Merge pull request #3000 from IQSS/2606-citation-date

added backend support for alternate citation dates #2606
IQSS · Mar 8, 2016 · 0e6f43b · 0e6f43b
2 parents 10a905f + 44dd4f6
commit 0e6f43b
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Showing 8 changed files with 220 additions and 24 deletions.
diff --git a/doc/sphinx-guides/source/api/native-api.rst b/doc/sphinx-guides/source/api/native-api.rst
@@ -139,6 +139,17 @@ Deletes the draft version of dataset ``$id``. Only the draft version can be dele
 
     DELETE http://$SERVER/api/datasets/$id/versions/:draft?key=$apiKey
 
+Sets the dataset field type to be used as the citation date for the given dataset (if the dataset does not include the dataset field type, the default logic is used). The name of the dataset field type should be sent in the body of the reqeust.
+To revert to the default logic, use ``:publicationDate`` as the ``$datasetFieldTypeName``.
+Note that the dataset field used has to be a date field::
+
+    PUT http://$SERVER/api/datasets/$id/citationdate?key=$apiKey
+    
+Restores the default logic of the field type to be used as the citation date. Same as ``PUT`` with ``:publicationDate`` body::
+    
+    DELETE http://$SERVER/api/datasets/$id/citationdate?key=$apiKey
+
+
 Builtin Users
 ~~~~~
 

diff --git a/scripts/database/upgrades/upgrade_v4.2.4_to_4.3.sql b/scripts/database/upgrades/upgrade_v4.2.4_to_4.3.sql
@@ -25,4 +25,12 @@ drop column sizeofcollection,
 drop column specialpermissions, 
 drop column studycompletion, 
 drop column termsofaccess, 
-drop column termsofuse;
+drop column termsofuse;
+
+-- Add new foreign ket to dataset for citation date (from datasetfieldtype)
+ALTER TABLE dataset ADD COLUMN citationdatedatasetfieldtype_id bigint;
+
+ALTER TABLE dataset
+  ADD CONSTRAINT fk_dataset_citationdatedatasetfieldtype_id FOREIGN KEY (citationdatedatasetfieldtype_id)
+      REFERENCES datasetfieldtype (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION;
diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataset.java b/src/main/java/edu/harvard/iq/dataverse/Dataset.java
@@ -13,6 +13,7 @@
 import javax.persistence.Entity;
 import javax.persistence.Index;
 import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
 import javax.persistence.NamedQueries;
 import javax.persistence.NamedQuery;
 import javax.persistence.OneToMany;
@@ -81,6 +82,18 @@ public void setDatasetLinkingDataverses(List<DatasetLinkingDataverse> datasetLin
     private boolean fileAccessRequest;
     @OneToMany(mappedBy = "dataset", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     private List<DataFileCategory> dataFileCategories = null;
+
+    @ManyToOne
+    @JoinColumn(name = "citationDateDatasetFieldType_id")
+    private DatasetFieldType citationDateDatasetFieldType;
+
+    public DatasetFieldType getCitationDateDatasetFieldType() {
+        return citationDateDatasetFieldType;
+    }
+
+    public void setCitationDateDatasetFieldType(DatasetFieldType citationDateDatasetFieldType) {
+        this.citationDateDatasetFieldType = citationDateDatasetFieldType;
+    }    
 
     public Dataset() {
         //this.versions = new ArrayList();

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -121,7 +121,16 @@ public List<Dataset> findAllOrSubset(long numPartitions, long partitionId, boole
         typedQuery.setParameter("partitionId", partitionId);
         return typedQuery.getResultList();
     }
-
+
+    /**
+     * Merges the passed dataset to the persistence context.
+     * @param ds the dataset whose new state we want to persist.
+     * @return The managed entity representing {@code ds}.
