Merge pull request #3904 from IQSS/3902-Fixing-lots-of-ugly-code

3902 fixing lots of ugly code
IQSS · Aug 2, 2017 · f23ed5f · f23ed5f
2 parents 5622911 + 29376d0
commit f23ed5f
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Showing 81 changed files with 829 additions and 964 deletions.
diff --git a/src/main/java/edu/harvard/iq/dataverse/BibtexCitation.java b/src/main/java/edu/harvard/iq/dataverse/BibtexCitation.java
@@ -21,7 +21,7 @@
  */
 public class BibtexCitation {
 
-    private List<String> authors = new ArrayList();
+    private List<String> authors = new ArrayList<>();
     private String title;
     private String year;
     private GlobalId persistentId;

diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValueServiceBean.java
@@ -5,13 +5,12 @@
  */
 package edu.harvard.iq.dataverse;
 
-import java.util.ArrayList;
 import java.util.List;
 import javax.ejb.Stateless;
 import javax.inject.Named;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import javax.persistence.TypedQuery;
 
 /**
  *
@@ -27,7 +26,7 @@ public class ControlledVocabularyValueServiceBean implements java.io.Serializabl
     public List<ControlledVocabularyValue> findByDatasetFieldTypeId(Long dsftId) {
 
         String queryString = "select o from ControlledVocabularyValue as o where o.datasetFieldType.id = " + dsftId + " ";
-        Query query = em.createQuery(queryString);
+        TypedQuery<ControlledVocabularyValue> query = em.createQuery(queryString, ControlledVocabularyValue.class);
         return query.getResultList();
 
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
@@ -20,6 +20,7 @@
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.persistence.Query;
+import javax.persistence.TypedQuery;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 import org.jsoup.nodes.Element;
@@ -118,7 +119,7 @@ public boolean testDOIExists(String identifier) {
     }
 
     public HashMap<String, String> getMetadata(String identifier) throws IOException {
-        HashMap<String, String> metadata = new HashMap();
+        HashMap<String, String> metadata = new HashMap<>();
         try (DataCiteRESTfullClient client = openClient()) {
             String xmlMetadata = client.getMetadata(identifier.substring(identifier.indexOf(":") + 1));
             DataCiteMetadataTemplate template = new DataCiteMetadataTemplate(xmlMetadata);
@@ -137,7 +138,7 @@ public HashMap<String, String> getMetadata(String identifier) throws IOException
     }
 
     public DOIDataCiteRegisterCache findByDOI(String doi) {
-        Query query = em.createNamedQuery("DOIDataCiteRegisterCache.findByDoi",
+        TypedQuery<DOIDataCiteRegisterCache> query = em.createNamedQuery("DOIDataCiteRegisterCache.findByDoi",
                 DOIDataCiteRegisterCache.class);
         query.setParameter("doi", doi);
         List<DOIDataCiteRegisterCache> rc = query.getResultList();
@@ -227,7 +228,7 @@ public DataCiteMetadataTemplate(String xmlMetaData) {
             identifier = identifierElements.get(0).html();
         }
         Elements creatorElements = doc.select("creatorName");
-        creators = new ArrayList();
+        creators = new ArrayList<>();
         for (Element creatorElement : creatorElements) {
             creators.add(creatorElement.html());
         }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteServiceBean.java
@@ -115,6 +115,7 @@ public HashMap<String, String> lookupMetadataFromIdentifier(String protocol, Str
      * @param dataset the Dataset whose metadata needs to be modified
      * @param metadata the new metadata for the Dataset
      * @return the Dataset identifier, or null if the modification failed
+     * @throws java.lang.Exception
      */
     @Override
     public String modifyIdentifier(Dataset dataset, HashMap<String, String> metadata) throws Exception {
@@ -168,7 +169,7 @@ public void deleteRecordFromCache(Dataset datasetIn){
     public void deleteIdentifier(Dataset datasetIn) throws Exception {
         logger.log(Level.FINE,"deleteIdentifier");
         String identifier = getIdentifierFromDataset(datasetIn);
-        HashMap<String, String> doiMetadata = new HashMap();
+        HashMap<String, String> doiMetadata = new HashMap<>();
         try {
             doiMetadata = doiDataCiteRegisterService.getMetadata(identifier);
         } catch (Exception e) {
@@ -179,7 +180,7 @@ public void deleteIdentifier(Dataset datasetIn) throws Exception {
             logger.log(Level.WARNING, "message {0}", e.getMessage());
         }
 
-        String idStatus = (String) doiMetadata.get("_status");
+        String idStatus = doiMetadata.get("_status");
 
         if (idStatus != null && idStatus.equals("reserved")) {
             logger.log(Level.INFO, "Delete status is reserved..");
@@ -200,6 +201,7 @@ public void deleteIdentifier(Dataset datasetIn) throws Exception {
         }
     }
 
