server: add BIONETDB_HOME parameter to web.xml and INSTALLATION.DIR t…

…o pom.xml
opencb · Mar 12, 2018 · 0d81b1b · 0d81b1b
1 parent 50c6637
commit 0d81b1b
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Showing 4 changed files with 78 additions and 58 deletions.
diff --git a/bionetdb-core/src/main/resources/configuration.yml b/bionetdb-core/src/main/resources/configuration.yml
@@ -2,7 +2,7 @@
 logLevel: null
 logFile: null
 
-## You can define more than one database, you can pass the database id to BioNetDBManager.
+## More than one database can be defined, you can pass the database id to BioNetDBManager.
 ## If not passed the default database will always be the first one.
 databases:
 - id: "${BIONETDB.DB.DATABASE}"
@@ -11,4 +11,4 @@ databases:
   port: "${BIONETDB.DB.PORT}"
   user: "${BIONETDB.DB.USER}"
   password: "${BIONETDB.DB.PASSWORD}"
-  options: null
+  options: null                         ## map containing specific database options
diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/GenericRestWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/GenericRestWSServer.java
@@ -8,6 +8,7 @@
 import com.fasterxml.jackson.module.jsonSchema.factories.SchemaFactoryWrapper;
 import com.google.common.base.Splitter;
 import io.swagger.annotations.ApiParam;
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.bionetdb.core.BioNetDBManager;
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
 import org.opencb.bionetdb.core.config.BioNetDBConfiguration;
@@ -18,13 +19,15 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
 import javax.ws.rs.core.*;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.*;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 /**
  * Created by imedina on 01/10/15.
@@ -73,45 +76,17 @@ public class GenericRestWSServer {
     protected static NetworkDBAdaptor networkDBAdaptor;
     protected static Map<String, BioNetDBManager> bioNetDBManagers;
 
+    protected static AtomicBoolean initialized;
+
     private static final int LIMIT_DEFAULT = 1000;
     private static final int LIMIT_MAX = 5000;
     private static final int DEFAULT_LIMIT = 2000;
     private static final int MAX_LIMIT = 5000;
 
     static {
-        logger = LoggerFactory.getLogger("org.opencb.cellbase.server.ws.GenericRestWSServer");
-        logger.info("Static block, creating Neo4JNetworkDBAdaptor");
-        try {
-            if (System.getenv("BIONETDB_HOME") != null) {
-                logger.info("Loading configuration from '{}'", System.getenv("BIONETDB_HOME") + "/configuration.yml");
-                bioNetDBConfiguration = BioNetDBConfiguration
-                        .load(new FileInputStream(new File(System.getenv("BIONETDB_HOME") + "/configuration.yml")));
-            } else {
-                logger.info("Loading configuration from '{}'",
-                        BioNetDBConfiguration.class.getClassLoader().getResourceAsStream("configuration.yml").toString());
-                bioNetDBConfiguration = BioNetDBConfiguration
-                        .load(BioNetDBConfiguration.class.getClassLoader().getResourceAsStream("configuration.yml"));
-            }
+        initialized = new AtomicBoolean(false);
 
-//            networkDBAdaptor = new Neo4JNetworkDBAdaptor("test1", bioNetDBConfiguration);
-//        } catch (BioNetDBException e) {
-//            e.printStackTrace();
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-
-        // Init the manager map with the managers, this will allow methods to query the right database
-        bioNetDBManagers = new HashMap<>();
-        if (bioNetDBConfiguration != null && bioNetDBConfiguration.getDatabases().size() > 0) {
-            try {
-                for (DatabaseConfiguration databaseConfiguration : bioNetDBConfiguration.getDatabases()) {
-                    BioNetDBManager bioNetDBManager = new BioNetDBManager(databaseConfiguration.getId(), bioNetDBConfiguration);
-                    bioNetDBManagers.put(databaseConfiguration.getId(), bioNetDBManager);
-                }
-            } catch (BioNetDBException e) {
-                e.printStackTrace();
-            }
-        }
+        logger = LoggerFactory.getLogger("org.opencb.bionetdb.server.rest.GenericRestWSServer");
 
         jsonObjectMapper = new ObjectMapper();
         jsonObjectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
@@ -126,18 +101,65 @@ public GenericRestWSServer(@PathParam("apiVersion") String apiVersion, @Context
         this.uriInfo = uriInfo;
         this.httpServletRequest = hsr;
 
-        logger.debug("Executing GenericRestWSServer constructor with no Species");
         init();
     }
 
-    protected void init() throws VersionException {
+    private void init() throws VersionException {
+        // This must be only executed once, this method loads the configuration and create the BioNetDBManagers
+        if (initialized.compareAndSet(false, true)) {
+            initBioNetDBObjects();
+        }
+
         query = new Query();
         queryOptions = new QueryOptions();
 
