V3_0.java [src/java/m/ghg/daycent] Revision: default Date:
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package m.ghg.daycent;
import csip.Config;
import csip.api.server.Executable;
import csip.ModelDataService;
import csip.api.client.ModelDataServiceCall;
import csip.api.server.ServiceException;
import csip.SessionLogger;
import csip.annotations.Description;
import csip.annotations.Name;
import csip.annotations.Options;
import csip.annotations.Resource;
import csip.utils.Parallel;
import csip.utils.TextParser;
import gisobjects.GISObject;
import gisobjects.GISObjectFactory;
import gisobjects.db.GISEngineFactory;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.StandardCopyOption;
import java.sql.Connection;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
import java.util.logging.Level;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.ws.rs.Path;
import m.ghg.ApplicationResources;
import static m.ghg.ApplicationResources.*;
import static m.ghg.daycent.V2_1.yieldConv;
import oms3.ObjectiveFunction;
import org.apache.commons.io.input.ReversedLinesFileReader;
import org.apache.velocity.Template;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.VelocityEngine;
import org.apache.velocity.runtime.RuntimeConstants;
import org.codehaus.jettison.json.JSONArray;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import util.CRLMODData;
import util.DateConversion;
import util.DayCentData;
import util.ObjFuncs.*;
import util.ObjFuncs.PBIAS;
import util.ServiceUtils;
import util.WeatherStatistics;
/**
*
* @author sidereus, od
*/
@Name("Daycent simulation execution")
@Description("Daycent CSIP service")
//@Path("m/daycent/3.0")
@Options(timeout = "P1H")
@Resource(from = ApplicationResources.class)
public class V3_0 extends ModelDataService {
private final WeatherStatistics ws = new WeatherStatistics();
protected String schedule;
protected String schedule_IC;
protected boolean fileAsJSON;
protected String aoaId;
protected JSONObject aoa_geometry;
protected double[] latlon = {Double.NaN, Double.NaN};
protected int weatherDuration;
protected int startingYear;
protected boolean useClimateWind;
protected double nlayer;
protected List<Double> profileDepths;
// slice by time (start and end) and convert it
protected JSONObject rotation;
protected List<Integer> crop_id;
protected Collection<String> JSONparams;
protected Integer cokey;
protected Double area;
protected Integer yearPractChange;
protected Integer staticYearPractChange = 2011;
protected Integer endPractChange;
protected int colGracc = 0;
protected int colAbove = 0;
protected int colBelow = 0;
protected int colSOM = 0;
protected CRLMODData crlmod;
protected DayCentData dayCentData;
@Override
protected void preProcess() throws ServiceException {
schedule = parameter().getString(SCHEDULE_FILE);
schedule_IC = parameter().getString(SCHEDULE_FILE_IC, "");
useClimateWind = parameter().getBoolean(USE_CLIMATE_WIND, false);
fileAsJSON = parameter().getBoolean(STREAM_FILE, false);
weatherDuration = parameter().getInt(WEATHER_DURATION_TXT);
startingYear = parameter().getInt(STARTING_YEAR_TXT);
schedule = ServiceUtils.checkRemoveExtension(schedule);
aoa_geometry = parameter().getJSON(soils.AoA.AOA_GEOMETRY);
cokey = parameter().getInt(soils.db.tables.TableComponent.COKEY);
area = parameter().getDouble("area");
yearPractChange = parameter().getInt("yearPractChange");
endPractChange = parameter().getInt("endPractChange", 2020);
JSONparams = parameter().getNames();
crlmod = new CRLMODData(parameter().getJSON("crlmod"));
dayCentData = new DayCentData(parameter().getNames(), parameter());
}
@Override
protected void doProcess() throws Exception {
// Get centroid of shape, if it is not a point already. (If it's a point, the centroid is the point)
try (Connection conn = resources().getJDBC(GISDB_SQLSVR)) {
GISObject shape = GISObjectFactory.createGISObject(aoa_geometry, GISEngineFactory.createGISEngine(conn));
// getLat/Lon functions get point value or the centroid of the shape.
