| @@ -24,7 +24,8 @@ |
| import ngmf.util.cosu.luca.of.TRMSE; |
| import oms.utils.Utils; |
| import oms.utils.Utils.PBIAS; |
| -import oms.utils.Utils.NS2LOG; |
| +import oms.utils.Utils.NSLOG; |
| +import oms.utils.Utils.NSLOG1P; |
| import oms3.ObjectiveFunction; |
| |
| /** |
| @@ -43,205 +44,210 @@ |
| @Resource(file = "${csip.dir}/bin/ages/simulation/ages.sim", type = REFERENCE, id = KEY_SCRIPT) |
| public class V1_0 extends ModelDataService { |
| |
| - public static final String KEY_SCRIPT = "ages.sim"; |
| - public static final String RUN_INC = "run.inc"; |
| + public static final String KEY_SCRIPT = "ages.sim"; |
| + public static final String RUN_INC = "run.inc"; |
| |
| - public static final String PAR_STARTTIME = "startTime"; |
| - public static final String PAR_ENDTIME = "endTime"; |
| + public static final String PAR_STARTTIME = "startTime"; |
| + public static final String PAR_ENDTIME = "endTime"; |
| |
| - static final Map<String, ObjectiveFunction> OF = new HashMap<>(); |
| + 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("rmse", new RMSE()); |
| - OF.put("trmse", new TRMSE()); |
| - OF.put("pbias", new PBIAS()); |
| + |
| + static { |
| + OF.put("kge", new KGE()); |
| + OF.put("ns", new NS()); |
| + OF.put("nslog", new NSLOG()); |
| + OF.put("nslog1p", new NSLOG1P()); |
| + OF.put("rmse", new RMSE()); |
| + OF.put("trmse", new TRMSE()); |
| + OF.put("pbias", new PBIAS()); |
| + } |
| + |
| + // required parameter |
| + String[] reqParams = { |
| + PAR_STARTTIME, |
| + PAR_ENDTIME |
| + }; |
| + |
| + // optional parameter |
| + String[] optParams = { |
| + "ACAdaptation", |
| + "BetaW", |
| + "Beta_min", |
| + "Beta_rsd", |
| + "FCAdaptation", |
| + "Ksink", |
| + "LExCoef", |
| + "N_delay_RG1", |
| + "N_delay_RG2", |
| + "a_rain", |
| + "a_snow", |
| + "angstrom_a", |
| + "angstrom_b", |
| + "baseTemp", |
| + "calib_clat_fact", |
| + "ccf_factor", |
| + "defaultCO2", |
| + "denitfac", |
| + "delayNitrification", |
| + "denitrificationRateCoefficient", |
| + "denitrificationSoilSaturationThreshold", |
| + "depdr", |
| + "deposition_factor", |
| + "drrad", |
| + "drspac", |
| + "f1", |
| + "f12", |
| + "f13", |
| + "f14", |
| + "f15", |
| + "f16", |
| + "f17", |
| + "f18", |
| + "f19", |
| + "f2", |
| + "f3", |
| + "f4", |
| + "f5", |
| + "f6", |
| + "f7", |
| + "f8", |
| + "flowRouteTA", |
| + "fmt_date", |
| + "fmt_double", |
| + "g_factor", |
| + "geoMaxPerc", |
| + "gwCapRise", |
| + "gwRG1Fact", |
| + "gwRG1RG2dist", |
| + "gwRG2Fact", |
| + "halflife_RG1", |
| + "halflife_RG2", |
| + "infil_conc_factor", |
| + "initLPS", |
| + "initMPS", |
| + "initN_concRG1", |
| + "initN_concRG2", |
| + "initRG1", |
| + "initRG2", |
| + "kdiff_layer", |
| + "kf_calib", |
| + "lagSurfaceRunoff", |
| + "lagInterflow", |
| + "locGrw", |
| + "longTZ", |
| + "nitri_delay", |
| + "nitrificationSoilTemperatureThreshold", |
| + "nitrificationSurfaceTemperatureThreshold", |
| + "opti", |
| + "piadin", |
| + "r_factor", |
| + "rootfactor", |
| + "sceno", |
| + "skipRegression", |
| + "snowCritDens", |
| + "snowDensConst", |
| + "snowFactorA", |
| + "snowFactorB", |
| + "snowFactorC", |
| + "snow_trans", |
| + "snow_trs", |
