/*
 * Copyright (c) 2003-2010 The Regents of the University of California.
 * All rights reserved.
 *
 * '$Author: crawl $'
 * '$Date: 2015-08-24 22:48:48 +0000 (Mon, 24 Aug 2015) $' 
 * '$Revision: 33634 $'
 * 
 * Permission is hereby granted, without written agreement and without
 * license or royalty fees, to use, copy, modify, and distribute this
 * software and its documentation for any purpose, provided that the above
 * copyright notice and the following two paragraphs appear in all copies
 * of this software.
 *
 * IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
 * FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
 * ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
 * THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 *
 * THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
 * PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
 * CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
 * ENHANCEMENTS, OR MODIFICATIONS.
 *
 */

//implements WmsdActor, which allows Kepler to control the wmsd system (in wmsd.jar at time of writing), which submits Encyclopedia of Life (EOL) tasks via APST system.
//EOL uses the Grid to predict 3D protein structures on entire genomes from homologous experimentally solved structures in support of rational drug design, ultimately in support of the pharmaceutical industry
//This extremely CPU-intensive process is considered "embarrassingly parallel" and thus an excellent application for the computational grid.
//Modeled protein structures are stored in an on-line, Internet accessible database.
//See more about the Encyclopedia of Life project at SDSC at http://eol.sdsc.edu

package org.eol;

import java.sql.Connection;
import java.util.ArrayList;

import org.geon.DBConnectionToken;

import edu.sdsc.eol.EolLog;
import edu.sdsc.eol.Wmsd;
import ptolemy.actor.TypedAtomicActor;
import ptolemy.actor.TypedIOPort;
import ptolemy.data.BooleanToken;
import ptolemy.data.StringToken;
import ptolemy.data.expr.FileParameter;
import ptolemy.data.expr.Parameter;
import ptolemy.data.expr.StringParameter;
import ptolemy.data.type.BaseType;
import ptolemy.kernel.CompositeEntity;
import ptolemy.kernel.util.IllegalActionException;
import ptolemy.kernel.util.NameDuplicationException;

/**
 * Description of the Class
 */
public class WmsdActor extends TypedAtomicActor {
        /**
         * Construct an actor with the given container and name.
         * 
         * @param container
         *            The container.
         * @param name
         *            The name of this actor.
         * @exception IllegalActionException
         *                If the actor cannot be contained by the proposed
         *                container.
         * @exception NameDuplicationException
         *                If the container already has an actor with this name.
         * @since
         */

        // inputs
        public TypedIOPort dbcon = new TypedIOPort(this, "dbcon", true, false); // wmsd

        // bookkeeping
        // database

        public TypedIOPort categoryDatabaseName = new TypedIOPort(this,
                        "categoryDatabaseName", true, false);

        public TypedIOPort sourceLabel = new TypedIOPort(this, "sourceLabel", true,
                        false);

        // outputs
        public TypedIOPort trigger = new TypedIOPort(this, "trigger", false, true);

        public TypedIOPort output_log = new TypedIOPort(this, "output_log", false,
                        true);

        public Parameter createDB = new Parameter(this, "CREATE_DB",
                        new BooleanToken(false));

        public Parameter init_apstd = new Parameter(this, "INIT_APSTD",
                        new BooleanToken(false));

        public Parameter dbPrefix = new StringParameter(this, "DB_PREFIX");

        public Parameter apstdHostColonPort = new StringParameter(this,
                        "APSTD_HOST_COLON_PORT");

        public FileParameter tmp_dir = new FileParameter(this, "TMP_DIR");

        public Parameter scp_user = new StringParameter(this, "SCP_USER");

        public Parameter scp_server = new StringParameter(this, "SCP_SERVER"); // Null

        // OK

        public Parameter scp_invoke_string = new StringParameter(this,
                        "SCP_INVOKE_STRING");

        public FileParameter resource_xml_file_name = new FileParameter(this,
                        "RESOURCE_XML_FILE_NAME");

        public FileParameter application_xml_file_name = new FileParameter(this,
                        "APPLICATION_XML_FILE_NAME");

        public Parameter enough_tasks = new Parameter(this, "ENOUGH_TASKS");

        public Parameter tasks_per_update = new Parameter(this, "TASKS_PER_UPDATE");