latlon[0] = shape.getLatitude();
latlon[1] = shape.getLongitude();
}
String sourcePath = workspace().getFile("fix.100").getAbsolutePath();
String destPath = workspace().getDir().getAbsolutePath()
.concat(File.separator).concat("fix_2.100");
File sourceTemplate = new File(sourcePath);
File destTemplate = new File(destPath);
Files.copy(sourceTemplate.toPath(), destTemplate.toPath());
Parallel.run(Config.getBoolean("ghg.serial.datafetch", false),
() -> {
fetchClimate();
computeWeatherStats();
},
() -> {
fetchSoil();
countLayers(); // testing if we need the fix structure in Black et al. 2017
}
);
dayCentData.preRunFixes();
// RENAME PRE-AG SCH
java.nio.file.Path source = workspace().getFile("pa_Truterra.sch").toPath();
Files.move(source, source.resolveSibling("Truterra.sch"), StandardCopyOption.REPLACE_EXISTING);
createConfig("crop.100");
createConfig(getSite100());
createConfig("fix.100"); // values from payload _pa
runDaycent();
runDaycentList();
source = workspace().getFile("Truterra.sch").toPath();
Files.move(source, source.resolveSibling("Truterra_pa.sch"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceBin = workspace().getFile("Truterra.bin").toPath();
Files.move(sourceBin, sourceBin.resolveSibling("Truterra_pa.bin"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceFix = workspace().getFile("fix.100").toPath();
Files.move(sourceFix, sourceFix.resolveSibling("fix_pa.100"), StandardCopyOption.REPLACE_EXISTING);
sourceFix = workspace().getFile("fix_2.100").toPath();
Files.move(sourceFix, sourceFix.resolveSibling("fix.100"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceLis = workspace().getFile("Truterra.lis").toPath();
Files.move(sourceLis, sourceLis.resolveSibling("Truterra_pa.lis"), StandardCopyOption.REPLACE_EXISTING);
Files.delete(workspace().getFile("year_summary.out").toPath());
dayCentData.postRunFixes();
// RENAME AG SCH
source = workspace().getFile("ag_Truterra.sch").toPath();
Files.move(source, source.resolveSibling("Truterra.sch"), StandardCopyOption.REPLACE_EXISTING);
createConfig("fix.100"); // values from payload _ag
schedule_IC = "Truterra_pa.bin";
runDaycent();
runDaycentList();
// checkHarvest();
}
@Override
protected void postProcess() throws Exception {
List<String> l = getRequestedObjfunc();
if (l.isEmpty()) {
parseLis();
} else {
calibrate(l);
}
}
protected String getSite100() throws IOException {
String scheduleWithExtension = schedule + ".sch";
return new TextParser(workspace().getFile(scheduleWithExtension))
.toLineContaining(".100")
.tokens().asStringArray()[0];
}
protected List<String> parseOutfile() throws IOException {
try (Stream<String> stream = workspace().lines("outfiles.in")) {
return stream
.filter(l -> l.startsWith("1"))
.map(l -> l.split("\\s+")[1])
.collect(Collectors.toList());
}
}
// because templates are currently inputs
private File renameInputTemplate(String template) throws IOException {
String sourcePath = workspace().getFile(template).getAbsolutePath();
String destPath = workspace().getDir().getAbsolutePath()
.concat(File.separator).concat(TMP100);
File sourceTemplate = new File(sourcePath);
File destTemplate = new File(destPath);
Files.copy(sourceTemplate.toPath(), destTemplate.toPath());
//Why? If copy suceeded, then they are equal.
