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Merge pull request #142 from SanojPunchihewa/bug-fixes
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Bug fixes
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@SanojPunchihewa
SanojPunchihewa authored Mar 20, 2020
2 parents 7c33c70 + bae386c commit fb959ee
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Showing 14 changed files with 405 additions and 414 deletions.
9 changes: 9 additions & 0 deletions app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -281,6 +281,15 @@ private static void configureDemoArgsFilePath(Argument argument, String folder)
if (argument.getArgID().equals("F5C_ALIGN_SUMMARY_OUTPUT_FILE")) {
argument.setArgValue(folder + "/event.summary.txt");
}

// f5c methylation frequency input/output files
if (argument.getArgID().equals("F5C_METH_FREQ_INPUT_FILE")) {
argument.setArgValue(folder + "/f5c-methylation.tsv");
}
if (argument.getArgID().equals("F5C_METH_FREQ_FILE")) {
argument.setArgValue(folder + "/f5c-methylation-freq.tsv");
}

}

}
11 changes: 7 additions & 4 deletions app/src/main/java/com/mobilegenomics/f5n/activity/ConfirmationActivity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
import android.os.Handler;
import android.provider.Settings;
import android.provider.Settings.SettingNotFoundException;
import android.text.Html;
import android.util.Log;
import android.view.View;
import android.view.View.OnClickListener;
Expand Down Expand Up @@ -267,10 +268,12 @@ public void run() {
linearLayout.addView(txtOuputFolderInfo);
}

TextView txtOuputFolderInfo = new TextView(this);
txtOuputFolderInfo.setText(
"Brightness will be reduced when running the pipeline to save power. Minimizing the app or turning off the display will abort the process");
linearLayout.addView(txtOuputFolderInfo);
TextView txtBrightnessInfo = new TextView(this);

txtBrightnessInfo.setText(Html.fromHtml(
"Brightness will reduce once the pipeline starts. <b>Do not</b> minimize or turn off the display, process may crash\n"));

linearLayout.addView(txtBrightnessInfo);

mp = MediaPlayer.create(this, R.raw.alarm);

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125 changes: 2 additions & 123 deletions app/src/main/java/com/mobilegenomics/f5n/activity/DownloadActivity.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,11 @@
package com.mobilegenomics.f5n.activity;

import android.annotation.SuppressLint;
import android.content.Intent;
import android.content.res.ColorStateList;
import android.graphics.Color;
import android.net.Uri;
import android.os.AsyncTask;
import android.os.Bundle;
import android.text.TextUtils;
import android.util.Log;
import android.view.View;
import android.view.View.OnClickListener;
import android.widget.Button;
Expand All @@ -21,112 +18,20 @@
import androidx.annotation.NonNull;
import androidx.annotation.Nullable;
import androidx.appcompat.app.AppCompatActivity;
import com.liulishuo.okdownload.DownloadTask;
import com.liulishuo.okdownload.core.Util;
import com.liulishuo.okdownload.core.cause.EndCause;
import com.mobilegenomics.f5n.GUIConfiguration;
import com.mobilegenomics.f5n.R;
import com.mobilegenomics.f5n.core.AppMode;
import com.mobilegenomics.f5n.support.DownloadListener;
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;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStream;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPClient;
import org.apache.commons.net.ftp.FTPFile;
import org.apache.commons.net.io.CopyStreamAdapter;

public class DownloadActivity extends AppCompatActivity {

class FTPDownloadTask extends AsyncTask<String, Long, Boolean> {

long downloadStartTime;

long fileSize;

boolean status;

@Override
protected Boolean doInBackground(String... urls) {
FTPClient con;
try {
con = new FTPClient();
con.setDefaultPort(8000);
con.connect(urls[0]);

con.setCopyStreamListener(new CopyStreamAdapter() {
@Override
public void bytesTransferred(long totalBytesTransferred, int bytesTransferred, long streamSize) {
publishProgress(totalBytesTransferred);
}