| + "soilDiffMPSLPS", |
| + "soilDistMPSLPS", |
| + "soilImpGT80", |
| + "soilImpLT80", |
| + "soilLatVertLPS", |
| + "soilLinRed", |
| + "soilMaxDPS", |
| + "soilMaxInfSnow", |
| + "soilMaxInfSummer", |
| + "soilMaxInfWinter", |
| + "soilMaxPerc", |
| + "soilOutLPS", |
| + "soilPolRed", |
| + "t_factor", |
| + "tempRes", |
| + "temp_lag" |
| + }; |
| + |
| + // simulation flags |
| + String[] flags = { |
| + "flagParallel", |
| + "flagRegionalization", |
| + "flagHRURouting", |
| + "flagReachRouting", |
| + "flagSort", |
| + "flagSplit", |
| + "flagInfiltration", |
| + "flagTillage", |
| + "flagTileDrain", |
| + "flagUPGM", |
| + "parallelismFactor", |
| + "parallelismThreads", |
| + "flagSaveState", |
| + "flagLoadState", |
| + "flagWB" |
| + }; |
| + |
| + |
| + @Override |
| + public void doProcess() throws Exception { |
| + String dsl = parameter().getString(KEY_SCRIPT, |
| + resources().getFile(KEY_SCRIPT).toString()); |
| + |
| + // pass request param to model runtime parameter -> run.inc |
| + Map<String, String> agesParam = new LinkedHashMap<>(); |
| + Utils.passReqQuotedParam(agesParam, parameter(), reqParams); |
| + |
| + // scalar parameter |
| + Utils.passOptParam(agesParam, parameter(), optParams); |
| + |
| + // optional flags |
| + Utils.passOptQuotedParam(agesParam, parameter(), flags); |
| + |
| + // create parameter include file |
| + Utils.createParamInclude(agesParam, getWorkspaceFile(RUN_INC)); |
| + |
| + String start = parameter().getString(PAR_STARTTIME); |
| + String end = parameter().getString(PAR_ENDTIME); |
| + |
| + File d = new File(dsl); |
| + if (!(d.isAbsolute() && d.exists())) { |
| + d = getWorkspaceFile(dsl); |
| } |
| |
| - // required parameter |
| - String[] reqParams = { |
| - PAR_STARTTIME, |
| - PAR_ENDTIME |
| - }; |
| + getWorkspaceFile("output").mkdirs(); |
| + getWorkspaceFile("logs").mkdirs(); |
| |
| - // optional parameter |
| - String[] optParams = { |
| - "ACAdaptation", |
| - "BetaW", |
| - "Beta_min", |
| - "Beta_rsd", |
| - "FCAdaptation", |
| - "Ksink", |
| - "LExCoef", |
| - "N_delay_RG1", |
| - "N_delay_RG2", |
| - "a_rain", |
| - "a_snow", |
| - "angstrom_a", |
| - "angstrom_b", |
| - "baseTemp", |
| - "calib_clat_fact", |
| - "ccf_factor", |
| - "defaultCO2", |
| - "denitfac", |
| - "delayNitrification", |
| - "denitrificationRateCoefficient", |
| - "denitrificationSoilSaturationThreshold", |
| - "depdr", |
| - "deposition_factor", |
| - "drrad", |
| - "drspac", |
| - "f1", |
| - "f12", |
| - "f13", |
| - "f14", |
| - "f15", |
| - "f16", |
| - "f17", |
| - "f18", |
| - "f19", |
| - "f2", |
| - "f3", |
| - "f4", |
| - "f5", |
| - "f6", |
| - "f7", |
| - "f8", |
| - "flowRouteTA", |
| - "fmt_date", |
| - "fmt_double", |
| - "g_factor", |
| - "geoMaxPerc", |
| - "gwCapRise", |
| - "gwRG1Fact", |
| - "gwRG1RG2dist", |
| - "gwRG2Fact", |
| - "halflife_RG1", |
| - "halflife_RG2", |
| - "infil_conc_factor", |
| - "initLPS", |
| - "initMPS", |
| - "initN_concRG1", |
| - "initN_concRG2", |
| - "initRG1", |
| - "initRG2", |
| - "kdiff_layer", |
| - "kf_calib", |
| - "lagSurfaceRunoff", |
| - "lagInterflow", |
| - "locGrw", |
| - "longTZ", |
| - "nitri_delay", |
| - "nitrificationSoilTemperatureThreshold", |
