models: add write method to Network in order to save it into a file i…

…n JSON format based, #58
opencb · Nov 30, 2020 · bb63017 · bb63017
1 parent abba9da
commit bb63017
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Showing 3 changed files with 67 additions and 26 deletions.
diff --git a/...b-app/src/main/java/org/opencb/bionetdb/app/cli/admin/executors/BuildCommandExecutor.java b/...b-app/src/main/java/org/opencb/bionetdb/app/cli/admin/executors/BuildCommandExecutor.java
@@ -1,33 +1,14 @@
 package org.opencb.bionetdb.app.cli.admin.executors;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.MapperFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import htsjdk.samtools.util.StringUtil;
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.opencb.bionetdb.app.cli.CommandExecutor;
 import org.opencb.bionetdb.app.cli.admin.AdminCliOptionsParser;
 import org.opencb.bionetdb.core.exceptions.BioNetDBException;
-import org.opencb.bionetdb.core.io.BioPaxParser;
-import org.opencb.bionetdb.core.io.SbmlParser;
-import org.opencb.bionetdb.core.io.SifParser;
-import org.opencb.bionetdb.core.models.network.Network;
-import org.opencb.bionetdb.core.models.network.Node;
-import org.opencb.bionetdb.core.models.network.Relation;
 import org.opencb.bionetdb.lib.BioNetDbManager;
-import org.opencb.bionetdb.lib.utils.Builder;
 import org.opencb.commons.utils.FileUtils;
-import org.opencb.commons.utils.ListUtils;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.*;
 
 /**
  * Created by imedina on 05/08/15.

diff --git a/bionetdb-app/src/test/java/org/opencb/bionetdb/app/BioNetDBMainTest.java b/bionetdb-app/src/test/java/org/opencb/bionetdb/app/BioNetDBMainTest.java
@@ -1,6 +1,7 @@
 package org.opencb.bionetdb.app;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
@@ -9,7 +10,7 @@
 import org.opencb.bionetdb.core.models.network.Relation;
 
 import java.io.File;
-import java.io.IOException;
+import java.io.FileNotFoundException;
 import java.util.ArrayList;
 
 public class BioNetDBMainTest {
@@ -20,7 +21,8 @@ public void createCsvClinicalAnalysis() {
         String cmdLine = "~/appl/bionetdb/build/bin/bionetdb.sh create-csv -i " + caPath + "/input/ -o csv/ --clinical-analysis";
     }
 
-    private void createNetworks() {
+
+    public void createNetworks() {
         long uid = 0;
 
         ObjectMapper mapper = new ObjectMapper();
@@ -43,12 +45,17 @@ private void createNetworks() {
                 Relation.Type.GENE__DRUG);
         network.getRelations().add(relation1);
 
+        File file = new File("/tmp/network1.json");
         try {
-            mapper.writer().writeValue(new File("/tmp/network1.json"), network);
-        } catch (IOException e) {
+            network.write(file);
+        } catch (FileNotFoundException | JsonProcessingException e) {
             e.printStackTrace();
         }
-
+//        try {
+//            mapper.writer().writeValue(, network);
+//        } catch (IOException e) {
+//            e.printStackTrace();
+//        }
 
         network = new Network("net2", "net2", "Network #2");
         network.setNodes(new ArrayList<>());
@@ -67,11 +74,17 @@ private void createNetworks() {
                 Relation.Type.GENE__DRUG);
         network.getRelations().add(relation3);
 
+        file = new File("/tmp/network2.json");
         try {
-            mapper.writer().writeValue(new File("/tmp/network2.json"), network);
-        } catch (IOException e) {
+            network.write(file);
+        } catch (FileNotFoundException | JsonProcessingException e) {
             e.printStackTrace();
         }
+//        try {
+//            mapper.writer().writeValue(new File("/tmp/network2.json"), network);
+//        } catch (IOException e) {
+//            e.printStackTrace();
+//        }
 
     }
 }
diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/models/network/Network.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/models/network/Network.java
@@ -1,5 +1,13 @@
 package org.opencb.bionetdb.core.models.network;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.MapperFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -14,6 +22,9 @@ public class Network extends Graph {
 
     private Map<String, Object> attributes;
 
+    private long numNodes;
+    private long numRelations;
+
     public Network() {
         this("", "", "");
     }
@@ -27,6 +38,32 @@ public Network(String id, String name, String description) {
         attributes = new HashMap<>();
     }
 
+    public void write(File file) throws FileNotFoundException, JsonProcessingException {
+        Network network = new Network(id, name, description);
+        network.setAttributes(attributes);
+        network.setNumNodes(nodes.size());
+        network.setNumRelations(relations.size());
+
+        ObjectMapper mapper = new ObjectMapper();
+        mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+        mapper.configure(MapperFeature.REQUIRE_SETTERS_FOR_GETTERS, true);
+
+        PrintWriter pw = new PrintWriter(file);
+
+        pw.println(mapper.writer().writeValueAsString(network));
+        for (Node node: nodes) {
+            pw.println(mapper.writer().writeValueAsString(node));
+        }
+        for (Relation relation: relations) {
+            pw.println(mapper.writer().writeValueAsString(relation));
+        }
+
+        pw.close();
+
+
+    }
+
+
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("Network{");
@@ -75,4 +112,14 @@ public Network setAttributes(Map<String, Object> attributes) {
         this.attributes = attributes;
         return this;
     }
+
+    public Network setNumNodes(long numNodes) {
+        this.numNodes = numNodes;
+        return this;
+    }
+
+    public Network setNumRelations(long numRelations) {
+        this.numRelations = numRelations;
+        return this;
+    }
 }