+     */
+    public Dataset merge( Dataset ds ) {
+        return em.merge(ds);
+    }
+
     public Dataset findByGlobalId(String globalId) {
 
         String protocol = "";

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
@@ -1,8 +1,10 @@
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.DatasetFieldType.FieldType;
 import edu.harvard.iq.dataverse.util.StringUtil;
 import java.io.Serializable;
 import java.sql.Timestamp;
+import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -12,6 +14,8 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -664,30 +668,40 @@ public String getCitation(boolean isOnlineVersion) {
         } else {
             str += getDatasetProducersString();
         }
+
+        Date citationDate = getCitationDate();    
+        if (citationDate != null) {
+          if (!StringUtil.isEmpty(str)) {
+                str += ", ";
+            }      
+          str += new SimpleDateFormat("yyyy").format(citationDate);
+
+        } else {
+            if (this.getDataset().getPublicationDate() == null || StringUtil.isEmpty(this.getDataset().getPublicationDate().toString())) {
 
-        if (this.getDataset().getPublicationDate() == null || StringUtil.isEmpty(this.getDataset().getPublicationDate().toString())) {
-
-            if (!this.getDataset().isHarvested()) {
-                //if not released use current year
-                if (!StringUtil.isEmpty(str)) {
-                    str += ", ";
-                }
-                str += new SimpleDateFormat("yyyy").format(new Timestamp(new Date().getTime()));
-            } else {
-                String distDate = getDistributionDate();
-                if (distDate != null) {
+                if (!this.getDataset().isHarvested()) {
+                    //if not released use current year
                     if (!StringUtil.isEmpty(str)) {
                         str += ", ";
                     }
-                    str += distDate;
+                    str += new SimpleDateFormat("yyyy").format(new Timestamp(new Date().getTime()));
+                } else {
+                    String distDate = getDistributionDate();
+                    if (distDate != null) {
+                        if (!StringUtil.isEmpty(str)) {
+                            str += ", ";
+                        }
+                        str += distDate;
+                    }
                 }
+            } else {
+                if (!StringUtil.isEmpty(str)) {
+                    str += ", ";
+                }
+                str += new SimpleDateFormat("yyyy").format(new Timestamp(this.getDataset().getPublicationDate().getTime()));
             }
-        } else {
-            if (!StringUtil.isEmpty(str)) {
-                str += ", ";
-            }
-            str += new SimpleDateFormat("yyyy").format(new Timestamp(this.getDataset().getPublicationDate().getTime()));
         }
+
         if (this.getTitle() != null) {
             if (!StringUtil.isEmpty(this.getTitle())) {
                 if (!StringUtil.isEmpty(str)) {
@@ -780,6 +794,31 @@ public String getCitation(boolean isOnlineVersion) {
          }*/
         return str;
     }
+
+    private Date getCitationDate() {
+        DatasetField citationDate = getDatasetField(this.getDataset().getCitationDateDatasetFieldType());        
+        if (citationDate != null && citationDate.getDatasetFieldType().getFieldType().equals(FieldType.DATE)){          
+            try {  
+                return new SimpleDateFormat("yyyy").parse( citationDate.getValue() );
+            } catch (ParseException ex) {
+                Logger.getLogger(DatasetVersion.class.getName()).log(Level.SEVERE, null, ex);
+            }
+        }
+
+        return null;
+    }
+
+    public DatasetField getDatasetField(DatasetFieldType dsfType) {
+        if (dsfType != null) {
+            for (DatasetField dsf : this.getFlatDatasetFields()) {
+                if (dsf.getDatasetFieldType().equals(dsfType)) {
+                    return dsf;
+                }
+            }
+        }
+        return null;
+
+    }
 
     public String getDistributionDate() {
         //todo get dist date from datasetfieldvalue table

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java b/src/main/java/edu/harvard/iq/dataverse/api/AbstractApiBean.java
@@ -31,14 +31,19 @@
 import edu.harvard.iq.dataverse.util.json.JsonParser;
 import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
 import edu.harvard.iq.dataverse.validation.BeanValidationServiceBean;
+import java.io.StringReader;
 import java.net.URI;
 import java.util.concurrent.Callable;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.json.Json;
 import javax.json.JsonArrayBuilder;
+import javax.json.JsonObject;
 import javax.json.JsonObjectBuilder;
+import javax.json.JsonReader;
+import javax.json.JsonValue;
+import javax.json.JsonValue.ValueType;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.servlet.http.HttpServletRequest;
@@ -83,10 +88,39 @@ public Response getResponse() {
          */
         public Response refineResponse( String message ) {
             final Status statusCode = Response.Status.fromStatusCode(response.getStatus());
-            final Throwable cause = getCause();
-            return errorResponse(statusCode, message
-                    + (cause!=null ? " "+cause.getMessage() : "")
-                    + " (" + statusCode.toString() + ")" );
+            String baseMessage = getWrappedMessageWhenJson();
+
+            if ( baseMessage == null ) {
+                final Throwable cause = getCause();
+                baseMessage = (cause!=null ? cause.getMessage() : "");
+            }
+            return errorResponse(statusCode, message+" "+baseMessage);
+        }
+
+        /**
+         * In the common case of the wrapped response being of type JSON,
+         * return the message field it has (if any).
+         * @return the content of a message field, or {@code null}.
