https://github.com/metadatacenter/cedar-project/issues/1198

src/main/java/org/metadatacenter/cadsr/ingestor/category/CategoryStats.java

@@ -1,8 +1,6 @@
 package org.metadatacenter.cadsr.ingestor.category;
 
-import java.util.ArrayList;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Set;
 
 /**

src/main/java/org/metadatacenter/cadsr/ingestor/cde/Value.java

@@ -91,10 +91,9 @@ public boolean equals(Object obj) {
     if (obj == null) {
       return false;
     }
-    if (!(obj instanceof Value)) {
+    if (!(obj instanceof Value other)) {
       return false;
     }
-    Value other = (Value) obj;
     return Objects.equals(id, other.id)
         && Objects.equals(version, other.version)
         && Objects.equals(dbLabel, other.dbLabel)
@@ -105,4 +104,4 @@ public boolean equals(Object obj) {
         && Objects.equals(beginDate, other.beginDate)
         && Objects.equals(endDate, other.endDate);
   }
-}
+}

src/main/java/org/metadatacenter/cadsr/ingestor/cde/action/AttachCdeToCategoriesAction.java

@@ -1,14 +1,11 @@
 package org.metadatacenter.cadsr.ingestor.cde.action;
 
-import org.metadatacenter.cadsr.ingestor.util.CdeUtil;
 import org.metadatacenter.cadsr.ingestor.util.CedarServices;
 import org.metadatacenter.cadsr.ingestor.util.Constants.CedarServer;
-import org.metadatacenter.model.ModelNodeNames;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.List;
-import java.util.Map;
 
 public class AttachCdeToCategoriesAction implements CdeAction {
 

src/main/java/org/metadatacenter/cadsr/ingestor/cde/action/LoadValueSetsOntologyAction.java

@@ -39,16 +39,13 @@ public String execute(CedarServer cedarEnvironment, String apiKey) {
         status = CedarServices.loadValueSetsOntologyStatus(cedarEnvironment, apiKey);
       }
 
-      if (status.equals("COMPLETE"))
-        return "Done";
-      else if (status.equals("ERROR"))
-        return "Error";
-      else if (status.equals("NOT_YET_INITIATED"))
-        return "Failed to start";
-      else if (status.equals("IN_PROGRESS"))
-        return "Failed to finish";
-      else
-        return "Error - unknown status";
+      return switch (status) {
+        case "COMPLETE" -> "Done";
+        case "ERROR" -> "Error";
+        case "NOT_YET_INITIATED" -> "Failed to start";
+        case "IN_PROGRESS" -> "Failed to finish";
+        default -> "Error - unknown status";
+      };
 
     } catch (IOException | InterruptedException e) {
       String message = "Error calling load value sets ontology endpoint: " + e.getMessage();

src/main/java/org/metadatacenter/cadsr/ingestor/cde/handler/UIHandler.java

@@ -2,7 +2,6 @@
 
 import org.metadatacenter.cadsr.cde.schema.DataElement;
 import org.metadatacenter.cadsr.cde.schema.VALUEDOMAIN;
-import org.metadatacenter.cadsr.ingestor.cde.CadsrConstants;
 import org.metadatacenter.cadsr.ingestor.exception.UnsupportedDataElementException;
 import org.metadatacenter.model.ModelNodeNames;
 import org.metadatacenter.model.ModelNodeValues;

src/main/java/org/metadatacenter/cadsr/ingestor/cde/handler/VersionHandler.java

@@ -25,7 +25,7 @@ public VersionHandler handle(DataElement dataElement) throws UnsupportedDataElem
   private void setDataElementStatus(DataElement dataElement) throws UnsupportedDataElementException {
     String status = dataElement.getWORKFLOWSTATUS().getContent();
     if (Strings.isNullOrEmpty(status)) {
-      String reason = String.format("Data element status is empty (Unknown)");
+      String reason = "Data element status is empty (Unknown)";
       throw new UnsupportedDataElementException(dataElement, reason);
     }
     if (!CadsrStatus.STATUS_LIST.contains(status)) {
@@ -40,7 +40,7 @@ private void setDataElementStatus(DataElement dataElement) throws UnsupportedDat
   private void setDataElementVersion(DataElement dataElement) throws UnsupportedDataElementException {
     String version = dataElement.getVERSION().getContent();
     if (Strings.isNullOrEmpty(version)) {
-      String reason = String.format("Data element version is empty (Unknown)");
+      String reason = "Data element version is empty (Unknown)";
       throw new UnsupportedDataElementException(dataElement, reason);
     }
     this.version = CdeUtil.reformatVersioningNumber(version);

src/main/java/org/metadatacenter/cadsr/ingestor/form/FormParseReporter.java

@@ -39,9 +39,7 @@ public List<String> getMessages(String reportId) {
   }
 
   public void remove(String reportId) {
-    if (messagesMap.containsKey(reportId)) {
-      messagesMap.remove(reportId);
-    }
+    messagesMap.remove(reportId);
   }
 
