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Merge pull request #122 from SanojPunchihewa/bug-fixes
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Bug fixes
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@SanojPunchihewa
SanojPunchihewa authored Feb 6, 2020
2 parents eb3b409 + 698b161 commit 4286231
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Showing 13 changed files with 418 additions and 108 deletions.
4 changes: 4 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 @@ -147,6 +147,10 @@ public static ArrayList<Step> getSteps() {
return steps;
}

public static void setSteps(ArrayList<Step> newSteps) {
steps = newSteps;
}

public static void configureLikedFileArgument(String fileName, String value) {
linkedFileArguments.put(fileName, value);
}
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9 changes: 9 additions & 0 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 @@ -30,6 +30,7 @@
import com.mobilegenomics.f5n.core.PipelineComponent;
import com.mobilegenomics.f5n.support.FileUtil;
import com.mobilegenomics.f5n.support.PipelineState;
import com.mobilegenomics.f5n.support.PreferenceUtil;
import com.mobilegenomics.f5n.support.TimeFormat;
import java.io.BufferedReader;
import java.io.File;
Expand Down Expand Up @@ -276,9 +277,17 @@ protected void onPostExecute(final String s) {
btnWriteLog.setVisibility(View.VISIBLE);
btnProceed.setEnabled(true);
mProgressBar.setVisibility(View.GONE);
PreferenceUtil
.setSharedPreferenceInt(R.string.id_app_mode, GUIConfiguration.getPipelineState().ordinal());

if (GUIConfiguration.getAppMode() == AppMode.SLAVE) {
mp.start();
mp.setLooping(true);
GUIConfiguration.setPipelineState(PipelineState.TO_BE_UPLOAD);
PreferenceUtil
.setSharedPreferenceInt(R.string.id_app_mode, GUIConfiguration.getPipelineState().ordinal());
PreferenceUtil
.setSharedPreferenceString(R.string.id_results_summary, resultsSummary);
btnSendResults.setVisibility(View.VISIBLE);
}
}
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2 changes: 2 additions & 0 deletions app/src/main/java/com/mobilegenomics/f5n/activity/DemoActivity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
import com.mobilegenomics.f5n.core.PipelineStep;
import com.mobilegenomics.f5n.support.DownloadListener;
import com.mobilegenomics.f5n.support.FileUtil;
import com.mobilegenomics.f5n.support.PipelineState;
import com.mobilegenomics.f5n.support.PreferenceUtil;
import com.mobilegenomics.f5n.support.TimeFormat;
import com.mobilegenomics.f5n.support.ZipListener;
Expand Down Expand Up @@ -137,6 +138,7 @@ public void onClick(final View v) {
GUIConfiguration.addPipelineStep(step);
}
GUIConfiguration.printList();
GUIConfiguration.setPipelineState(PipelineState.CONFIGURED);
GUIConfiguration.configureSteps(DemoActivity.this,
Environment.getExternalStorageDirectory() + "/" + folderName + "/"
+ fileName.substring(0, fileName.lastIndexOf(".")));
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2 changes: 1 addition & 1 deletion app/src/main/java/com/mobilegenomics/f5n/activity/DownloadActivity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -317,7 +317,7 @@ public void onComplete(@NonNull final EndCause cause, @Nullable final Exception

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

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197 changes: 177 additions & 20 deletions app/src/main/java/com/mobilegenomics/f5n/activity/MinITActivity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,33 +3,42 @@
import android.content.ClipData;
import android.content.ClipboardManager;
import android.content.Context;
import android.content.DialogInterface;
import android.content.DialogInterface.OnDismissListener;
import android.content.Intent;
import android.os.AsyncTask;
import android.os.Bundle;
import android.os.Handler;
import android.text.TextUtils;
import android.util.Log;
import android.view.View;
import android.view.View.OnClickListener;
import android.widget.Button;
import android.widget.EditText;
import android.widget.ProgressBar;
import android.widget.TableRow;
import android.widget.TextView;
import android.widget.Toast;
import androidx.annotation.NonNull;
import androidx.annotation.Nullable;
import androidx.appcompat.app.AlertDialog;
import androidx.appcompat.app.AppCompatActivity;
import com.liulishuo.okdownload.core.Util;
import com.mobilegenomics.f5n.BuildConfig;
import com.mobilegenomics.f5n.GUIConfiguration;
import com.mobilegenomics.f5n.R;
import com.mobilegenomics.f5n.dto.State;
import com.mobilegenomics.f5n.dto.WrapperObject;
import com.mobilegenomics.f5n.support.PipelineState;
import com.mobilegenomics.f5n.support.PreferenceUtil;
import com.mobilegenomics.f5n.support.ServerCallback;
import com.mobilegenomics.f5n.support.ServerConnectionUtils;
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.FileInputStream;
import java.util.ArrayList;
import java.util.Objects;
import net.gotev.uploadservice.UploadService;
import org.apache.commons.net.ftp.FTP;
Expand All @@ -48,6 +57,10 @@ class FTPUploadTask extends AsyncTask<String, Long, Boolean> {
protected Boolean doInBackground(String... urls) {
FTPClient con;
try {

