Merge pull request #65 from SanojPunchihewa/bug-fixes

Bug fixes

app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java

@@ -103,9 +103,13 @@ public static void createPipeline() {
     public static void runPipeline() {
         for (PipelineComponent pipelineComponent : pipelineComponents) {
             long start = System.currentTimeMillis();
-            pipelineComponent.run();
+            int returnCode = pipelineComponent.run();
             long time = System.currentTimeMillis() - start;
-            pipelineComponent.setRuntime(TimeFormat.millisToShortDHMS(time));
+            String status = returnCode == 0 ? "Success" : "Error";
+            pipelineComponent.setRuntime(TimeFormat.millisToShortDHMS(time) + " status = " + status);
+            if (returnCode != 0) {
+                break;
+            }
         }
     }
 

app/src/main/java/com/mobilegenomics/f5n/activity/ConfirmationActivity.java

@@ -1,6 +1,6 @@
 package com.mobilegenomics.f5n.activity;
 
-import android.app.ProgressDialog;
+import android.content.DialogInterface;
 import android.content.res.ColorStateList;
 import android.graphics.Color;
 import android.os.AsyncTask;
@@ -14,11 +14,12 @@
 import android.widget.LinearLayout;
 import android.widget.LinearLayout.LayoutParams;
 import android.widget.ProgressBar;
-import android.widget.ScrollView;
 import android.widget.TextView;
 import android.widget.Toast;
 import androidx.annotation.Nullable;
+import androidx.appcompat.app.AlertDialog;
 import androidx.appcompat.app.AppCompatActivity;
+import androidx.core.widget.NestedScrollView;
 import com.mobilegenomics.f5n.GUIConfiguration;
 import com.mobilegenomics.f5n.R;
 import com.mobilegenomics.f5n.core.PipelineComponent;
@@ -41,11 +42,13 @@ public class ConfirmationActivity extends AppCompatActivity {
 
     private static final String TAG_SAMTOOLS = "samtools-native";
 
-    private ProgressDialog progressDialog;
+    private int isPipelineRunning = 0;
+
+    private boolean logWrittenToFile = false;
 
     TextView txtLogs;
 
-    ScrollView scrollView;
+    NestedScrollView scrollView;
 
     LinearLayout linearLayout;
 
@@ -101,7 +104,7 @@ public void onClick(final View v) {
         separator1.setBackgroundColor(Color.parseColor("#000000"));
         linearLayout.addView(separator1);
 
-        scrollView = new ScrollView(this);
+        scrollView = new NestedScrollView(this);
         linearLayout.addView(scrollView);
 
         txtLogs = new TextView(this);
@@ -134,6 +137,7 @@ public class RunPipeline extends AsyncTask<String, Integer, String> {
         @Override
         protected void onPreExecute() {
             super.onPreExecute();
+            isPipelineRunning = 1;
         }
 
         @Override
@@ -161,6 +165,7 @@ protected void onPostExecute(final String s) {
                         pipelineComponent.getPipelineStep().getCommand() + " took " + pipelineComponent.getRuntime());
                 linearLayout.addView(txtRuntime);
             }
+            isPipelineRunning = 2;
             btnWriteLog.setVisibility(View.VISIBLE);
             btnProceed.setEnabled(true);
             mProgressBar.setVisibility(View.GONE);
@@ -265,12 +270,68 @@ private void writeLogToFile() {
             myOutWriter.close();
             fOut.close();
             Toast.makeText(getApplicationContext(), "Finished writing to mobile-genomics in home", Toast.LENGTH_LONG)
-                    .show(); //##5
+                    .show();
+            logWrittenToFile = true;
         } catch (Exception e) {
             Toast.makeText(getApplicationContext(), "Write failure", Toast.LENGTH_SHORT).show(); //##6
             Log.e("TAG", e.toString());
         }
 
