Add option to run a Demo

app/src/main/AndroidManifest.xml

@@ -14,7 +14,8 @@
         android:roundIcon="@mipmap/ic_launcher_round"
         android:supportsRtl="true"
         android:theme="@style/AppTheme"
-        tools:ignore="GoogleAppIndexingWarning">
+        tools:ignore="GoogleAppIndexingWarning"
+        android:usesCleartextTraffic="true">
         <activity android:name=".activity.MainActivity">
             <intent-filter>
                 <action android:name="android.intent.action.MAIN" />
@@ -28,6 +29,7 @@
         <activity android:name=".activity.DownloadActivity" />
         <activity android:name=".activity.MinITActivity" />
         <activity android:name=".activity.TerminalActivity" />
+        <activity android:name=".activity.DemoActivity" />
     </application>
 
 </manifest>

app/src/main/java/com/mobilegenomics/f5n/GUIConfiguration.java

@@ -45,11 +45,11 @@ public static void printList() {
         }
     }
 
-    public static void configureSteps(Context context) {
+    public static void configureSteps(Context context, String folderPath) {
         // clear() vs new check what is better
         steps = new ArrayList<>();
         for (PipelineStep pipelineStep : selectedPipelineSteps) {
-            ArrayList<Argument> arguments = configureArguments(context, pipelineStep);
+            ArrayList<Argument> arguments = configureArguments(context, pipelineStep, folderPath);
             Step step = new Step(pipelineStep, arguments);
             steps.add(step);
         }
@@ -125,7 +125,8 @@ public static String getLinkedFileArgument(String fileName) {
         return linkedFileArguments.containsKey(fileName) ? linkedFileArguments.get(fileName) : "";
     }
 
-    private static ArrayList<Argument> configureArguments(Context context, PipelineStep pipelineStep) {
+    private static ArrayList<Argument> configureArguments(Context context, PipelineStep pipelineStep,
+            String folderPath) {
         int rawFile = 0;
         switch (pipelineStep) {
             case MINIMAP2_SEQUENCE_ALIGNMENT:
@@ -150,18 +151,87 @@ private static ArrayList<Argument> configureArguments(Context context, PipelineS
                 Log.e(TAG, "Invalid Pipeline Step");
                 break;
         }
-        return buildArgumentsFromJson(context, rawFile);
+        return buildArgumentsFromJson(context, rawFile, folderPath);
     }
 
-    private static ArrayList<Argument> buildArgumentsFromJson(Context context, @RawRes int file) {
+    private static ArrayList<Argument> buildArgumentsFromJson(Context context, @RawRes int file, String folderPath) {
         ArrayList<Argument> arguments = new ArrayList<>();
         JsonObject argsJson = JSONFileHelper.rawtoJsonObject(context, file);
         JsonArray argsJsonArray = argsJson.getAsJsonArray("args");
         for (JsonElement element : argsJsonArray) {
             Argument argument = new Gson().fromJson(element, Argument.class);
+            if (folderPath != null) {
+                configureDemoArgsFilePath(argument, folderPath);
+            }
             arguments.add(argument);
         }
         return arguments;
     }
 
+    private static void configureDemoArgsFilePath(Argument argument, String folder) {
+
+        if (argument.isFile()) {
+            argument.setSetByUser(true);
+        }
+
+        // minimap2 input/output files
+        if (argument.getArgID().equals("MINIMAP2_REF_FILE")) {
+            argument.setArgValue(folder + "/draft.fa");
+        }
+        if (argument.getArgID().equals("MINIMAP2_QUERY_FILE")) {
+            argument.setArgValue(folder + "/reads.fasta");
+        }
+        if (argument.getArgID().equals("MINIMAP2_OUTPUT_FILE")) {
+            argument.setArgValue(folder + "/minimap2-out.sam");
+        }
+
+        // samtools input/output files
+        if (argument.getArgID().equals("SAMTOOL_SORT_INPUT_FILE")) {
+            argument.setArgValue(folder + "/minimap2-out.sam");
+        }
+        if (argument.getArgID().equals("SAMTOOL_SORT_OUTPUT_FILE")) {
+            argument.setArgValue(folder + "/reads.sorted.bam");
+        }
+
+        if (argument.getArgID().equals("SAMTOOL_INDEX_INPUT_FILE")) {
+            argument.setArgValue(folder + "/reads.sorted.bam");
+        }
+
+        // f5c index input/output files
+        if (argument.getArgID().equals("F5C_INDEX_FAST5_FILE")) {
+            argument.setArgValue(folder + "/fast5_files");
+        }
+        if (argument.getArgID().equals("F5C_INDEX_FASTA_FILE")) {
+            argument.setArgValue(folder + "/reads.fasta");
+        }
+
+        // f5c methylation input/output files
+        if (argument.getArgID().equals("F5C_METH_FASTA_FILE")) {
+            argument.setArgValue(folder + "/reads.fasta");
+        }
+        if (argument.getArgID().equals("F5C_METH_SORTED_FILE")) {
+            argument.setArgValue(folder + "/reads.sorted.bam");
+        }
+        if (argument.getArgID().equals("F5C_METH_REF_FILE")) {
+            argument.setArgValue(folder + "/draft.fa");
+        }
+        if (argument.getArgID().equals("F5C_METH_OUTPUT_FILE")) {
+            argument.setArgValue(folder + "/f5c-methylation.tsv");
+        }
+
+        // f5c event alignment input/output files
+        if (argument.getArgID().equals("F5C_ALIGN_FASTA_FILE")) {
+            argument.setArgValue(folder + "/reads.fasta");
+        }
+        if (argument.getArgID().equals("F5C_ALIGN_SORTED_FILE")) {
+            argument.setArgValue(folder + "/reads.sorted.bam");
+        }
+        if (argument.getArgID().equals("F5C_ALIGN_REF_FILE")) {
+            argument.setArgValue(folder + "/draft.fa");
+        }
+        if (argument.getArgID().equals("F5C_ALIGN_OUTPUT_FILE")) {
+            argument.setArgValue(folder + "/f5c-event-alignment.txt");
+        }
+    }
+
 }

