Use more generics, less trailing whitespace in the dataverse package (#775)

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

@@ -149,7 +149,7 @@ public DataTable getDataTable() {
 
     public void setDataTable(DataTable dt) {
         if (this.getDataTables() == null) {
-            this.setDataTables( new ArrayList() );
+            this.setDataTables( new ArrayList<DataTable>() );
         } else {
             this.getDataTables().clear();
         }
@@ -191,7 +191,7 @@ public IngestReport getIngestReport() {
 
     public void setIngestReport(IngestReport report) {
         if (ingestReports == null) {
-            ingestReports = new ArrayList();
+            ingestReports = new ArrayList<IngestReport>();
         } else {
             ingestReports.clear();
         }
@@ -508,11 +508,11 @@ public String getMapItFileDownloadURL(String serverName){
         return serverName + "/api/access/datafile/" + this.getId();
     }
 
-    /* 
+    /**
      * If this is tabular data, the corresponding dataTable may have a UNF -
      * "numeric fingerprint" signature - generated:
+     * @return the file's UNF or null if it doesn't exist
      */
-
     public String getUnf() {
         if (this.isTabularData()) {
             // (isTabularData() method above verifies that that this file
@@ -530,6 +530,10 @@ public String getUnf() {
     inverseJoinColumns = @JoinColumn(name = "authenticated_user_id"))
     private List<AuthenticatedUser> fileAccessRequesters;
 
+    /**
+     * Get the users who requested access to this file.
+     * @return a list of AuthenticatedUsers who requested access to this file
+     */
     public List<AuthenticatedUser> getFileAccessRequesters() {
         return fileAccessRequesters;
     }

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

@@ -21,6 +21,7 @@
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.Query;
+import javax.persistence.TypedQuery;
 
 /**
  *
@@ -118,7 +119,7 @@ public class DataFileServiceBean implements java.io.Serializable {
     private static final String MIME_TYPE_UNDETERMINED_BINARY = "application/binary";
 
     public DataFile find(Object pk) {
-        return (DataFile) em.find(DataFile.class, pk);
+        return em.find(DataFile.class, pk);
     }   
 
     /*public DataFile findByMD5(String md5Value){
@@ -136,14 +137,14 @@ public List<DataFile> findByDatasetId(Long studyId) {
            Sure, we don't have *studies* any more, in 4.0; it's a tribute 
            to the past. -- L.A.
         */
-        Query query = em.createQuery("select o from DataFile o where o.owner.id = :studyId order by o.id");
+        TypedQuery<DataFile> query = em.createQuery("select o from DataFile o where o.owner.id = :studyId order by o.id", DataFile.class);
         query.setParameter("studyId", studyId);
         return query.getResultList();
     }  
 
     public List<DataFile> findIngestsInProgress() {
         if ( em.isOpen() ) {
-            Query query = em.createQuery("select object(o) from DataFile as o where o.ingestStatus =:scheduledStatusCode or o.ingestStatus =:progressStatusCode order by o.id");
+            TypedQuery<DataFile> query = em.createQuery("select object(o) from DataFile as o where o.ingestStatus =:scheduledStatusCode or o.ingestStatus =:progressStatusCode order by o.id", DataFile.class);
             query.setParameter("scheduledStatusCode", DataFile.INGEST_STATUS_SCHEDULED);
             query.setParameter("progressStatusCode", DataFile.INGEST_STATUS_INPROGRESS);
             return query.getResultList();
@@ -160,7 +161,7 @@ public DataTable findDataTableByFileId(Long fileId) {
     }
 
     public List<DataFile> findAll() {
-        return em.createQuery("select object(o) from DataFile as o order by o.id").getResultList();
+        return em.createQuery("select object(o) from DataFile as o order by o.id", DataFile.class).getResultList();
     }
 
     public DataFile save(DataFile dataFile) {
@@ -170,9 +171,9 @@ public DataFile save(DataFile dataFile) {
     }
 
     public Boolean isPreviouslyPublished(Long fileId){
-        Query query = em.createQuery("select object(o) from FileMetadata as o where o.dataFile.id =:fileId");
+        TypedQuery<FileMetadata> query = em.createQuery("select object(o) from FileMetadata as o where o.dataFile.id =:fileId", FileMetadata.class);
         query.setParameter("fileId", fileId);
-        List retList = query.getResultList();
+        List<FileMetadata> retList = query.getResultList();
         return (retList.size() > 1);
     }
 