if (!Files.readAllLines(sourceTemplate.toPath()).equals(Files.readAllLines(destTemplate.toPath()))) {
throw new IOException("File not fully copied");
} else {
Files.delete(sourceTemplate.toPath());
}
return sourceTemplate;
}
private void cleanUpWorkspace() throws IOException {
Files.delete(workspace().getFile(TMP100).toPath());
}
protected void createConfig(String template) throws IOException {
VelocityEngine velocity = new VelocityEngine();
velocityInit(velocity);
VelocityContext context = new VelocityContext();
context.put(DAYCENT.toLowerCase(), this);
File filledTemplate = renameInputTemplate(template);
try (FileWriter w = new FileWriter(filledTemplate.getAbsolutePath())) {
Template vt = velocity.getTemplate(TMP100, "utf-8");
vt.merge(context, w);
}
cleanUpWorkspace();
}
public void velocityInit(VelocityEngine velocity) {
velocity.setProperty(RuntimeConstants.FILE_RESOURCE_LOADER_PATH,
workspace().getDir().getAbsolutePath());
velocity.init();
}
private void throwError(int ret, Executable exe) throws IOException, ServiceException {
File stderr = exe.stderr();
File stdout = exe.stdout();
String err = "ret: " + ret + "\n";
if (stderr.exists() && stderr.length() > 0) {
err = err + "stderr: \n" + workspace().readString(stderr.getName());
}
if (stdout.exists() && stdout.length() > 0) {
String out = "";
ReversedLinesFileReader r = new ReversedLinesFileReader(stdout, Charset.forName("UTF-8"));
for (int i = 0; i < 20; i++) {
String l = r.readLine();
if (l == null) {
break;
}
out = l + '\n' + out;
}
r.close();
err = err + "stdout (last 10 lines): ...\n" + out;
}
throw new ServiceException("Error running " + exe.getName() + ": " + err);
}
private Executable buildExe(Executable exe) {
exe.addArguments(
"-s", schedule,
"-n", schedule
);
return exe;
}
private Executable buildExeIC(Executable exe) {
schedule_IC = ServiceUtils.checkRemoveExtension(schedule_IC);
exe.addArguments(
"-s", schedule,
"-n", schedule,
"-e", schedule_IC
);
return exe;
}
protected boolean simulationFailure(Executable exe) throws IOException {
try (Stream<String> stream = workspace().lines(exe.stderr())) {
return stream
.filter(l -> l.toLowerCase().contains("execution success"))
.collect(Collectors.toList())
.isEmpty();
}
}
protected boolean lisFailure(Executable exe) throws IOException {
try (Stream<String> stream = workspace().lines(exe.stdout())) {
return stream
.filter(l -> l.contains("Done."))
.collect(Collectors.toList())
.isEmpty();
}
}
protected void runDaycent() throws ServiceException, IOException {
Executable exe = resources().getExe(DAYCENT);
exe = (schedule_IC.isEmpty()) ? buildExe(exe) : buildExeIC(exe);
int ret = exe.exec();
if (ret != 0 || simulationFailure(exe)) {
throwError(ret, exe);
}
}
protected void runDaycentList() throws ServiceException, IOException {
Executable exe = resources().getExe(DAYCENT_LIST);
exe.addArguments(
schedule,
schedule,
"outvars.txt"
);
int ret = exe.exec();
if (ret != 0 || lisFailure(exe)) {
throwError(ret, exe);
}
}
protected void computeWeatherStats() throws IOException, Exception {
try (Stream<String> stream = workspace().lines(DAYCENT_WEATHER)) {
ws.compute(stream);
}
}
protected void fetchClimate() throws Exception {
ModelDataServiceCall mds = new ModelDataServiceCall()
.put(STARTING_YEAR_TXT, startingYear)
.put(WEATHER_DURATION_TXT, weatherDuration)
.put(STREAM_FILE, fileAsJSON)
.put(USE_CLIMATE_WIND, useClimateWind)
.put(soils.AoA.AOA_GEOMETRY, new JSONObject()
.put(TYPE, aoa_geometry.get(TYPE))
.put(COORDINATES, aoa_geometry.get(COORDINATES)))
.url(Config.getString(WEATHER_URL_KEY,
request().getCodebase() + "d/weather/cligen/1.0"))
.call();
if (mds.serviceFinished()) {
mds.download(DAYCENT_WEATHER, workspace().getFile(DAYCENT_WEATHER));
} else {
throw new ServiceException("GHG Weather service error: " + mds.getError());
}
}
//////////// Calibration
void calibrate(List<String> l) throws Exception {
for (String ofName : l) {
// 2 values
String[] data = parameter().getStringArray(ofName);
if (data.length != 2) {
throw new ServiceException("Invalid of content, 2 elements expected");
}
// data[0] : calibration target (e.g. yield)
// data[1] : calibration details (startyear/endyear)