app/src/main/java/com/mobilegenomics/f5n/activity/DemoActivity.java

@@ -0,0 +1,207 @@
+package com.mobilegenomics.f5n.activity;
+
+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;
+
+public class DemoActivity extends AppCompatActivity {
+
+    private static final String TAG = DemoActivity.class.getSimpleName();
+
+    private static final String ecoliDataSetURL = "https://zanojmobiapps.com/_tmp/genome/ecoli/ecoli-data-set.zip";
+
+    private static final String folderName = "mobile-genomics";
+
+    private static final String fileName = "ecoli-data-set.zip";
+
+    private long downloadID;
+
+    private LinearLayout linearLayout;
+
+    private TextView txtLogView;
+
+    private Button btnRunPipeline;
+
+    private File logFile;
+
+    private FileOutputStream fOut;
+
+    private OutputStreamWriter myOutWriter;
+
+    @Override
+    protected void onCreate(@Nullable final Bundle savedInstanceState) {
+        super.onCreate(savedInstanceState);
+        setContentView(R.layout.layout_vertical);
+
+        String dirPath = Environment.getExternalStorageDirectory() + "/" + folderName;
+        File dir = new File(dirPath);
+        if (!dir.exists()) {
+            dir.mkdirs();
+        }
+
+        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);
+            }
+        }
+
+        registerReceiver(onDownloadComplete, new IntentFilter(DownloadManager.ACTION_DOWNLOAD_COMPLETE));
+
+        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);
+        }
+
+        linearLayout = findViewById(R.id.vertical_linear_layout);
+
+        TextView txtInfo = new TextView(this);
+        txtInfo.setText(getResources().getString(R.string.pipeline_description));
+        linearLayout.addView(txtInfo);
+
+        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);
+
+        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);
+
+        txtLogView = new TextView(this);
+//        txtLogView.setTextSize(f);
+        linearLayout.addView(txtLogView);
+
+        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);
+
+    }
+
+    private void downloadDataSet(String url) {
+        // TODO check wifi connectivity
+
+        writeToLogFile("Downloading data set...\n");
+
+        DownloadManager downloadmanager = (DownloadManager) getSystemService(Context.DOWNLOAD_SERVICE);
+        Uri uri = Uri.parse(url);
+
+        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));
+
+            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");
+        }
+    }
+
+    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));
+            }
+        }
+    };
+
+    @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();
+        }
+    }
+
+    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);
+    }
+
+    private void writeToLogFile(String lines) {
+        txtLogView.append(lines);
+        try {
+            myOutWriter.append(lines);
+            myOutWriter.flush();
+        } catch (IOException e) {
+            Log.e(TAG, "Error : " + e);
+        }
+    }
+
+}

app/src/main/java/com/mobilegenomics/f5n/activity/MainActivity.java

@@ -11,11 +11,9 @@
 import androidx.annotation.NonNull;
 import androidx.appcompat.app.AppCompatActivity;
 import androidx.core.app.ActivityCompat;
-
 import com.mobilegenomics.f5n.R;
 import com.mobilegenomics.f5n.support.PermissionResultCallback;
 import com.mobilegenomics.f5n.support.PermissionUtils;
-
 import java.util.ArrayList;
 
 public class MainActivity extends AppCompatActivity implements
@@ -57,6 +55,10 @@ public void startMinITMode(View view) {
         startActivity(new Intent(MainActivity.this, MinITActivity.class));
     }
 
+    public void startDemoMode(View view) {
+        startActivity(new Intent(MainActivity.this, DemoActivity.class));
+    }
+
     /////////////////////////////
     // Permission functions
     /////////////////////////////

app/src/main/java/com/mobilegenomics/f5n/activity/PipelineActivity.java

@@ -9,11 +9,9 @@
 import android.widget.LinearLayout;
 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 java.util.ArrayList;
 
 public class PipelineActivity extends AppCompatActivity {
@@ -73,7 +71,7 @@ private void initPipelineSteps(int mode) {
         }
         if (!clickedNone) {
             GUIConfiguration.printList();
-            GUIConfiguration.configureSteps(PipelineActivity.this);
+            GUIConfiguration.configureSteps(PipelineActivity.this, null);
             if (mode == MODE_GUI) {
                 startActivity(new Intent(PipelineActivity.this, StepActivity.class));
             } else {