Several fixes and minor improvements

opencb · Sep 16, 2016 · 4914993 · 4914993
1 parent f3cb35a
commit 4914993
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Showing 7 changed files with 506 additions and 494 deletions.
diff --git a/bionetdb-app/pom.xml b/bionetdb-app/pom.xml
@@ -36,11 +36,11 @@
             <groupId>org.opencb.commons</groupId>
             <artifactId>commons-lib</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.sbml.libsbml</groupId>
-            <artifactId>libsbml</artifactId>
-            <systemPath>${basedir}/app/ext-libs/libsbmlj.jar</systemPath>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.sbml.libsbml</groupId>-->
+            <!--<artifactId>libsbml</artifactId>-->
+            <!--<systemPath>${basedir}/app/ext-libs/libsbmlj.jar</systemPath>-->
+        <!--</dependency>-->
 
         <dependency>
             <groupId>com.beust</groupId>
@@ -136,14 +136,14 @@
                                     <arg value="${build.dir}"/>
                                 </exec>
 
-                                <echo>Copying ext-libs to ${build.dir}/libs</echo>
-                                <exec executable="cp">
-                                    <arg value="${app.dir}/ext-libs/libsbml.so.5.11.4"/>
-                                    <arg value="${app.dir}/ext-libs/libsbml-static.a"/>
-                                    <arg value="${app.dir}/ext-libs/libsbmlj.jar"/>
-                                    <arg value="${app.dir}/ext-libs/libsbmlj.so"/>
-                                    <arg value="${build.dir}/libs/"/>
-                                </exec>
+                                <!--<echo>Copying ext-libs to ${build.dir}/libs</echo>-->
+                                <!--<exec executable="cp">-->
+                                    <!--<arg value="${app.dir}/ext-libs/libsbml.so.5.11.4"/>-->
+                                    <!--<arg value="${app.dir}/ext-libs/libsbml-static.a"/>-->
+                                    <!--<arg value="${app.dir}/ext-libs/libsbmlj.jar"/>-->
+                                    <!--<arg value="${app.dir}/ext-libs/libsbmlj.so"/>-->
+                                    <!--<arg value="${build.dir}/libs/"/>-->
+                                <!--</exec>-->
                             </target>
                         </configuration>
                         <goals>

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
@@ -29,16 +29,29 @@ public void execute() {
         try {
             Path inputPath = Paths.get(loadCommandOptions.input);
             FileUtils.checkFile(inputPath);
+
+//            ObjectMapper objectMapper = new ObjectMapper();
+//            ObjectReader objectReader = objectMapper.readerFor(Network.class);
+//            Network network = objectReader.readValue(inputPath.toFile());
+
+
+            // From biopax
             BioPaxParser bioPaxParser = new BioPaxParser("L3");
             Network network = bioPaxParser.parse(inputPath);
 
-            if (loadCommandOptions.database == null || loadCommandOptions.database.isEmpty()) {
-                DatabaseConfiguration databaseConfiguration = createDatabaseConfigurationFromCLI("unknown", loadCommandOptions.host,
-                        loadCommandOptions.port, loadCommandOptions.user, loadCommandOptions.password);
-                configuration.getDatabases().add(databaseConfiguration);
+            String database = loadCommandOptions.database;;
+            if (database == null || database.isEmpty()) {
+                if (configuration.getDatabases() != null && configuration.getDatabases().size() > 0) {
+                    database = configuration.getDatabases().get(0).getId();
+                } else {
+                    database = "unknown";
+                    DatabaseConfiguration databaseConfiguration = createDatabaseConfigurationFromCLI("unknown",
+                            loadCommandOptions.host, loadCommandOptions.port, loadCommandOptions.user, loadCommandOptions.password);
+                    configuration.getDatabases().add(databaseConfiguration);
+                }
             }
 
-            NetworkDBAdaptor networkDBAdaptor = new Neo4JNetworkDBAdaptor("unknown", configuration, true);
+            NetworkDBAdaptor networkDBAdaptor = new Neo4JNetworkDBAdaptor(database, configuration, true);
             networkDBAdaptor.insert(network, null);
 
         } catch (Exception e) {

diff --git a/bionetdb-core/pom.xml b/bionetdb-core/pom.xml
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>org.neo4j.driver</groupId>
             <artifactId>neo4j-java-driver</artifactId>
-            <version>1.0.4</version>
+            <version>1.0.5</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.dataformat</groupId>
@@ -47,11 +47,11 @@
             <groupId>org.biopax.paxtools</groupId>
             <artifactId>paxtools-core</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.sbml.libsbml</groupId>
-            <artifactId>libsbml</artifactId>
-            <systemPath>${basedir}/../bionetdb-app/app/ext-libs/libsbmlj.jar</systemPath>
-        </dependency>
+        <!--<dependency>-->
+            <!--<groupId>org.sbml.libsbml</groupId>-->
+            <!--<artifactId>libsbml</artifactId>-->
+            <!--<systemPath>${basedir}/../bionetdb-app/app/ext-libs/libsbmlj.jar</systemPath>-->
+        <!--</dependency>-->
         <dependency>
             <groupId>psidev.psi.mi</groupId>
             <artifactId>psimitab</artifactId>