Merge pull request #54 from allan-shoup/system-exit

Converted System.exit to throw exceptions, cleaned up leaked …
scify · Aug 27, 2021 · eb8d063 · eb8d063
2 parents 3eb67fc + ac37156
commit eb8d063
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Showing 60 changed files with 267 additions and 453 deletions.
diff --git a/src/main/java/org/scify/jedai/blockbuilding/AbstractBlockBuilding.java b/src/main/java/org/scify/jedai/blockbuilding/AbstractBlockBuilding.java
@@ -107,7 +107,7 @@ public int getTotalNoOfEntities() {
         if (entityProfilesD2 == null) {
             return noOfEntitiesD1;
         }
-        return noOfEntitiesD1 + noOfEntitiesD2;
+        return Math.addExact(noOfEntitiesD1, noOfEntitiesD2);
     }
 
     protected void indexEntities(Map<String, TIntList> index, List<EntityProfile> entities) {

diff --git a/src/main/java/org/scify/jedai/blockprocessing/AbstractBlockProcessing.java b/src/main/java/org/scify/jedai/blockprocessing/AbstractBlockProcessing.java
@@ -36,6 +36,6 @@ protected void printOriginalStatistics(List<AbstractBlock> inputBlocks) {
         }
 
         Log.info("Original blocks\t:\t" + inputBlocks.size());
-        Log.info("Original comparisons\t:\t" + ((long)comparisons));
+        Log.info("Original comparisons\t:\t" + comparisons);
     }
 }
diff --git a/src/main/java/org/scify/jedai/blockprocessing/blockcleaning/BlockFiltering.java b/src/main/java/org/scify/jedai/blockprocessing/blockcleaning/BlockFiltering.java
@@ -105,10 +105,10 @@ protected void getBilateralLimits(List<AbstractBlock> blocks) {
         });
 
         for (int i = 0; i < limitsD1.length; i++) {
-            limitsD1[i] = (int) Math.round(ratio * limitsD1[i]);
+            limitsD1[i] = Math.round(ratio * limitsD1[i]);
         }
         for (int i = 0; i < limitsD2.length; i++) {
-            limitsD2[i] = (int) Math.round(ratio * limitsD2[i]);
+            limitsD2[i] = Math.round(ratio * limitsD2[i]);
         }
     }
 
@@ -193,7 +193,7 @@ protected void getUnilateralLimits(List<AbstractBlock> blocks) {
         });
 
         for (int i = 0; i < limitsD1.length; i++) {
-            limitsD1[i] = (int) Math.round(ratio * limitsD1[i]);
+            limitsD1[i] = Math.round(ratio * limitsD1[i]);
         }
     }
 

diff --git a/src/main/java/org/scify/jedai/blockprocessing/blockcleaning/SizeBasedBlockPurging.java b/src/main/java/org/scify/jedai/blockprocessing/blockcleaning/SizeBasedBlockPurging.java
@@ -63,7 +63,7 @@ private int getMaxBlockSize(List<AbstractBlock> blocks) {
             entities.addAll(uBlock.getEntities());
         });
 
-        return (int) Math.round(entities.size()*purgingFactor);
+        return Math.round(entities.size()*purgingFactor);
     }
 
     private int getMaxInnerBlockSize(List<AbstractBlock> blocks) {
@@ -76,7 +76,7 @@ private int getMaxInnerBlockSize(List<AbstractBlock> blocks) {
             d2Entities.addAll(bBlock.getIndex2Entities());
         });
 
-        return (int) Math.round(Math.min(d1Entities.size(), d2Entities.size())*purgingFactor);
+        return Math.round(Math.min(d1Entities.size(), d2Entities.size())*purgingFactor);
     }
 
     @Override

diff --git a/src/main/java/org/scify/jedai/blockprocessing/comparisoncleaning/CanopyClustering.java b/src/main/java/org/scify/jedai/blockprocessing/comparisoncleaning/CanopyClustering.java
@@ -15,7 +15,6 @@
  */
 package org.scify.jedai.blockprocessing.comparisoncleaning;
 
