Merge pull request #124 from SanojPunchihewa/bug-fixes

Bug fixes
SanojPunchihewa · Feb 14, 2020 · 5db20d3 · 5db20d3
2 parents 4286231 + 503e77d
commit 5db20d3
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Showing 5 changed files with 48 additions and 34 deletions.
diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/DemoActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/DemoActivity.java
@@ -119,13 +119,15 @@ protected void onCreate(@Nullable final Bundle savedInstanceState) {
             @Override
             public void onClick(final View v) {
                 btnDownloadAndExtract.setEnabled(false);
+                String datasetFolder = Environment.getExternalStorageDirectory() + "/" + folderName
+                        + "/ecoli-data-set";
+                FileUtil.deleteFolder(new File(datasetFolder));
                 downloadDataSet(ecoliDataSetURL);
             }
         });
         linearLayout.addView(btnDownloadAndExtract);
 
         txtLogView = new TextView(this);
-//        txtLogView.setTextSize(f);
         linearLayout.addView(txtLogView);
 
         btnRunPipeline = new Button(this);

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/DownloadActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/DownloadActivity.java
@@ -31,6 +31,7 @@
 import com.mobilegenomics.f5n.support.DownloadManager;
 import com.mobilegenomics.f5n.support.PipelineState;
 import com.mobilegenomics.f5n.support.PreferenceUtil;
+import com.mobilegenomics.f5n.support.TimeFormat;
 import com.mobilegenomics.f5n.support.ZipListener;
 import com.mobilegenomics.f5n.support.ZipManager;
 import com.obsez.android.lib.filechooser.ChooserDialog;
@@ -46,6 +47,8 @@ public class DownloadActivity extends AppCompatActivity {
 
     class FTPDownloadTask extends AsyncTask<String, Long, Boolean> {
 
+        long downloadStartTime;
+
         long fileSize;
 
         boolean status;
@@ -93,8 +96,10 @@ public void bytesTransferred(long totalBytesTransferred, int bytesTransferred, l
         protected void onPostExecute(final Boolean downloadSuccess) {
             super.onPostExecute(downloadSuccess);
             Log.i(TAG, "Download Finished");
+            long downloadTime = System.currentTimeMillis() - downloadStartTime;
             if (downloadSuccess) {
-                statusTextView.setText("Download Completed");
+                String time = TimeFormat.millisToShortDHMS(downloadTime);
+                statusTextView.setText("Download Completed in " + time);
             } else {
                 statusTextView.setText("Download Error");
             }
@@ -105,6 +110,7 @@ protected void onPostExecute(final Boolean downloadSuccess) {
         protected void onPreExecute() {
             super.onPreExecute();
             Log.i(TAG, "Download Started");
+            downloadStartTime = System.currentTimeMillis();
             statusTextView.setText("Download Started");
             progressBar.setMax(100);
             disableButtons();

diff --git a/app/src/main/java/com/mobilegenomics/f5n/activity/MinITActivity.java b/app/src/main/java/com/mobilegenomics/f5n/activity/MinITActivity.java
@@ -33,6 +33,7 @@
 import com.mobilegenomics.f5n.support.PreferenceUtil;
 import com.mobilegenomics.f5n.support.ServerCallback;
 import com.mobilegenomics.f5n.support.ServerConnectionUtils;
+import com.mobilegenomics.f5n.support.TimeFormat;
 import com.mobilegenomics.f5n.support.ZipListener;
 import com.mobilegenomics.f5n.support.ZipManager;
 import com.obsez.android.lib.filechooser.ChooserDialog;
@@ -53,6 +54,8 @@ class FTPUploadTask extends AsyncTask<String, Long, Boolean> {
 
         long fileSize;
 
+        long uploadStartTime;
+
         @Override
         protected Boolean doInBackground(String... urls) {
             FTPClient con;
@@ -107,11 +110,13 @@ protected void onCancelled() {
         protected void onPostExecute(final Boolean uploadSuccess) {
             super.onPostExecute(uploadSuccess);
             Log.i(TAG, "Upload Finished");
+            long uploadTime = System.currentTimeMillis() - uploadStartTime;
             if (uploadSuccess) {
+                String time = TimeFormat.millisToShortDHMS(uploadTime);
                 GUIConfiguration.setPipelineState(PipelineState.COMPLETED);
                 PreferenceUtil
                         .setSharedPreferenceInt(R.string.id_app_mode, GUIConfiguration.getPipelineState().ordinal());
-                statusTextView.setText("Upload Completed");
+                statusTextView.setText("Upload Completed in " + time);
                 sendJobResults();
             } else {
                 statusTextView.setText("Upload Error");
@@ -121,6 +126,7 @@ protected void onPostExecute(final Boolean uploadSuccess) {
         @Override
         protected void onPreExecute() {
             super.onPreExecute();
+            uploadStartTime = System.currentTimeMillis();
             statusTextView.setText("Upload started");
         }
 

