/src/egats/EGATSProcess.java
Java | 479 lines | 267 code | 50 blank | 162 comment | 30 complexity | 9443ac2a89610d55c827e2f72e605a63 MD5 | raw file
- package egats;
- import com.mongodb.BasicDBList;
- import com.mongodb.DBObject;
- import com.mongodb.util.JSON;
- import java.io.File;
- import java.lang.reflect.Method;
- /**
- * The verbs.
- *
- * @author Augie Hill - augie@umich.edu
- */
- public class EGATSProcess extends DataObject implements Runnable {
- public static final DataObjectCache<EGATSProcess> CACHE = new DataObjectCache<EGATSProcess>(Data.PROCESSES, EGATSProcess.class);
- public static final String STATUS_CREATED = "Created";
- public static final String STATUS_SUBMITTED = "Submitted";
- public static final String STATUS_RUNNING = "Running";
- public static final String STATUS_COMPLETED = "Completed";
- public static final String STATUS_FAILED = "Failed";
- // Transient variables are not serialized
- private transient Server server;
- private String status;
- private String exceptionMessage;
- private Long createTime;
- private Long startTime;
- private Long finishTime;
- private String name;
- private String methodPath;
- private String[] args = new String[0];
- private String outputID;
- /**
- *
- */
- @Override
- public final void run() {
- try {
- // Set up
- setStatus(STATUS_RUNNING);
- setStartTime(System.currentTimeMillis());
- save();
- // Checks
- if (methodPath == null) {
- throw new Exception("Method path is not set.");
- }
- if (args == null) {
- throw new Exception("Argument list is not set.");
- }
- // Is this a python script or a java method?
- if (server.getToolkit().containsPyScript(methodPath)) {
- // Check the args
- String[] mArgs = args;
- if (mArgs == null) {
- mArgs = new String[0];
- }
- // Replace requests for egats object file references
- String[] pyArgs = new String[mArgs.length];
- for (int i = 0; i < pyArgs.length; i++) {
- if (mArgs[i].startsWith("egats-obj-file:")) {
- EGATSObject o = EGATSObject.CACHE.get(mArgs[i].replaceFirst("egats-obj-file:", ""));
- EGATSObjectFile of = Data.GSON.fromJson(o.getObject(), EGATSObjectFile.class);
- File file = server.getWorkFileManager().getFile(o, of);
- pyArgs[i] = file.getAbsolutePath();
- } else {
- pyArgs[i] = mArgs[i];
- }
- }
- // Execute
- StringBuilder command = new StringBuilder();
- // To run python on Windows (which is what I'm running when I test)
- // command.append("C:/Windows/System32/cmd.exe /c C:/Python32/python.exe ");
- command.append("python ");
- command.append(server.getToolkit().getToolkitDirectoryPath());
- command.append(File.separator);
- command.append(methodPath);
- for (String arg : pyArgs) {
- command.append(" ");
- command.append(arg);
- }
- // Create an output buffer
- StringBuffer buffer = new StringBuffer();
- // Execute the command
- Process p = Runtime.getRuntime().exec(command.toString());
- // Stream the output amd error in to a buffer
- StreamToBufferThread outThread = new StreamToBufferThread(p.getInputStream(), buffer);
- StreamToBufferThread errThread = new StreamToBufferThread(p.getErrorStream(), buffer);
- outThread.start();
- errThread.start();
- // Wait on the script to complete execution (waitFor doesn't always work)
- boolean exited = false;
- while (!exited) {
- try {
- p.exitValue();
- exited = true;
- } catch (IllegalThreadStateException e) {
- Thread.sleep(1000);
- }
- }
- // Make sure the output and error has been written to the file
- outThread.join();
- errThread.join();
- // Create an EGATSObject from the output
- EGATSObject o = new EGATSObject();
- o.setClassPath(String.class.getName());
- o.setObject(buffer.toString());
- // Save it
- o.save();
- // Add it to the cache
- EGATSObject.CACHE.insert(o.getID(), o);
- // Save the ID of the output object
- setOutputID(o.getID().intern());
- } else {
- // Convert all '/' to '.'
