Make it work with latest versions of gate-interaction, weka-wrapper, …

…and sklearn-wrapper.
GateNLP · Jul 11, 2016 · 0aea2b1 · 0aea2b1
1 parent 069108b
commit 0aea2b1
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Showing 4 changed files with 54 additions and 15 deletions.
diff --git a/creole.xml b/creole.xml
@@ -1,7 +1,7 @@
 <!-- creole.xml for Learning_Framework -->
 <CREOLE-DIRECTORY
   ID="gate.LearningFramework"
-  VERSION="3.4-gamma"
+  VERSION="3.4"
   DESCRIPTION="Learning Framework"
   HELPURL="https://github.com/GateNLP/gateplugin-LearningFramework/wiki"
 >

diff --git a/lib-static/interaction-1.0-SNAPSHOT.jar b/lib-static/interaction-1.0-SNAPSHOT.jar
diff --git a/src/gate/plugin/learningframework/engines/EngineSklearnExternal.java b/src/gate/plugin/learningframework/engines/EngineSklearnExternal.java
@@ -20,6 +20,7 @@
 import java.io.FileInputStream;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -137,19 +138,22 @@ private File findWrapperCommand(File dataDirectory, boolean apply) {
 
   @Override
   protected void loadModel(File directory, String parms) {
+    ArrayList<String> finalCommand = new ArrayList<String>();
     // Instead of loading a model, this establishes a connection with the 
     // external sklearn process. 
 
     File commandFile = findWrapperCommand(directory, true);
     String modelFileName = new File(directory,"sklmodel").getAbsolutePath();
-    String finalCommand = commandFile.getAbsolutePath()+" "+wrapperhome+" "+modelFileName;
+    finalCommand.add(commandFile.getAbsolutePath());
+    finalCommand.add(wrapperhome);
+    finalCommand.add(modelFileName);
     // if we have a shell command prepend that, and if we have shell parms too, include them
     if(shellcmd != null) {
       String tmp = shellcmd;
       if(shellparms != null) {
         shellcmd += " " + shellparms;
       }
-      finalCommand = shellcmd + " " + finalCommand;
+      finalCommand.add(0,shellcmd);
     }
     System.err.println("Running: "+finalCommand);
     // Create a fake Model jsut to make LF_Apply... happy which checks if this is null
@@ -168,13 +172,15 @@ protected void saveModel(File directory) {
 
   @Override
   public void trainModel(File dataDirectory, String instanceType, String parms) {
+    ArrayList<String> finalCommand = new ArrayList<String>();
     // invoke the sklearn wrapper for training
     // NOTE: for this the first word in parms must be the full sklearn class name, the rest are parms
-    if(parms == null || parms.isEmpty()) {
+    if(parms == null || parms.trim().isEmpty()) {
       throw new GateRuntimeException("Cannot train using SklearnWrapper, algorithmParameter must contain fulle SciKit Learn algorithm class name as first word");
     }
     String sklearnClass = null;
     String sklearnParms = "";
+    parms = parms.trim();
     int spaceIdx = parms.indexOf(" ");
     if(spaceIdx<0) {
       sklearnClass = parms;
@@ -192,16 +198,27 @@ public void trainModel(File dataDirectory, String instanceType, String parms) {
             Exporter.EXPORTER_MATRIXMARKET2_CLASS, dataDirectory, instanceType, parms);
     String dataFileName = dataDirectory.getAbsolutePath()+File.separator;
     String modelFileName = new File(dataDirectory, "sklmodel").getAbsolutePath();
-    String finalCommand = commandFile.getAbsolutePath()+" "+wrapperhome+" "+dataFileName+" "+modelFileName+" "+sklearnClass+" "+sklearnParms;
+    finalCommand.add(commandFile.getAbsolutePath());
+    finalCommand.add(wrapperhome);
+    finalCommand.add(dataFileName);
+    finalCommand.add(modelFileName);
+    finalCommand.add(sklearnClass);
+    if(!sklearnParms.isEmpty()) {
+      String[] tmp = sklearnParms.split("\\s+",-1);
+      finalCommand.addAll(Arrays.asList(tmp));
+    }
     // if we have a shell command prepend that, and if we have shell parms too, include them
     if(shellcmd != null) {
       String tmp = shellcmd;
       if(shellparms != null) {
         shellcmd += " " + shellparms;
       }
-      finalCommand = shellcmd + " " + finalCommand;
+      finalCommand.add(0,shellcmd);
+    }
+    System.err.println("Running: ");
+    for(int i=0; i<finalCommand.size();i++) {
+      System.err.println(i+": >"+finalCommand.get(i)+"<");
     }
-    System.err.println("Running: "+finalCommand);
     // Create a fake Model jsut to make LF_Apply... happy which checks if this is null
     model = "ExternalSklearnWrapperModel";
 

diff --git a/src/gate/plugin/learningframework/engines/EngineWekaExternal.java b/src/gate/plugin/learningframework/engines/EngineWekaExternal.java
@@ -19,6 +19,7 @@
 import java.io.FileInputStream;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 import org.yaml.snakeyaml.Yaml;
@@ -49,6 +50,8 @@ public class EngineWekaExternal extends Engine {
   private String shellcmd = null;
   private String shellparms = null;
   private String wrapperhome = null;
+  private boolean linuxLike = true;
+  private boolean windowsLike = false;
 