         parseQueryParams();
+
         startTime = System.currentTimeMillis();
     }
 
+    /**
+     * This method loads the configuration and create the BioNetDB mangers, must be called once.
+     */
+    private void initBioNetDBObjects() {
+        try {
+            if (System.getenv("BIONETDB_HOME") != null) {
+                logger.info("Loading configuration from '{}'", System.getenv("BIONETDB_HOME") + "/configuration.yml");
+                bioNetDBConfiguration = BioNetDBConfiguration
+                        .load(new FileInputStream(new File(System.getenv("BIONETDB_HOME") + "/configuration.yml")));
+            } else {
+                // We read 'BIONETDB_HOME' parameter from the web.xml file
+                ServletContext context = httpServletRequest.getServletContext();
+                String bionetdbHome = context.getInitParameter("BIONETDB_HOME");
+                if (StringUtils.isNotEmpty(bionetdbHome)) {
+                    logger.info("Loading configuration from '{}'", bionetdbHome + "/configuration.yml");
+                    bioNetDBConfiguration = BioNetDBConfiguration
+                            .load(new FileInputStream(new File(bionetdbHome + "/configuration.yml")));
+                } else {
+                    logger.info("Loading configuration from '{}'",
+                            BioNetDBConfiguration.class.getClassLoader().getResourceAsStream("configuration.yml").toString());
+                    bioNetDBConfiguration = BioNetDBConfiguration
+                            .load(BioNetDBConfiguration.class.getClassLoader().getResourceAsStream("configuration.yml"));
+                }
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+
+        // Init the manager map with the managers, this will allow methods to query the right database
+        bioNetDBManagers = new HashMap<>();
+        if (bioNetDBConfiguration != null && bioNetDBConfiguration.getDatabases().size() > 0) {
+            try {
+                for (DatabaseConfiguration databaseConfiguration : bioNetDBConfiguration.getDatabases()) {
+                    BioNetDBManager bioNetDBManager = new BioNetDBManager(databaseConfiguration.getId(), bioNetDBConfiguration);
+                    bioNetDBManagers.put(databaseConfiguration.getId(), bioNetDBManager);
+                }
+            } catch (BioNetDBException e) {
+                e.printStackTrace();
+            }
+        }
+    }
+
     private void parseQueryParams() throws VersionException {
         // If by any reason 'apiVersion' is null we try to read it from the URI path, if not present an Exception is thrown
         if (this.apiVersion == null) {

diff --git a/bionetdb-server/src/main/webapp/WEB-INF/web.xml b/bionetdb-server/src/main/webapp/WEB-INF/web.xml
@@ -1,4 +1,4 @@
-<?xml apiVersion="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8"?>
 <!--
   ~ Copyright 2015 OpenCB
   ~
@@ -18,10 +18,15 @@
 <web-app version="2.5"
          xmlns="http://java.sun.com/xml/ns/javaee"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd">
+         xsi:schemaLocation="http://jBIONETDB_HOMEava.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd">
 
     <display-name>BioNetDB Server</display-name>
 
+    <context-param>
+        <param-name>BIONETDB_HOME</param-name>
+        <param-value>${BIONETDB.INSTALLATION.DIR}</param-value>
+    </context-param>
+
     <servlet>
         <servlet-name>BioNetDBServer</servlet-name>
         <servlet-class>org.glassfish.jersey.servlet.ServletContainer</servlet-class>
@@ -31,11 +36,6 @@
             <param-value>io.swagger.jaxrs.listing;org.opencb.bionetdb.server.rest;com.jersey.jaxb;com.fasterxml.jackson.jaxrs.json</param-value>
         </init-param>
 
-        <!--<init-param>-->
-            <!--<param-name>jersey.config.server.provider.classnames</param-name>-->
-            <!--<param-value>org.glassfish.jersey.media.multipart.MultiPartFeature</param-value>-->
-        <!--</init-param>-->
-
         <init-param>
             <param-name>BIONETDB_HOME</param-name>
             <param-value>~/appl/bionetdb/build</param-value>
@@ -59,21 +59,6 @@
         <url-pattern>*</url-pattern>
     </filter-mapping>
 
-    <!--swagger-->
-    <!--<servlet>-->
-        <!--<servlet-name>JerseyJaxrsConfig</servlet-name>-->
-        <!--<servlet-class>io.swagger.jersey.config.JerseyJaxrsConfig</servlet-class>-->
-
-        <!--<init-param>-->
-            <!--<param-name>api.apiVersion</param-name>-->
-            <!--<param-value>1.0.0</param-value>-->
-        <!--</init-param>-->
-        <!--<init-param>-->
-            <!--<param-name>swagger.api.basepath</param-name>-->
-            <!--<param-value>/cellbase/webservices/rest</param-value>-->
-        <!--</init-param>-->
-        <!--<load-on-startup>2</load-on-startup>-->
-    <!--</servlet>-->
 
     <servlet>
         <servlet-name>Jersey2Config</servlet-name>

diff --git a/pom.xml b/pom.xml
@@ -86,6 +86,16 @@
                 <groupId>org.opencb.biodata</groupId>
                 <artifactId>biodata-models</artifactId>
                 <version>${biodata.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>com.google.protobuf</groupId>
+                        <artifactId>protobuf-lite</artifactId>
+                    </exclusion>
+                    <exclusion>
+                        <groupId>org.mortbay.jetty</groupId>
+                        <artifactId>servlet-api</artifactId>
+                    </exclusion>
+                </exclusions>
             </dependency>
             <dependency>
                 <groupId>org.opencb.commons</groupId>
@@ -200,7 +210,10 @@
                 <activeByDefault>true</activeByDefault>
             </activation>
             <properties>
+                <BIONETDB.INSTALLATION.DIR>/opt/bionetdb</BIONETDB.INSTALLATION.DIR>
+
                 <BIONETDB.DB.DATABASE>scerevisiae</BIONETDB.DB.DATABASE>
+                <BIONETDB.DB.SPECIES>scerevisiae</BIONETDB.DB.SPECIES>
                 <BIONETDB.DB.HOST>localhost</BIONETDB.DB.HOST>
                 <BIONETDB.DB.PORT>7687</BIONETDB.DB.PORT>
                 <BIONETDB.DB.USER>neo4j</BIONETDB.DB.USER>