- String cMethodPath = methodPath.replaceAll("/", ".").trim();
- String methodClassPath = cMethodPath;
- if (cMethodPath.lastIndexOf(".") >= 0) {
- methodClassPath = cMethodPath.substring(0, cMethodPath.lastIndexOf("."));
- }
- Class methodClass = server.getToolkit().getClass(methodClassPath);
- if (methodClass == null) {
- throw new Exception("Method class not found in toolkit: " + methodClassPath);
- }
- String methodName = cMethodPath.substring(cMethodPath.lastIndexOf(".") + 1);
- // Check the args
- String[] mArgs = args;
- if (mArgs == null) {
- mArgs = new String[0];
- }
- // Get the objects from the cache
- EGATSObject[] argEObjs = new EGATSObject[mArgs.length];
- for (int i = 0; i < mArgs.length; i++) {
- argEObjs[i] = EGATSObject.CACHE.get(mArgs[i]);
- if (argEObjs[i] == null) {
- throw new Exception("Could not find object with id \"" + mArgs[i] + "\".");
- }
- }
- // Generate objects
- Class[] argCObjs = new Class[argEObjs.length];
- Object[] argObjs = new Object[argEObjs.length];
- for (int i = 0; i < argEObjs.length; i++) {
- String classPath = argEObjs[i].getClassPath().replaceAll("/", ".").trim();
- argCObjs[i] = server.getToolkit().getClass(classPath);
- argObjs[i] = argCObjs[i].cast(Data.GSON.fromJson(argEObjs[i].getObject(), argCObjs[i]));
- }
- // Instantiate the method to be run
- Method method = methodClass.getMethod(methodName, argCObjs);
- if (method == null) {
- throw new Exception("Unknown method name and argument class combination.");
- }
- // Execute the static method (need to create a dummy instance even though it's a static method)
- Object output = method.invoke(methodClass.newInstance(), argObjs);
- // Create an EGATSObject from the output
- EGATSObject o = new EGATSObject();
- o.setClassPath(method.getReturnType().getName());
- o.setObject(Data.GSON.toJson(output));
- // Save it
- o.save();
- // Add it to the cache
- EGATSObject.CACHE.insert(o.getID(), o);
- // Save the ID of the output object
- setOutputID(o.getID().intern());
- }
- // All done
- setStatus(STATUS_COMPLETED);
- } catch (Exception e) {
- if (e instanceof NullPointerException) {
- setExceptionMessage("Null pointer encountered.");
- } else if (e instanceof NoSuchMethodException) {
- setExceptionMessage("No such method.");
- } else {
- setExceptionMessage(e.getMessage());
- }
- setStatus(STATUS_FAILED);
- } finally {
- setFinishTime(System.currentTimeMillis());
- }
- try {
- save();
- } catch (Exception e) {
- // Log
- // TODO
- }
- }
- /**
- *
- * @return
- */
- public final Server getServer() {
- return server;
- }
- /**
- *
- * @param server
- */
- public final void setServer(Server server) {
- this.server = server;
- }
- /**
- *
- * @return
- */
- public final String[] getArgs() {
- return args;
- }
- /**
- *
- * @param args
- */
- public final void setArgs(String[] args) {
- this.args = args;
- put("args", args);
- }
- /**
- *
- */
- public final Long getCreateTime() {
- return createTime;
- }
- /**
- *
- * @param time
- */
- private void setCreateTime(Long time) {
- this.createTime = time;
- put("createTime", time);
- }
- /**
- *
- * @return
- */
- public final String getExceptionMessage() {
- return exceptionMessage;
- }
- /**
- *
- * @param message
- */
- private void setExceptionMessage(String message) {
- this.exceptionMessage = message;
- put("exceptionMessage", message);
- }
- /**
- *
- * @return
- */
- public final Long getFinishTime() {
- return finishTime;
- }
- /**
- *
- * @param time
- */
- private void setFinishTime(Long time) {