   /**
    * Try to find the script running the Weka-Wrapper command.
@@ -110,8 +113,8 @@ private File findWrapperCommand(File dataDirectory, boolean apply) {
     // we use the simple heuristic that if the file separator is "/" 
     // we assume we can use the bash script, if it is "\" we use the windows
     // script and otherwise we give up
-    boolean linuxLike = System.getProperty("file.separator").equals("/");
-    boolean windowsLike = System.getProperty("file.separator").equals("\\");
+    linuxLike = System.getProperty("file.separator").equals("/");
+    windowsLike = System.getProperty("file.separator").equals("\\");
     if(linuxLike) {
       if(apply) 
         commandFile = new File(new File(wrapperHome,"bin"),"wekaWrapperApply.sh");
@@ -137,6 +140,7 @@ private File findWrapperCommand(File dataDirectory, boolean apply) {
 
   @Override
   protected void loadModel(File directory, String parms) {
+    ArrayList<String> finalCommand = new ArrayList<String>();
     // Instead of loading a model, this establishes a connection with the 
     // external weka process. For this, we expect an additional file in the 
     // directory, weka.yaml, which describes how to run the weka wrapper
@@ -149,14 +153,18 @@ protected void loadModel(File directory, String parms) {
     if(!new File(header).exists()) {
       throw new GateRuntimeException("File not found: "+header);
     }
-    String finalCommand = commandFile.getAbsolutePath()+" "+wrapperhome+" "+modelFileName+" "+header;
+    finalCommand.add(commandFile.getAbsolutePath());
+    finalCommand.add(wrapperhome);
+    finalCommand.add(modelFileName);
+    finalCommand.add(header);
+
     // if we have a shell command prepend that, and if we have shell parms too, include them
     if(shellcmd != null) {
       String tmp = shellcmd;
       if(shellparms != null) {
         shellcmd += " " + shellparms;
       }
-      finalCommand = shellcmd + " " + finalCommand;
+      finalCommand.add(0,shellcmd);
     }
     System.err.println("Running: "+finalCommand);
     // Create a fake Model jsut to make LF_Apply... happy which checks if this is null
@@ -175,13 +183,15 @@ protected void saveModel(File directory) {
 
   @Override
   public void trainModel(File dataDirectory, String instanceType, String parms) {
+    ArrayList<String> finalCommand = new ArrayList<String>();
     // TODO: invoke the weka wrapper
     // NOTE: for this the first word in parms must be the full weka class name, the rest are parms
-    if(parms == null || parms.isEmpty()) {
+    if(parms == null || parms.trim().isEmpty()) {
       throw new GateRuntimeException("Cannot train using WekaWrapper, algorithmParameter must contain Weka algorithm class as first word");
     }
     String wekaClass = null;
     String wekaParms = "";
+    parms = parms.trim();
     int spaceIdx = parms.indexOf(" ");
     if(spaceIdx<0) {
       wekaClass = parms;
@@ -199,16 +209,28 @@ public void trainModel(File dataDirectory, String instanceType, String parms) {
             Exporter.EXPORTER_ARFF_CLASS, dataDirectory, instanceType, parms);
     String dataFileName = new File(dataDirectory,Globals.dataBasename+".arff").getAbsolutePath();
     String modelFileName = new File(dataDirectory, FILENAME_MODEL).getAbsolutePath();
-    String finalCommand = commandFile.getAbsolutePath()+" "+wrapperhome+" "+dataFileName+" "+modelFileName+" "+wekaClass+" "+wekaParms;
+
+    finalCommand.add(commandFile.getAbsolutePath());
+    finalCommand.add(wrapperhome);
+    finalCommand.add(dataFileName);
+    finalCommand.add(modelFileName);
+    finalCommand.add(wekaClass);
+    if(!wekaParms.isEmpty()) {
+      String[] tmp = wekaParms.split("\\s+",-1);
+      finalCommand.addAll(Arrays.asList(tmp));
+    }
     // if we have a shell command prepend that, and if we have shell parms too, include them
     if(shellcmd != null) {
       String tmp = shellcmd;
       if(shellparms != null) {
         shellcmd += " " + shellparms;
       }
-      finalCommand = shellcmd + " " + finalCommand;
+      finalCommand.add(0,shellcmd);
+    }
+    System.err.println("Running: ");
+    for(int i=0; i<finalCommand.size();i++) {
+      System.err.println(i+": >"+finalCommand.get(i)+"<");
     }
-    System.err.println("Running: "+finalCommand);
     // Create a fake Model jsut to make LF_Apply... happy which checks if this is null
     model = "ExternalWekaWrapperModel";