Some minor fixes and performance improvements

bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/ExpressionCommandExecutor.java

@@ -6,6 +6,7 @@
 import org.opencb.bionetdb.core.models.Network;
 import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor;
 import org.opencb.commons.utils.FileUtils;
+import org.opencb.datastore.core.QueryOptions;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -35,13 +36,16 @@ public void execute() {
             ExpressionParser expressionParser = new ExpressionParser(metadata);
             NetworkDBAdaptor networkDBAdaptor = new Neo4JNetworkDBAdaptor(expressionCommandOptions.database);
 
+            QueryOptions options = new QueryOptions();
+            options.put("addNodes", this.expressionCommandOptions.add);
+
             Map<String, Map<String, String>> allExpressionFiles = expressionParser.getMyFiles();
             for (String tissue : allExpressionFiles.keySet()) {
                 for (String timeseries : allExpressionFiles.get(tissue).keySet()) {
                     if ((expressionCommandOptions.tissues == null || expressionCommandOptions.tissues.contains(tissue)) &&
                             (expressionCommandOptions.timeseries == null || expressionCommandOptions.timeseries.contains(timeseries))) {
                         List<Expression> myExpression = expressionParser.parse(tissue, timeseries);
-                        networkDBAdaptor.addExpressionData(tissue, timeseries, myExpression, expressionCommandOptions.add);
+                        networkDBAdaptor.addExpressionData(tissue, timeseries, myExpression, options);
                     }
                 }
             }

bionetdb-core/pom.xml

@@ -20,6 +20,10 @@
             <groupId>org.opencb.datastore</groupId>
             <artifactId>datastore-core</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>org.neo4j</groupId>

bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java

@@ -1,6 +1,6 @@
 package org.opencb.bionetdb.core.api;
 
-import org.opencb.bionetdb.core.exceptions.DBException;
+import org.opencb.bionetdb.core.exceptions.NetworkDBException;
 import org.opencb.bionetdb.core.models.Expression;
 import org.opencb.bionetdb.core.models.Network;
 import org.opencb.bionetdb.core.models.Xref;
@@ -45,18 +45,18 @@ enum NetworkQueryParams implements QueryParam {
     }
 
 
-    void insert(Network network, QueryOptions queryOptions) throws DBException;
+    void insert(Network network, QueryOptions queryOptions) throws NetworkDBException;
 
     void addXrefs(String nodeID, List<Xref> xref_list);
 
     /**
      *
      * @param tissue Tissue of the current expression experiment
-     * @param timeseries Timeseries of the current expression experiment
+     * @param timeSeries Timeseries of the current expression experiment
      * @param myExpression List of expression data to be add in the database
-     * @param add Boolean to know if nodes not found in the database have to be created and insert their expression or not
+     * @param options Boolean to know if nodes not found in the database have to be created and insert their expression or not
      */
-    void addExpressionData(String tissue, String timeseries, List<Expression> myExpression, boolean addNodes);
+    void addExpressionData(String tissue, String timeSeries, List<Expression> myExpression, QueryOptions options);
 
     //TODO: To remove
     //public QueryResult getXrefs(String idNode);

bionetdb-core/src/main/java/org/opencb/bionetdb/core/exceptions/NetworkDBException.java

@@ -0,0 +1,20 @@
+package org.opencb.bionetdb.core.exceptions;
+
+/**
+ * Created by pfurio on 10/9/15.
+ */
+public class NetworkDBException extends Exception {
+
+    public NetworkDBException(String message) {
+        super(message);
+    }
+
+    public NetworkDBException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    public NetworkDBException(Throwable cause) {
+        super(cause);
+    }
+
+}

bionetdb-core/src/main/java/org/opencb/bionetdb/core/io/ExpressionParser.java

@@ -1,16 +1,18 @@
 package org.opencb.bionetdb.core.io;
 
 import org.opencb.bionetdb.core.models.Expression;
+import org.opencb.commons.utils.FileUtils;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import static java.nio.file.Files.readAllLines;
-
 /**
  * Created by pfurio on 8/9/15.
  */
@@ -19,81 +21,103 @@ public class ExpressionParser {
     private Map<String, Map<String, String>> myFiles;
 
     public ExpressionParser(Path metadata) throws IOException {
+        FileUtils.checkFile(metadata);
+
         myFiles = new HashMap<>();
-        List<String> allLines = readAllLines(metadata);
+        List<String> allLines = Files.readAllLines(metadata);
         for (String line : allLines) {
             String[] fields = line.split("\t");
-            Map<String, String> timeseries;
-            if (myFiles.containsKey(fields[0]))
-                timeseries = myFiles.get(fields[0]);
-            else
-                timeseries = new HashMap<>();
-            timeseries.put(fields[1], metadata.getParent().toString() + "/" + fields[2]);
+            Map<String, String> timeSeries;
+            if (myFiles.containsKey(fields[0])) {
+                timeSeries = myFiles.get(fields[0]);
+            } else {
+                timeSeries = new HashMap<>();
+            }
+            timeSeries.put(fields[1], metadata.getParent().toString() + "/" + fields[2]);
             if (!myFiles.containsKey(fields[0]))
-                myFiles.put(fields[0], timeseries);
+                myFiles.put(fields[0], timeSeries);
         }
     }
 
-    public Map<String, Map<String, String>> getMyFiles() {
-        return myFiles;
-    }
-
     public List<Expression> parse(String tissue, String time) throws IOException {
-
         String expressionFile = myFiles.get(tissue).get(time);
         List<Expression> myExpressionList = new ArrayList<>();
 
-        // Open expression file
-        BufferedReader br = new BufferedReader(new FileReader(expressionFile));
-        String currentLine = br.readLine();
+        int colId = -1;
+        int colExpr = -1;
+        int colPval = -1;
+        int colOdds = -1;
+        int colUpreg = -1;
 