 }

src/main/java/org/metadatacenter/cadsr/ingestor/form/FormParser.java

@@ -9,7 +9,6 @@
 import org.metadatacenter.cadsr.ingestor.util.CdeUtil;
 import org.metadatacenter.cadsr.ingestor.util.CedarServerUtil;
 import org.metadatacenter.cadsr.ingestor.util.Constants;
-import org.metadatacenter.cadsr.ingestor.util.Constants.*;
 import org.metadatacenter.cadsr.ingestor.util.GeneralUtil;
 import org.metadatacenter.config.CedarConfig;
 import org.metadatacenter.config.environment.CedarEnvironmentVariableProvider;
@@ -21,10 +20,7 @@
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import static org.metadatacenter.cadsr.ingestor.util.Constants.*;
 
@@ -188,17 +184,15 @@ private static Object setDefaultUi() {
 
   // Target: required
   private static Object setRequired() {
-    return Arrays.asList(new String[]{
-        ModelNodeNames.JSON_LD_CONTEXT,
+    return Arrays.asList(ModelNodeNames.JSON_LD_CONTEXT,
         ModelNodeNames.JSON_LD_ID,
         ModelNodeNames.SCHEMA_IS_BASED_ON,
         ModelNodeNames.SCHEMA_ORG_NAME,
         ModelNodeNames.SCHEMA_ORG_DESCRIPTION,
         ModelNodeNames.PAV_CREATED_ON,
         ModelNodeNames.PAV_CREATED_BY,
         ModelNodeNames.PAV_LAST_UPDATED_ON,
-        ModelNodeNames.OSLC_MODIFIED_BY,
-    });
+        ModelNodeNames.OSLC_MODIFIED_BY);
   }
 
   // Target: properties
@@ -278,7 +272,7 @@ private static Object setDefaultPropertiesContextPropertiesUri(String uri) {
     Map<String, Object> content = Maps.newHashMap();
     content.put(ModelNodeNames.JSON_SCHEMA_TYPE, ModelNodeValues.STRING);
     content.put(ModelNodeNames.JSON_SCHEMA_FORMAT, ModelNodeValues.URI);
-    content.put(ModelNodeNames.JSON_SCHEMA_ENUM, Arrays.asList(new String[]{uri}));
+    content.put(ModelNodeNames.JSON_SCHEMA_ENUM, Collections.singletonList(uri));
     return content;
   }
 
@@ -297,7 +291,7 @@ private static Object setDefaultPropertiesContextPropertiesAtTypeObject(String t
     // Target: X.properties.@type
     Map<String, Object> contentPropertiesAtType = Maps.newHashMap();
     contentPropertiesAtType.put(ModelNodeNames.JSON_SCHEMA_TYPE, ModelNodeValues.STRING);
-    contentPropertiesAtType.put(ModelNodeNames.JSON_SCHEMA_ENUM, Arrays.asList(new String[]{type}));
+    contentPropertiesAtType.put(ModelNodeNames.JSON_SCHEMA_ENUM, Collections.singletonList(type));
 
     // Target: X.properties
     Map<String, Object> contentProperties = Maps.newHashMap();
@@ -333,7 +327,7 @@ private static Map<String, Object> setStringMinLength() {
 
   private static Map<String, Object> setUriStringOrNull() {
     Map<String, Object> uriString = Maps.newHashMap();
-    uriString.put(ModelNodeNames.JSON_SCHEMA_TYPE, Arrays.asList(new String[]{ModelNodeValues.STRING, ModelNodeValues.NULL}));
+    uriString.put(ModelNodeNames.JSON_SCHEMA_TYPE, List.of(ModelNodeValues.STRING, ModelNodeValues.NULL));
     uriString.put(ModelNodeNames.JSON_SCHEMA_FORMAT, ModelNodeValues.URI);
     return uriString;
   }
@@ -358,7 +352,7 @@ private static Map<String, Object> setUriStringArray() {
 