| - "nitrificationSurfaceTemperatureThreshold", |
| - "opti", |
| - "piadin", |
| - "r_factor", |
| - "rootfactor", |
| - "sceno", |
| - "skipRegression", |
| - "snowCritDens", |
| - "snowDensConst", |
| - "snowFactorA", |
| - "snowFactorB", |
| - "snowFactorC", |
| - "snow_trans", |
| - "snow_trs", |
| - "soilDiffMPSLPS", |
| - "soilDistMPSLPS", |
| - "soilImpGT80", |
| - "soilImpLT80", |
| - "soilLatVertLPS", |
| - "soilLinRed", |
| - "soilMaxDPS", |
| - "soilMaxInfSnow", |
| - "soilMaxInfSummer", |
| - "soilMaxInfWinter", |
| - "soilMaxPerc", |
| - "soilOutLPS", |
| - "soilPolRed", |
| - "t_factor", |
| - "tempRes", |
| - "temp_lag" |
| - }; |
| + Utils.runAges(d, getWorkspaceDir(), parameter(), resources(), LOG); |
| |
| - // simulation flags |
| - String[] flags = { |
| - "flagParallel", |
| - "flagRegionalization", |
| - "flagHRURouting", |
| - "flagReachRouting", |
| - "flagSort", |
| - "flagSplit", |
| - "flagInfiltration", |
| - "flagTillage", |
| - "flagTileDrain", |
| - "flagUPGM", |
| - "parallelismFactor", |
| - "parallelismThreads", |
| - "flagSaveState", |
| - "flagLoadState", |
| - "flagWB" |
| - }; |
| + for (String ofName : getRequestedObjfunc(OF.keySet())) { |
| + String[] data = parameter().getStringArray(ofName); |
| + double v = calc_of(OF.get(ofName), data[0], data[1], start, end); |
| + results().put(ofName, v); |
| + } |
| +// results().put(getWorkspaceFile("output")); |
| + } |
| |
| - @Override |
| - public void doProcess() throws Exception { |
| - String dsl = parameter().getString(KEY_SCRIPT, |
| - resources().getFile(KEY_SCRIPT).toString()); |
| |
| - // pass request param to model runtime parameter -> run.inc |
| - Map<String, String> agesParam = new LinkedHashMap<>(); |
| - Utils.passReqQuotedParam(agesParam, parameter(), reqParams); |
| + private List<String> getRequestedObjfunc(Set<String> names) { |
| + List<String> l = new ArrayList<>(); |
| + for (String ofName : names) { |
| + if (parameter().has(ofName)) { |
| + l.add(ofName); |
| + } |
| + } |
| + return l; |
| + } |
| |
| - // scalar parameter |
| - Utils.passOptParam(agesParam, parameter(), optParams); |
| |
| - // optional flags |
| - Utils.passOptQuotedParam(agesParam, parameter(), flags); |
| - |
| - // create parameter include file |
| - Utils.createParamInclude(agesParam, getWorkspaceFile(RUN_INC)); |
| - |
| - String start = parameter().getString(PAR_STARTTIME); |
| - String end = parameter().getString(PAR_ENDTIME); |
| - |
| - File d = new File(dsl); |
| - if (!(d.isAbsolute() && d.exists())) { |
| - d = getWorkspaceFile(dsl); |
| - } |
| - |
| - getWorkspaceFile("output").mkdirs(); |
| - getWorkspaceFile("logs").mkdirs(); |
| - |
| - Utils.runAges(d, getWorkspaceDir(), parameter(), resources(), LOG); |
| - |
| - for (String ofName : getRequestedObjfunc(OF.keySet())) { |
| - String[] data = parameter().getStringArray(ofName); |
| - double v = calc_of(OF.get(ofName), data[0], data[1], start, end); |
| - results().put(ofName, v); |
| - } |
| -// results().put(getWorkspaceFile("output")); |
| - } |
| - |
| - private List<String> getRequestedObjfunc(Set<String> names) { |
| - List<String> l = new ArrayList<>(); |
