core: new configuration functionality added

bionetdb-app/pom.xml

@@ -134,6 +134,7 @@
                                     <arg value="${project.basedir}/target/appassembler/bin"/>
                                     <arg value="${project.basedir}/target/appassembler/libs"/>
                                     <arg value="${app.dir}/examples"/>
+                                    <arg value="${project.basedir}/../bionetdb-core/target/classes/configuration.yml"/>
                                     <arg value="${project.basedir}/../bionetdb-server/target/bionetdb.war"/>
                                     <arg value="${project.basedir}/../LICENSE"/>
                                     <arg value="${project.basedir}/../README.md"/>

bionetdb-core/pom.xml

@@ -29,6 +29,10 @@
             <artifactId>commons-lib</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>com.fasterxml.jackson.dataformat</groupId>
+            <artifactId>jackson-dataformat-yaml</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.neo4j</groupId>
             <artifactId>neo4j</artifactId>
@@ -47,7 +51,7 @@
             <groupId>psidev.psi.mi</groupId>
             <artifactId>psimitab</artifactId>
         </dependency>
-<dependency>
+        <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
         </dependency>

bionetdb-core/src/main/java/org/opencb/bionetdb/core/config/BioNetDBConfiguration.java

@@ -0,0 +1,179 @@
+package org.opencb.bionetdb.core.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created by imedina on 05/10/15.
+ */
+public class BioNetDBConfiguration {
+
+    private String defaultDatabase;
+    private String logLevel;
+    private String logFile;
+
+    private List<DatabaseConfiguration> databases;
+
+    protected static Logger logger = LoggerFactory.getLogger(BioNetDBConfiguration.class);
+
+    public BioNetDBConfiguration() {
+        this("", new ArrayList<>());
+    }
+
+    public BioNetDBConfiguration(String defaultDatabase, List<DatabaseConfiguration> databaseConfigurations) {
+        this.defaultDatabase = defaultDatabase;
+        this.databases = databaseConfigurations;
+
+    }
+
+    /*
+     * This method attempts to find and load the configuration from installation directory,
+     * if not exists then loads JAR storage-configuration.yml.
+     */
+    @Deprecated
+    public static BioNetDBConfiguration load() throws IOException {
+        String appHome = System.getProperty("app.home", System.getenv("BIONETDB_HOME"));
+        Path path = Paths.get(appHome + "/configuration.yml");
+        if (appHome != null && Files.exists(path)) {
+            logger.debug("Loading configuration from '{}'", appHome + "/configuration.yml");
+            return BioNetDBConfiguration
+                    .load(new FileInputStream(new File(appHome + "/configuration.yml")));
+        } else {
+            logger.debug("Loading configuration from '{}'",
+                    BioNetDBConfiguration.class.getClassLoader()
+                            .getResourceAsStream("configuration.yml")
+                            .toString());
+            return BioNetDBConfiguration
+                    .load(BioNetDBConfiguration.class.getClassLoader().getResourceAsStream("configuration.yml"));
+        }
+    }
+
+    public static BioNetDBConfiguration load(InputStream configurationInputStream) throws IOException {
+        return load(configurationInputStream, "yaml");
+    }
+
+    public static BioNetDBConfiguration load(InputStream configurationInputStream, String format) throws IOException {
+        BioNetDBConfiguration bioNetDBConfiguration;
+        ObjectMapper objectMapper;
+        switch (format) {
+            case "json":
+                objectMapper = new ObjectMapper();
+                bioNetDBConfiguration = objectMapper.readValue(configurationInputStream, BioNetDBConfiguration.class);
+                break;
+            case "yml":
+            case "yaml":
+            default:
+                objectMapper = new ObjectMapper(new YAMLFactory());
+                bioNetDBConfiguration = objectMapper.readValue(configurationInputStream, BioNetDBConfiguration.class);
+                break;
+        }
+
+        return bioNetDBConfiguration;
+    }
+
+    public void serialize(OutputStream configurationOututStream) throws IOException {
+        ObjectMapper jsonMapper = new ObjectMapper(new YAMLFactory());
+        jsonMapper.writerWithDefaultPrettyPrinter().writeValue(configurationOututStream, this);
+    }
+
+    public DatabaseConfiguration findDatabase() {
+        if (defaultDatabase != null && !defaultDatabase.isEmpty()) {
+            return findDatabase(defaultDatabase);
+        } else {
+            if (databases.size() > 0) {
+                return databases.get(0);
+            } else {
+                return null;
+            }
+        }
+    }
+
+    public DatabaseConfiguration findDatabase(String database) {
+        DatabaseConfiguration databaseConfiguration = null;
+        for (DatabaseConfiguration databaseConf : databases) {
+            if (databaseConf.getId().equals(database)) {
+                databaseConfiguration = databaseConf;
+                break;
+            }
+        }
+
+        return databaseConfiguration;
+    }
+
+    public void addDatabase(InputStream configurationInputStream) throws IOException {
+        addDatabase(configurationInputStream, "yaml");
+    }
+
+    public void addDatabase(InputStream configurationInputStream, String format) throws IOException {
+        DatabaseConfiguration databaseConfiguration;
+        ObjectMapper objectMapper;
+        switch (format) {
+            case "json":
+                objectMapper = new ObjectMapper();
+                databaseConfiguration = objectMapper.readValue(configurationInputStream, DatabaseConfiguration.class);
+                break;
+            case "yml":
+            case "yaml":
+            default:
+                objectMapper = new ObjectMapper(new YAMLFactory());
+                databaseConfiguration = objectMapper.readValue(configurationInputStream, DatabaseConfiguration.class);
+                break;
+        }
+
+        if (databaseConfiguration != null) {
+            this.databases.add(databaseConfiguration);
+        }
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("BioNetDBConfiguration{");
+        sb.append("defaultDatabase='").append(defaultDatabase).append('\'');
+        sb.append(", logLevel='").append(logLevel).append('\'');
+        sb.append(", logFile='").append(logFile).append('\'');
+        sb.append(", databases=").append(databases);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getDefaultDatabase() {
+        return defaultDatabase;
+    }
+
+    public void setDefaultDatabase(String defaultDatabase) {
+        this.defaultDatabase = defaultDatabase;
+    }
+
+    public String getLogLevel() {
+        return logLevel;
+    }
+
+    public void setLogLevel(String logLevel) {
+        this.logLevel = logLevel;
+    }
+
+    public String getLogFile() {
+        return logFile;
+    }
+
+    public void setLogFile(String logFile) {
+        this.logFile = logFile;
+    }
+
+    public List<DatabaseConfiguration> getDatabases() {
+        return databases;
+    }
+
+    public void setDatabases(List<DatabaseConfiguration> databases) {
+        this.databases = databases;
+    }
+}