diff --git a/app/src/main/java/com/mobilegenomics/f5n/support/FileUtil.java b/app/src/main/java/com/mobilegenomics/f5n/support/FileUtil.java
@@ -235,4 +235,16 @@ public static boolean isFileInExternalSdCard(String filePath) {
         return !filePath.contains(internalStorage);
     }
 
+    /**
+     * Delete a folder and its content
+     */
+    public static void deleteFolder(File fodler) {
+        if (fodler.isDirectory()) {
+            for (File child : fodler.listFiles()) {
+                deleteFolder(child);
+            }
+        }
+        fodler.delete();
+    }
+
 }
diff --git a/app/src/main/res/raw/f5c_call_methylation_arguments.json b/app/src/main/res/raw/f5c_call_methylation_arguments.json
@@ -62,14 +62,14 @@
     },
     {
       "argName": "batch size",
-      "argValue": "512",
-      "argDescription": "batch size -max number of reads loaded at once [512]",
+      "argValue": "256",
+      "argDescription": "batch size -max number of reads loaded at once [256]",
       "flag": "-K",
       "argID": "tobedecided",
       "isDependentOn": "argIDofanotherArg",
       "hasFlag": true,
       "flagOnly": false,
-      "required": false,
+      "required": true,
       "isFile": false
     },
     {
@@ -84,33 +84,21 @@
       "required": true,
       "isFile": false
     },
-    {
-      "argName": "help",
-      "argValue": null,
-      "argDescription": "help",
-      "flag": "-h",
-      "argID": "tobedecided",
-      "isDependentOn": "argIDofanotherArg",
-      "hasFlag": true,
-      "flagOnly": true,
-      "required": false,
-      "isFile": false
-    },
     {
       "argName": "min map quality",
-      "argValue": "0",
+      "argValue": null,
       "argDescription": "minimum mapping quality [30]",
       "flag": "--min-mapq",
       "argID": "tobedecided",
       "isDependentOn": "argIDofanotherArg",
       "hasFlag": true,
       "flagOnly": false,
-      "required": true,
+      "required": false,
       "isFile": false
     },
     {
       "argName": "consider secondary map",
-      "argValue": "no",
+      "argValue": null,
       "argDescription": "consider secondary mappings or not [no]",
       "flag": "--secondary=",
       "argID": "tobedecided",
@@ -121,22 +109,22 @@
       "isFile": false
     },
     {
-      "argName": "skip unreadable or terminate",
-      "argValue": "yes",
-      "argDescription": "skip any unreadable fast5 or terminate program [yes]",
-      "flag": "--skip-unreadable=",
+      "argName": "skip ultra long reads and write to file",
+      "argValue": null,
+      "argDescription": "skip ultra long reads and write those entries to the bam file provided as the argument",
+      "flag": "--skip-ultra",
       "argID": "tobedecided",
       "isDependentOn": "argIDofanotherArg",
       "hasFlag": true,
       "flagOnly": false,
       "required": false,
-      "isFile": false
+      "isFile": true
     },
     {
-      "argName": "verbosity",
-      "argValue": "0",
-      "argDescription": "verbosity level [0]",
-      "flag": "--verbose",
+      "argName": "threshold to skip ultra long reads",
+      "argValue": null,
+      "argDescription": "threshold to skip ultra long reads [100000]",
+      "flag": "--ultra-thresh",
       "argID": "tobedecided",
       "isDependentOn": "argIDofanotherArg",
       "hasFlag": true,
@@ -145,14 +133,14 @@
       "isFile": false
     },
     {
-      "argName": "version",
+      "argName": "verbosity",
       "argValue": null,
-      "argDescription": "print version",
-      "flag": "--version",
+      "argDescription": "verbosity level [0]",
+      "flag": "--verbose",
       "argID": "tobedecided",
       "isDependentOn": "argIDofanotherArg",
       "hasFlag": true,
-      "flagOnly": true,
+      "flagOnly": false,
       "required": false,
       "isFile": false
     }