+         */
+        String getWrappedMessageWhenJson() {
+            if ( response.getMediaType().equals(MediaType.APPLICATION_JSON_TYPE) ) {
+                Object entity = response.getEntity();
+                if ( entity == null ) return null;
+
+                String json = entity.toString();
+                try ( StringReader rdr = new StringReader(json) ){
+                    JsonReader jrdr = Json.createReader(rdr);
+                    JsonObject obj = jrdr.readObject();
+                    if ( obj.containsKey("message") ) {
+                        JsonValue message = obj.get("message");
+                        return message.getValueType() == ValueType.STRING ? obj.getString("message") : message.toString();
+                    } else {
+                        return null;
+                    }
+                }
+            } else {
+                return null;
+            }
         }
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.DOIEZIdServiceBean;
 import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.DatasetField;
+import edu.harvard.iq.dataverse.DatasetFieldType;
 import edu.harvard.iq.dataverse.DatasetServiceBean;
 import edu.harvard.iq.dataverse.DatasetVersion;
 import edu.harvard.iq.dataverse.Dataverse;
@@ -22,6 +23,7 @@
 import edu.harvard.iq.dataverse.engine.command.impl.GetLatestPublishedDatasetVersionCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.ListVersionsCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetCommand;
+import edu.harvard.iq.dataverse.engine.command.impl.SetDatasetCitationDateCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetTargetURLCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
 import edu.harvard.iq.dataverse.export.DDIExportServiceBean;
@@ -124,7 +126,42 @@ public Response destroyDataset( @PathParam("id") Long id) {
 		} catch (WrappedResponse ex) {
 			return ex.refineResponse( "Failed to detroy dataset " + id );
 		}		
-	}        
+	}
+
+	@PUT
+	@Path("{id}/citationdate")
+	public Response setCitationDate( @PathParam("id") Long id, String dsfTypeName) {
+            try {
+                if ( dsfTypeName.trim().isEmpty() ){
+                    throw new WrappedResponse( badRequest("Please provide a dataset field type in the requst body.") );
+                }
+                DatasetFieldType dsfType = null;
+                if (!":publicationDate".equals(dsfTypeName)) {
+                    dsfType = datasetFieldSvc.findByName(dsfTypeName);
+                    if (dsfType == null) {
+                        throw new WrappedResponse( badRequest("Dataset Field Type Name " + dsfTypeName + " not found.") );
+                    }
+                }
+
+                execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), dsfType));
+
+                return okResponse("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default"));
+
+            } catch (WrappedResponse ex) {
+                return ex.refineResponse("Unable to set citation date for dataset " + id + ".");
+            }
+	}    
+
+	@DELETE
+	@Path("{id}/citationdate")
+	public Response useDefaultCitationDate( @PathParam("id") Long id) {
+            try {
+                execCommand(new SetDatasetCitationDateCommand(createDataverseRequest(findUserOrDie()), findDatasetOrDie(id), null));
+                return okResponse("Citation Date for dataset " + id + " set to default");
+            } catch (WrappedResponse ex) {
+                return ex.refineResponse("Unable to restore default citation date for dataset " + id + ".");
+            }
+	}         
 
 	@GET
 	@Path("{id}/versions")

diff --git a/...main/java/edu/harvard/iq/dataverse/engine/command/impl/SetDatasetCitationDateCommand.java b/...main/java/edu/harvard/iq/dataverse/engine/command/impl/SetDatasetCitationDateCommand.java
@@ -0,0 +1,45 @@
+package edu.harvard.iq.dataverse.engine.command.impl;
+
+import edu.harvard.iq.dataverse.Dataset;
+import edu.harvard.iq.dataverse.DatasetFieldType;
+import edu.harvard.iq.dataverse.DatasetFieldType.FieldType;
+import edu.harvard.iq.dataverse.authorization.Permission;
+import edu.harvard.iq.dataverse.engine.command.AbstractCommand;
+import edu.harvard.iq.dataverse.engine.command.CommandContext;
+import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
+import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
+import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
+import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
+
+/**
+ *
+ * @author gdurand
+ */
+@RequiredPermissions( Permission.PublishDataset )
+public class SetDatasetCitationDateCommand extends AbstractCommand<Dataset>{
+
+
+	private final DatasetFieldType dsfType;
+	private final Dataset dataset;
+
+	public SetDatasetCitationDateCommand( DataverseRequest aRequest, Dataset dataset, DatasetFieldType dsfType ) {
+		super( aRequest, dataset );
+		this.dataset = dataset;
+		this.dsfType = dsfType;
+	}
+
+	@Override
+	public Dataset execute(CommandContext ctxt) throws CommandException {
+            if ( dsfType == null || dsfType.getFieldType().equals(FieldType.DATE) ) {
+                dataset.setCitationDateDatasetFieldType(dsfType);           
+            } else {
+                throw new IllegalCommandException("Provided DatasetFieldtype is not a Date", this);
+            }
+
+            Dataset savedDataset = ctxt.datasets().merge(dataset);
+            ctxt.index().indexDataset(savedDataset, false); 
+            return savedDataset;
+	}
+
+}
+