| - for (String ofName : names) { |
| - if (parameter().has(ofName)) { |
| - l.add(ofName); |
| - } |
| - } |
| - return l; |
| - } |
| - |
| - private double calc_of(ObjectiveFunction of, String obs, |
| - String sim, String start, String end) throws IOException, ServiceException { |
| - // e.g. obs_data02_14.csv/obs/orun[1] |
| - double[] obsData = Utils.getData(obs, getWorkspaceDir(), start, end); |
| - // e.g. output/csip_run/out/Outlet.csv/output/catchmentSimRunoff |
| - double[] simData = Utils.getData(sim, getWorkspaceDir(), start, end); |
| - return of.calculate(obsData, simData, parameter().getDouble("missing", -9999d)); |
| - } |
| + private double calc_of(ObjectiveFunction of, String obs, |
| + String sim, String start, String end) throws IOException, ServiceException { |
| + // e.g. obs_data02_14.csv/obs/orun[1] |
| + double[] obsData = Utils.getData(obs, getWorkspaceDir(), start, end); |
| + // e.g. output/csip_run/out/Outlet.csv/output/catchmentSimRunoff |
| + double[] simData = Utils.getData(sim, getWorkspaceDir(), start, end); |
| + return of.calculate(obsData, simData, parameter().getDouble("missing", -9999d)); |
| + } |
| |
| } |
| @@ -33,251 +33,324 @@ |
| */ |
| public class Utils { |
| |
| - // parameter keys |
| - public static final String KEY_LOGLEVEL = "loglevel"; |
| - public static final String KEY_OPTIONS = "java.options"; |
| + // parameter keys |
| + public static final String KEY_LOGLEVEL = "loglevel"; |
| + public static final String KEY_OPTIONS = "java.options"; |
| |
| - public static final String ID_AGES_JAR = "ages.jar"; |
| + public static final String ID_AGES_JAR = "ages.jar"; |
| |
| - /** |
| - * |
| - */ |
| - public static class PBIAS implements ObjectiveFunction { |
| + /** |
| + * |
| + */ |
| + public static class PBIAS implements ObjectiveFunction { |
| |
| - @Override |
| - public double calculate(double[] obs, double[] sim, double missing) { |
| - if (sim.length != obs.length) { |
| - throw new IllegalArgumentException("obs/sim length differ: " + obs.length + "!=" + sim.length); |
| - } |
| - double diffsum = 0; |
| - double obssum = 0; |
| - for (int i = 0; i < sim.length; i++) { |
| - if (obs[i] > missing) { |
| - diffsum += sim[i] - obs[i]; |
| - obssum += obs[i]; |
| - } |
| - } |
| - return (diffsum / obssum) * 100.0; |
| + @Override |
| + public double calculate(double[] obs, double[] sim, double missing) { |
| + if (sim.length != obs.length) { |
| + throw new IllegalArgumentException("obs/sim length differ: " + obs.length + "!=" + sim.length); |
| + } |
| + double diffsum = 0; |
| + double obssum = 0; |
| + for (int i = 0; i < sim.length; i++) { |
| + if (obs[i] > missing) { |
| + diffsum += sim[i] - obs[i]; |
| + obssum += obs[i]; |
| } |
| - |
| - @Override |
| - public boolean positiveDirection() { |
| - return false; |
| - } |
| + } |
| + return (diffsum / obssum) * 100.0; |
| } |
| |
| - public static class NS2LOG implements ObjectiveFunction { |
| |
| - @Override |
| - public double calculate(double[] obs, double[] sim, double missing) { |
| - int pre_size = sim.length; |
| - int val_size = obs.length; |
| - int steps = 0; |
| - double sum_log_pd = 0; |
| - double sum_log_vd = 0; |