@@ -331,6 +332,9 @@ public boolean ingestableAsTabular(DataFile dataFile) {
          * main code base, so we can just go through a hard-coded list of mime 
          * types. -- L.A. 
          */
+        if (dataFile == null) {
+            return false;
+        }
 
         String mimeType = dataFile.getContentType();
 
@@ -372,6 +376,10 @@ public String getFileClassById (Long fileId) {
     }
 
     public String getFileClass (DataFile file) {
+        if (file == null) {
+            return null;
+        }
+
         if (isFileClassImage(file)) {
             return FILE_CLASS_IMAGE;
         }

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

@@ -81,7 +81,7 @@ public enum TagType {Survey, TimeSeries, Panel, Event, Genomics, Network, Geospa
     }
 
     public static List<String> listTags() {
-        List<String> retlist = new ArrayList();
+        List<String> retlist = new ArrayList<>();
 
         for(TagType t : TagType.values()) {
             retlist.add(TagTypeToLabels.get(t));

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

@@ -57,47 +57,47 @@ public DataTable() {
     @Column( nullable = false )
     private String unf;
 
-    /*
+    /**
      * caseQuantity: Number of observations
      */
     private Long caseQuantity;
 
 
-    /*
+    /**
      * varQuantity: Number of variables
      */
     private Long varQuantity;
 
-    /*
+    /**
      * recordsPerCase: this property is specific to fixed-field data files
      * in which rows of observations may represented by *multiple* lines.
      * The only known use case (so far): the fixed-width data files from
      * ICPSR.
      */
     private Long recordsPerCase;
 
-     /*
+    /**
      * DataFile that stores the data for this DataTable
      */
     @ManyToOne
     @JoinColumn(nullable=false)
     private DataFile dataFile;
 
-     /*
+    /**
      * DataVariables in this DataTable:
      */
     @OneToMany (mappedBy="dataTable", cascade={ CascadeType.REMOVE, CascadeType.MERGE,CascadeType.PERSIST})
     @OrderBy ("fileOrder")
     private List<DataVariable> dataVariables;
 
-    /* 
+    /**
      * originalFileType: the format of the file from which this data table was
      * extracted (STATA, SPSS, R, etc.)
      * Note: this was previously stored in the StudyFile.
      */
     private String originalFileFormat;
 
-    /*
+    /**
      * originalFormatVersion: the version/release number of the original file
      * format; for example, STATA 9, SPSS 12, etc.
      */

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

@@ -42,7 +42,7 @@ public class Dataset extends DvObjectContainer {
     private static final long serialVersionUID = 1L;
 
     @OneToMany(mappedBy = "owner", cascade = CascadeType.MERGE)
-    private List<DataFile> files = new ArrayList();
+    private List<DataFile> files = new ArrayList<>();
 
