diff --git a/src/main/html/webapp/components/admin/settings/server/server.stache b/src/main/html/webapp/components/admin/settings/server/server.stache
index f681fe16..437f685d 100644
--- a/src/main/html/webapp/components/admin/settings/server/server.stache
+++ b/src/main/html/webapp/components/admin/settings/server/server.stache
@@ -95,7 +95,9 @@
{{else}}
{{name}}
- {{{error}}}
+
{{/enabled}}
diff --git a/src/main/java/cloudgene/mapred/plugins/docker/DockerBinary.java b/src/main/java/cloudgene/mapred/plugins/docker/DockerBinary.java
index 4f0f469f..04101742 100644
--- a/src/main/java/cloudgene/mapred/plugins/docker/DockerBinary.java
+++ b/src/main/java/cloudgene/mapred/plugins/docker/DockerBinary.java
@@ -38,12 +38,11 @@ public String getVersion() {
if (isInstalled()) {
String binary = getBinary();
Command command = new Command(binary, "version");
- command.saveStdOut(FileUtil.path("docker-version.txt"));
+ StringBuffer stdout = new StringBuffer();
+ command.writeStdout(stdout);
command.setSilent(true);
command.execute();
- String version = FileUtil.readFileAsString("docker-version.txt");
- FileUtil.deleteFile("docker-version.txt");
- return version;
+ return stdout.toString();
} else {
return "Docker not installed.";
}
diff --git a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java b/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java
index 85347d26..b32aca2e 100644
--- a/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java
+++ b/src/main/java/cloudgene/mapred/plugins/nextflow/NextflowBinary.java
@@ -63,12 +63,11 @@ public boolean isInstalled() {
public String getVersion() {
if (isInstalled()) {
Command command = new Command(binary, "info");
- command.saveStdOut(FileUtil.path("info-version.txt"));
+ StringBuffer stdout = new StringBuffer();
+ command.writeStdout(stdout);
command.setSilent(true);
command.execute();
- String version = FileUtil.readFileAsString("info-version.txt");
- FileUtil.deleteFile("info-version.txt");
- return version;
+ return stdout.toString();
} else {
return "Nextflow not installed.";
}
diff --git a/src/main/java/cloudgene/mapred/server/controller/ServerAdminController.java b/src/main/java/cloudgene/mapred/server/controller/ServerAdminController.java
index 005bebb8..1490ff63 100644
--- a/src/main/java/cloudgene/mapred/server/controller/ServerAdminController.java
+++ b/src/main/java/cloudgene/mapred/server/controller/ServerAdminController.java
@@ -14,6 +14,7 @@
import cloudgene.mapred.server.responses.ServerResponse;
import cloudgene.mapred.server.responses.StatisticsResponse;
import cloudgene.mapred.server.services.ServerService;
+import cloudgene.mapred.util.TextUtil;
import genepi.io.FileUtil;
import io.micronaut.core.annotation.Nullable;
import io.micronaut.http.MediaType;
@@ -88,8 +89,7 @@ public String getDetails() {
public String getLogs() {
File file = new File(LOG_FILENAME);
if (file.exists()) {
- String content = serverService.tail(file, 1000);
- return content;
+ return TextUtil.tail(file, 1000);
} else {
return "No log file available.";
}
diff --git a/src/main/java/cloudgene/mapred/server/services/ServerService.java b/src/main/java/cloudgene/mapred/server/services/ServerService.java
index 000dd2b4..f2f1af57 100644
--- a/src/main/java/cloudgene/mapred/server/services/ServerService.java
+++ b/src/main/java/cloudgene/mapred/server/services/ServerService.java
@@ -3,15 +3,12 @@
import java.io.File;
import java.io.IOException;
import java.net.URL;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
+import java.util.*;
import java.util.jar.Attributes;