double v = calcObjFunc(LOG,
workspace().getFile("Truterra.sch"),
workspace().getFile("Truterra.lis"),
data[0], data[1]);
results().put(ofName, v);
}
}
static double getAvg(SessionLogger LOG, File schFile, File lisFile, String column,
int starty, int endy, String croptype, String termination) throws Exception {
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, String> c = ServiceUtils.getMapFor(lisFile, column);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("caggr : " + c);
}
// lisDates of harvest from schedule file
List<String> harvestDates = getDates(LOG, starty, endy, schFile, croptype, termination);
// extract the values based on keys (harvest dates) into columnVals
List<String> columnVals = new ArrayList<>();
for (String harvestDate : harvestDates) {
String caggr = c.get(harvestDate);
if (caggr == null) {
throw new ServiceException("No caggr value for harvestDate: " + harvestDate);
}
columnVals.add(c.get(harvestDate));
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("columnVals " + columnVals);
}
// create the average of those values
double avg = columnVals.stream().mapToDouble(Double::parseDouble).average().getAsDouble();
if (LOG.isLoggable(Level.INFO)) {
LOG.info("avg: " + avg);
}
return avg;
}
public static boolean isLeapYear(int year) {
Calendar cal = Calendar.getInstance();
cal.set(Calendar.YEAR, year);
return cal.getActualMaximum(Calendar.DAY_OF_YEAR) > 365;
}
static double getVal(SessionLogger LOG, File schFile, File lisFile, String column,
int year) throws Exception {
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, String> c = ServiceUtils.getMapFor(lisFile, column);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("caggr : " + c);
}
String tdate;
if (isLeapYear(year)) {
tdate = String.valueOf(year) + ".366";
} else {
tdate = String.valueOf(year) + ".365";
}
String date = DateConversion.date2daycentLis(tdate);
// extract the values based on keys (harvest dates) into columnVals
String somsc = c.get(date);
if (somsc == null) {
throw new ServiceException("No somsc value for year: " + year);
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("somsc " + somsc);
}
return Double.parseDouble(somsc);
}
static List<String> getDates(SessionLogger LOG, int starty, int endy,
File schFile, String croptype, String termination) throws IOException {
List<String> schDates = ServiceUtils.getCropHarvest(schFile, croptype, termination);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("schDates: " + schDates);
}
List<String> filtered_schDates = new ArrayList<>();
// filter by date range (starty - endy)
for (String schDate : schDates) {
String[] sd = schDate.split("\\.");
int y = Integer.parseInt(sd[0]);
if (y >= starty && y <= endy) {
filtered_schDates.add(schDate);
}
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("Filtered dates: " + filtered_schDates);
}
// convert all schDates to lisDates
List<String> lisDates = new ArrayList<>();
for (String schDate : filtered_schDates) {
lisDates.add(DateConversion.date2daycentLis(schDate));
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("lisDates: " + lisDates);
}
return lisDates;
}
public static void main(String[] args) throws Exception {
calcObjFunc(new SessionLogger(),
new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.sch"),
new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.lis"),
"yield", "50.9, 1935, 1960, SYBN1");
calcObjFunc(new SessionLogger(),
new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.sch"),
new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.lis"),
"soc", "50.9, 2019");
calcObjFunc(new SessionLogger(),
new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.sch"),
new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.lis"),
"biomass", "120, 2011, 2020, CC2");
}
static double calcObjFunc(SessionLogger LOG, File schFile, File lisFile,
String target, String targetInfo) throws Exception {
if (target.equals("yield")) {
String[] ti = targetInfo.split("\\s*,\\s*");
if (ti.length != 4) {
throw new ServiceException("Invalid targetinfo for yield.");
}
String obsValStr = ti[0]; // obs data value for period
String start = ti[1]; // start