     private String protocol;
     private String authority;
@@ -56,7 +56,7 @@ public class Dataset extends DvObjectContainer {
     private String identifier;
     @OneToMany(mappedBy = "dataset", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     @OrderBy("versionNumber DESC, minorVersionNumber DESC")
-    private List<DatasetVersion> versions = new ArrayList();
+    private List<DatasetVersion> versions = new ArrayList<>();
     @OneToOne(mappedBy = "dataset", cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     private DatasetLock datasetLock;
     @OneToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
@@ -87,7 +87,7 @@ public Dataset() {
         DatasetVersion datasetVersion = new DatasetVersion();
         datasetVersion.setDataset(this);
         datasetVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
-        datasetVersion.setFileMetadatas(new ArrayList());
+        datasetVersion.setFileMetadatas(new ArrayList<FileMetadata>());
         datasetVersion.setVersionNumber(new Long(1));
         datasetVersion.setMinorVersionNumber(new Long(0));
         versions.add(datasetVersion);
@@ -218,7 +218,7 @@ public void setVersions(List<DatasetVersion> versions) {
     private DatasetVersion createNewDatasetVersion(Template template) {
         DatasetVersion dsv = new DatasetVersion();
         dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
-        dsv.setFileMetadatas(new ArrayList());
+        dsv.setFileMetadatas(new ArrayList<FileMetadata>());
         DatasetVersion latestVersion = null;
 
         //if the latest version has values get them copied over
@@ -273,7 +273,7 @@ private DatasetVersion createNewDatasetVersion(Template template) {
         if (template == null) {
             getVersions().add(0, dsv);
         } else {
-            this.setVersions(new ArrayList());
+            this.setVersions(new ArrayList<DatasetVersion>());
             getVersions().add(0, dsv);
         }
 
@@ -301,9 +301,9 @@ public DatasetVersion getCreateVersion() {
         dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
         dsv.setDataset(this);
         dsv.setDatasetFields(dsv.initDatasetFields());;
-        dsv.setFileMetadatas(new ArrayList());
+        dsv.setFileMetadatas(new ArrayList<FileMetadata>());
 
-        this.setVersions(new ArrayList());
+        this.setVersions(new ArrayList<DatasetVersion>());
         getVersions().add(0, dsv);
 
         return dsv;

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

@@ -170,7 +170,7 @@ public void setParentDatasetFieldCompoundValue(DatasetFieldCompoundValue parentD
 
     @OneToMany(mappedBy = "parentDatasetField", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     @OrderBy("displayOrder ASC")
-    private List<DatasetFieldCompoundValue> datasetFieldCompoundValues = new ArrayList();
+    private List<DatasetFieldCompoundValue> datasetFieldCompoundValues = new ArrayList<>();
 
     public List<DatasetFieldCompoundValue> getDatasetFieldCompoundValues() {
         return datasetFieldCompoundValues;
@@ -182,7 +182,7 @@ public void setDatasetFieldCompoundValues(List<DatasetFieldCompoundValue> datase
 
     @OneToMany(mappedBy = "datasetField", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     @OrderBy("displayOrder ASC")
-    private List<DatasetFieldValue> datasetFieldValues = new ArrayList();
+    private List<DatasetFieldValue> datasetFieldValues = new ArrayList<>();
 
     public List<DatasetFieldValue> getDatasetFieldValues() {
         return this.datasetFieldValues;
@@ -194,7 +194,7 @@ public void setDatasetFieldValues(List<DatasetFieldValue> datasetFieldValues) {
 
     @ManyToMany(cascade = {CascadeType.MERGE})
     @JoinTable(indexes = {@Index(columnList="datasetfield_id"),@Index(columnList="controlledvocabularyvalues_id")})
-    private List<ControlledVocabularyValue> controlledVocabularyValues = new ArrayList();
+    private List<ControlledVocabularyValue> controlledVocabularyValues = new ArrayList<>();
 
     public List<ControlledVocabularyValue> getControlledVocabularyValues() {
         return controlledVocabularyValues;
@@ -271,7 +271,7 @@ public String getCompoundDisplayValue() {
     }
 
     public List<String> getValues() {
-        List returnList = new ArrayList();
+        List<String> returnList = new ArrayList<>();
         if (!datasetFieldValues.isEmpty()) {
             for (DatasetFieldValue dsfv : datasetFieldValues) {
                 returnList.add(dsfv.getValue());

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

@@ -64,7 +64,7 @@ public static DatasetFieldCompoundValue createNewEmptyDatasetFieldCompoundValue(
 