+    @Override
     protected HashMap<String, String> getUpdateMetadataFromDataset(Dataset datasetIn) {
         logger.log(Level.FINE,"getUpdateMetadataFromDataset");
         HashMap<String, String> metadata = super.getUpdateMetadataFromDataset(datasetIn);

diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFile.java b/src/main/java/edu/harvard/iq/dataverse/DataFile.java
@@ -27,7 +27,6 @@
 import java.text.SimpleDateFormat;
 import java.util.Arrays;
 import java.util.HashMap;
-import java.util.Iterator;
 import java.util.Map;
 import java.util.logging.Logger;
 import javax.json.Json;
@@ -71,7 +70,7 @@ public class DataFile extends DvObject implements Comparable {
     public static final char INGEST_STATUS_INPROGRESS = 67;
     public static final char INGEST_STATUS_ERROR = 68; 
 
-    public static final Long ROOT_DATAFILE_ID_DEFAULT = new Long(-1);
+    public static final Long ROOT_DATAFILE_ID_DEFAULT = (long) -1;
 
     private String name;
 
@@ -258,7 +257,7 @@ public DataTable getDataTable() {
 
     public void setDataTable(DataTable dt) {
         if (this.getDataTables() == null) {
-            this.setDataTables( new ArrayList() );
+            this.setDataTables( new ArrayList<>() );
         } else {
             this.getDataTables().clear();
         }
@@ -275,11 +274,9 @@ public List<String> getTagLabels(){
         List<DataFileTag> currentDataTags = this.getTags();
         List<String> tagStrings = new ArrayList<>();
 
-        if (( currentDataTags != null)||(!currentDataTags.isEmpty())){
+        if (( currentDataTags != null)&&(!currentDataTags.isEmpty())){
 
-            Iterator itr = currentDataTags.iterator();
-            while (itr.hasNext()){
-                DataFileTag element = (DataFileTag)itr.next();
+            for (DataFileTag element : currentDataTags) {
                 tagStrings.add(element.getTypeLabel());
              }
         }
@@ -297,9 +294,7 @@ public JsonArrayBuilder getTagLabelsAsJsonArrayBuilder(){
         }
 
 
-        Iterator itr = currentDataTags.iterator();
-        while (itr.hasNext()){
-            DataFileTag element = (DataFileTag)itr.next();
+        for (DataFileTag element : currentDataTags) {
             builder.add(element.getTypeLabel());            
         }
         return builder;
@@ -358,7 +353,7 @@ public IngestReport getIngestReport() {
 
     public void setIngestReport(IngestReport report) {
         if (ingestReports == null) {
-            ingestReports = new ArrayList();
+            ingestReports = new ArrayList<>();
         } else {
             ingestReports.clear();
         }
@@ -489,9 +484,10 @@ private FileMetadata getLatestFileMetadata() {
             if (fmd == null || fileMetadata.getDatasetVersion().getVersionNumber().compareTo( fmd.getDatasetVersion().getVersionNumber() ) > 0 ) {
                 fmd = fileMetadata;
             } else if ((fileMetadata.getDatasetVersion().getVersionNumber().compareTo( fmd.getDatasetVersion().getVersionNumber())==0 )&& 
-                   ( fileMetadata.getDatasetVersion().getMinorVersionNumber().compareTo( fmd.getDatasetVersion().getMinorVersionNumber()) > 0 )   )
+                   ( fileMetadata.getDatasetVersion().getMinorVersionNumber().compareTo( fmd.getDatasetVersion().getMinorVersionNumber()) > 0 )   ) {
                 fmd = fileMetadata;
         }
+        }
         return fmd;
     }
 
@@ -594,10 +590,7 @@ public boolean isImage() {
     }
 
     public boolean isFilePackage() {
-        if (DataFileServiceBean.MIME_TYPE_PACKAGE_FILE.equalsIgnoreCase(contentType)) {
-            return true;
-        }
-        return false;
+        return DataFileServiceBean.MIME_TYPE_PACKAGE_FILE.equalsIgnoreCase(contentType);
     }
 
     public void setIngestStatus(char ingestStatus) {
@@ -916,7 +909,7 @@ public JsonObject asGsonObject(boolean prettyPrint){
         // ----------------------------------        
         // Checksum
         // ----------------------------------
-        Map<String, String> checkSumMap = new HashMap<String, String>();
+        Map<String, String> checkSumMap = new HashMap<>();
         checkSumMap.put("type", getChecksumType().toString());
         checkSumMap.put("value", getChecksumValue());