-import com.esotericsoftware.minlog.Log;
 import org.scify.jedai.datamodel.AbstractBlock;
 import org.scify.jedai.utilities.enumerations.WeightingScheme;
 import gnu.trove.iterator.TIntIterator;
@@ -56,8 +55,8 @@ public CanopyClustering(float inThr, float outThr, WeightingScheme scheme) {
         exclusiveThreshold = outThr;
         inclusiveThreshold = inThr;
         if (exclusiveThreshold < inclusiveThreshold) {
-            Log.error(getMethodName(), "The " + getParameterName(1) + " cannot be smaller than the " + getParameterName(0));
-            System.exit(-1);
+            throw new IllegalStateException(
+                "The " + getParameterName(1) + " cannot be smaller than the " + getParameterName(0));
         }
     }
 

diff --git a/...ain/java/org/scify/jedai/blockprocessing/comparisoncleaning/ExtendedCanopyClustering.java b/...ain/java/org/scify/jedai/blockprocessing/comparisoncleaning/ExtendedCanopyClustering.java
@@ -15,7 +15,6 @@
  */
 package org.scify.jedai.blockprocessing.comparisoncleaning;
 
-import com.esotericsoftware.minlog.Log;
 import org.scify.jedai.datamodel.AbstractBlock;
 import org.scify.jedai.datamodel.Comparison;
 import org.scify.jedai.utilities.enumerations.WeightingScheme;
@@ -60,8 +59,7 @@ public ExtendedCanopyClustering(int inThr, int outThr, WeightingScheme scheme) {
         exclusiveThreshold = outThr;
         inclusiveThreshold = inThr;
         if (inclusiveThreshold < exclusiveThreshold) {
-            Log.error(getMethodName(), "The Exclusive Threshold cannot be larger than the Inclusive one.");
-            System.exit(-1);
+            throw new IllegalStateException("The Exclusive Threshold cannot be larger than the Inclusive one.");
         }
     }
 
@@ -133,7 +131,7 @@ protected List<AbstractBlock> pruneEdges() {
 
         excludedEntities = new TIntHashSet();
         nearestEntities = new HashSet[noOfEntities];
-        topKEdges = new PriorityQueue<>((int) (2 * inclusiveThreshold), new IncComparisonWeightComparator());
+        topKEdges = new PriorityQueue<>(2 * inclusiveThreshold, new IncComparisonWeightComparator());
         if (weightingScheme.equals(WeightingScheme.ARCS)) {
             while (iterator.hasNext()) {
                 int currentId = iterator.next();

diff --git a/...in/java/org/scify/jedai/configuration/randomsearch/AbstractRandomSearchConfiguration.java b/...in/java/org/scify/jedai/configuration/randomsearch/AbstractRandomSearchConfiguration.java
@@ -27,10 +27,10 @@ public abstract class AbstractRandomSearchConfiguration implements IRandomSearch
 
     protected final static Random RANDOM_GEN = new Random();
 
-    protected final List selectedRandomValues;
+    protected final List<Object> selectedRandomValues;
 
     public AbstractRandomSearchConfiguration() {
-        selectedRandomValues = new ArrayList();
+        selectedRandomValues = new ArrayList<>();
     }
 