Log.e(TAG, "Address = " + urls[0]);
Log.e(TAG, "File path = " + urls[1]);

con = new FTPClient();
con.setDefaultPort(8000);
con.connect(urls[0]);
Expand All @@ -70,7 +83,8 @@ public void bytesTransferred(long totalBytesTransferred, int bytesTransferred, l
fileSize = fileIn.length();

FileInputStream in = new FileInputStream(fileIn);
boolean result = con.storeFile(new File(urls[1]).getName(), in);
String filePath = "outputs/" + new File(urls[1]).getName();
boolean result = con.storeFile(filePath, in);
in.close();
status = result;
con.logout();
Expand All @@ -94,6 +108,9 @@ protected void onPostExecute(final Boolean uploadSuccess) {
super.onPostExecute(uploadSuccess);
Log.i(TAG, "Upload Finished");
if (uploadSuccess) {
GUIConfiguration.setPipelineState(PipelineState.COMPLETED);
PreferenceUtil
.setSharedPreferenceInt(R.string.id_app_mode, GUIConfiguration.getPipelineState().ordinal());
statusTextView.setText("Upload Completed");
sendJobResults();
} else {
Expand Down Expand Up @@ -126,11 +143,17 @@ protected void onProgressUpdate(final Long... values) {

TextView statusTextView;

private Button btnSendResult;
private TableRow trSendResults;

private String folderPath;
private Button btnProcessJob;

private Button btnRequestJob;

private boolean ranPipeline = false;
private Button btnCompressFiles;

private Button btnSendResults;

private String folderPath;

private String resultsSummary;

Expand All @@ -140,6 +163,8 @@ protected void onProgressUpdate(final Long... values) {

private String zipFileName;

private ArrayList<String> fileList;

public static void logHandler(Handler handler) {
handler.post(new Runnable() {
@Override
Expand All @@ -157,6 +182,12 @@ protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
setContentView(R.layout.activity_minit);

if (PreferenceUtil.getSharedPreferenceInt(R.string.id_app_mode) == PipelineState.MINIT_RUNNING.ordinal() &&
PreferenceUtil.getSharedPreferenceStepList(R.string.id_step_list) != null &&
PreferenceUtil.getSharedPreferenceObject(R.string.id_wrapper_obj) != null) {
showResumeMessage(PipelineState.MINIT_RUNNING);
}

statusTextView = findViewById(R.id.txt_status);
progressBar = findViewById(R.id.progress_upload_status);

Expand All @@ -165,19 +196,28 @@ protected void onCreate(Bundle savedInstanceState) {
serverAddressInput = findViewById(R.id.input_server_address);

connectionLogText = findViewById(R.id.text_conn_log);
final Button btnRquestJob = findViewById(R.id.btn_request_job);
btnSendResult = findViewById(R.id.btn_send_result);

trSendResults = findViewById(R.id.tr_select_files_send);

btnRequestJob = findViewById(R.id.btn_request_job);
btnProcessJob = findViewById(R.id.btn_process_job);
btnCompressFiles = findViewById(R.id.btn_select_files);
btnSendResults = findViewById(R.id.btn_send_result);

if (getIntent().getExtras() != null) {
resultsSummary = getIntent().getExtras().getString("PIPELINE_STATUS");
folderPath = getIntent().getExtras().getString("FOLDER_PATH");
if (resultsSummary != null && !TextUtils.isEmpty(resultsSummary)) {
ranPipeline = true;
btnRquestJob.setText("Send Results");
btnRequestJob.setVisibility(View.GONE);
trSendResults.setVisibility(View.VISIBLE);
}
} else {
if (PreferenceUtil.getSharedPreferenceInt(R.string.id_app_mode) == PipelineState.TO_BE_UPLOAD.ordinal()) {
showResumeMessage(PipelineState.TO_BE_UPLOAD);
}
}

btnRquestJob.setOnClickListener(new View.OnClickListener() {
btnRequestJob.setOnClickListener(new View.OnClickListener() {
@Override
public void onClick(View v) {

Expand All @@ -186,21 +226,41 @@ public void onClick(View v) {
serverIP = serverAddressInput.getText().toString().trim();

ServerConnectionUtils.setServerAddress(serverIP);
if (ranPipeline) {
uploadDataSet();
} else {
requestJob();
}
requestJob();
} else {
Toast.makeText(MinITActivity.this, "Please input a server IP", Toast.LENGTH_SHORT).show();
}
}
});

btnCompressFiles.setOnClickListener(new OnClickListener() {
@Override
public void onClick(final View v) {
openFileManager(false, true);
}
});

btnSendResults.setOnClickListener(new OnClickListener() {
@Override
public void onClick(final View v) {
if (serverAddressInput.getText() != null && !TextUtils
.isEmpty(serverAddressInput.getText().toString().trim())) {
serverIP = serverAddressInput.getText().toString().trim();
ServerConnectionUtils.setServerAddress(serverIP);
openFileManager(false, false);
} else {
Toast.makeText(MinITActivity.this, "Please input a server IP", Toast.LENGTH_SHORT).show();
}
}
});

btnSendResult.setOnClickListener(new View.OnClickListener() {
btnProcessJob.setOnClickListener(new View.OnClickListener() {
@Override
public void onClick(View v) {