| + @Override |
| + public boolean positiveDirection() { |
| + return false; |
| + } |
| + } |
| |
| - /** |
| - * checking if both data arrays have the same number of elements |
| - */ |
| - if (pre_size != val_size) { |
| - return missing; |
| - } else { |
| - steps = pre_size; |
| - } |
| + /** |
| + * |
| + */ |
| + public static class NSLOG implements ObjectiveFunction { |
| |
| - /** |
| - * calculating logarithmic values of both data sets. Sets 0 if data |
| - * is 0 |
| - */ |
| - double[] log_preData = new double[pre_size]; |
| - double[] log_valData = new double[val_size]; |
| + @Override |
| + public double calculate(double[] obs, double[] sim, double missing) { |
| + int pre_size = sim.length; |
| + int val_size = obs.length; |
| + int steps = 0; |
| + double sum_log_pd = 0; |
| + double sum_log_vd = 0; |
| |
| - for (int i = 0; i < steps; i++) { |
| - if (sim[i] >= 0 && obs[i] >= 0) { |
| - |
| - if (sim[i] == 0) { |
| - log_preData[i] = 0; |
| - } else { |
| - log_preData[i] = Math.log(sim[i]); |
| - } |
| + /** |
| + * checking if both data arrays have the same number of elements |
| + */ |
| + if (pre_size != val_size) { |
| + return missing; |
| + } else { |
| + steps = pre_size; |
| + } |
| |
| - if (obs[i] == 0) { |
| - log_valData[i] = 0; |
| - } else { |
| - log_valData[i] = Math.log(obs[i]); |
| - } |
| - } |
| - } |
| + /** |
| + * calculating logarithmic values of both data sets. Sets 0 if data is 0 |
| + */ |
| + double[] log_preData = new double[pre_size]; |
| + double[] log_valData = new double[val_size]; |
| |
| - /** |
| - * summing up both data sets |
| - */ |
| - for (int i = 0; i < log_valData.length; i++) { |
| - sum_log_pd += log_preData[i]; |
| - sum_log_vd += log_valData[i]; |
| - } |
| + for (int i = 0; i < steps; i++) { |
| + if (sim[i] >= 0 && obs[i] >= 0) { |
| |
| - /** |
| - * calculating mean values for both data sets |
| - */ |
| - double mean_log_pd = sum_log_pd / log_valData.length; |
| - double mean_log_vd = sum_log_vd / log_valData.length; |
| + if (sim[i] == 0) { |
| + log_preData[i] = 0; |
| + } else { |
| + log_preData[i] = Math.log(sim[i]); |
| + } |
| |
| - /** |
| - * calculating mean pow deviations |
| - */ |
| - double pd_log_vd = 0; |
| - double vd_log_mean = 0; |
| - for (int i = 0; i < log_valData.length; i++) { |
| - pd_log_vd = pd_log_vd + (Math.pow(Math.abs(log_valData[i] - log_preData[i]), 2)); |
| - vd_log_mean = vd_log_mean + (Math.pow(Math.abs(log_valData[i] - mean_log_vd), 2)); |
| - } |
| + if (obs[i] == 0) { |
| + log_valData[i] = 0; |
| + } else { |
| + log_valData[i] = Math.log(obs[i]); |
| + } |
| + } |
| + } |
| |
| - /** |
| - * calculating efficiency after Nash & Sutcliffe (1970) |
| - */ |
| - double log_efficiency = 1 - (pd_log_vd / vd_log_mean); |
| - return log_efficiency; |
| - } |
| + /** |
| + * summing up both data sets |
| + */ |
| + for (int i = 0; i < log_valData.length; i++) { |
| + sum_log_pd += log_preData[i]; |
| + sum_log_vd += log_valData[i]; |
| + } |
| |
| - @Override |
| - public boolean positiveDirection() { // ??? |
| - return false; |
| - } |
| + /** |
| + * calculating mean values for both data sets |
| + */ |
| + double mean_log_pd = sum_log_pd / log_valData.length; |