        // Until the DBconnect actor is fixed, when we won't need these anymore.
        public Parameter db_jdbc_connection_string = new StringParameter(this,
                        "DB_JDBC_CONNECTION_STRING");

        public Parameter db_username = new StringParameter(this, "DB_USERNAME");

        public Parameter db_password = new StringParameter(this, "DB_PASSWORD");

        private String DB_PREFIX;

        private String APSTD_HOST_COLON_PORT, TMP_DIR, SCP_USER, SCP_SERVER,
                        SCP_INVOKE_STRING;

        private String RESOURCE_XML_FILE_NAME, APPLICATION_XML_FILE_NAME,
                        TASKS_PER_UPDATE, ENOUGH_TASKS;

        // Only needed if DBconnection input isn't provided, which happened during
        // testing because DBconnection was broken, or at least configuration
        // was broken.

        private String DB_JDBC_CONNECTION_STRING, DB_USERNAME, DB_PASSWORD;

        public WmsdActor(CompositeEntity container, String name)
                        throws NameDuplicationException, IllegalActionException {

                super(container, name);

                // make these booleans radio buttons
                createDB.setTypeEquals(BaseType.BOOLEAN);
                attributeChanged(createDB);

                init_apstd.setTypeEquals(BaseType.BOOLEAN);
                attributeChanged(init_apstd);

                enough_tasks.setTypeEquals(BaseType.INT);
                attributeChanged(enough_tasks);

                tasks_per_update.setTypeEquals(BaseType.INT);
                attributeChanged(tasks_per_update);

                dbcon.setTypeEquals(DBConnectionToken.DBCONNECTION);

                categoryDatabaseName.setTypeEquals(BaseType.STRING);
                sourceLabel.setTypeEquals(BaseType.STRING);

                trigger.setTypeEquals(BaseType.STRING);
                output_log.setTypeEquals(BaseType.STRING);

        }

        /**
         * initialize
         * 
         * @throws IllegalActionException
         */
        public void initialize() throws IllegalActionException {
                // WGK: this is the way others do it, but one can imagine
                // an object that acts as an array encapsulating Parameter,
                // private String, and string descriptor, and a loop here.
                // More elegant, less verbose, less prone to bugs.

                DB_JDBC_CONNECTION_STRING = dequoteAndLog(db_jdbc_connection_string,
                                "DB_JDBC_CONNECTION_STRING");
                DB_USERNAME = dequoteAndLog(db_username, "DB_USERNAME");
                DB_PASSWORD = dequoteAndLog(db_password, "DB_PASSWORD");
                DB_PREFIX = dequoteAndLog(dbPrefix, "DB_PREFIX");
                APSTD_HOST_COLON_PORT = dequoteAndLog(apstdHostColonPort,
                                "APSTD_HOST_COLON_PORT");
                SCP_USER = dequoteAndLog(scp_user, "SCP_USER");
                SCP_SERVER = dequoteAndLog(scp_server, "SCP_SERVER");
                SCP_INVOKE_STRING = dequoteAndLog(scp_invoke_string,
                                "SCP_INVOKE_STRING");

                if (resource_xml_file_name.getToken() != null) {
                        RESOURCE_XML_FILE_NAME = resource_xml_file_name.asFile().toString();
                        writeLogLn("RESOURCE_XML_FILE_NAME: " + RESOURCE_XML_FILE_NAME);
                }

                if (application_xml_file_name.getToken() != null) {
                        APPLICATION_XML_FILE_NAME = application_xml_file_name.asFile()
                                        .toString();
                        writeLogLn("APPLICATION_XML_FILE_NAME: "
                                        + APPLICATION_XML_FILE_NAME);
                }

                if (tmp_dir.getToken() != null) {
                        TMP_DIR = tmp_dir.asFile().toString();
                        writeLogLn("TMP_DIR: " + TMP_DIR);
                }

