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Merge pull request #96 from SanojPunchihewa/bug-fixes
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Use a Pipe to read log messages
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@SanojPunchihewa
SanojPunchihewa authored Dec 17, 2019
2 parents cd781c0 + 05f1579 commit bf228b0
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Showing 7 changed files with 103 additions and 111 deletions.
33 changes: 30 additions & 3 deletions app/src/main/cpp/native-lib.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,13 @@
#include <setjmp.h>
#include <signal.h>
#include <unistd.h>
#include <sys/stat.h>
#include <fcntl.h>
#include<android/log.h>

#define FILE_CLOSE_TAG "EOF"
const char *outfile;
int fdo;

#include "interface_minimap.h"
#include "interface_f5c.h"
Expand Down Expand Up @@ -73,9 +80,6 @@ Java_com_mobilegenomics_f5n_core_NativeCommands_init(JNIEnv *env, jobject, jstri
// Convert command to cpp
//TODO:casting not good
char *command_c = (char *) env->GetStringUTFChars(command, nullptr);
// if(!command_c) {throwJavaError(env, "jvm could not allocate memory");return;};
// std::string command_s = command_c;


enum { kMaxArgs = 64 };
int argc = 0;
Expand Down Expand Up @@ -217,4 +221,27 @@ Java_com_mobilegenomics_f5n_core_NativeCommands_initsamtool(JNIEnv *env, jobject


return result;
}

extern "C"
JNIEXPORT jint JNICALL
Java_com_mobilegenomics_f5n_core_NativeCommands_startPipeline(JNIEnv *env, jobject thiz, jstring pipe_path) {
outfile = env->GetStringUTFChars(pipe_path, nullptr);

int out = mkfifo(outfile, 0664);
fdo = open(outfile, O_WRONLY);

dup2(fdo, STDERR_FILENO);
setvbuf(stderr, 0, _IONBF, 0);
return 0;
}

extern "C"
JNIEXPORT jint JNICALL
Java_com_mobilegenomics_f5n_core_NativeCommands_finishPipeline(JNIEnv *env, jobject thiz, jstring pipe_path) {
fprintf(stderr, FILE_CLOSE_TAG);
fflush(stderr);
close(fdo);
env->ReleaseStringUTFChars(pipe_path, outfile);
return 0;
}
177 changes: 69 additions & 108 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 @@ -8,6 +8,7 @@
import android.os.AsyncTask;
import android.os.Bundle;
import android.os.Environment;
import android.os.Handler;
import android.util.Log;
import android.view.View;
import android.view.View.OnClickListener;
Expand All @@ -25,27 +26,23 @@
import com.mobilegenomics.f5n.GUIConfiguration;
import com.mobilegenomics.f5n.R;
import com.mobilegenomics.f5n.core.AppMode;
import com.mobilegenomics.f5n.core.NativeCommands;
import com.mobilegenomics.f5n.core.PipelineComponent;
import com.mobilegenomics.f5n.support.TimeFormat;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class ConfirmationActivity extends AppCompatActivity {

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

private static final String TAG_F5C = "f5c-android";

private static final String TAG_MINIMAP2 = "minimap2-native";

private static final String TAG_SAMTOOLS = "samtools-native";
private static final String FILE_CLOSE_TAG = "EOF";

private String resultsSummary;

Expand All @@ -71,13 +68,37 @@ public class ConfirmationActivity extends AppCompatActivity {

MediaPlayer mp;

ShowLogCat showLogCatTask;
Handler mHandler;

String logPipePath;

File logPipeFile;

@Override
protected void onCreate(@Nullable final Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
setContentView(R.layout.layout_vertical);

String dirPath = Environment.getExternalStorageDirectory() + "/" + "mobile-genomics";

File dir = new File(dirPath);
if (!dir.exists()) {
dir.mkdirs();
}

logPipeFile = new File(dir.getAbsolutePath() + "/pipe-out");
logPipePath = dir.getAbsolutePath() + "/pipe-out";
if (!logPipeFile.exists()) {
try {
logPipeFile.createNewFile();
} catch (IOException e) {
Toast.makeText(this, "Error creating log file, Please check permissions", Toast.LENGTH_SHORT).show();
Log.e(TAG, "Error : " + e);
}
}

mHandler = new Handler();

linearLayout = findViewById(R.id.vertical_linear_layout);