| + double mean_log_vd = sum_log_vd / log_valData.length; |
| + |
| + /** |
| + * calculating mean pow deviations |
| + */ |
| + double pd_log_vd = 0; |
| + double vd_log_mean = 0; |
| + for (int i = 0; i < log_valData.length; i++) { |
| + pd_log_vd = pd_log_vd + (Math.pow(Math.abs(log_valData[i] - log_preData[i]), 2)); |
| + vd_log_mean = vd_log_mean + (Math.pow(Math.abs(log_valData[i] - mean_log_vd), 2)); |
| + } |
| + |
| + /** |
| + * calculating efficiency after Nash & Sutcliffe (1970) |
| + */ |
| + double log_efficiency = 1 - (pd_log_vd / vd_log_mean); |
| + return log_efficiency; |
| } |
| |
| - /** |
| - * create a 'sim' include file for the run part. |
| - */ |
| - public static void createParamInclude(Map<String, String> p, |
| - File file) throws IOException { |
| - StringBuilder b = new StringBuilder(); |
| - b.append("parameter {\n"); |
| - p.keySet().forEach((name) -> { |
| - b.append(" ").append(name).append(" ").append(p.get(name)).append("\n"); |
| - }); |
| - b.append("}\n"); |
| - FileUtils.writeStringToFile(file, b.toString()); |
| + |
| + @Override |
| + public boolean positiveDirection() { |
| + return true; |
| + } |
| + } |
| + |
| + /** |
| + * |
| + */ |
| + public static class NSLOG1P implements ObjectiveFunction { |
| + |
| + @Override |
| + public double calculate(double[] obs, double[] sim, double missing) { |
| + if (sim.length != obs.length) { |
| + throw new IllegalArgumentException("obs/sim length differ: " + obs.length + "!=" + sim.length); |
| + } |
| + |
| + /** |
| + * calculating logarithmic values of both data sets. Sets 0 if data is 0 |
| + */ |
| + double[] log_sim = new double[sim.length]; |
| + double[] log_obs = new double[sim.length]; |
| + |
| + int valid = 0; |
| + double sum_log_obs = 0.0; |
| + |
| + for (int i = 0; i < sim.length; i++) { |
| + //either prediction or validation shows a negative value. |
| + //in this case the pair is excluded from the further calculation, |
| + //simply by setting the values to -1 and not increasing valid pairs |
| + // this will also handle missing values |
| + if (sim[i] < 0.0 || obs[i] < 0.0) { |
| + log_sim[i] = -1; |
| + log_obs[i] = -1; |
| + continue; |
| + } |
| + //both prediction and validation are equal or greater than zero |
| + //no problem for the calculation |
| + log_sim[i] = Math.log1p(sim[i]); |
| + log_obs[i] = Math.log1p(obs[i]); |
| + |
| + // summing up |
| + sum_log_obs += log_obs[i]; |
| + valid++; |
| + } |
| + |
| + // calculating mean |
| + double mean_log_obs = sum_log_obs / valid; |
| + |
| + // calculating mean pow deviations |
| + double sum1 = 0.0; |
| + double sum_mean = 0.0; |
| + for (int i = 0; i < sim.length; i++) { |
| + if (log_sim[i] >= 0) { |
| + sum1 += Math.pow(Math.abs(log_obs[i] - log_sim[i]), 2); |
| + sum_mean += Math.pow(Math.abs(log_obs[i] - mean_log_obs), 2); |
| + } |
| + } |
| + return 1 - (sum1 / sum_mean); |
| } |
| |
| - /** |
| - * pass a required parameter, quoted (string). |
| - */ |
| - public static void passReqQuotedParam(Map<String, String> p, |
| - PayloadParameter param, String... names) throws ServiceException { |
| - for (String name : names) { |