     @Override

diff --git a/src/main/java/org/scify/jedai/datamodel/Comparison.java b/src/main/java/org/scify/jedai/datamodel/Comparison.java
@@ -65,7 +65,6 @@ public int getEntityId2() {
     /**
      * Returns the measure of the weight or similarity between two entities.
      * Higher utility measures correspond to greater weight or stronger similarity.
-     * @return 
      */
     public float getUtilityMeasure() {
         return utilityMeasure;

diff --git a/src/main/java/org/scify/jedai/datamodel/GomoryHuTree.java b/src/main/java/org/scify/jedai/datamodel/GomoryHuTree.java
@@ -90,7 +90,7 @@ public SimpleGraph<Integer, DefaultEdge> MinCutTree() {
 
             final Set<V> sourcePartition = minSourceSinkCut.getSourcePartition();
 //            float flowValue = minSourceSinkCut.getCutWeight();
-            DefaultWeightedEdge e = (DefaultWeightedEdge) returnGraphClone.addEdge(vertex, predecessor);
+            DefaultWeightedEdge e = returnGraphClone.addEdge(vertex, predecessor);
             returnGraph.addEdge(Integer.parseInt(vertex + ""), Integer.parseInt(predecessor + ""));
             returnGraphClone.setEdgeWeight(e, flowValue);
 

diff --git a/src/main/java/org/scify/jedai/datamodel/SimilarityPairs.java b/src/main/java/org/scify/jedai/datamodel/SimilarityPairs.java
@@ -15,9 +15,7 @@
  */
 package org.scify.jedai.datamodel;
 
-import com.esotericsoftware.minlog.Log;
 import java.io.Serializable;
-
 import java.util.List;
 import org.scify.jedai.utilities.IConstants;
 
@@ -64,10 +62,9 @@ private long countComparisons(List<AbstractBlock> blocks) {
             comparisons += block.getNoOfComparisons();
         }
 
-        if (MAX_COMPARISONS < comparisons) {
-            Log.error("Very high number of comparisons to be executed! "
-                    + "Maximum allowed number is : " + MAX_COMPARISONS);
-            System.exit(-1);
+        if (comparisons > MAX_COMPARISONS) {
+            throw new IllegalStateException("Very high number of comparisons to be executed. "
+                + "Maximum allowed number is : " + MAX_COMPARISONS);
         }
         return comparisons;
     }

diff --git a/src/main/java/org/scify/jedai/datamodel/joins/Category.java b/src/main/java/org/scify/jedai/datamodel/joins/Category.java
@@ -50,8 +50,8 @@ public Category(int len, float threshold, int categoryN) {
         Category.THRESHOLD = threshold;
         Category.N = categoryN;
         s_len = len;
-        e_len = (int) ((float) (s_len / THRESHOLD));
-        K = (int) (2 * (1 - THRESHOLD) / (1 + THRESHOLD) * (float) e_len);
+        e_len = (int) (s_len / THRESHOLD);
+        K = (int) (2 * (1 - THRESHOLD) / (1 + THRESHOLD) * e_len);
         N1 = K + 1;
         N2 = 2;
 

diff --git a/src/main/java/org/scify/jedai/datareader/entityreader/EntityDBReader.java b/src/main/java/org/scify/jedai/datareader/entityreader/EntityDBReader.java
@@ -19,8 +19,7 @@
 import org.apache.jena.atlas.json.JsonArray;
 import org.apache.jena.atlas.json.JsonObject;
 import org.scify.jedai.datamodel.EntityProfile;
-
-import java.io.IOException;
+import org.scify.jedai.utilities.DBUtils;
 import java.sql.*;
 import java.util.*;
 
@@ -60,33 +59,25 @@ public List<EntityProfile> getEntityProfiles() {
             return null;
         }
 
-        //inputFilePath is assigned the Database URL
-        try {
-            if (user == null) {
-                Log.error("Database user has not been set!");
-                return null;
-            }
-            if (password == null) {
-                Log.error("Database password has not been set!");
-                return null;
-            }
-            if (table == null) {
-                Log.error("Database table has not been set!");
-                return null;
-            }
-
-            Connection conn;
-            if (inputFilePath.startsWith("mysql")) {
-                conn = getMySQLconnection(inputFilePath);
-            } else if (inputFilePath.startsWith("postgresql")) {
-                conn = getPostgreSQLconnection(inputFilePath);
-            } else {
-                Log.error("Only MySQL and PostgreSQL are supported for the time being!");
-                return null;
-            }
+        if (user == null) {
+            Log.error("Database user has not been set!");
+            return null;
+        }
+        if (password == null) {
+            Log.error("Database password has not been set!");
+            return null;
+        }
+        if (table == null) {
+            Log.error("Database table has not been set!");
+            return null;
+        }
 