import java.util.jar.Manifest;
import cloudgene.mapred.plugins.nextflow.NextflowPlugin;
+import cloudgene.mapred.util.command.Command;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.ObjectNode;
@@ -211,6 +208,34 @@ public String getClusterDetails() {
plugins.add(pluginObject);
}
+ //check user defined resources
+ for (Map resource: application.getSettings().getResources()){
+ String name = resource.get("name");
+ ObjectNode pluginObject = mapper.createObjectNode();
+ pluginObject.put("name", name);
+ if (!resource.containsKey("command")) {
+ pluginObject.put("error", "Command defined in resource '" + name + "'");
+ }
+ String cmd = resource.get("command");
+ String[] tiles = cmd.split(" ");
+ String[] params = Arrays.copyOfRange(tiles, 1, tiles.length);
+ Command command = new Command(tiles[0], params);
+ command.setSilent(true);
+ StringBuffer output = new StringBuffer();
+ StringBuffer error = new StringBuffer();
+ command.writeStdout(output);
+ command.writeStderr(error);
+ int exitCode = command.execute();
+ if (exitCode == 0) {
+ pluginObject.put("enabled", true);
+ pluginObject.put("details", output.toString());
+ }else {
+ pluginObject.put("enabled", false);
+ pluginObject.put("error", output.toString()+ "\n" + error.toString());
+ }
+ plugins.add(pluginObject);
+ }
+
// database
object.put("db_max_active", application.getDatabase().getDataSource().getMaxActive());
object.put("db_active", application.getDatabase().getDataSource().getNumActive());
@@ -222,53 +247,6 @@ public String getClusterDetails() {
return object.toString();
}
- public String tail(File file, int lines) {
- java.io.RandomAccessFile fileHandler = null;
- try {
- fileHandler = new java.io.RandomAccessFile(file, "r");
- long fileLength = fileHandler.length() - 1;
- StringBuilder sb = new StringBuilder();
- int line = 0;
-
- for (long filePointer = fileLength; filePointer != -1; filePointer--) {
- fileHandler.seek(filePointer);
- int readByte = fileHandler.readByte();
-
- if (readByte == 0xA) {
- line = line + 1;
- if (line == lines) {
- if (filePointer == fileLength) {
- continue;
- }
- break;
- }
- } else if (readByte == 0xD) {
- line = line + 1;
- if (line == lines) {
- if (filePointer == fileLength - 1) {
- continue;
- }
- break;
- }
- }
- sb.append((char) readByte);
- }
-
- String lastLine = sb.reverse().toString();
- return lastLine;
- } catch (java.io.IOException e) {
- log.error("Parsing log file failed.", e);
- return null;
- } finally {
- if (fileHandler != null)
- try {
- fileHandler.close();
- } catch (IOException e) {
- log.error("Parsing log file failed.", e);
- }
- }
- }
-
public void updateNextflowConfig(String content) {
NextflowPlugin plugin = (NextflowPlugin) PluginManager.getInstance().getPlugin(NextflowPlugin.ID);
String filename = plugin.getNextflowConfig();
diff --git a/src/main/java/cloudgene/mapred/util/Settings.java b/src/main/java/cloudgene/mapred/util/Settings.java
index d2520b6a..32da184e 100644
--- a/src/main/java/cloudgene/mapred/util/Settings.java
+++ b/src/main/java/cloudgene/mapred/util/Settings.java
@@ -48,6 +48,8 @@ public class Settings {
private List> errorHandlers = new Vector>();
+ private List> resources = new Vector<>();
+
private int autoRetireInterval = 5;
private int retireAfter = 6;
@@ -389,6 +391,14 @@ public List> getErrorHandlers() {
return errorHandlers;
}
+ public void setResources(List> resources) {
+ this.resources = resources;
+ }
+
+ public List> getResources() {
+ return resources;
+ }
+
public void setRepository(ApplicationRepository repository) {
