Java tutorial
/************************************************************************* * * * 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(); } } }