookAndStartFileDownload(GuestbookResponse guestbookRespon
         }
 
         // Make sure to set the "do not write Guestbook response" flag to TRUE when calling the Access API:
-        redirectToDownloadAPI(format, fileMetadata.getDataFile().getId(), true);
+        redirectToDownloadAPI(format, fileMetadata.getDataFile().getId(), true, fileMetadata.getId());
         logger.fine("issued file download redirect for filemetadata "+fileMetadata.getId()+", datafile "+fileMetadata.getDataFile().getId());
     }
 
@@ -215,8 +215,8 @@ private void redirectToBatchDownloadAPI(String multiFileString, Boolean guestboo
 
     }
 
-    private void redirectToDownloadAPI(String downloadType, Long fileId, boolean guestBookRecordAlreadyWritten) {
-        String fileDownloadUrl = FileUtil.getFileDownloadUrlPath(downloadType, fileId, guestBookRecordAlreadyWritten);
+    private void redirectToDownloadAPI(String downloadType, Long fileId, boolean guestBookRecordAlreadyWritten, Long fileMetadataId) {
+        String fileDownloadUrl = FileUtil.getFileDownloadUrlPath(downloadType, fileId, guestBookRecordAlreadyWritten, fileMetadataId);
         logger.fine("Redirecting to file download url: " + fileDownloadUrl);
         try {
             FacesContext.getCurrentInstance().getExternalContext().redirect(fileDownloadUrl);
@@ -226,7 +226,7 @@ private void redirectToDownloadAPI(String downloadType, Long fileId, boolean gue
     }
 
     private void redirectToDownloadAPI(String downloadType, Long fileId) {
-        redirectToDownloadAPI(downloadType, fileId, true);
+        redirectToDownloadAPI(downloadType, fileId, true, null);
     }
 
     private void redirectToBatchDownloadAPI(String multiFileString, Boolean downloadOriginal){
@@ -258,7 +258,7 @@ public void explore(GuestbookResponse guestbookResponse, FileMetadata fmd, Exter
         if(dataFile.getFileMetadata()==null) {
             dataFile=datafileService.find(dataFile.getId());
         }
-        ExternalToolHandler externalToolHandler = new ExternalToolHandler(externalTool, dataFile, apiToken);
+        ExternalToolHandler externalToolHandler = new ExternalToolHandler(externalTool, dataFile, apiToken, fmd);
         // Back when we only had TwoRavens, the downloadType was always "Explore". Now we persist the name of the tool (i.e. "TwoRavens", "Data Explorer", etc.)
         guestbookResponse.setDownloadtype(externalTool.getDisplayName());
         String toolUrl = externalToolHandler.getToolUrlWithQueryParams();
@@ -479,4 +479,4 @@ public void sendRequestFileAccessNotification(Dataset dataset, Long fileId, Auth
 
 
 
-}
+}

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

@@ -182,7 +182,7 @@ public class Access extends AbstractApiBean {
     @Path("datafile/bundle/{fileId}")
     @GET
     @Produces({"application/zip"})
-    public BundleDownloadInstance datafileBundle(@PathParam("fileId") String fileId, @QueryParam("gbrecs") boolean gbrecs, @QueryParam("key") String apiToken, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/ {
+    public BundleDownloadInstance datafileBundle(@PathParam("fileId") String fileId, @QueryParam("fileMetadataId") Long fileMetadataId,@QueryParam("gbrecs") boolean gbrecs, @QueryParam("key") String apiToken, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/ {
 
 
         GuestbookResponse gbr = null;
@@ -207,9 +207,14 @@ public BundleDownloadInstance datafileBundle(@PathParam("fileId") String fileId,
 