String end = ti[2]; // end
String ct = ti[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double obsVal = Double.parseDouble(obsValStr);
// simulated yield
double simVal = getAvg(LOG, schFile, lisFile,
"cgracc", Integer.parseInt(start), Integer.parseInt(end), ct, "HARV");
Double conv = yieldConv.get(ct);
if (conv == null) {
throw new ServiceException("No yield conversion factor for: " + ct);
}
simVal = simVal * conv;
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim yield: " + simVal);
}
return obsVal - simVal;
} else if (target.equals("biomass")) {
String[] ti = targetInfo.split("\\s*,\\s*");
if (ti.length != 4) {
throw new ServiceException("Invalid targetinfo for yield.");
}
String obsValStr = ti[0]; // obs data value for period
String start = ti[1]; // start
String end = ti[2]; // end
String ct = ti[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double obsVal = Double.parseDouble(obsValStr);
// simulated yield
double simVal = getAvg(LOG, schFile, lisFile,
"agcacc", Integer.parseInt(start), Integer.parseInt(end), ct, "HERB");
//
// Double conv = yieldConv.get(ct);
// if (conv == null) {
// throw new ServiceException("No yield conversion factor for: " + ct);
// }
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim biomass: " + simVal);
}
return obsVal - simVal;
} else if (target.equals("soc")) {
String[] ti = targetInfo.split("\\s*,\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for yield.");
}
String obsValStr = ti[0]; // obs data value for period
String year = ti[1]; // year
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double simVal = getVal(LOG, schFile, lisFile,
"somsc", Integer.parseInt(year));
double obsVal = Double.parseDouble(obsValStr);
return obsVal - simVal;
} else {
throw new Exception("calibration target not supported: " + target);
}
}
static final Map<String, ObjectiveFunction> OF = new HashMap<>();
static {
// OF.put("kge", new KGE());
// OF.put("ns", new NS());
// OF.put("nslog", new NS2LOG());
// OF.put("nslog1p", new NSLOG1P());
// OF.put("nslog2", new NSLOG2());
// OF.put("rmse", new RMSE());
// OF.put("trmse", new TRMSE());
OF.put("pbias", new PBIAS());
}
private List<String> getRequestedObjfunc() {
List<String> l = new ArrayList<>();
for (String p : parameter().getNames()) {
if (p.toLowerCase().startsWith("pbias.")) {
l.add(p);
}
}
return l;
}
/////////////////////
protected void parseLis() throws FileNotFoundException, JSONException {
List<Integer> practiceChange = new LinkedList<>();
// adjusted to get
for (int i = staticYearPractChange; i <= endPractChange; i++) {
practiceChange.add(i);
}
String filename = schedule + ".lis";
int lineNumber = 1;
int colTime = 0;
boolean skiplastline = Boolean.FALSE;
try (Scanner scanner = new Scanner(workspace().getFile(filename));) {
String[] prevData = null;
Integer yearNewMgt = practiceChange.remove(0); // first element always
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
double prevCgain = 0;
if (lineNumber == 1) {
// read header
String[] data = line.split("\\s+");
for (int col = 0; col < data.length; col++) {
if (data[col].equals("cgracc")) {
colGracc = col;
} else if (data[col].equals("agcprd")) {
colAbove = col;
} else if (data[col].equals("bgcjprd")) {
colBelow = col;
} else if (data[col].equals("somsc")) {
colSOM = col;
} else if (data[col].equals("time")) {
colTime = col;
}
}
} else if (lineNumber == 2) {
// skip line because empty
} else {
// check the line
String[] data = line.split("\\s+");
double year = Double.parseDouble(data[colTime]);
if (prevData == null && year == (yearNewMgt + MODEL_OFFSET)) {
prevData = data;
}
if (!skiplastline) {
// +2000 because 4000 years of simulation
// +1 because of extra year - December 2012 = 2013.00 from Daycent .lis file
if (year == (yearNewMgt + MODEL_OFFSET + 1)) {
double som = Double.parseDouble(prevData[colSOM]);
prevCgain = som * 0.00404686 * area;
Integer actYear = yearNewMgt;
results().put(actYear.toString(), getValues(data, prevCgain));
prevData = data;
// last year is duplicated and need to skip it
if (!practiceChange.isEmpty()) {
yearNewMgt = practiceChange.remove(0);
} else {
skiplastline = Boolean.TRUE;
}
}
}
}
lineNumber++;