-            final Statement stmt = conn.createStatement();
-            final ResultSet rs = stmt.executeQuery("SELECT * FROM " + table);//retrieve the appropriate table
+        //inputFilePath is assigned the Database URL
+        try (Connection conn = DBUtils.getDBConnection(inputFilePath, user, password, ssl);
+            Statement stmt = conn.createStatement();
+            ResultSet rs = stmt.executeQuery("SELECT * FROM " + table);//retrieve the appropriate table
+            ) {
+
             final ResultSetMetaData rsmd = rs.getMetaData();
             int columnsNum = rsmd.getColumnCount();
             String[] columns = new String[columnsNum];
@@ -113,7 +104,7 @@ public List<EntityProfile> getEntityProfiles() {
                 }
             }
             rs.close();
-        } catch (IOException | SQLException ex) {
+        } catch (SQLException ex) {
             Log.error("Error in entities reading!", ex);
             return null;
         }
@@ -157,16 +148,6 @@ public String getMethodParameters() {
                 + "6)" + getParameterDescription(5) + ".";
     }
 
-    private Connection getMySQLconnection(String dbURL) throws IOException {
-        try {
-            Class.forName("com.mysql.jdbc.Driver");
-            return DriverManager.getConnection("jdbc:" + dbURL + "?user=" + user + "&password=" + password);
-        } catch (Exception ex) {
-            Log.error("Error with database connection!", ex);
-            return null;
-        }
-    }
-
     @Override
     public JsonArray getParameterConfiguration() {
         final JsonObject obj1 = new JsonObject();
@@ -273,25 +254,6 @@ public String getParameterName(int parameterId) {
         }
     }
 
-    private Connection getPostgreSQLconnection(String dbURL) throws IOException {
-        try {
-            final Properties props = new Properties();
-            if (!(user == null)) {
-                props.setProperty("user", user);
-            }
-            if (!(password == null)) {
-                props.setProperty("password", password);
-            }
-            if (ssl) {
-                props.setProperty("ssl", "true");
-            }
-            return DriverManager.getConnection("jdbc:" + dbURL, props);
-        } catch (SQLException ex) {
-            Log.error("Error with database connection!", ex);
-            return null;
-        }
-    }
-
     public void setAttributesToExclude(String[] attributesNamesToExclude) {
         attributesToExclude.addAll(Arrays.asList(attributesNamesToExclude));
     }

diff --git a/src/main/java/org/scify/jedai/datareader/entityreader/EntityJSONRDFReader.java b/src/main/java/org/scify/jedai/datareader/entityreader/EntityJSONRDFReader.java
@@ -19,10 +19,8 @@
 import org.apache.jena.atlas.json.JSON;
 import org.apache.jena.atlas.json.JsonArray;
 import org.apache.jena.atlas.json.JsonObject;
-import org.rdfhdt.hdt.exceptions.NotFoundException;
 import org.scify.jedai.datamodel.EntityProfile;
 
-import java.io.IOException;
 import java.util.*;
 
 /**
@@ -57,11 +55,9 @@ public List<EntityProfile> getEntityProfiles() {
         //load the rdf model from the input file
         try {
             readModel(inputFilePath);
-        } catch (IOException ex) {
+        } catch (Exception ex) {
             Log.error("Error in entities reading!", ex);
             return null;
-        } catch (NotFoundException e) {
-            Log.error(e.getMessage());
         }
 
         return entityProfiles;
@@ -145,7 +141,7 @@ public String getParameterName(int parameterId) {
         }
     }
 
