Several configuration improvements:

* we can use Maven profiles to setup the configuration connection * Load CLI accepts database credentials
opencb · Jul 20, 2016 · 925b6d3 · 925b6d3
1 parent af561e8
commit 925b6d3
Show file tree

Hide file tree

Showing 5 changed files with 55 additions and 12 deletions.
diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java
@@ -121,6 +121,18 @@ public class LoadCommandOptions {
         @Parameter(names = {"--database"}, description = "Data model type to be loaded, i.e. genome, gene, ...", required = false, arity = 1)
         public String database;
 
+        @Parameter(names = {"--host"}, description = "...", required = false, arity = 1)
+        public String host = "localhost";
+
+        @Parameter(names = {"--port"}, description = "...", required = false, arity = 1)
+        public int port = 7687;
+
+        @Parameter(names = {"-u", "--user"}, description = "Data model type to be loaded, i.e. genome, gene, ...", required = false, arity = 1)
+        public String user;
+
+        @Parameter(names = {"-p", "--password"}, description = "Data model type to be loaded, i.e. genome, gene, ...", password = true, arity = 1)
+        public String password;
+
         @Parameter(names = {"-l", "--loader"}, description = "Database specific data loader to be used", required = false, arity = 1)
         public String loader = "org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor";
 

diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/LoadCommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/LoadCommandExecutor.java
@@ -1,15 +1,12 @@
 package org.opencb.bionetdb.app.cli;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.ObjectReader;
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
+import org.opencb.bionetdb.core.config.DatabaseConfiguration;
 import org.opencb.bionetdb.core.io.BioPaxParser;
 import org.opencb.bionetdb.core.models.Network;
 import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor;
 import org.opencb.commons.utils.FileUtils;
 
-import java.io.IOException;
-import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -35,11 +32,19 @@ public void execute() {
             BioPaxParser bioPaxParser = new BioPaxParser("L3");
             Network network = bioPaxParser.parse(inputPath);
 
-//            ObjectReader objectReader = new ObjectMapper().readerFor(Network.class);
-//            Network network = objectReader.readValue(Files.newBufferedReader(inputPath));
+            if (loadCommandOptions.database == null || loadCommandOptions.database.isEmpty()) {
+                loadCommandOptions.database = "unknown";
 
-            NetworkDBAdaptor networkDBAdaptor = new Neo4JNetworkDBAdaptor(loadCommandOptions.database, configuration, true);
+                DatabaseConfiguration databaseConfiguration = new DatabaseConfiguration(loadCommandOptions.database, null);
+                databaseConfiguration.setHost(loadCommandOptions.host);
+                databaseConfiguration.setPort(loadCommandOptions.port);
+                databaseConfiguration.setUser(loadCommandOptions.user);
+                databaseConfiguration.setPassword(loadCommandOptions.password);
+
+                configuration.getDatabases().add(databaseConfiguration);
+            }
 
+            NetworkDBAdaptor networkDBAdaptor = new Neo4JNetworkDBAdaptor(loadCommandOptions.database, configuration, true);
             networkDBAdaptor.insert(network, null);
 
         } catch (Exception e) {

diff --git a/bionetdb-core/pom.xml b/bionetdb-core/pom.xml
@@ -66,4 +66,13 @@
         </dependency>
     </dependencies>
 
+    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <filtering>true</filtering>
+            </resource>
+        </resources>
+    </build>
+
 </project>
diff --git a/bionetdb-core/src/main/resources/configuration.yml b/bionetdb-core/src/main/resources/configuration.yml
@@ -3,11 +3,11 @@ defaultDatabase: "scerevisiae"
 logLevel: null
 logFile: null
 databases:
-- id: "scerevisiae"
-  host: "localhost"
-  port: "7687"
-  user: "neo4j"
-  password: "neo4j"
+- id: "${BIONETDB.DATABASE}"
+  host: "${BIONETDB.CATALOG.DB.HOST}"
+  port: "${BIONETDB.CATALOG.DB.PORT}"
+  user: "${BIONETDB.CATALOG.DB.USER}"
+  password: "${BIONETDB.CATALOG.DB.PASSWORD}"
   options: null
 - id: "hsapiens"
   host: "localhost"

diff --git a/pom.xml b/pom.xml
@@ -246,6 +246,23 @@
         </plugins>
     </build>
 
+    <profiles>
+        <profile>
+            <id>default-config</id>
+            <activation>
+                <activeByDefault>true</activeByDefault>
+            </activation>
+            <properties>
+                <opencga.war.name>opencga-${bionetdb.version}</opencga.war.name>
+
+                <BIONETDB.DATABASE>scerevisiae</BIONETDB.DATABASE>
+                <BIONETDB.CATALOG.DB.HOST>localhost</BIONETDB.CATALOG.DB.HOST>
+                <BIONETDB.CATALOG.DB.PORT>7687</BIONETDB.CATALOG.DB.PORT>
+                <BIONETDB.CATALOG.DB.USER></BIONETDB.CATALOG.DB.USER>
+                <BIONETDB.CATALOG.DB.PASSWORD></BIONETDB.CATALOG.DB.PASSWORD>
+            </properties>
+        </profile>
+    </profiles>
     <distributionManagement>
         <repository>
             <id>ossrh</id>