variables metadata into meta-db

.gitignore

@@ -4,4 +4,3 @@ target/
 .DS_Store
 .m2
 *.jar
-src/main/resources/data/

src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java

@@ -47,6 +47,13 @@ public class PersistenceConfiguration {
         return new JdbcTemplate(dataSource());
     }
 
+    @Bean
+    @Autowired
+    @Qualifier("jdbcTemplateMeta")
+    public JdbcTemplate jdbcTemplateMeta() {
+        return new JdbcTemplate(metaDataSource());
+    }
+
     @Bean(name = "metaEntityManagerFactory")
     @DependsOn("flyway")
     public LocalContainerEntityManagerFactoryBean metaEntityManagerFactory() {

src/main/java/eu/hbp/mip/controllers/GroupsApi.java

@@ -7,22 +7,22 @@ package eu.hbp.mip.controllers;
 import com.google.gson.Gson;
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
-import com.google.gson.stream.JsonReader;
 import eu.hbp.mip.model.Group;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiResponse;
 import io.swagger.annotations.ApiResponses;
 import org.apache.log4j.Logger;
+import org.postgresql.util.PGobject;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.http.ResponseEntity;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.support.rowset.SqlRowSet;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RestController;
 
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-
 import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
 
 @RestController
@@ -32,10 +32,12 @@ public class GroupsApi {
 
     private static final Logger LOGGER = Logger.getLogger(GroupsApi.class);
 
-    private static final String VARIABLES_FILE = "data/variables.json";
-
     private static String groups;
 
+    @Autowired
+    @Qualifier("jdbcTemplateMeta")
+    private JdbcTemplate jdbcTemplateMeta;
+
 
     @ApiOperation(value = "Get the root group (containing all subgroups)", response = Group.class)
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@@ -48,20 +50,22 @@ public class GroupsApi {
         return ResponseEntity.ok(new Gson().fromJson(groups, Object.class));
     }
 
-    private static void loadGroups() {
+    private void loadGroups() {
         if(groups == null)
         {
-            InputStream is = VariablesApi.class.getClassLoader().getResourceAsStream(VARIABLES_FILE);
-            InputStreamReader isr = new InputStreamReader(is);
-            BufferedReader br = new BufferedReader(isr);
+            String sqlQuery = "SELECT * FROM meta_variables";
+            SqlRowSet data = jdbcTemplateMeta.queryForRowSet(sqlQuery);
+            data.next();
+            String json = ((PGobject) data.getObject("hierarchy")).getValue();
+
+            JsonObject root = new Gson().fromJson(json, JsonObject.class);
 
-            JsonObject root = new Gson().fromJson(new JsonReader(br), JsonObject.class);
             removeVariablesRecursive(root);
             groups = new Gson().toJson(root);
         }
     }
 
-    private static void removeVariablesRecursive(JsonObject element) {
+    private void removeVariablesRecursive(JsonObject element) {
         if (element.has("groups")){
             for(JsonElement child : element.getAsJsonArray("groups")) {
                 removeVariablesRecursive(child.getAsJsonObject());

src/main/java/eu/hbp/mip/controllers/VariablesApi.java

@@ -9,16 +9,16 @@ import com.google.gson.Gson;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
-import com.google.gson.stream.JsonReader;
-import eu.hbp.mip.model.Variable;
 import io.swagger.annotations.*;
 import org.apache.log4j.Logger;
+import org.postgresql.util.PGobject;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.http.ResponseEntity;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.support.rowset.SqlRowSet;
 import org.springframework.web.bind.annotation.*;
 
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.util.LinkedList;
 import java.util.List;
 
@@ -31,10 +31,12 @@ public class VariablesApi {
 
     private static final Logger LOGGER = Logger.getLogger(VariablesApi.class);
 
-    private static final String VARIABLES_FILE = "data/variables.json";
-
     private static LinkedList<String> variables;
 
+    @Autowired
+    @Qualifier("jdbcTemplateMeta")
+    private JdbcTemplate jdbcTemplateMeta;
+
 
     @ApiOperation(value = "Get variables", response = List.class, responseContainer = "List")
     @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@@ -123,31 +125,33 @@ public class VariablesApi {
     )  {
         LOGGER.info("Get groups and variables hierarchy");
 
-        InputStream is = Variable.class.getClassLoader().getResourceAsStream(VARIABLES_FILE);
-        InputStreamReader isr = new InputStreamReader(is);
-        BufferedReader br = new BufferedReader(isr);
+        String sqlQuery = "SELECT * FROM meta_variables";
+        SqlRowSet data = jdbcTemplateMeta.queryForRowSet(sqlQuery);
+        data.next();
+        String json = ((PGobject) data.getObject("hierarchy")).getValue();
 
-        Object hierarchy = new Gson().fromJson(new JsonReader(br), Object.class);
+        Object hierarchy = new Gson().fromJson(json, Object.class);
 
         return ResponseEntity.ok(hierarchy);
     }
 
 
-    private static void loadVariables() {
+    private void loadVariables() {
         if(variables == null)
         {
-            InputStream is = VariablesApi.class.getClassLoader().getResourceAsStream(VARIABLES_FILE);
-            InputStreamReader isr = new InputStreamReader(is);
-            BufferedReader br = new BufferedReader(isr);
+            String sqlQuery = "SELECT * FROM meta_variables";
+            SqlRowSet data = jdbcTemplateMeta.queryForRowSet(sqlQuery);
+            data.next();
+            String json = ((PGobject) data.getObject("hierarchy")).getValue();
 
-            JsonObject root = new Gson().fromJson(new JsonReader(br), JsonObject.class);
-            variables = new LinkedList<>();
+            JsonObject root = new Gson().fromJson(json, JsonObject.class);
 
+            variables = new LinkedList<>();
             extractVariablesRecursive(root);
         }
     }
 
-    private static void extractVariablesRecursive(JsonObject element) {
+    private void extractVariablesRecursive(JsonObject element) {
         if (element.has("groups")){
             for(JsonElement child : element.getAsJsonArray("groups")) {
                 extractVariablesRecursive(child.getAsJsonObject());