this.repository = repository;
}
diff --git a/src/main/java/cloudgene/mapred/util/TextUtil.java b/src/main/java/cloudgene/mapred/util/TextUtil.java
new file mode 100644
index 00000000..38d45056
--- /dev/null
+++ b/src/main/java/cloudgene/mapred/util/TextUtil.java
@@ -0,0 +1,59 @@
+package cloudgene.mapred.util;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+
+public class TextUtil {
+
+ private static final Logger log = LoggerFactory.getLogger(TextUtil.class);
+
+ public static String tail(File file, int lines) {
+ java.io.RandomAccessFile fileHandler = null;
+ try {
+ fileHandler = new java.io.RandomAccessFile(file, "r");
+ long fileLength = fileHandler.length() - 1;
+ StringBuilder sb = new StringBuilder();
+ int line = 0;
+
+ for (long filePointer = fileLength; filePointer != -1; filePointer--) {
+ fileHandler.seek(filePointer);
+ int readByte = fileHandler.readByte();
+
+ if (readByte == 0xA) {
+ line = line + 1;
+ if (line == lines) {
+ if (filePointer == fileLength) {
+ continue;
+ }
+ break;
+ }
+ } else if (readByte == 0xD) {
+ line = line + 1;
+ if (line == lines) {
+ if (filePointer == fileLength - 1) {
+ continue;
+ }
+ break;
+ }
+ }
+ sb.append((char) readByte);
+ }
+
+ String lastLine = sb.reverse().toString();
+ return lastLine;
+ } catch (java.io.IOException e) {
+ log.error("Parsing log file failed.", e);
+ return null;
+ } finally {
+ if (fileHandler != null)
+ try {
+ fileHandler.close();
+ } catch (IOException e) {
+ log.error("Parsing log file failed.", e);
+ }
+ }
+ }
+}
diff --git a/src/main/java/cloudgene/mapred/util/command/Command.java b/src/main/java/cloudgene/mapred/util/command/Command.java
index 5d6df9e8..314b7842 100644
--- a/src/main/java/cloudgene/mapred/util/command/Command.java
+++ b/src/main/java/cloudgene/mapred/util/command/Command.java
@@ -3,9 +3,6 @@
import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
-
-import org.apache.commons.codec.digest.DigestUtils;
public class Command {
@@ -15,19 +12,15 @@ public class Command {
private boolean silent = false;
- private boolean deleteInput = false;
-
private String directory = null;
- private StringBuffer stout = new StringBuffer();
-
private String stdoutFileName = null;
private String stderrFileName = null;
- private List inputs = new Vector();
+ private StringBuffer stdout;
- private List outputs = new Vector();
+ private StringBuffer stderr;
public Command(String cmd, String... params) {
this.cmd = cmd;
@@ -38,7 +31,7 @@ public Command(String cmd) {
this.cmd = cmd;
}
- public void setParams(String... params) {
+ public void setArgs(String... params) {
this.params = params;
}
@@ -49,6 +42,15 @@ public void setParams(List params) {
}
}
+ public void writeStdout(StringBuffer stdout) {
+ this.stdout = stdout;
+ }
+
+ public void writeStderr(StringBuffer stderr) {
+ this.stderr = stderr;
+ }
+
+
public void saveStdOut(String filename) {
this.stdoutFileName = filename;
}
@@ -72,19 +74,20 @@ public int execute() {
try {
ProcessBuilder builder = new ProcessBuilder(command);
- // builder.redirectErrorStream(true);
+ // ensure it works on MacOS
+ builder.environment().put("PATH", builder.environment().get("PATH") + ":" + "/usr/local/bin/");
if (directory != null) {
builder.directory(new File(directory));
}
Process process = builder.start();
- CommandStreamHandler handler = new CommandStreamHandler(
- process.getInputStream(), stdoutFileName);
+ CommandStreamHandler handler = new CommandStreamHandler(process.getInputStream(), stdoutFileName);
+ handler.setStringBuffer(stdout);
handler.setSilent(silent);