-        int col_id, col_expr, col_pval, col_odds, col_upreg;
-        col_id = col_expr = col_pval = col_odds = col_upreg = -1;
-        String[] headers = currentLine.split("\t", -1);
-        if (headers.length == 2 || headers.length == 5) {
+        // Open expression file, this can be gzipped
+        Path expressionFilePath = Paths.get(expressionFile);
+        BufferedReader br = FileUtils.newBufferedReader(expressionFilePath);
 
+        // Finding the index position for each column
+        String currentLine = br.readLine();
+        String[] headers = currentLine.split("\t", -1);
+        if (headers.length > 1) {
             // Get the column where we can find each of the columns
             for (int i = 0; i < headers.length; i++) {
                 switch(headers[i]) {
                     case "ID":
-                        col_id = i;
+                        colId = i;
                         break;
                     case "Expression":
-                        col_expr = i;
+                        colExpr = i;
                         break;
                     case "Pvalue":
-                        col_pval = i;
+                        colPval = i;
                         break;
                     case "Odds":
-                        col_odds = i;
+                        colOdds = i;
                         break;
                     case "Upregulated":
-                        col_upreg = i;
+                        colUpreg = i;
                         break;
                     default:
                         break;
                 }
             }
 
             // It we have the geneID at least and some expression, pvalues, odds or upregulations...
-            if (col_id != -1 && (col_expr != -1 ||col_odds != -1 ||col_pval != -1 ||col_upreg != -1)) {
+            if (colId != -1 && (colExpr != -1 ||colOdds != -1 ||colPval != -1 ||colUpreg != -1)) {
                 while ((currentLine = br.readLine()) != null) {
                     String[] line_spl = currentLine.split("\t", -1);
-                    Expression myexpr = new Expression(line_spl[col_id]);
-                    if (col_expr != -1)
-                        myexpr.setExpression(Double.parseDouble(line_spl[col_expr]));
-                    if (col_odds != -1)
-                        myexpr.setOdds(Double.parseDouble(line_spl[col_odds]));
-                    if (col_pval != -1)
-                        myexpr.setPvalue(Double.parseDouble(line_spl[col_pval]));
-                    if (col_upreg != -1)
-                        myexpr.setUpregulated(Integer.parseInt(line_spl[col_upreg]));
-                    myExpressionList.add(myexpr);
+                    Expression myExpr = new Expression(line_spl[colId]);
+                    if (colExpr != -1) {
+                        myExpr.setExpression(Double.parseDouble(line_spl[colExpr]));
+                    }
+                    if (colOdds != -1) {
+                        myExpr.setOdds(Double.parseDouble(line_spl[colOdds]));
+                    }
+                    if (colPval != -1) {
+                        myExpr.setPvalue(Double.parseDouble(line_spl[colPval]));
+                    }
+                    if (colUpreg != -1) {
+                        myExpr.setUpregulated(Integer.parseInt(line_spl[colUpreg]));
+                    }
+                    myExpressionList.add(myExpr);
                 }
             }
         }
 
         return myExpressionList;
     }
 
+    @Override
+    public String toString() {
+        return "ExpressionParser{" +
+                "myFiles=" + myFiles +
+                '}';
+    }
+
+    public Map<String, Map<String, String>> getMyFiles() {
+        return myFiles;
+    }
+
+    public void setMyFiles(Map<String, Map<String, String>> myFiles) {
+        this.myFiles = myFiles;
+    }
+
 }

bionetdb-core/src/main/java/org/opencb/bionetdb/core/io/XrefAnnotationParser.java

@@ -32,7 +32,6 @@ public class XrefAnnotationParser {
      * Unknown info is represented as an empty string.
      */
     public Map<String, Xref> parseXrefAnnotationFile(Path path) throws IOException {
-
         // Reading GZip input stream
         InputStream inputStream;
         if (path.toFile().getName().endsWith(".gz")) {

bionetdb-core/src/main/java/org/opencb/bionetdb/core/models/Expression.java

@@ -13,6 +13,10 @@ public class Expression {
     private double odds;
     private int upregulated;
 
+    public Expression() {
+        this("");
+    }
+
     public Expression(String id) {
         this.id = id;
         this.expression = -1;
@@ -21,40 +25,55 @@ public Expression(String id) {
         this.upregulated = -1;
     }
 
-    public void setExpression(double expression) {
-        this.expression = expression;
-    }
-
-    public void setPvalue(double pvalue) {
-        this.pvalue = pvalue;
-    }
-
-    public void setOdds(double odds) {
-        this.odds = odds;
-    }
-
-    public void setUpregulated(int upregulated) {
-        this.upregulated = upregulated;
+    @Override
+    public String toString() {
+        return "Expression{" +
+                "id='" + id + '\'' +
+                ", expression=" + expression +
+                ", pvalue=" + pvalue +
+                ", odds=" + odds +
+                ", upregulated=" + upregulated +
+                '}';
     }
 
     public String getId() {
         return id;
     }
 
+    public void setId(String id) {
+        this.id = id;
+    }
+
     public double getExpression() {
         return expression;
     }
 
+    public void setExpression(double expression) {
+        this.expression = expression;
+    }
+
     public double getPvalue() {
         return pvalue;
     }
 
+    public void setPvalue(double pvalue) {
+        this.pvalue = pvalue;
+    }
+
     public double getOdds() {
         return odds;
     }
 
+    public void setOdds(double odds) {
+        this.odds = odds;
+    }
+
     public int getUpregulated() {
         return upregulated;
     }
 
+    public void setUpregulated(int upregulated) {
+        this.upregulated = upregulated;
+    }
+
 }