PreferenceUtil
.setSharedPreferenceObject(R.string.id_wrapper_obj, ServerConnectionUtils.getWrapperObject());

Intent intent = new Intent(MinITActivity.this, DownloadActivity.class);
// TODO Fix the following
// Protocol, file server IP and Port
Expand Down Expand Up @@ -248,7 +308,7 @@ public void onSuccess(final WrapperObject job) {
public void run() {
GUIConfiguration.configureSteps(job.getSteps());
zipFileName = job.getPrefix();
btnSendResult.setVisibility(View.VISIBLE);
btnProcessJob.setVisibility(View.VISIBLE);
}
});
}
Expand All @@ -275,8 +335,16 @@ public void run() {
});
}

private void uploadDataSet() {
private void uploadDataSet(String filePath) {
new FTPUploadTask().execute(serverIP, filePath);
}

private void compressDataSet() {
// TODO check wifi connectivity
folderPath = fileList.get(fileList.size() - 1);
String zipFileName = folderPath + "/" + folderPath.substring(folderPath.lastIndexOf("/") + 1)
+ ".out.zip";

ZipManager zipManager = new ZipManager(MinITActivity.this, new ZipListener() {
@Override
public void onStarted(@NonNull final long totalBytes) {
Expand Down Expand Up @@ -308,16 +376,105 @@ public void onComplete(@NonNull final boolean success, @Nullable final Exception
public void run() {
if (success) {
statusTextView.setText("Zip Successful");
String path = folderPath + ".out.zip";
new FTPUploadTask().execute(serverIP, path);
} else {
statusTextView.setText("Zip Error");
}
}
});
}
});
zipManager.zip(folderPath);

fileList.remove(fileList.size() - 1);
zipManager.zip(fileList, zipFileName);
}

private void openFileManager(boolean dirOnly, boolean toCompress) {
fileList = new ArrayList<>();

if (toCompress) {
new ChooserDialog(MinITActivity.this)
.withFilter(dirOnly, false)
.enableMultiple(true)
.withChosenListener(new ChooserDialog.Result() {
@Override
public void onChoosePath(String path, File pathFile) {
if (fileList.contains(path)) {
fileList.remove(path);
} else {
fileList.add(path);
}
}
})
// to handle the back key pressed or clicked outside the dialog:
.withOnCancelListener(new DialogInterface.OnCancelListener() {
public void onCancel(DialogInterface dialog) {
dialog.cancel();
}
})
.withOnDismissListener(new OnDismissListener() {
@Override
public void onDismiss(final DialogInterface dialog) {
compressDataSet();
}
})
.withResources(R.string.title_choose_any_file, R.string.title_choose, R.string.dialog_cancel)
.build()
.show();
} else {
new ChooserDialog(MinITActivity.this)
.withFilter(dirOnly, false)
// to handle the result(s)
.withChosenListener(new ChooserDialog.Result() {
@Override
public void onChoosePath(String path, File pathFile) {
uploadDataSet(path);
}
})
.build()
.show();
}
}

private void showResumeMessage(PipelineState state) {

String msg;

if (state == PipelineState.TO_BE_UPLOAD) {
msg = "You can upload the data from previous job";
} else {
msg = "You can re run the previous job";
}

new AlertDialog.Builder(this)
.setTitle("Resume App State")
.setMessage(msg)
.setPositiveButton("Resume", new DialogInterface.OnClickListener() {
public void onClick(DialogInterface dialog, int which) {
dialog.dismiss();
ServerConnectionUtils.setWrapperObject(
(WrapperObject) PreferenceUtil
.getSharedPreferenceObject(R.string.id_wrapper_obj));
if (state == PipelineState.TO_BE_UPLOAD) {
btnRequestJob.setVisibility(View.GONE);
trSendResults.setVisibility(View.VISIBLE);
resultsSummary = PreferenceUtil.getSharedPreferenceString(R.string.id_results_summary);
} else {
GUIConfiguration.setPipelineState(PipelineState.CONFIGURED);
GUIConfiguration
.setSteps(PreferenceUtil.getSharedPreferenceStepList(R.string.id_step_list));
Intent intent = new Intent(MinITActivity.this, TerminalActivity.class);
startActivity(intent);
}
}
})
.setNegativeButton("Get new Job", new DialogInterface.OnClickListener() {
@Override
public void onClick(final DialogInterface dialog, final int which) {
dialog.dismiss();
}
})
.setCancelable(false)
.show();
}

private boolean validateIPAddress(final String ip) {
Expand Down
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