| - p.put(name, "\"" + param.getString(name) + "\""); |
| - } |
| + |
| + @Override |
| + public boolean positiveDirection() { |
| + return true; |
| + } |
| + } |
| + |
| + |
| + /** |
| + * create a 'sim' include file for the run part. |
| + */ |
| + public static void createParamInclude(Map<String, String> p, |
| + File file) throws IOException { |
| + StringBuilder b = new StringBuilder(); |
| + b.append("parameter {\n"); |
| + p.keySet().forEach((name) -> { |
| + b.append(" ").append(name).append(" ").append(p.get(name)).append("\n"); |
| + }); |
| + b.append("}\n"); |
| + FileUtils.writeStringToFile(file, b.toString()); |
| + } |
| + |
| + |
| + /** |
| + * pass a required parameter, quoted (string). |
| + */ |
| + public static void passReqQuotedParam(Map<String, String> p, |
| + PayloadParameter param, String... names) throws ServiceException { |
| + for (String name : names) { |
| + p.put(name, "\"" + param.getString(name) + "\""); |
| + } |
| + } |
| + |
| + |
| + /** |
| + * pass optional parameter, no quotes. |
| + */ |
| + public static void passOptParam(Map<String, String> p, |
| + PayloadParameter param, String... names) throws ServiceException { |
| + for (String name : names) { |
| + if (param.has(name)) { |
| + p.put(name, param.getString(name)); |
| + } |
| + } |
| + } |
| + |
| + |
| + public static void passOptQuotedParam(Map<String, String> p, |
| + PayloadParameter param, String... names) throws ServiceException { |
| + for (String name : names) { |
| + if (param.has(name)) { |
| + p.put(name, "\"" + param.getString(name) + "\""); |
| + } |
| + } |
| + } |
| + |
| + |
| + /** |
| + * Run Ages |
| + * |
| + * @param dsl |
| + * @param options |
| + * @throws Exception |
| + */ |
| + public static void runAges(File dsl, File ws, PayloadParameter param, |
| + ServiceResources res, SessionLogger LOG) throws Exception { |
| + |
| + // Create/execute a Ages. |
| + Executable p = createProcess(dsl, ws, param, res, LOG); |
| + int result = p.exec(); |
| + if (result != 0) { |
| + FilenameFilter ff = new WildcardFileFilter("java*stderr.txt", IOCase.INSENSITIVE); |
| + File[] f = ws.listFiles(ff); |
| + if (f != null && f.length > 0) { |
| + String err = FileUtils.readFileToString(f[0]); |
| + LOG.info("Ages execution error. " + f[0] + ":\n" + err); |
| + throw new ServiceException("Ages execution error. " + f[0] + ":\n" + err); |
| + } |
| + throw new ServiceException("Ages execution error." + result); |
| + } |
| + } |
| + |
| + |
| + /** |
| + * Create the external Ages process. |
| + */ |
| + public static Executable createProcess(File dsl, File ws, |
| + PayloadParameter param, ServiceResources res, SessionLogger LOG) throws Exception { |
| + |
| + Map<String, String> sysprops = new HashMap(); |
| + sysprops.put("oms_prj", ws.toString()); |
| + sysprops.put("csip_ages", res.getFile(ID_AGES_JAR).getParent()); |
| + |
| + String[] jvmOptions = Binaries.asSysProps(sysprops); |
| + String options = param.getString(KEY_OPTIONS, ""); |
| + if (options != null && !options.isEmpty()) { |
| + jvmOptions = (String[]) ArrayUtils.addAll(jvmOptions, options.split("\\s+")); |
| } |
| |
| - /** |
| - * pass optional parameter, no quotes. |
| - */ |