   private static Map<String, Object> setDateTimeStringOrNull() { // We allow null because the value is set by the server
     Map<String, Object> uriString = Maps.newHashMap();
-    uriString.put(ModelNodeNames.JSON_SCHEMA_TYPE, Arrays.asList(new String[]{ModelNodeValues.STRING, ModelNodeValues.NULL}));
+    uriString.put(ModelNodeNames.JSON_SCHEMA_TYPE, List.of(ModelNodeValues.STRING, ModelNodeValues.NULL));
     uriString.put(ModelNodeNames.JSON_SCHEMA_FORMAT, ModelNodeValues.DATE_TIME);
     return uriString;
   }

src/main/java/org/metadatacenter/cadsr/ingestor/form/handler/TemplateFieldsHandler.java

@@ -17,7 +17,8 @@
 import java.io.IOException;
 import java.util.*;
 
-import static org.metadatacenter.cadsr.ingestor.util.Constants.*;
+import static org.metadatacenter.cadsr.ingestor.util.Constants.LARGE_PAGE_SIZE;
+import static org.metadatacenter.cadsr.ingestor.util.Constants.MOVE_ACTIONS_THRESHOLD;
 import static org.metadatacenter.model.ModelNodeNames.*;
 
 public class TemplateFieldsHandler implements ModelHandler {
@@ -137,8 +138,7 @@ private Map<String, Object> customizeCdeValues(Map<String, Object> cde, List<Val
       // also sort them alphabetically in the UI, so we need to make that comparison. We cannot retrieve the values
       // alphabetically sorted by BioPortal, so we sort them here. We will compare their position to the valid values
       // display order later (see generateMoveActions method) to determine if it's necessary to generate move actions.
-      Collections.sort(cdeValues,
-          (v1, v2) -> v1.get("notation").compareTo(v2.get("notation")));
+      cdeValues.sort((v1, v2) -> v1.get("notation").compareTo(v2.get("notation")));
 
       // Create Map with the values indexed by prefLabel to access them quickly. We save the position as a new
       // attribute. We'll use it to generate the move actions
@@ -156,8 +156,7 @@ private Map<String, Object> customizeCdeValues(Map<String, Object> cde, List<Val
       // 2. Compare (ignoring case) the retrieved values to the values in the form's XML to identify exclusions
       // Correspondences between CEDAR's CDE model and the form's xml validValue model:
       //  - notation <-> value
-      Map<String, Map<String, String>> excludedCdeValuesMap = new HashMap<>();
-      excludedCdeValuesMap.putAll(cdeValuesMap);
+      Map<String, Map<String, String>> excludedCdeValuesMap = new HashMap<>(cdeValuesMap);
       for (ValidValue validValue : validValues) {
         String valueKey = validValue.getValue().toLowerCase();
         if (excludedCdeValuesMap.containsKey(valueKey)) {
@@ -252,11 +251,9 @@ private Map<String, Object> getUpdatedUi(String fieldName, String fieldDescripti
   private Map<String, Object> getUpdatedPropertiesContextProperties(String fieldName, Map<String, Object> templateMap) {
     Map<String, Object> properties = (Map<String, Object>) templateMap.get(JSON_SCHEMA_PROPERTIES);
     Map<String, Object> propertiesContext = (Map<String, Object>) properties.get(JSON_LD_CONTEXT);
-    Map<String, Object> propertiesContextProperties =
-        (Map<String, Object>) propertiesContext.get(JSON_SCHEMA_PROPERTIES);
+    Map<String, Object> propertiesContextProperties = (Map<String, Object>) propertiesContext.get(JSON_SCHEMA_PROPERTIES);
     propertiesContextProperties.put(fieldName, new HashMap<String, List<String>>() {{
-      put(JSON_SCHEMA_ENUM,
-          Arrays.asList(new String[]{"https://schema.metadatacenter.org/properties/" + UUID.randomUUID()}));
+      put(JSON_SCHEMA_ENUM, List.of("https://schema.metadatacenter.org/properties/" + UUID.randomUUID()));
     }});
     return propertiesContextProperties;
   }
@@ -285,17 +282,15 @@ private List<String> getUpdatedRequired(String fieldName, Map<String, Object> te
    * @param modules
    */
   private void sortModules(List<Module> modules) {
-    Collections.sort(modules, new Comparator<>() {
-      public int compare(Module m1, Module m2) {
-        if (m1.getDisplayOrder() == null && m2.getDisplayOrder() == null) {
-          return 0;
-        } else if (m1.getDisplayOrder() == null) {
-          return 1;
-        } else if (m2.getDisplayOrder() == null) {
-          return -1;
-        }
-        return Integer.compare(Integer.parseInt(m1.getDisplayOrder()), Integer.parseInt(m2.getDisplayOrder()));
+    modules.sort((m1, m2) -> {
+      if (m1.getDisplayOrder() == null && m2.getDisplayOrder() == null) {
+        return 0;
+      } else if (m1.getDisplayOrder() == null) {
+        return 1;
+      } else if (m2.getDisplayOrder() == null) {
+        return -1;
       }
+      return Integer.compare(Integer.parseInt(m1.getDisplayOrder()), Integer.parseInt(m2.getDisplayOrder()));
     });
   }
 