                if (enough_tasks.getToken() != null) {
                        // Integer type.
                        ENOUGH_TASKS = enough_tasks.getToken().toString();
                        writeLogLn("ENOUGH_TASKS: " + ENOUGH_TASKS);
                }

                if (tasks_per_update.getToken() != null) {
                        // Integer type.
                        TASKS_PER_UPDATE = tasks_per_update.getToken().toString();
                        writeLogLn("TASKS_PER_UPDATE: " + TASKS_PER_UPDATE);
                }

                if (DB_PREFIX == null || TMP_DIR == null || SCP_USER == null
                                || RESOURCE_XML_FILE_NAME == null
                                || APPLICATION_XML_FILE_NAME == null
                                || SCP_INVOKE_STRING == null || APSTD_HOST_COLON_PORT == null) {
                        throw new IllegalActionException(
                                        "The parameters CREATE_DB, DB_PREFIX, APSTD_HOST_COLON_PORT "
                                                        + "TMP_DIR, SCP_USER, SCP_INVOKE_STRING, INIT_APSTD must have valid values.  CREATE_DB specifies whether to create bookkeeping database tables must be TRUE or FALSE."
                                                        + "DB_PREFIX gives the wmsd bookkeeping database table prefixes."
                                                        + "APST_HOST_COLON_PORT is gives the host and port (separated by a colon)"
                                                        + "where an apstd is listening. (Typically localhost:6660). SCP_INVOKE_STRING provides the local path and command arguments (e.g. identity file) that will be used to start scp. SCP_USER gives the username to be used to scp/ssh login on the apstd host. SCP_SERVER, optional, gives the SCP server when it is different from the apstd connection (due to, say, ssh port forwarding as a result of a firewall.) INIT_APSTD must be TRUE or FALSE, and specifies whether to clear the Apstd and load in the resource file. TMP_DIR gives the name of a temporary directory on the local machine (required)."
                                                        + "RESOURCE_XML_FILE_NAME must be set to the local location of the XML computation resources file in APSTD format. APPLICATION_XML_FILE_NAME species in the XML file (in WMSD pseudo-Apstd task format) that gives the per-protein and per-genome tasks to be submitted, with variable substitution. ENOUGH_TASKS (optional) specifies the maximum number of tasks apst is allowed to run at any given time --- set larger than cpus in the cluster. TASKS_PER_UPDATE (optional) specifies the max submitted to apstd at any given time. Please provide these values and re-execute.");
                }

        }

        /**
         * @return Description of the Returned Value
         * @exception IllegalActionException
         *                Description of Exception
         * @since
         */
        public boolean prefire() throws IllegalActionException {
                return super.prefire();
        }

        /**
         * Send a random number with a uniform distribution to the output. This
         * number is only changed in the prefire() method, so it will remain
         * constant throughout an iteration.
         * 
         * @exception IllegalActionException
         *                If there is no director.
         * @since
         */
        public void fire() throws IllegalActionException {
                writeLogLn("firing Wmsd Actor");
                super.fire();

                // convert inputs to string types

                String categoryDatabaseNameStr = ((StringToken) categoryDatabaseName
                                .get(0)).stringValue();
                String sourceLabelStr = ((StringToken) sourceLabel.get(0))
                                .stringValue();

                ArrayList atemp = new ArrayList();

                // String createDbOption = "--create_db";

                String[] argsTemp = { "--resources", RESOURCE_XML_FILE_NAME,
                                "--applications", APPLICATION_XML_FILE_NAME, "--apstcontact",
                                APSTD_HOST_COLON_PORT, "--category", categoryDatabaseNameStr,
                                "--source", sourceLabelStr, "--dbprefix", DB_PREFIX,
                                "--tmpdir", TMP_DIR, "--scp_user", SCP_USER,
                                "--scp_invoke_string", SCP_INVOKE_STRING, };
                // convert to ArrayList because Java doesn't support dynamic array sizes
                for (int i = 0; i < argsTemp.length; i++) {
                        atemp.add(argsTemp[i]);
                }

                if (((BooleanToken) createDB.getToken()).booleanValue() == true) {
                        // we've already tested that this is either true or false.
                        // if it is true, the default value above is used.
                        atemp.add("--create_db");
                }