     }
 
+    @Override
+    public void onBackPressed() {
+        if (isPipelineRunning == 0) {
+            super.onBackPressed();
+        } else if (isPipelineRunning == 1) {
+            showStopPipelineDialog();
+        } else if (isPipelineRunning == 2) {
+            if (!logWrittenToFile) {
+                showWriteToFileDialog();
+            } else {
+                super.onBackPressed();
+            }
+        }
+    }
+
+    private void showWriteToFileDialog() {
+
+        new AlertDialog.Builder(ConfirmationActivity.this)
+                .setTitle("Save log")
+                .setMessage("Are you sure you want to save log?")
+                .setPositiveButton("Yes", new DialogInterface.OnClickListener() {
+                    public void onClick(DialogInterface dialog, int which) {
+                        writeLogToFile();
+                        ConfirmationActivity.super.onBackPressed();
+                    }
+                })
+                .setNegativeButton("No", new DialogInterface.OnClickListener() {
+                    @Override
+                    public void onClick(final DialogInterface dialog, final int which) {
+                        ConfirmationActivity.super.onBackPressed();
+                    }
+                })
+                .show();
+
+    }
+
+    private void showStopPipelineDialog() {
+
+        new AlertDialog.Builder(ConfirmationActivity.this)
+                .setTitle("Stop Running")
+                .setMessage("Are you sure to stop the pipeline?")
+                .setPositiveButton("Yes", new DialogInterface.OnClickListener() {
+                    public void onClick(DialogInterface dialog, int which) {
+                        // TODO Kill the native process
+                        ConfirmationActivity.super.onBackPressed();
+                    }
+                })
+                .setNegativeButton("No", new DialogInterface.OnClickListener() {
+                    @Override
+                    public void onClick(final DialogInterface dialog, final int which) {
+                        dialog.dismiss();
+                    }
+                })
+                .show();
+    }
 }

app/src/main/java/com/mobilegenomics/f5n/activity/DemoActivity.java

@@ -71,9 +71,6 @@ protected void onCreate(@Nullable final Bundle savedInstanceState) {
                 Log.e(TAG, "Error : " + e);
             }
         }
-
-        registerReceiver(onDownloadComplete, new IntentFilter(DownloadManager.ACTION_DOWNLOAD_COMPLETE));
-
         try {
             fOut = new FileOutputStream(logFile, true);
             myOutWriter = new OutputStreamWriter(fOut);
@@ -117,14 +114,15 @@ public void onClick(final View v) {
         btnRunPipeline.setOnClickListener(new OnClickListener() {
             @Override
             public void onClick(final View v) {
+                GUIConfiguration.eraseSelectedPipeline();
                 for (PipelineStep step : PipelineStep.values()) {
                     GUIConfiguration.addPipelineStep(step);
                 }
                 GUIConfiguration.printList();
                 GUIConfiguration.configureSteps(DemoActivity.this,
                         Environment.getExternalStorageDirectory() + "/" + folderName + "/"
                                 + fileName.substring(0, fileName.lastIndexOf(".")));
-                startActivity(new Intent(DemoActivity.this, ConfirmationActivity.class));
+                startActivity(new Intent(DemoActivity.this, TerminalActivity.class));
             }
         });
         linearLayout.addView(btnRunPipeline);
@@ -172,10 +170,21 @@ public void onReceive(Context context, Intent intent) {
         }
     };
 
+    @Override
+    protected void onStart() {
+        super.onStart();
+        registerReceiver(onDownloadComplete, new IntentFilter(DownloadManager.ACTION_DOWNLOAD_COMPLETE));
+    }
+
+    @Override
+    protected void onPause() {
+        super.onPause();
+        unregisterReceiver(onDownloadComplete);
+    }
+
     @Override
     protected void onStop() {
         super.onStop();
-        unregisterReceiver(onDownloadComplete);
         try {
             myOutWriter.append("-------------------- End of Log --------------------\n\n");
             myOutWriter.flush();

app/src/main/java/com/mobilegenomics/f5n/core/Argument.java

@@ -117,7 +117,11 @@ public String toString() {
         // TODO Check for NULL
         if (this.setByUser) {
             if (this.argValue != null) {
-                return this.hasFlag ? this.flag + " " + this.argValue : this.argValue;
+                if (this.hasFlag) {
+                    return this.flag.endsWith("=") ? this.flag + this.argValue : this.flag + " " + this.argValue;
+                } else {
+                    return this.argValue;
+                }
             } else {
                 return this.flag;
             }

app/src/main/res/raw/minimap2.json

@@ -1,5 +1,17 @@
 {
   "args": [
+    {
+      "argName": "Temporary Prefix for multi-part index",
+      "argValue": "temp.minimap",
+      "argDescription": "Prefix to create temporary files. Typically used for a multi-part index",
+      "flag": "--multi-prefix=",
+      "argID": "MINIMAP2_TEMP_FILE",
+      "isDependentOn": "null",
+      "hasFlag": true,
+      "flagOnly": false,
+      "required": false,
+      "isFile": true
+    },
     {
       "argName": "reference index",
       "argValue": null,