}
}
}
private JSONArray getValues(String[] data, double prevCgain) throws JSONException {
double comp_crop_yld_c = Double.parseDouble(data[colGracc]) * 0.00404686 * area;
double comp_crop_res_c = (Double.parseDouble(data[colAbove])
+ Double.parseDouble(data[colBelow])) * 0.00404686 * area;
double comp_soil_c_stock = Double.parseDouble(data[colSOM]) * 0.00404686 * area;
double comp_soil_c_stock_unit_area = Double.parseDouble(data[colSOM]);
double comp_soil_c_gain = comp_soil_c_stock - prevCgain;
JSONObject jy = new JSONObject()
.put("name", "comp_crop_yld_c")
.put("description", "Crop yield carbon of intersected mapunit soil component leaving field")
.put("units", "Metric tons")
.put("value", comp_crop_yld_c);
JSONObject jc = new JSONObject()
.put("name", "comp_crop_res_c")
.put("description", "Crop residue carbon above and below ground of intersected mapunit soil component remaining in field")
.put("units", "Metric tons")
.put("value", comp_crop_res_c);
JSONObject js = new JSONObject()
.put("name", "comp_soil_c_stock")
.put("description", "Soil carbon stock of intersected mapunit soil component at the end of crop")
.put("units", "Metric tons")
.put("value", comp_soil_c_stock);
JSONObject jg = new JSONObject()
.put("name", "comp_soil_c_gain")
.put("description", "Soil carbon stock gain or loss for intersected mapunit soil component through crop year")
.put("units", "Metric tons")
.put("value", comp_soil_c_gain);
JSONObject jsua = new JSONObject()
.put("name", "comp_soil_c_stock_unit_area")
.put("description", "Soil carbon stock per unit area of intersected mapunit soil component at the end of crop")
.put("units", "g per meter squared")
.put("value", comp_soil_c_stock_unit_area);
JSONArray ja = new JSONArray()
.put(jy)
.put(jc)
.put(js)
.put(jg)
.put(jsua);
return ja;
}
public void checkHarvest() throws FileNotFoundException, ServiceException {
String filename = schedule + ".lis";
int lineNumber = 1;
int colGracc = 0;
int colTime = 0;
try (Scanner scanner = new Scanner(workspace().getFile(filename));) {
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
if (lineNumber == 1) {
// read header
String[] data = line.split("\\s+");
for (int col = 0; col < data.length; col++) {
if (data[col].equals("cgracc")) {
colGracc = col;
} else if (data[col].equals("time")) {
colTime = col;
}
}
} else if (lineNumber == 2) {
// skip line because empty
} else {
// check the line
String[] data = line.split("\\s+");
double year = Double.parseDouble(data[colTime]);
if (year > 4010 && year < 4021) {
double grainHarvest = Double.parseDouble(data[colGracc]);
if (grainHarvest == 0.0) {
String msg = "cgracc for year " + year + " is " + grainHarvest;
throw new ServiceException(msg);
}
}
}
lineNumber++;
}
}
}
protected void countLayers() throws ServiceException {
try {
profileDepths = new LinkedList<>();
List<Double> profiles = Files.lines(workspace().getFile("soils.in").toPath())
.map(str -> str.split("\\s+"))
.map(str -> Double.parseDouble(str[1]))
.collect(Collectors.toList());
double[] defaultProfile = new double[]{10, 20, 15, 15, 30, 30, 30, 30, 30, 30};
double val = 0;
double bottom = profiles.get(profiles.size() - 1);
for (int i = 0; i < defaultProfile.length; i++) {
double prof = defaultProfile[i];
val += prof;
if (val == bottom) {
profileDepths.add(prof);
break;
} else if (val > bottom) {
double tmpval = val - prof;
profileDepths.add(bottom - tmpval);
break;
} else {
profileDepths.add(prof);
}
}
nlayer = profileDepths.size(); // - 2; // the first three layers are meshed into 1
} catch (IOException ex) {
throw new ServiceException(ex.getMessage());
}
}
protected void fetchSoil() throws Exception {
ModelDataServiceCall mds = new ModelDataServiceCall()
.put(STREAM_FILE, fileAsJSON)
.put("cokey", cokey)
.put(soils.AoA.AOA_GEOMETRY, new JSONObject()
.put(TYPE, aoa_geometry.get(TYPE))
.put(COORDINATES, aoa_geometry.get(COORDINATES)))
.url(Config.getString("ghg.soilfile.url",
request().getCodebase() + "d/insoilfile/2.2"))
.call();
if (mds.serviceFinished()) {
mds.download("soils.in", workspace().getFile("soils.in"));
} else {
throw new ServiceException("GHG Soil service error: " + mds.getError());
}
}
}