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Merge pull request #61 from SanojPunchihewa/dev-demo
Add option to run a Demo
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207 changes: 207 additions & 0 deletions
207
app/src/main/java/com/mobilegenomics/f5n/activity/DemoActivity.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,207 @@ | ||
| package com.mobilegenomics.f5n.activity; | ||
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| import android.app.DownloadManager; | ||
| import android.content.BroadcastReceiver; | ||
| import android.content.Context; | ||
| import android.content.Intent; | ||
| import android.content.IntentFilter; | ||
| import android.net.Uri; | ||
| import android.os.Bundle; | ||
| import android.os.Environment; | ||
| import android.util.Log; | ||
| import android.view.View; | ||
| import android.view.View.OnClickListener; | ||
| import android.widget.Button; | ||
| import android.widget.LinearLayout; | ||
| import android.widget.TextView; | ||
| import android.widget.Toast; | ||
| import androidx.annotation.Nullable; | ||
| import androidx.appcompat.app.AppCompatActivity; | ||
| import com.mobilegenomics.f5n.GUIConfiguration; | ||
| import com.mobilegenomics.f5n.R; | ||
| import com.mobilegenomics.f5n.core.PipelineStep; | ||
| import com.mobilegenomics.f5n.support.Decompress; | ||
| import com.mobilegenomics.f5n.support.TimeFormat; | ||
| import java.io.File; | ||
| import java.io.FileOutputStream; | ||
| import java.io.IOException; | ||
| import java.io.OutputStreamWriter; | ||
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| public class DemoActivity extends AppCompatActivity { | ||
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| private static final String TAG = DemoActivity.class.getSimpleName(); | ||
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| private static final String ecoliDataSetURL = "https://zanojmobiapps.com/_tmp/genome/ecoli/ecoli-data-set.zip"; | ||
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| private static final String folderName = "mobile-genomics"; | ||
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| private static final String fileName = "ecoli-data-set.zip"; | ||
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| private long downloadID; | ||
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| private LinearLayout linearLayout; | ||
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| private TextView txtLogView; | ||
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| private Button btnRunPipeline; | ||
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| private File logFile; | ||
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| private FileOutputStream fOut; | ||
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| private OutputStreamWriter myOutWriter; | ||
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| @Override | ||
| protected void onCreate(@Nullable final Bundle savedInstanceState) { | ||
| super.onCreate(savedInstanceState); | ||
| setContentView(R.layout.layout_vertical); | ||
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| String dirPath = Environment.getExternalStorageDirectory() + "/" + folderName; | ||
| File dir = new File(dirPath); | ||
| if (!dir.exists()) { | ||
| dir.mkdirs(); | ||
| } | ||
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| logFile = new File(dir.getAbsolutePath() + "/f5n-log.txt"); | ||
| if (!logFile.exists()) { | ||
| try { | ||
| logFile.createNewFile(); | ||
| } catch (IOException e) { | ||
| Toast.makeText(this, "Error creating log file, Please check permissions", Toast.LENGTH_SHORT).show(); | ||
| Log.e(TAG, "Error : " + e); | ||
| } | ||
| } | ||
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| registerReceiver(onDownloadComplete, new IntentFilter(DownloadManager.ACTION_DOWNLOAD_COMPLETE)); | ||
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| try { | ||
| fOut = new FileOutputStream(logFile, true); | ||
| myOutWriter = new OutputStreamWriter(fOut); | ||
| String header = "----------- Log for Demo app session " + TimeFormat | ||
| .millisToDateTime(System.currentTimeMillis()) | ||
| + " -----------\n"; | ||
| myOutWriter.append(header); | ||
| } catch (Exception e) { | ||
| Log.e(TAG, "Error : " + e); | ||
| } | ||
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| linearLayout = findViewById(R.id.vertical_linear_layout); | ||
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| TextView txtInfo = new TextView(this); | ||
| txtInfo.setText(getResources().getString(R.string.pipeline_description)); | ||
| linearLayout.addView(txtInfo); | ||