@@ -305,17 +300,15 @@ public int compare(Module m1, Module m2) {
    * @param questions
    */
   private void sortQuestions(List<Question> questions) {
-    Collections.sort(questions, new Comparator<>() {
-      public int compare(Question q1, Question q2) {
-        if (q1.getDisplayOrder() == null && q2.getDisplayOrder() == null) {
-          return 0;
-        } else if (q1.getDisplayOrder() == null) {
-          return 1;
-        } else if (q2.getDisplayOrder() == null) {
-          return -1;
-        }
-        return Integer.compare(Integer.parseInt(q1.getDisplayOrder()), Integer.parseInt(q2.getDisplayOrder()));
+    questions.sort((q1, q2) -> {
+      if (q1.getDisplayOrder() == null && q2.getDisplayOrder() == null) {
+        return 0;
+      } else if (q1.getDisplayOrder() == null) {
+        return 1;
+      } else if (q2.getDisplayOrder() == null) {
+        return -1;
       }
+      return Integer.compare(Integer.parseInt(q1.getDisplayOrder()), Integer.parseInt(q2.getDisplayOrder()));
     });
   }
 

src/main/java/org/metadatacenter/cadsr/ingestor/form/handler/TemplateHeaderAndFooterHandler.java

@@ -1,17 +1,10 @@
 package org.metadatacenter.cadsr.ingestor.form.handler;
 
 import org.metadatacenter.cadsr.form.schema.Form;
-import org.metadatacenter.cadsr.form.schema.Module;
-import org.metadatacenter.cadsr.form.schema.Question;
-import org.metadatacenter.cadsr.ingestor.util.CedarFieldUtil;
-import org.metadatacenter.cadsr.ingestor.util.CedarServices;
-import org.metadatacenter.cadsr.ingestor.util.Constants.CedarServer;
-import org.metadatacenter.model.ModelNodeNames;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import javax.annotation.Nullable;
-import java.io.IOException;
 import java.util.*;
 
 import static org.metadatacenter.model.ModelNodeNames.*;

src/main/java/org/metadatacenter/cadsr/ingestor/form/handler/VersionHandler.java

@@ -1,17 +1,5 @@
 package org.metadatacenter.cadsr.ingestor.form.handler;
 
-import com.google.common.base.Strings;
-import org.metadatacenter.cadsr.cde.schema.DataElement;
-import org.metadatacenter.cadsr.form.schema.Form;
-import org.metadatacenter.cadsr.ingestor.cde.CadsrStatus;
-import org.metadatacenter.cadsr.ingestor.cde.handler.ModelHandler;
-import org.metadatacenter.cadsr.ingestor.exception.UnsupportedDataElementException;
-import org.metadatacenter.model.BiboStatus;
-import org.metadatacenter.model.ModelNodeNames;
-
-import javax.annotation.Nullable;
-import java.util.Map;
-
 //public class VersionHandler implements ModelHandler {
 //
 //  private String status = null;

src/main/java/org/metadatacenter/cadsr/ingestor/tools/form/CadsrFormImportTool.java

@@ -2,15 +2,10 @@
 
 import com.google.common.base.Stopwatch;
 import org.metadatacenter.cadsr.form.schema.Form;
-import org.metadatacenter.cadsr.ingestor.form.FormParser;
 import org.metadatacenter.cadsr.ingestor.form.FormUtil;
 import org.metadatacenter.cadsr.ingestor.tools.form.config.ConfigSettings;
 import org.metadatacenter.cadsr.ingestor.tools.form.config.ConfigSettingsParser;
-import org.metadatacenter.cadsr.ingestor.util.CedarServices;
 import org.metadatacenter.cadsr.ingestor.util.GeneralUtil;
-import org.metadatacenter.config.CedarConfig;
-import org.metadatacenter.config.environment.CedarEnvironmentVariableProvider;
-import org.metadatacenter.model.SystemComponent;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/metadatacenter/cadsr/ingestor/tools/form/config/ConfigSettings.java