         DownloadInfo dInfo = new DownloadInfo(df);
         BundleDownloadInstance downloadInstance = new BundleDownloadInstance(dInfo);
-
-        FileMetadata fileMetadata = df.getFileMetadata();
-        DatasetVersion datasetVersion = df.getOwner().getLatestVersion();
+
+        FileMetadata fileMetadata = null;
+
+        if (fileMetadataId == null) {
+            fileMetadata = df.getFileMetadata();
+        } else {
+            fileMetadata = dataFileService.findFileMetadata(fileMetadataId);
+        }
 
         downloadInstance.setFileCitationEndNote(new DataCitation(fileMetadata).toEndNoteString());
         downloadInstance.setFileCitationRIS(new DataCitation(fileMetadata).toRISString());
@@ -223,7 +228,8 @@ public BundleDownloadInstance datafileBundle(@PathParam("fileId") String fileId,
                     dfId,
                     outStream,
                     null,
-                    null);
+                    null,
+                    fileMetadataId);
 
             downloadInstance.setFileDDIXML(outStream.toString());
 
@@ -382,8 +388,8 @@ public DownloadInstance datafile(@PathParam("fileId") String fileId, @QueryParam
     @Path("datafile/{fileId}/metadata")
     @GET
     @Produces({"text/xml"})
-    public String tabularDatafileMetadata(@PathParam("fileId") String fileId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException, ServiceUnavailableException /*, PermissionDeniedException, AuthorizationRequiredException*/ { 
-        return tabularDatafileMetadataDDI(fileId, exclude, include, header, response);
+    public String tabularDatafileMetadata(@PathParam("fileId") String fileId, @QueryParam("fileMetadataId") Long fileMetadataId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException, ServiceUnavailableException /*, PermissionDeniedException, AuthorizationRequiredException*/ {
+        return tabularDatafileMetadataDDI(fileId, fileMetadataId, exclude, include, header, response);
     }
 
     /* 
@@ -393,7 +399,7 @@ public String tabularDatafileMetadata(@PathParam("fileId") String fileId, @Query
     @Path("datafile/{fileId}/metadata/ddi")
     @GET
     @Produces({"text/xml"})
-    public String tabularDatafileMetadataDDI(@PathParam("fileId") String fileId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException, ServiceUnavailableException /*, PermissionDeniedException, AuthorizationRequiredException*/ {
+    public String tabularDatafileMetadataDDI(@PathParam("fileId") String fileId,  @QueryParam("fileMetadataId") Long fileMetadataId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException, ServiceUnavailableException /*, PermissionDeniedException, AuthorizationRequiredException*/ {
         String retValue = "";
 
         DataFile dataFile = null; 
@@ -406,8 +412,16 @@ public String tabularDatafileMetadataDDI(@PathParam("fileId") String fileId, @Qu
         }
 
         response.setHeader("Content-disposition", "attachment; filename=\"dataverse_files.zip\"");
-
-        String fileName = dataFile.getFileMetadata().getLabel().replaceAll("\\.tab$", "-ddi.xml");
+
+        FileMetadata fm = null;
+        if (fileMetadataId == null) {
+            fm = dataFile.getFileMetadata();
+        } else {
+            fm = dataFileService.findFileMetadata(fileMetadataId);
+        }
+
+        String fileName = fm.getLabel().replaceAll("\\.tab$", "-ddi.xml");
+
         response.setHeader("Content-disposition", "attachment; filename=\""+fileName+"\"");
         response.setHeader("Content-Type", "application/xml; name=\""+fileName+"\"");
 
@@ -419,7 +433,8 @@ public String tabularDatafileMetadataDDI(@PathParam("fileId") String fileId, @Qu
                     dataFileId,
                     outStream,
                     exclude,
-                    include);
+                    include,
+                    fileMetadataId);
 
             retValue = outStream.toString();
 
@@ -439,7 +454,7 @@ public String tabularDatafileMetadataDDI(@PathParam("fileId") String fileId, @Qu
     @GET
     @Produces({ "application/xml" })
 
-    public String dataVariableMetadataDDI(@PathParam("varId") Long varId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/ {
+    public String dataVariableMetadataDDI(@PathParam("varId") Long varId, @QueryParam("fileMetadataId") Long fileMetadataId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/ {
         String retValue = "";
 
         ByteArrayOutputStream outStream = null;
@@ -450,7 +465,8 @@ public String dataVariableMetadataDDI(@PathParam("varId") Long varId, @QueryPara
                     varId,
                     outStream,
                     exclude,
-                    include);
+                    include,
+                    fileMetadataId);
         } catch (Exception e) {
             // For whatever reason we've failed to generate a partial 
             // metadata record requested. We simply return an empty string.