});

if (con.login("test", "test")) {
con.enterLocalPassiveMode(); // important!
con.setFileType(FTP.BINARY_FILE_TYPE);
con.setBufferSize(1024000);
FTPFile[] ff = con.listFiles(urls[1]);

if (ff != null) {
fileSize = (ff[0].getSize());
}

OutputStream out = new FileOutputStream(new File(folderPath + "/" + urls[1]));
status = con.retrieveFile(urls[1], out);
out.close();
con.logout();
con.disconnect();
}
} catch (Exception e) {
Log.e(TAG, "Error: " + e);
status = false;
}
return status;
}

@Override
protected void onPostExecute(final Boolean downloadSuccess) {
super.onPostExecute(downloadSuccess);
Log.i(TAG, "Download Finished");
long downloadTime = System.currentTimeMillis() - downloadStartTime;
if (downloadSuccess) {
String time = TimeFormat.millisToShortDHMS(downloadTime);
statusTextView.setText("Download Completed in " + time);
} else {
statusTextView.setText("Download Error");
}
enableButtons();
}

@Override
protected void onPreExecute() {
super.onPreExecute();
Log.i(TAG, "Download Started");
downloadStartTime = System.currentTimeMillis();
statusTextView.setText("Download Started");
progressBar.setMax(100);
disableButtons();
}

@Override
protected void onProgressUpdate(final Long... values) {
super.onProgressUpdate(values);
String total = Util.humanReadableBytes(fileSize, true);
String downloaded = Util.humanReadableBytes(values[0], true);
statusTextView.setText("Downloading: " + downloaded + "/" + total);
float percent = (float) values[0] / fileSize;
progressBar.setProgress((int) percent * progressBar.getMax());
}
}

private static final String TAG = DownloadActivity.class.getSimpleName();

private static String folderPath;
Expand Down Expand Up @@ -155,8 +60,6 @@ protected void onProgressUpdate(final Long... values) {

EditText urlInputPath;

private DownloadTask downloadTask;

@SuppressLint("ClickableViewAccessibility")
@Override
protected void onCreate(@Nullable final Bundle savedInstanceState) {
Expand Down Expand Up @@ -211,8 +114,7 @@ public void onClick(final View v) {
@Override
public void onClick(final View v) {
if (urlInputPath.getText() != null && !TextUtils.isEmpty(urlInputPath.getText().toString().trim())) {
//downloadDataSet(urlInputPath.getText().toString().trim());
downloadDatasetFTP(urlInputPath.getText().toString().trim());
downloadDataSet(urlInputPath.getText().toString().trim());
} else {
Toast.makeText(DownloadActivity.this, "Please input a URL", Toast.LENGTH_SHORT).show();
}
Expand Down Expand Up @@ -273,26 +175,9 @@ public void onClick(final View v) {

TextView txtSDCardWarning = new TextView(this);
txtSDCardWarning.setText(
"Cannot download or extract to SD card? Please check Help -> View Tutorial");
"Cannot download or extract to SD card? Please check Settings");
txtSDCardWarning.setTextColor(getResources().getColor(R.color.colorRead));
linearLayout.addView(txtSDCardWarning);

if (GUIConfiguration.getAppMode() == AppMode.SLAVE) {
btnRunPipeline = new Button(this);
btnRunPipeline.setText("Run Pipeline");
btnRunPipeline.setVisibility(View.GONE);
linearLayout.addView(btnRunPipeline);
btnRunPipeline.setOnClickListener(new OnClickListener() {
@Override
public void onClick(final View v) {
GUIConfiguration.setPipelineState(PipelineState.TO_BE_CONFIGURED);
Intent intent = new Intent(DownloadActivity.this, TerminalActivity.class);
intent.putExtra("FOLDER_PATH", folderPath.substring(0, folderPath.lastIndexOf(".")));
startActivity(intent);
}
});
}

}

private void enableButtons() {
Expand Down Expand Up @@ -321,12 +206,6 @@ public void onComplete(@NonNull final EndCause cause, @Nullable final Exception
downloadManager.download(DownloadActivity.this, treeUri);
}

private void downloadDatasetFTP(String url) {
String[] urlData = url.split("/");
Log.d(TAG, "URL=" + urlData[1]);
new FTPDownloadTask().execute(urlData[0], urlData[1]);
}

private void extractZip(String filepath) {

ZipManager zipManager = new ZipManager(DownloadActivity.this, new ZipListener() {
Expand Down
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