                if (((BooleanToken) init_apstd.getToken()).booleanValue() == true) {
                        // we've already tested that this is either true or false.
                        // if it is true, the default value above is used.
                        atemp.add("--init_apstd");
                }

                if (SCP_SERVER != null && !SCP_SERVER.equals("")) {
                        atemp.add("--scp_server");
                        atemp.add(SCP_SERVER);
                }

                if (ENOUGH_TASKS != null) {
                        ENOUGH_TASKS = (new Integer(ENOUGH_TASKS)).toString(); // make sure
                        // integer
                        // value.
                        atemp.add("--enough_tasks");
                        atemp.add(ENOUGH_TASKS);
                }

                if (TASKS_PER_UPDATE != null) {
                        TASKS_PER_UPDATE = (new Integer(TASKS_PER_UPDATE)).toString(); // make
                        // sure
                        // integer
                        // value.
                        atemp.add("--tasks_per_update");
                        atemp.add(TASKS_PER_UPDATE);
                }

                try {
                        Wmsd wm = null;
                        if (dbcon.numberOfSources() > 0 && dbcon.hasToken(0)) {
                                String[] args = (String[]) atemp.toArray(new String[atemp
                                                .size()]);

                                DBConnectionToken _dbcon = (DBConnectionToken) dbcon.get(0);
                                Connection _con;
                                try {
                                        _con = _dbcon.getValue();

                                } catch (Exception e) {
                                        throw new IllegalActionException(this, e,
                                                        "CONNECTION FAILURE");
                                }

                                wm = new Wmsd(args, _con);

                        } else {
                                // DB connect broken, user putting in db parameters manually.
                                // :-(
                                // this stuff will be eliminated once DBconnect actor is again
                                // working reliably.

                                if (DB_JDBC_CONNECTION_STRING == null || DB_USERNAME == null
                                                || DB_PASSWORD == null) {
                                        throw new IllegalActionException(
                                                        "In the absence of an DBconnect input, DB_JDBC_CONNECTION_STRING, DB_USERNAME, DB_PASSWORD must not be null but provide the db connection parameters for the Wmsd bookkeeping database.");
                                }
                                atemp.add("--dbhost");
                                atemp.add(DB_JDBC_CONNECTION_STRING);
                                atemp.add("--dbuser");
                                atemp.add(DB_USERNAME);
                                atemp.add("--dbpassword");
                                atemp.add(DB_PASSWORD);

                                String[] args = (String[]) atemp.toArray(new String[atemp
                                                .size()]);
                                wm = new Wmsd(args);
                        }
                        wm.run();

                } catch (Exception e) {
                        e.printStackTrace();
                        throw new IllegalActionException("Unexpected error: "
                                        + e.getMessage());
                }

                copyToLog(EolLog.getAndClearOutData());
                broadcastToLog();

                trigger.broadcast(new StringToken(categoryDatabaseNameStr));
                writeLogLn("Wmsd Actor done");

        }

        private void writeLogLn(String msg) {
                System.out.println(msg);
                copyToLog(msg + "\n");
        }

        private String logString = null;

        private void copyToLog(String msg) {
                if (logString == null) {
                        logString = new String();
                }
                logString += msg;
        }

        private void broadcastToLog() {
                if (logString != null) {
                        try {
                                output_log.broadcast(new StringToken(logString));
                        } catch (IllegalActionException e) {
                                e.printStackTrace();
                        }
                }
        }

        private String dequote(String mystring) {
                return (mystring.substring(1, mystring.length() - 1));
        }

        private String dequoteAndLog(String mystring, String name) {
                mystring = dequote(mystring);
                writeLogLn(name + ": " + mystring);
                return (mystring);
        }

        private String dequoteAndLog(Parameter myparm, String name)
                        throws IllegalActionException {
                if (myparm.getToken() != null) {
                        // only fix and print if not equal to null.
                        String mystring = ((StringToken) myparm.getToken()).toString();
                        return (dequoteAndLog(mystring, name));
                }
                return (null);
        }

}