bionetdb-core/src/main/java/org/opencb/bionetdb/core/config/DatabaseConfiguration.java

@@ -0,0 +1,103 @@
+package org.opencb.bionetdb.core.config;
+
+import org.opencb.datastore.core.ObjectMap;
+
+/**
+ * Created by imedina on 05/10/15.
+ */
+public class DatabaseConfiguration {
+
+    private String id;
+
+    private String host;
+    private int port;
+    private String user;
+    private String password;
+
+    private String path;
+
+    /**
+     * options parameter defines database-specific parameters.
+     */
+    private ObjectMap options;
+
+
+    public DatabaseConfiguration() {
+
+    }
+
+    public DatabaseConfiguration(String id, ObjectMap options) {
+        this.id = id;
+        this.options = options;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("DatabaseConfiguration{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", host='").append(host).append('\'');
+        sb.append(", port=").append(port);
+        sb.append(", user='").append(user).append('\'');
+        sb.append(", password='").append(password).append('\'');
+        sb.append(", path='").append(path).append('\'');
+        sb.append(", options=").append(options);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public String getHost() {
+        return host;
+    }
+
+    public void setHost(String host) {
+        this.host = host;
+    }
+
+    public int getPort() {
+        return port;
+    }
+
+    public void setPort(int port) {
+        this.port = port;
+    }
+
+    public String getUser() {
+        return user;
+    }
+
+    public void setUser(String user) {
+        this.user = user;
+    }
+
+    public String getPassword() {
+        return password;
+    }
+
+    public void setPassword(String password) {
+        this.password = password;
+    }
+
+    public String getPath() {
+        return path;
+    }
+
+    public void setPath(String path) {
+        this.path = path;
+    }
+
+    public ObjectMap getOptions() {
+        return options;
+    }
+
+    public void setOptions(ObjectMap options) {
+        this.options = options;
+    }
+}

bionetdb-core/src/main/resources/configuration.yml

@@ -0,0 +1,12 @@
+---
+defaultDatabase: "testDB"
+logLevel: null
+logFile: null
+databases:
+- id: "testDB"
+  host: null
+  port: 0
+  user: null
+  password: null
+  path: null
+  options: null

bionetdb-core/src/test/java/org/opencb/bionetdb/core/config/BioNetDBConfigurationTest.java

@@ -0,0 +1,30 @@
+package org.opencb.bionetdb.core.config;
+
+import org.junit.Test;
+
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.Assert.*;
+
+/**
+ * Created by imedina on 05/10/15.
+ */
+public class BioNetDBConfigurationTest {
+
+    @Test
+    public void testSerialize() throws Exception {
+
+        BioNetDBConfiguration bioNetDBConfiguration = new BioNetDBConfiguration();
+
+        bioNetDBConfiguration.setDefaultDatabase("testDB");
+
+        List<DatabaseConfiguration> databases = new ArrayList<>();
+        databases.add(new DatabaseConfiguration("testDB", null));
+
+        bioNetDBConfiguration.setDatabases(databases);
+
+        bioNetDBConfiguration.serialize(new FileOutputStream("/tmp/bionetdb-configuration-test.yml"));
+    }
+}

pom.xml

@@ -136,6 +136,11 @@
                 <artifactId>jackson-databind</artifactId>
                 <version>${jackson.version}</version>
             </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.dataformat</groupId>
+                <artifactId>jackson-dataformat-yaml</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
             <dependency>
                 <groupId>com.fasterxml.jackson.module</groupId>
                 <artifactId>jackson-module-jsonSchema</artifactId>