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

@@ -73,7 +73,7 @@ public class Meta {
     @GET
     @Produces({ "application/xml" })
 
-    public String variable(@PathParam("varId") Long varId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/ {
+    public String variable(@PathParam("varId") Long varId, @QueryParam("fileMetadataId") Long fileMetadataId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) /*throws NotFoundException, ServiceUnavailableException, PermissionDeniedException, AuthorizationRequiredException*/ {
         String retValue = "";
 
         ByteArrayOutputStream outStream = null;
@@ -84,7 +84,8 @@ public String variable(@PathParam("varId") Long varId, @QueryParam("exclude") St
                     varId,
                     outStream,
                     exclude,
-                    include);
+                    include,
+                    fileMetadataId);
         } catch (Exception e) {
             // For whatever reason we've failed to generate a partial 
             // metadata record requested. We simply return an empty string.
@@ -103,7 +104,7 @@ public String variable(@PathParam("varId") Long varId, @QueryParam("exclude") St
     @Path("datafile/{fileId}")
     @GET
     @Produces({"text/xml"})
-    public String datafile(@PathParam("fileId") Long fileId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException, ServiceUnavailableException /*, PermissionDeniedException, AuthorizationRequiredException*/ {
+    public String datafile(@PathParam("fileId") Long fileId, @QueryParam("fileMetadataId") Long fileMetadataId, @QueryParam("exclude") String exclude, @QueryParam("include") String include, @Context HttpHeaders header, @Context HttpServletResponse response) throws NotFoundException, ServiceUnavailableException /*, PermissionDeniedException, AuthorizationRequiredException*/ {
         String retValue = "";
 
         DataFile dataFile = null; 
@@ -129,7 +130,8 @@ public String datafile(@PathParam("fileId") Long fileId, @QueryParam("exclude")
                     fileId,
                     outStream,
                     exclude,
-                    include);
+                    include,
+                    fileMetadataId);
 
             retValue = outStream.toString();
 

src/main/java/edu/harvard/iq/dataverse/datavariable/VariableMetadata.java

@@ -56,6 +56,12 @@ public class VariableMetadata implements Serializable  {
     @Column(columnDefinition="TEXT")
     private String literalquestion;
 
+    /**
+     * postquestion: post question, metadata variable field.
+     */
+    @Column(columnDefinition="TEXT")
+    private String postquestion;
+
     /**
      * interviewinstruction: Interview Instruction, metadata variable field.
      */
@@ -147,6 +153,10 @@ public void setLiteralquestion(String literalquestion) {
         this.literalquestion = literalquestion;
     }
 
+    public String getPostquestion() {return this.postquestion;}
+
+    public void setPostquestion(String postquestion) {this.postquestion = postquestion;}
+
     public String getInterviewinstruction() {
         return this.interviewinstruction;
     }

src/main/java/edu/harvard/iq/dataverse/datavariable/VariableMetadataDDIParser.java

@@ -164,6 +164,9 @@ private void processQstn(XMLStreamReader xmlr, VariableMetadata newVM) throws XM
                 } else if (xmlr.getLocalName().equals("ivuInstr")) {
                     String text = parseText(xmlr, false);
                     newVM.setInterviewinstruction(text);
+                } else if (xmlr.getLocalName().equals("postQTxt")) {
+                    String text = parseText(xmlr, false);
+                    newVM.setPostquestion(text);
                 }
             } else if (event == XMLStreamConstants.END_ELEMENT) {
                 if (xmlr.getLocalName().equals("qstn")) return;