Merge pull request #125 from SanojPunchihewa/bug-fixes

Bug fixes
SanojPunchihewa · Feb 16, 2020 · 87d81f5 · 87d81f5
2 parents 5db20d3 + 5afe035
commit 87d81f5
Show file tree

Hide file tree

Showing 8 changed files with 34 additions and 8 deletions.
diff --git a/app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java b/app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java
@@ -230,6 +230,11 @@ private static void configureDemoArgsFilePath(Argument argument, String folder)
         if (argument.getArgID().equals("SAMTOOL_SORT_OUTPUT_FILE")) {
             argument.setArgValue(folder + "/reads.sorted.bam");
         }
+        // For the Demo we need to use 100M max memory for samtools sort
+        if (argument.getArgID().equals("SAMTOOL_MAX_MEMORY")) {
+            argument.setSetByUser(true);
+            argument.setArgValue("100M");
+        }
 
         if (argument.getArgID().equals("SAMTOOL_INDEX_INPUT_FILE")) {
             argument.setArgValue(folder + "/reads.sorted.bam");

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/ConfirmationActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/ConfirmationActivity.java
@@ -206,6 +206,13 @@ public void run() {
         separator2.setBackgroundColor(Color.parseColor("#000000"));
         linearLayout.addView(separator2);
 
+        if (GUIConfiguration.getAppMode() == AppMode.STANDALONE) {
+            TextView txtOuputFolderInfo = new TextView(this);
+            txtOuputFolderInfo.setText(
+                    "By default, output files are written to the mobile-genomics folder in your main storage. If you have updated the output paths please check the respective folders");
+            linearLayout.addView(txtOuputFolderInfo);
+        }
+
         mp = MediaPlayer.create(this, R.raw.alarm);
 
         btnWriteLog = new Button(this);

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/StepActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/StepActivity.java
@@ -6,6 +6,7 @@
 import android.content.Context;
 import android.content.Intent;
 import android.os.Bundle;
+import android.os.Environment;
 import android.text.Editable;
 import android.text.TextUtils;
 import android.text.TextWatcher;
@@ -66,12 +67,16 @@ public class StepActivity extends AppCompatActivity {
 
     private List<String> fileNames;
 
+    private String MOBILE_GENOMICS_FOLDER_PATH;
+
     @SuppressLint("ClickableViewAccessibility")
     @Override
     protected void onCreate(@Nullable final Bundle savedInstanceState) {
         super.onCreate(savedInstanceState);
         setContentView(R.layout.layout_step);
 
+        MOBILE_GENOMICS_FOLDER_PATH = Environment.getExternalStorageDirectory() + "/" + "mobile-genomics/";
+
         fileNames = new ArrayList<>();
 
         adapter = new ArrayAdapter<>(this,
@@ -220,19 +225,23 @@ public void onItemClick(final AdapterView<?> parent, final View view, final int
                             editText.setText(folderPath + "/" + parent.getAdapter().getItem(position));
                         }
                     });
-                } else {
-                    editText = new EditText(this);
-                }
-                editText.setId(argument_id + 1000);
-                if (argument.isFile()) {
                     if (argument.getIsDependentOn() != null) {
                         editText.setText(GUIConfiguration.getLinkedFileArgument(argument.getIsDependentOn()));
                     } else if (argument.getArgValue() != null) {
                         editText.setText(argument.getArgValue());
                     }
+                    if (argument.getArgID().contains("OUTPUT") || argument.getArgID().contains("TEMP")) {
+                        if (editText.getText() != null && !TextUtils.isEmpty(editText.getText().toString())) {
+                            editText.setText(MOBILE_GENOMICS_FOLDER_PATH + editText.getText().toString());
+                        } else {
+                            editText.setText(MOBILE_GENOMICS_FOLDER_PATH);
+                        }
+                    }
                 } else {
+                    editText = new EditText(this);
                     editText.setText(argument.getArgValue());
                 }
+                editText.setId(argument_id + 1000);
                 linearLayout.addView(editText);
                 LinearLayout.LayoutParams editText_LayoutParams =
                         new LinearLayout.LayoutParams(LayoutParams.MATCH_PARENT,
@@ -260,6 +269,10 @@ public void onClick(final View v) {
                         if (!argument.isFlagOnly()) {
                             EditText editText = findViewById(arg_id + 1000);
                             if (editText.getText() != null && !TextUtils.isEmpty(editText.getText().toString())) {
+                                if (argument.isFile() && editText.getText().toString().endsWith("/")) {
+                                    haveSetAllRequiredArgs = false;
+                                    editText.setError("Please specify a file name");
+                                }
                                 String argValue = editText.getText().toString();
                                 if (argument.isFile()) {
                                     GUIConfiguration

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/TerminalActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/TerminalActivity.java
@@ -203,7 +203,8 @@ private void replaceDirectoryPath(String path) {
     private void showCrashError() {
         new AlertDialog.Builder(this)
                 .setTitle("F5N Crashed")
-                .setMessage("App Crashed due to Out Of Memory")
+                .setMessage(
+                        "One of the Native libraries has encountered a problem, most probably an Out Of Memory. Refer tmp.log in main storage/mobile-genomics folder for more information")
                 .setPositiveButton("Go to Start page", new DialogInterface.OnClickListener() {
                     public void onClick(DialogInterface dialog, int which) {
                         dialog.dismiss();

diff --git a/app/src/main/jniLibs/arm64-v8a/libf5cshared.so b/app/src/main/jniLibs/arm64-v8a/libf5cshared.so
diff --git a/app/src/main/jniLibs/armeabi-v7a/libf5cshared.so b/app/src/main/jniLibs/armeabi-v7a/libf5cshared.so
diff --git a/app/src/main/res/raw/f5c_event_align_arguments.json b/app/src/main/res/raw/f5c_event_align_arguments.json
@@ -52,7 +52,7 @@
       "argName": "event summary file",
       "argValue": "event.summary.txt",
       "argDescription": "path to event summary file",
-      "flag": "--event-summary=",
+      "flag": "--summary",
       "argID": "F5C_ALIGN_SUMMARY_OUTPUT_FILE",
       "isDependentOn": null,
       "hasFlag": true,

diff --git a/app/src/main/res/raw/samtool_sort_arguments.json b/app/src/main/res/raw/samtool_sort_arguments.json
@@ -29,7 +29,7 @@
       "argValue": "768M",
       "argDescription": "max memory per thread; suffix K/M/G recognized",
       "flag": "-m",
-      "argID": "tobedecided",
+      "argID": "SAMTOOL_MAX_MEMORY",
       "isDependentOn": "argIDofanotherArg",
       "hasFlag": true,
       "flagOnly": false,