/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package com.twentyn.bioreactor.pH;
import com.fasterxml.jackson.databind.Module;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.twentyn.bioreactor.util.Time;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import com.fasterxml.jackson.datatype.joda.JodaModule;
import org.joda.time.DateTime;
import com.twentyn.bioreactor.sensors.PHSensorData;
public class ControlSystem {
private static final Logger LOGGER = LogManager.getFormatterLogger(ControlSystem.class);
private static final String SENSOR_READING_FILE_LOCATION = "/tmp/sensors/v1/pH/reading.json";
private static final Double MARGIN_OF_ACCEPTANCE_IN_PH = 0.5;
private static final Integer WAIT_TIME = 20000;
private static final Integer PUMP_TIME_WAIT_IN_MILLI_SECONDS = 1000;
private static final Integer WAIT_TIME_BETWEEN_ACTION_IN_MILLI_SECONDS = 100;
private static final String OPTION_TARGET_PH = "p";
private static final String OPTION_SENSOR_READING_FILE_LOCATION = "s";
private static final String OPTION_CONTROL_SOLUTION = "c";
private static final String HELP_MESSAGE = "This class runs the control system of one fermentation run";
public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {{
add(Option.builder(OPTION_SENSOR_READING_FILE_LOCATION)
.argName("sensor reading file location")
.desc("The file location of sensor reading data")
.hasArg()
.longOpt("sensor-reading-file-location")
);
add(Option.builder(OPTION_TARGET_PH)
.argName("target ph")
.desc("The target pH of the system")
.hasArg().required()
.longOpt("target-ph")
);
add(Option.builder(OPTION_CONTROL_SOLUTION)
.argName("control solution")
.desc("The solution from which we can control the pH. The control solution can have two values: ACID or BASE.")
.hasArg().required()
.longOpt("control-solution")
);
add(Option.builder("h")
.argName("help")
.desc("Prints this help message")
.longOpt("help")
);
}};
public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();
static {
HELP_FORMATTER.setWidth(100);
}
public enum SOLUTION {
ACID,
BASE
}
private MotorPinConfiguration motorPinConfiguration;
private SOLUTION solution;
private Double targetPH;
private ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private File pHSensorDataFile;
public ControlSystem(MotorPinConfiguration initializedMotorPinConfiguration,
SOLUTION solution,
Double targetPH,
File pHSensorDataFile) {
this.motorPinConfiguration = initializedMotorPinConfiguration;
this.solution = solution;
this.targetPH = targetPH;
this.pHSensorDataFile = pHSensorDataFile;
}
public void registerModuleForObjectMapper(Module module) {
this.OBJECT_MAPPER.registerModule(module);
}
// TODO: Move this functionality to the sensor module in the future since the control system is not responsible
// for where the data is in a file or not.
private PHSensorData readPhSensorData(File sensorDataFile) throws IOException {
PHSensorData sensorData = OBJECT_MAPPER.readValue(sensorDataFile, PHSensorData.class);
return sensorData;
}
private void takeAction() throws InterruptedException {
LOGGER.info("Pump more solution");
this.motorPinConfiguration.switchMotorOn();
Thread.sleep(PUMP_TIME_WAIT_IN_MILLI_SECONDS);
LOGGER.info("Stop pumping");
this.motorPinConfiguration.switchMotorOff();
}
private Long timeDifference(DateTime longerTime, DateTime shorterTime) {
return longerTime.getMillis() - shorterTime.getMillis();
}
private void shutdownFermentation() {
this.motorPinConfiguration.shutdownFermentation();
}
private Boolean pHOutOfRange(Double phValue) {
return (phValue < this.targetPH - MARGIN_OF_ACCEPTANCE_IN_PH && this.solution.equals(SOLUTION.BASE)) ||
(phValue > this.targetPH + MARGIN_OF_ACCEPTANCE_IN_PH && this.solution.equals(SOLUTION.ACID));
}
private void run() throws InterruptedException {
DateTime lastTimeSinceDoseAdministered = Time.now();
DateTime currTime;
while (true) {
try {
Thread.sleep(WAIT_TIME_BETWEEN_ACTION_IN_MILLI_SECONDS);
currTime = Time.now();
Long timeDiff = timeDifference(currTime, lastTimeSinceDoseAdministered);
PHSensorData phSensorData = readPhSensorData(this.pHSensorDataFile);
Double phValue = phSensorData.getpH();
LOGGER.info("PH value is %d", phValue);
if (timeDiff <= WAIT_TIME || !pHOutOfRange(phValue)) {
continue;
}
takeAction();
LOGGER.info("Took action when pH was %d", phValue);
lastTimeSinceDoseAdministered = new DateTime();
} catch (IOException e) {
LOGGER.error("Could not read pH value due to IOException. Error is %s:", e.getMessage());
} catch (InterruptedException e) {
LOGGER.error("Could not read pH value due to InterruptedException. Error is %s:", e.getMessage());
}
}
}
public static void main(String[] args) throws Exception {
Options opts = new Options();
for (Option.Builder b : OPTION_BUILDERS) {
opts.addOption(b.build());
}
CommandLine cl = null;
try {
CommandLineParser parser = new DefaultParser();
cl = parser.parse(opts, args);
} catch (ParseException e) {
LOGGER.error(String.format("Argument parsing failed: %s\n", e.getMessage()));
HELP_FORMATTER.printHelp(ControlSystem.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
System.exit(1);
}
if (cl.hasOption("help")) {
HELP_FORMATTER.printHelp(ControlSystem.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
return;
}
SOLUTION solution = null;
String acidOrBase = cl.getOptionValue(OPTION_CONTROL_SOLUTION);
if (acidOrBase.equals(SOLUTION.ACID.name())) {
solution = SOLUTION.ACID;
}
if (acidOrBase.equals(SOLUTION.BASE.name())) {
solution = SOLUTION.BASE;
}
if (solution == null) {
LOGGER.error("Input solution is neither %s or %s", SOLUTION.ACID.name(), SOLUTION.BASE.name());
return;
}
Double targetPH = Double.parseDouble(cl.getOptionValue(OPTION_TARGET_PH));
File sensorReadingDataFile = new File(cl.getOptionValue(OPTION_SENSOR_READING_FILE_LOCATION, SENSOR_READING_FILE_LOCATION));
MotorPinConfiguration motorPinConfiguration = new MotorPinConfiguration(MotorPinConfiguration.PinNumberingScheme.BOARD);
motorPinConfiguration.initializeGPIOPinsAndSetConfigToStartState();
ControlSystem controlSystem = new ControlSystem(motorPinConfiguration, solution, targetPH, sensorReadingDataFile);
controlSystem.registerModuleForObjectMapper(new JodaModule());
try {
controlSystem.run();
} finally {
LOGGER.info("Shutting down");
controlSystem.shutdownFermentation();
}
}
}