-    private void readModel(String inpFIle) throws IOException, NotFoundException {
+    private void readModel(String inpFIle) {
         //read each ntriples
         JsonObject jsonObject = JSON.read(inpFIle);
         String key = jsonObject.keys().toArray()[0].toString();

diff --git a/src/main/java/org/scify/jedai/datareader/entityreader/EntityRDFReader.java b/src/main/java/org/scify/jedai/datareader/entityreader/EntityRDFReader.java
@@ -22,7 +22,6 @@
 import org.apache.jena.riot.RDFDataMgr;
 import org.scify.jedai.datamodel.EntityProfile;
 
-import java.io.IOException;
 import java.util.*;
 
 /**
@@ -58,7 +57,7 @@ public List<EntityProfile> getEntityProfiles() {
         try {
             final Model model = RDFDataMgr.loadModel(inputFilePath);
             readModel(model);
-        } catch (IOException ex) {
+        } catch (Exception ex) {
             Log.error("Error in entities reading!", ex);
             return null;
         }
@@ -144,7 +143,7 @@ public String getParameterName(int parameterId) {
         }
     }
 
-    private void readModel(Model m) throws IOException {
+    private void readModel(Model m) {
         //read each ntriples
         //get spo, create a separate profile for each separate subject,
         //with Attribute=predicate and Value=object

diff --git a/src/main/java/org/scify/jedai/datareader/entityreader/EntitySPARQLReader.java b/src/main/java/org/scify/jedai/datareader/entityreader/EntitySPARQLReader.java
@@ -19,7 +19,6 @@
 
 import com.esotericsoftware.minlog.Log;
 
-import java.io.IOException;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -69,7 +68,7 @@ public List<EntityProfile> getEntityProfiles() {
         //load the rdf model from the input file
         try {
             readEndpoint(inputFilePath);
-        } catch (IOException ex) {
+        } catch (Exception ex) {
             Log.error("Error in data reading", ex);
             return null;
         }
@@ -189,7 +188,7 @@ public String getParameterName(int parameterId) {
         }
     }
 
-    private void readEndpoint(String endpointUrl) throws IOException {
+    private void readEndpoint(String endpointUrl) {
         //read each ntriples
         //get spo, create a separate profile for each separate subject,
         //with Attribute=predicate and Value=object

diff --git a/src/main/java/org/scify/jedai/datareader/entityreader/EntityXMLreader.java b/src/main/java/org/scify/jedai/datareader/entityreader/EntityXMLreader.java
@@ -142,7 +142,7 @@ public String getParameterName(int parameterId) {
         }
     }
 
-    private void readXMLdoc(Document document) throws IOException {
+    private void readXMLdoc(Document document) {
         final Element classElement = document.getRootElement();
 
         final List<Element> dblpRoot = classElement.getChildren();

diff --git a/src/main/java/org/scify/jedai/datareader/groundtruthreader/AbstractGtReader.java b/src/main/java/org/scify/jedai/datareader/groundtruthreader/AbstractGtReader.java
@@ -43,14 +43,14 @@ public abstract class AbstractGtReader extends AbstractReader implements IGround
     protected final Set<IdDuplicates> idDuplicates;
     protected final TObjectIntMap<String> urlToEntityId1;
     protected final TObjectIntMap<String> urlToEntityId2;
-    protected final SimpleGraph duplicatesGraph;
+    protected final SimpleGraph<Integer, DefaultEdge> duplicatesGraph;
 
     public AbstractGtReader (String filePath) {
         super(filePath);
         idDuplicates = new HashSet<>();
-        duplicatesGraph = new SimpleGraph(DefaultEdge.class);
-        urlToEntityId1 = new TObjectIntHashMap();
-        urlToEntityId2 = new TObjectIntHashMap();
+        duplicatesGraph = new SimpleGraph<>(DefaultEdge.class);
+        urlToEntityId1 = new TObjectIntHashMap<>();
+        urlToEntityId2 = new TObjectIntHashMap<>();
     }
 
     @Override