     @OneToMany(mappedBy = "parentDatasetFieldCompoundValue", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     @OrderBy("datasetFieldType ASC")
-    private List<DatasetField> childDatasetFields = new ArrayList();
+    private List<DatasetField> childDatasetFields = new ArrayList<>();
 
     public Long getId() {
         return id;
@@ -134,7 +134,7 @@ public DatasetFieldCompoundValue copy(DatasetField parent) {
     public Map<DatasetField,String> getDisplayValueMap() {
         // todo - this currently only supports child datasetfields with single values
         // need to determine how we would want to handle multiple
-        Map fieldMap = new LinkedHashMap();
+        Map<DatasetField, String> fieldMap = new LinkedHashMap<>();
 
         for (DatasetField childDatasetField : childDatasetFields) {
             // skip the value if it is empty or N/A

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

@@ -29,7 +29,7 @@ public class DatasetFieldServiceBean implements java.io.Serializable {
     private static final String NAME_QUERY = "SELECT dsfType from DatasetFieldType dsfType where dsfType.name= :fieldName";
 
     public List<DatasetFieldType> findAllAdvancedSearchFieldTypes() {
-        return em.createQuery("select object(o) from DatasetFieldType as o where o.advancedSearchFieldType = true and o.title != '' order by o.id").getResultList();
+        return em.createQuery("select object(o) from DatasetFieldType as o where o.advancedSearchFieldType = true and o.title != '' order by o.id", DatasetFieldType.class).getResultList();
     }
 
     public List<DatasetFieldType> findAllFacetableFieldTypes() {
@@ -44,24 +44,24 @@ public List<DatasetFieldType> findFacetableFieldTypesByMetadataBlock(Long metada
     }
 
     public List<DatasetFieldType> findAllRequiredFields() {
-        return em.createQuery("select object(o) from DatasetFieldType as o where o.required = true order by o.id").getResultList();
+        return em.createQuery("select object(o) from DatasetFieldType as o where o.required = true order by o.id", DatasetFieldType.class).getResultList();
     }
 
     public List<DatasetFieldType> findAllOrderedById() {
-        return em.createQuery("select object(o) from DatasetFieldType as o order by o.id").getResultList();
+        return em.createQuery("select object(o) from DatasetFieldType as o order by o.id", DatasetFieldType.class).getResultList();
     }
 
     public List<DatasetFieldType> findAllOrderedByName() {
-        return em.createQuery("select object(o) from DatasetFieldType as o order by o.name").getResultList();
+        return em.createQuery("select object(o) from DatasetFieldType as o order by o.name", DatasetFieldType.class).getResultList();
     }
 
     public DatasetFieldType find(Object pk) {
-        return (DatasetFieldType) em.find(DatasetFieldType.class, pk);
+        return em.find(DatasetFieldType.class, pk);
     }
 
     public DatasetFieldType findByName(String name) {
         try {
-            return  (DatasetFieldType) em.createQuery(NAME_QUERY).setParameter("fieldName", name).getSingleResult();
+            return em.createQuery(NAME_QUERY, DatasetFieldType.class).setParameter("fieldName", name).getSingleResult();
         } catch (NoResultException e) {
             return null;
         }
@@ -107,7 +107,7 @@ public ForeignMetadataFieldMapping findFieldMapping(String formatName, String pa
     }
 
     public ControlledVocabularyValue findControlledVocabularyValue(Object pk) {
-        return (ControlledVocabularyValue) em.find(ControlledVocabularyValue.class, pk);
+        return em.find(ControlledVocabularyValue.class, pk);
     }
 
     /**
@@ -155,8 +155,8 @@ public ControlledVocabAlternate findControlledVocabAlternateByControlledVocabula
         } catch (NoResultException e) {
             return null;
         } catch (NonUniqueResultException ex){
-           List results = typedQuery.getResultList();
-           return (ControlledVocabAlternate) results.get(0);
+           List<ControlledVocabAlternate> results = typedQuery.getResultList();
+           return results.get(0);
         }
     }