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| TextView txtSkipDownload = new TextView(this); | ||
| txtSkipDownload.setText( | ||
| "If you have already downloaded and extracted the ecoli data set to main-storage/mobile-genomics folder, you can skip Download & Extract"); | ||
| txtSkipDownload.setPadding(0, 10, 0, 0); | ||
| linearLayout.addView(txtSkipDownload); | ||
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| Button btnDownloadAndExtract = new Button(this); | ||
| btnDownloadAndExtract.setText("Download & Extract"); | ||
| btnDownloadAndExtract.setOnClickListener(new OnClickListener() { | ||
| @Override | ||
| public void onClick(final View v) { | ||
| btnDownloadAndExtract.setEnabled(false); | ||
| downloadDataSet(ecoliDataSetURL); | ||
| } | ||
| }); | ||
| linearLayout.addView(btnDownloadAndExtract); | ||
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| txtLogView = new TextView(this); | ||
| // txtLogView.setTextSize(f); | ||
| linearLayout.addView(txtLogView); | ||
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| btnRunPipeline = new Button(this); | ||
| btnRunPipeline.setText("Run Pipeline"); | ||
| btnRunPipeline.setOnClickListener(new OnClickListener() { | ||
| @Override | ||
| public void onClick(final View v) { | ||
| 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)); | ||
| } | ||
| }); | ||
| linearLayout.addView(btnRunPipeline); | ||
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| } | ||
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| private void downloadDataSet(String url) { | ||
| // TODO check wifi connectivity | ||
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| writeToLogFile("Downloading data set...\n"); | ||
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| DownloadManager downloadmanager = (DownloadManager) getSystemService(Context.DOWNLOAD_SERVICE); | ||
| Uri uri = Uri.parse(url); | ||
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| try { | ||
| DownloadManager.Request request = new DownloadManager.Request(uri); | ||
| request.setTitle(fileName); | ||
| request.setDescription("Downloading"); | ||
| request.setNotificationVisibility(DownloadManager.Request.VISIBILITY_VISIBLE_NOTIFY_COMPLETED); | ||
| request.setVisibleInDownloadsUi(true); | ||
| request.setDestinationUri( | ||
| Uri.parse("file://" + Environment.getExternalStorageDirectory() + "/" + folderName + "/" | ||
| + fileName)); | ||
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| downloadID = downloadmanager.enqueue(request); | ||
| } catch (Exception e) { | ||
| Toast.makeText(this, "Invalid URL", Toast.LENGTH_SHORT).show(); | ||
| Log.e(TAG, "Exception: " + e); | ||
| writeToLogFile("[Error] Downloading data set: " + e + "\n"); | ||
| } | ||
| } | ||
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| private BroadcastReceiver onDownloadComplete = new BroadcastReceiver() { | ||
| @Override | ||
| public void onReceive(Context context, Intent intent) { | ||
| //Fetching the download id received with the broadcast | ||
| long id = intent.getLongExtra(DownloadManager.EXTRA_DOWNLOAD_ID, -1); | ||
| //Checking if the received broadcast is for our enqueued download by matching download id | ||
| if (downloadID == id) { | ||
| Toast.makeText(DemoActivity.this, "Download Completed", Toast.LENGTH_SHORT).show(); | ||
| writeToLogFile("Downloading data set completed\n"); | ||
| extractZip(new File(Environment.getExternalStorageDirectory() + "/" + folderName + "/" | ||
| + fileName)); | ||
| } | ||
| } | ||
| }; | ||
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| @Override | ||
| protected void onStop() { | ||
| super.onStop(); | ||
| unregisterReceiver(onDownloadComplete); | ||
| try { | ||
| myOutWriter.append("-------------------- End of Log --------------------\n\n"); | ||
| myOutWriter.flush(); | ||
| myOutWriter.close(); | ||
| fOut.close(); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
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| private void extractZip(File file) { | ||
| writeToLogFile("Extracting data set...\n"); | ||
| Decompress decompress = new Decompress(DemoActivity.this, file); | ||
| decompress.unzip(); | ||
| writeToLogFile("Extracting data set completed\n"); | ||
| btnRunPipeline.setVisibility(View.VISIBLE); | ||
| } | ||
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| private void writeToLogFile(String lines) { | ||
| txtLogView.append(lines); | ||
| try { | ||
| myOutWriter.append(lines); | ||
| myOutWriter.flush(); | ||
| } catch (IOException e) { | ||
| Log.e(TAG, "Error : " + e); | ||
| } | ||
| } | ||
|
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||
| } |
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