Thread inputStreamHandler = new Thread(handler);
- CommandStreamHandler handler2 = new CommandStreamHandler(
- process.getErrorStream(), stderrFileName);
+ CommandStreamHandler handler2 = new CommandStreamHandler(process.getErrorStream(), stderrFileName);
+ handler2.setStringBuffer(stderr);
handler2.setSilent(silent);
Thread errorStreamHandler = new Thread(handler2);
@@ -104,11 +107,8 @@ public int execute() {
process.destroy();
}
- if (deleteInput) {
- new File(cmd).delete();
- }
-
return 0;
+
} catch (Exception e) {
e.printStackTrace();
return -1;
@@ -123,14 +123,6 @@ public void setSilent(boolean silent) {
this.silent = silent;
}
- public boolean isDeleteInput() {
- return deleteInput;
- }
-
- public void setDeleteInput(boolean deleteInput) {
- this.deleteInput = deleteInput;
- }
-
public void setDirectory(String directory) {
this.directory = directory;
}
@@ -150,43 +142,6 @@ public String toString() {
return result;
}
- public String getStdOut() {
- return stout.toString();
- }
-
- public void addInput(String input) {
- inputs.add(input);
- }
-
- public void addOutput(String output) {
- outputs.add(output);
- }
-
- public List getInputs() {
- return inputs;
- }
-
- public List getOutputs() {
- return outputs;
- }
-
- private boolean isNoFile(String param) {
- return !inputs.contains(param) && !outputs.contains(param);
- }
-
- public String getSignature() {
-
- String fullCommand = cmd;
- for (String param : params) {
- if (isNoFile(param)) {
- fullCommand += param;
- }
- }
-
- return DigestUtils.md5Hex(fullCommand);
-
- }
-
public String getName() {
return cmd;
}
diff --git a/src/main/java/cloudgene/mapred/util/command/CommandStreamHandler.java b/src/main/java/cloudgene/mapred/util/command/CommandStreamHandler.java
index 35e94811..7aae1ba3 100644
--- a/src/main/java/cloudgene/mapred/util/command/CommandStreamHandler.java
+++ b/src/main/java/cloudgene/mapred/util/command/CommandStreamHandler.java
@@ -1,25 +1,23 @@
package cloudgene.mapred.util.command;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
public class CommandStreamHandler implements Runnable {
- private InputStream is;
-
- //private StringBuffer stdout = new StringBuffer();;
+ private BufferedReader is;
private boolean silent = false;
private String filename = null;
+ private StringBuffer memory;
+
public CommandStreamHandler(InputStream is) {
- this.is = is;
+ this.is = new BufferedReader(new InputStreamReader(is));
}
public CommandStreamHandler(InputStream is, String filename) {
- this.is = is;
+ this.is = new BufferedReader(new InputStreamReader(is));
this.filename = filename;
}
@@ -27,6 +25,10 @@ public void setSilent(boolean silent) {
this.silent = silent;
}
+ public void setStringBuffer(StringBuffer memory) {
+ this.memory = memory;
+ }
+
public void setFilename(String filename) {
this.filename = filename;
}
@@ -37,24 +39,25 @@ public void run() {
try {
boolean save = (filename != null && !filename.isEmpty());
- FileOutputStream writer = null;
+ BufferedWriter writer = null;
byte[] buffer = new byte[200];
if (save) {
- writer = new FileOutputStream(filename);
+ writer = new BufferedWriter(new FileWriter(filename));
}
- int size = 0;
-
- while ((size = is.read(buffer)) > 0) {
- //stdout.append(line);
+ String line = null;
+ while ((line = is.readLine()) != null) {
+ if (memory != null) {
+ memory.append(line).append("\n");
+ }
if (!silent) {
- String line = new String(buffer, 0, size);
- System.out.println(line);
+ System.out.println(" > " + line);
}
if (save) {
- writer.write(buffer, 0, size);
+ writer.write(line);
+ writer.newLine();
}
}