- this.finishTime = time;
- put("finishTime", time);
- }
- /**
- *
- * @return
- */
- public final String getMethodPath() {
- return methodPath;
- }
- /**
- *
- * @param methodPath
- */
- public final void setMethodPath(String methodPath) {
- this.methodPath = methodPath;
- put("methodPath", methodPath);
- }
- /**
- *
- * @return
- */
- public final String getName() {
- return name;
- }
- /**
- *
- * @param name
- */
- public final void setName(String name) {
- this.name = name;
- put("name", name);
- }
- /**
- *
- * @return
- */
- public final String getOutputID() {
- return outputID;
- }
- /**
- *
- * @param outputID
- */
- private void setOutputID(String outputID) {
- this.outputID = outputID;
- put("outputID", outputID);
- }
- /**
- *
- * @return
- */
- public final Long getStartTime() {
- return startTime;
- }
- /**
- *
- * @param time
- */
- private void setStartTime(Long time) {
- this.startTime = time;
- put("startTime", time);
- }
- /**
- *
- * @return
- */
- public final String getStatus() {
- return status;
- }
- /**
- *
- * @param status
- */
- private void setStatus(String status) {
- this.status = status;
- put("status", status);
- }
- /**
- *
- * @throws Exception
- */
- protected final void save() throws Exception {
- Data.save(Data.PROCESSES, this);
- }
- /**
- *
- * @return
- */
- public final String getJSON() {
- return JSON.serialize(this);
- }
- /**
- *
- * @return
- */
- @Override
- public int hashCode() {
- return toString().hashCode();
- }
- /**
- *
- * @param o
- * @return
- */
- @Override
- public boolean equals(Object o) {
- if (!(o instanceof EGATSProcess)) {
- return false;
- }
- return toString().equals(((EGATSProcess) o).toString());
- }
- /**
- *
- * @return
- */
- @Override
- public String toString() {
- return getJSON();
- }
- /**
- *
- * @param json
- * @return
- * @throws Exception
- */
- public static EGATSProcess create(String json) throws Exception {
- // Read the DBObject (attributes must be set separately)
- EGATSProcess o = CACHE.convert((DBObject) JSON.parse(json));
- // Set the attributes the user can set
- o.setName(o.getString("name"));
- o.setMethodPath(o.getString("methodPath"));
- o.setArgs(((BasicDBList) o.get("args")).toArray(new String[0]));
- // Set everything the client can't set
- o.removeField(DataObject.ATTR_ID);
- o.setCreateTime(System.currentTimeMillis());
- o.removeField("outputID");
- o.setStatus(STATUS_CREATED);
- o.removeField("exceptionMessage");
- o.removeField("startTime");
- o.removeField("finishTime");
- // Create a new entry in the database
- o.save();
- // Add it to the cache now because it will probably be referenced soon
- CACHE.insert(o.getID(), o);
- return o;
- }
- /**
- *
- * @param json
- * @return
- * @throws Exception
- */
- public static EGATSProcess read(String json) throws Exception {
- return read((DBObject) JSON.parse(json));
- }
- /**
- *
- * @param dbo
- * @return
- * @throws Exception
- */
- public static EGATSProcess read(DBObject dbo) throws Exception {
- EGATSProcess o = CACHE.convert(dbo);
- o.setName(o.getString("name"));
- o.setMethodPath(o.getString("methodPath"));
- o.setArgs(((BasicDBList) o.get("args")).toArray(new String[0]));
- o.setCreateTime(o.getLong("createTime"));
- o.setOutputID(o.getString("outputID"));
- o.setStatus(o.getString("status"));
- o.setExceptionMessage(o.getString("exceptionMessage"));
- o.setStartTime(o.getLong("startTime"));
- if (o.containsField("finishTime")) {
- o.setFinishTime(o.getLong("finishTime"));
- }
- return o;
- }
- }