Merge branch 'dev/46180_bugfixes_for_svarog_dmg_under_mac' into 'development'

#46180 bugfixes_for_svarog_dmg_under_mac dev

See merge request brain/svarog2!184

svarog/src/main/java/org/signalml/app/method/mp5/MP5ExecutorManager.java

@@ -21,6 +21,9 @@
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.annotations.Annotations;
 import com.thoughtworks.xstream.annotations.XStreamAlias;
+import java.io.File;
+import java.nio.file.Files;
+import org.signalml.method.mp5.MP5BundledProcessExecutor;
 
 /** MP5ExecutorManager
  *
@@ -37,9 +40,23 @@
 	private transient EventListenerList listenerList = new EventListenerList();
 
 	public MP5ExecutorManager() {
-		defaultExecutor = MP5LocalProcessExecutor.pathExecutor();
+                MP5Executor path_executor = MP5LocalProcessExecutor.pathExecutor();
+                MP5BundledProcessExecutor bundled_executor = new MP5BundledProcessExecutor();
+                String execPath = bundled_executor.getMp5ExecutablePath();
+                File execFile = new File(execPath);
+                if (execFile.exists())
+                {
+                    defaultExecutor = bundled_executor;
+                }
+                else
+                {
+                    defaultExecutor = path_executor;
+                }
+                
 		executors = new ArrayList<MP5Executor>();
-		executors.add(defaultExecutor);
+		executors.add(path_executor);
+                executors.add(bundled_executor);
+
 	}
 
 	@Override
@@ -55,7 +72,8 @@ private XStream createExecutorStreamer() {
 		Annotations.configureAliases(
 			streamer,
 			MP5ExecutorManager.class,
-			MP5LocalProcessExecutor.class
+			MP5LocalProcessExecutor.class,
+                        MP5BundledProcessExecutor.class
 			//MP5RemoteExecutor.class,
 			//MP5RemotePasswordExecutor.class
 		);

svarog/src/main/java/org/signalml/domain/signal/filter/export/IIRMultichannelSingleFilterForExport.java

@@ -29,8 +29,8 @@
 	/**
 	 * Files that are used to store temporary filtering results.
 	 */
-	private File temporaryFile1 = new File("exportsub1.bin.tmp");
-	private File temporaryFile2 = new File("exportsub2.bin.tmp");
+	private File temporaryFile1 = File.createTempFile("svarog_IIR_", "exportsub1.bin.tmp");
+	private File temporaryFile2 = File.createTempFile("svarog_IIR_", "exportsub2.bin.tmp");
 
 	/**
 	 * A {@link RawSignalWriter} for writing the temporary results to files.

svarog/src/main/java/org/signalml/domain/signal/filter/export/MultichannelSampleFilterForExport.java

@@ -2,6 +2,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
 
 import org.signalml.app.model.signal.SignalExportDescriptor;
 import org.signalml.domain.montage.Montage;
@@ -27,8 +28,8 @@
 	/**
 	 * Files storing the temporary results of the filtering.
 	 */
-	private File inputFile = new File("export2.bin.tmp");
-	private File outputFile = new File("export1.bin.tmp");
+	private File inputFile = File.createTempFile("svarog_filter_", "export2.bin");
+	private File outputFile = File.createTempFile("svarog_filter_", "export1.bin");
 	private RawSignalWriter rawSignalWriter = new RawSignalWriter();
 