String[] commands = GUIConfiguration.getSelectedCommandStrings();
Expand All @@ -101,8 +122,43 @@ public void onClick(final View v) {
btnProceed.setEnabled(false);
mProgressBar.setVisibility(View.VISIBLE);
GUIConfiguration.createPipeline();
showLogCatTask = new ShowLogCat();
showLogCatTask.executeOnExecutor(AsyncTask.THREAD_POOL_EXECUTOR);
new Thread(new Runnable() {
@Override
public void run() {
BufferedReader reader = null;
try {
reader = new BufferedReader(new FileReader(logPipePath));
while (true) {
String line = reader.readLine();
if (line == null) {
//wait until there is more of the file for us to read
try {
Thread.sleep(500);
} catch (InterruptedException e) {
e.printStackTrace();
}
} else {
if (line.equals(FILE_CLOSE_TAG)) {
break;
}
mHandler.post(new Runnable() {
@Override
public void run() {
txtLogs.append(line + "\n");
}
});
}
}
reader.close();
} catch (FileNotFoundException e) {
Log.e(TAG, "Pipe Not found: " + e);
} catch (IOException e) {
Log.e(TAG, "IO Exception: " + e);
} finally {
logPipeFile.delete();
}
}
}).start();
new RunPipeline().executeOnExecutor(AsyncTask.THREAD_POOL_EXECUTOR);
}
});
Expand Down Expand Up @@ -176,6 +232,7 @@ public class RunPipeline extends AsyncTask<String, Integer, String> {
@Override
protected void onPreExecute() {
super.onPreExecute();
NativeCommands.getNativeInstance().startPipeline(logPipePath);
isPipelineRunning = 1;
}

Expand All @@ -197,6 +254,7 @@ protected void onProgressUpdate(final Integer... values) {
@Override
protected void onPostExecute(final String s) {
super.onPostExecute(s);
NativeCommands.getNativeInstance().finishPipeline(logPipePath);
List<PipelineComponent> pipelineComponents = GUIConfiguration.getPipeline();
for (PipelineComponent pipelineComponent : pipelineComponents) {
TextView txtRuntime = new TextView(ConfirmationActivity.this);
Expand All @@ -216,100 +274,6 @@ protected void onPostExecute(final String s) {
}
}

public class ShowLogCat extends AsyncTask<Void, String, Void> {

BufferedReader bufferedReader;

InputStreamReader inputStreamReader;

Process process;

@Override
protected void onPreExecute() {
try {
process = Runtime.getRuntime().exec("logcat -c");
process = Runtime.getRuntime().exec("logcat");
inputStreamReader = new InputStreamReader(process.getInputStream());
bufferedReader = new BufferedReader(inputStreamReader);
} catch (IOException e) {
Log.e(TAG, "Error clearing logcat: " + e);
}
}

@Override
protected Void doInBackground(Void... params) {
try {

String line = "", filtered = "";

Pattern pattern = Pattern
.compile(TAG_F5C + "(.*)|" + TAG_MINIMAP2 + "(.*)|" + TAG_SAMTOOLS + "(.*)", 0);
Matcher matcher;

while ((line = bufferedReader.readLine()) != null) {

if (isCancelled()) {
break;
}

matcher = pattern.matcher(line);
if (!matcher.find()) {
continue;
}
// TODO find a better way to append all the matching groups
if (matcher.group(1) != null) {
filtered = TAG_F5C + matcher.group(1);
} else if (matcher.group(2) != null) {
filtered = TAG_MINIMAP2 + matcher.group(2);
} else if (matcher.group(3) != null) {
filtered = TAG_SAMTOOLS + matcher.group(3);
}
publishProgress(filtered);

}
} catch (IOException e) {
Log.e(TAG, "Error reading logcat: " + e);
}
return null;
}

@Override
protected void onProgressUpdate(String... values) {
txtLogs.append(values[0] + "\n");
scrollView.post(new Runnable() {
@Override
public void run() {
scrollView.fullScroll(View.FOCUS_DOWN);
}
});
}

@Override
protected void onPostExecute(final Void aVoid) {
super.onPostExecute(aVoid);
txtLogs.setText("");
try {
bufferedReader.close();
inputStreamReader.close();
} catch (IOException e) {
Log.e(TAG, "Error closing streams: " + e);
}
}

@Override
protected void onCancelled(final Void aVoid) {
super.onCancelled(aVoid);
txtLogs.setText("");
try {
bufferedReader.close();
inputStreamReader.close();
process.destroy();
} catch (IOException e) {
Log.e(TAG, "Error closing streams: " + e);
}
}
}

private void writeLogToFile() {

StringBuilder stringBuilder = new StringBuilder();
Expand Down Expand Up @@ -367,9 +331,6 @@ private void writeLogToFile() {
@Override
protected void onStop() {
super.onStop();
if (showLogCatTask != null) {
showLogCatTask.cancel(true);
}
}

@Override
Expand Down
4 changes: 4 additions & 0 deletions app/src/main/java/com/mobilegenomics/f5n/core/NativeCommands.java
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Expand Up @@ -20,6 +20,10 @@ public static NativeCommands getNativeInstance() {
return nativeCommands;
}

public native int startPipeline(String pipePath);

public native int finishPipeline(String pipePath);

public native int init(String command);

public native int initminimap2(String command);
Expand Down
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Binary file modified app/src/main/jniLibs/armeabi-v7a/libminimapshared.so
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