Added settings class to store global paths to run the server on a custom server

frontend/src/main/java/de/thm/positionData/AssemblyGuesser.java

@@ -17,6 +17,7 @@
 package de.thm.positionData;
 
 import de.thm.misc.Genome;
+import de.thm.spring.backend.Settings;
 import org.apache.commons.exec.CommandLine;
 import org.apache.commons.exec.DefaultExecutor;
 import org.apache.commons.exec.ExecuteStreamHandler;
@@ -71,10 +72,7 @@ public class AssemblyGuesser {
                 assemblies.add(assembly.toString());
 
         // get contigs file for each assembly
-        if (!System.getenv("HOME").contains("menzel"))
-            assemblies.forEach(a -> contigsPaths.add("/home/mmnz21/con/contigs_" + a));
-        else //on local pc:
-            assemblies.forEach(a -> contigsPaths.add( "/home/menzel/Desktop/THM/promotion/enhort/dat/" + a + "/inout/contigs"));
+        assemblies.forEach(a -> contigsPaths.add(Settings.getContigsPath() + "contigs_" + a));
 
         Pattern p = Pattern.compile("[\r\n]");
 

frontend/src/main/java/de/thm/spring/backend/BackendConnector.java

@@ -65,14 +65,10 @@ public final class BackendConnector {
     private String secret;
 
 
-    BackendConnector(){
+    BackendConnector(String ip) {
 
         this.port = 42412;
-
-        if (System.getenv("HOME").contains("menzel"))
-            this.ip = "127.0.0.1";
-        else
-            this.ip = "bioinf-ladon.mni.thm.de";
+        this.ip = ip;
 
         id = clientID.getAndIncrement();
 

frontend/src/main/java/de/thm/spring/backend/Session.java

@@ -53,7 +53,7 @@ public final class Session {
         this.customTracks = customTracks;
 
         StatisticsCollector.getInstance().addSessionC();
-        connector = new BackendConnector();
+        connector = new BackendConnector(Settings.getBackendip());
     }
 
     Session(String key, Date date) {
@@ -61,7 +61,7 @@ public final class Session {
         this.date = date;
 
         StatisticsCollector.getInstance().addSessionC();
-        connector = new BackendConnector();
+        connector = new BackendConnector(Settings.getBackendip());
     }
 
     public String getKey() {

frontend/src/main/java/de/thm/spring/backend/Settings.java

 package de.thm.spring.backend;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.net.InetAddress;
+import java.nio.file.Path;
+
 public class Settings {
+    private static String contigsPath;
+    private static String backendip;
+    private static Path logfile;
+
+    private static Logger logger = LoggerFactory.getLogger(StatisticsCollector.class);
+
+    public static String getBackendip() {
+        return backendip;
+    }
+
+    public static void setBackendip(String ip) {
+        try {
+            InetAddress address = InetAddress.getByName(ip);
+
+            if (!address.isReachable(1000))
+                throw new Exception("Backend Server " + ip + " not reachable");
+
+        } catch (Exception e) {
+            logger.error("Exception {}", e.getMessage(), e);
+        }
+
+        Settings.backendip = ip;
+    }
+
+    public static Path getLogfile_path() {
+        return logfile;
+    }
+
+    public static void setLogfile_path(String logfile_path) {
+        Settings.logfile = new File(logfile_path).toPath().toAbsolutePath();
+    }
+
+    public static String getContigsPath() {
+        return contigsPath;
+    }
+
+    public static void setContigsPath(String contigsPath) {
+        if (!new File(contigsPath).exists())
+            logger.error("Exception {}", "Contigs path missing", "The contigs path " + contigsPath + " is missing");
+
+        Settings.contigsPath = contigsPath;
+    }
 }
+

frontend/src/main/java/de/thm/spring/backend/StatisticsCollector.java

@@ -20,7 +20,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.BufferedWriter;
-import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -37,7 +36,7 @@ import java.util.stream.Stream;
  */
 public final class StatisticsCollector {
 
-    private static final StatisticsCollector instance = new StatisticsCollector(new File("/home/mmnz21/enhort.log").toPath());
+    private static final StatisticsCollector instance = new StatisticsCollector(Settings.getLogfile_path());
     private final Path logPath;
     private final Logger logger = LoggerFactory.getLogger(StatisticsCollector.class);
 
@@ -72,7 +71,6 @@ public final class StatisticsCollector {
             downloadCount = new AtomicInteger(0);
             date = new Date();
 
-
             saveStats();
 
             try {
@@ -97,7 +95,9 @@ public final class StatisticsCollector {
                 downloadCount = new AtomicInteger(Integer.parseInt(values[4]));
                 date = new SimpleDateFormat("EEE MMM dd HH:mm:ss zzz yyyy").parse(values[5]);
 
-                lines.close();
+            } catch (ArrayIndexOutOfBoundsException e) {
+                logPath.toFile().delete();
+                logger.error("Exception {}", "Corrupt log file", "The logfile was corrupt and was deleted. Please restart the server to enable logging again");
 
             } catch (IOException | ParseException e) {
                 logger.error("Exception {}", e.getMessage(), e);

frontend/src/main/java/de/thm/spring/controller/BatchController.java

@@ -97,7 +97,7 @@ public class BatchController {
         }
 
         Comparator<TestResult> byPackage = Comparator.comparing(t -> t.getTrack().getPack());
-        Comparator<TestResult> byTrack = byPackage.thenComparing(Comparator.comparing(t -> t.getTrack().getName()));
+        Comparator<TestResult> byTrack = byPackage.thenComparing(t -> t.getTrack().getName());
         Comparator<String> byIndex = Comparator.comparing(names::indexOf); // sort by index of names of user uploaded bed file names
 
         for (MultipartFile mf : files) {
@@ -164,6 +164,8 @@ public class BatchController {
                     List<Number> tmp = new ArrayList<>();
 
                     //TODO CSV:
+                    //TODO real fold change
+                    //csv.append(tr.getTrack().getName()).append(" Fold change (log2): ").append(tr.getEffectSize()).append(" In sites: ").append(tr.getMeasuredIn()).append(" In control: ").append(tr.getExpectedIn()).append(" Out sites: ").append(tr.getMeasuredOut()).append(" Out control: ").append(tr.getExpectedOut()).append(" P value: ").append(tr.getpValue());
                     csv.append(tr.getTrack().getName()).append(" Fold change (log2): ").append(tr.getEffectSize()).append(" In sites: ").append(tr.getMeasuredIn()).append(" In control: ").append(tr.getExpectedIn()).append(" Out sites: ").append(tr.getMeasuredOut()).append(" Out control: ").append(tr.getExpectedOut()).append(" P value: ").append(tr.getpValue());
                     csv.append(lb);
 

frontend/src/main/java/de/thm/spring/run/Webinterface.java

@@ -17,6 +17,7 @@
 package de.thm.spring.run;
 
 import de.thm.spring.backend.Sessions;
+import de.thm.spring.backend.Settings;
 import de.thm.spring.backend.StatisticsCollector;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -37,8 +38,14 @@ public class Webinterface {
 
     public static void main(String[] args) {
 
+        /* Set up Settings */
+
+        Settings.setBackendip(args[0]);
+        Settings.setContigsPath(args[1]);
+        Settings.setLogfile_path(args[2]);
 
         try {
+
             SpringApplication.run(Webinterface.class, args);
 
             Sessions.getInstance().addSession("monitorsession");