 	/**

svarog/src/main/java/org/signalml/method/mp5/MP5BundledProcessExecutor.java

+package org.signalml.method.mp5;
+
+import com.thoughtworks.xstream.annotations.XStreamAlias;
+import java.io.File;
+import java.util.Locale;
+import static org.signalml.app.util.i18n.SvarogI18n._;
+
+@XStreamAlias("mp5bundledexecutor")
+public class MP5BundledProcessExecutor extends MP5LocalProcessExecutor{
+    
+        public MP5BundledProcessExecutor()
+        {
+            super();
+            setName(_("execute from bundled executor"));
+
+        }
+
+        @Override
+        public void setMp5ExecutablePath(String mp5ExecutablePath) {
+	}
+
+        @Override
+	public String getMp5ExecutablePath() {
+            File jar = new File(MP5LocalProcessExecutor.class.getProtectionDomain().getCodeSource().getLocation().getPath());
+            String jarDir = jar.getParentFile().getPath();
+            String executor_folder;
+            String OS = System.getProperty("os.name", "generic").toLowerCase(Locale.ENGLISH);
+            String bits = System.getProperty("sun.arch.data.model");
+            
+            if ((OS.contains("mac")) || (OS.contains("darwin"))) {
+                executor_folder = "/mp/osx64/empi-osx64";
+              } else if (OS.contains("win")) {
+                executor_folder = "/mp/win" + bits + "/empi-win"+ bits+ ".exe";
+                
+              } else if (OS.indexOf("nux") >= 0) {
+                executor_folder = "/mp/linux/empi-lin" + bits;
+              } else {
+                executor_folder = "";
+              }
+            
+            return jarDir + executor_folder;
+	}
+    
+}

svarog/src/main/java/org/signalml/method/mp5/MP5LocalProcessExecutor.java

@@ -21,6 +21,8 @@
 import org.signalml.method.MethodExecutionTracker;
 
 import com.thoughtworks.xstream.annotations.XStreamAlias;
+import java.net.URLDecoder;
+import java.util.Locale;
 
 /** MP5LocalProcessExecutor
  *
@@ -37,7 +39,7 @@
 	private String uid;
 
 	private String name;
-	private String mp5ExecutablePath;
+	protected String mp5ExecutablePath;
 
 	private transient MP5ConfigCreator configCreator = new MP5ConfigCreator();
 	private transient RawSignalWriter rawSignalWriter = new RawSignalWriter();
@@ -138,7 +140,7 @@ public boolean execute(MP5Data data, int segment, File resultFile, MethodExecuti
 
 		tracker.setMessage(_("Starting executable"));
 
-		boolean executionOk = processController.executeProcess(workingDirectory, mp5ExecutablePath, configFile, tracker);
+		boolean executionOk = processController.executeProcess(workingDirectory, getMp5ExecutablePath(), configFile, tracker);
 		if (!executionOk) {
 			return false;
 		}

svarog/src/main/resources/org/signalml/schema/rawsignal.xsd

@@ -234,6 +234,15 @@
     		<minExclusive value="0"></minExclusive>
     	</restriction>
     </simpleType>
+    
+    <simpleType name="isBackup">
+    	<annotation>
+    		<documentation>
+    			LEGACY OPTION FOR BACKWARD COMPATABILITY, DOES NOTHING
+    		</documentation>
+    	</annotation>
+    	<restriction base="boolean" />
+    </simpleType>
 
     <complexType name="rawSignalInfo">
     	<sequence minOccurs="1" maxOccurs="1">
@@ -404,6 +413,11 @@
 		    <documentation>The timestamp of the first sample in the signal.</documentation>
 		</annotation>
 		</element>
+                <element name="isBackup" type="rs:isBackup" maxOccurs="1" minOccurs="0">
+                <annotation>
+                    <documentation>LEGACY OPTION FOR BACKWARD COMPATABILITY, DOES NOTHING</documentation>
+                </annotation>
+                </element>
     	</sequence>
     </complexType>
 
@@ -418,6 +432,7 @@
     		<element name="calibrationParam" type="rs:calibrationParam" minOccurs="1" maxOccurs="unbounded"></element>
     	</sequence>
     </complexType>
+    
 
     <element name="rawSignal" type="rs:rawSignalInfo">
     	<annotation>
@@ -425,4 +440,5 @@
     	</annotation>
     </element>
 
+
 </schema>