@@ -1,6 +1,5 @@
 package org.metadatacenter.cadsr.ingestor.tools.form.config;
 
-import org.metadatacenter.cadsr.ingestor.util.Constants.CedarServer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/metadatacenter/cadsr/ingestor/tools/form/config/ConfigSettingsParser.java

@@ -1,8 +1,6 @@
 package org.metadatacenter.cadsr.ingestor.tools.form.config;
 
 import org.apache.commons.cli.*;
-import org.metadatacenter.cadsr.ingestor.util.CedarServerUtil;
-import org.metadatacenter.cadsr.ingestor.util.Constants;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/metadatacenter/cadsr/ingestor/util/CdeUtil.java

@@ -131,8 +131,7 @@ public static Map<String, CdeSummary> getExistingCedarCdeSummaries(String cedarF
                                                                      String apiKey) throws IOException {
     // Retrieve existing CDEs from CEDAR
     logger.info("Retrieving current CDEs from CEDAR (folder id: " + cedarFolderId + ").");
-    List fieldNamesToInclude = new ArrayList(Arrays.asList(new String[]{"schema:identifier", "pav:version",
-        "sourceHash"}));
+    List fieldNamesToInclude = new ArrayList(List.of("schema:identifier", "pav:version", "sourceHash"));
     List<CdeSummary> cdeSummaries = CedarServices.findCdeSummariesInFolder(cedarFolderId,
         fieldNamesToInclude, true, cedarEnvironment, apiKey);
     logger.info("Number of CDEs retrieved from CEDAR: " + cdeSummaries.size() + ".");
@@ -188,9 +187,7 @@ public static Map<String, Object> removeNonRelevantKeysFromCdeFieldMap(Map<Strin
   public static String reformatVersioningNumber(String version) {
     String[] originalVersion = version.split("\\.");
     String[] baseVersion = {"0", "0", "0"};
-    for (int i = 0; i < originalVersion.length; i++) {
-      baseVersion[i] = originalVersion[i];
-    }
+    System.arraycopy(originalVersion, 0, baseVersion, 0, originalVersion.length);
     return String.join(".", baseVersion);
   }
 

src/main/java/org/metadatacenter/cadsr/ingestor/util/CedarServices.java

@@ -182,7 +182,7 @@ public static boolean isFieldInPath(String fieldId, String folderPath, CedarServ
   public static Optional<Map<String, Object>> searchCdeByPublicIdAndVersion(String publicId, String version,
                                                                             CedarServer cedarServer, String apiKey) throws IOException {
     String reformattedVersion = CdeUtil.reformatVersioningNumber(version);
-    List<CedarResourceType> resourceTypes = Arrays.asList(new CedarResourceType[]{CedarResourceType.FIELD});
+    List<CedarResourceType> resourceTypes = List.of(CedarResourceType.FIELD);
     String searchEndpoint = CedarServerUtil.getSearchEndPoint(publicId, resourceTypes, cedarServer);
     HttpURLConnection connection = ConnectionUtil.createAndOpenConnection("GET", searchEndpoint, apiKey);
     int responseCode = connection.getResponseCode();
@@ -235,9 +235,7 @@ public static String createCde(Map<String, Object> cdeFieldMap, String cdeHashCo
 
       // Extract the categories from the map if they are still there. They are not part of the CEDAR model, so we
       // don't want to post them
-      if (cdeFieldMap.containsKey(CDE_CATEGORY_IDS_FIELD)) {
-        cdeFieldMap.remove(CDE_CATEGORY_IDS_FIELD);
-      }
+      cdeFieldMap.remove(CDE_CATEGORY_IDS_FIELD);
 
       String payload = objectMapper.writeValueAsString(cdeFieldMap);
       conn = ConnectionUtil.createAndOpenConnection("POST", templateFieldsEndpoint, apiKey);
@@ -448,8 +446,8 @@ public static void attachCdeToCategories(String cedarCdeId, List<String> cedarCa
 
     if (cedarCategoryIds.size() > 0) {
       logger.info("Attaching CDE to the following categories: ");
-      for (int i=0; i<cedarCategoryIds.size(); i++) {
-        logger.info(" - " + cedarCategoryIds.get(i));
+      for (String cedarCategoryId : cedarCategoryIds) {
+        logger.info(" - " + cedarCategoryId);
       }
     }