| - public static void passOptParam(Map<String, String> p, |
| - PayloadParameter param, String... names) throws ServiceException { |
| - for (String name : names) { |
| - if (param.has(name)) { |
| - p.put(name, param.getString(name)); |
| - } |
| - } |
| + // java -Doms_prj=. -cp "dist/AgES.jar" oms3.CLI -l OFF -r "projects/sfir30/simulation/sfir30.sim" |
| + return Binaries.getResourceOMSDSL( |
| + dsl, // the dsl file to run |
| + jvmOptions, // jvm options |
| + ws, // workspace dir |
| + Arrays.asList(res.getFile(ID_AGES_JAR)), // the ages jar file |
| + param.getString(KEY_LOGLEVEL, "INFO"), // The log level |
| + LOG); // This session logger |
| + } |
| + |
| + private static final int FILE = 0; |
| + private static final int TABLE = 1; |
| + private static final int COLUMN = 2; |
| + |
| + |
| + /** |
| + * |
| + * @param d |
| + * @param workspace |
| + * @param start |
| + * @param end |
| + * @return |
| + * @throws IOException |
| + */ |
| + public static double[] getData(String d, File workspace, |
| + String start, String end) throws IOException { |
| + if (d == null) { |
| + throw new IllegalArgumentException("Missing data property: " + d); |
| + } |
| + String[] parts = DataIO.parseCsvFilename(d); |
| + if (parts.length != 3) { |
| + throw new IllegalArgumentException("invalid: " + d + " expected:: <file>/<table>/<column>"); |
| } |
| |
| - public static void passOptQuotedParam(Map<String, String> p, |
| - PayloadParameter param, String... names) throws ServiceException { |
| - for (String name : names) { |
| - if (param.has(name)) { |
| - p.put(name, "\"" + param.getString(name) + "\""); |
| - } |
| - } |
| - } |
| +// System.out.println(Arrays.toString(parts)); |
| + CSTable t = DataIO.table(new File(workspace, parts[FILE]), parts[TABLE]); |
| |
| - /** |
| - * Run Ages |
| - * |
| - * @param dsl |
| - * @param options |
| - * @throws Exception |
| - */ |
| - public static void runAges(File dsl, File ws, PayloadParameter param, |
| - ServiceResources res, SessionLogger LOG) throws Exception { |
| - |
| - // Create/execute a Ages. |
| - Executable p = createProcess(dsl, ws, param, res, LOG); |
| - int result = p.exec(); |
| - if (result != 0) { |
| - FilenameFilter ff = new WildcardFileFilter("java*stderr.txt", IOCase.INSENSITIVE); |
| - File[] f = ws.listFiles(ff); |
| - if (f != null && f.length > 0) { |
| - String err = FileUtils.readFileToString(f[0]); |
| - LOG.info("Ages execution error. " + f[0] + ":\n" + err); |
| - throw new ServiceException("Ages execution error. " + f[0] + ":\n" + err); |
| - } |
| - throw new ServiceException("Ages execution error." + result); |
| - } |
| - } |
| - |
| - /** |
| - * Create the external Ages process. |
| - */ |
| - public static Executable createProcess(File dsl, File ws, |
| - PayloadParameter param, ServiceResources res, SessionLogger LOG) throws Exception { |
| - |
| - Map<String, String> sysprops = new HashMap(); |
| - sysprops.put("oms_prj", ws.toString()); |
| - sysprops.put("csip_ages", res.getFile(ID_AGES_JAR).getParent()); |
| - |
| - String[] jvmOptions = Binaries.asSysProps(sysprops); |
| - String options = param.getString(KEY_OPTIONS, ""); |
| - if (options != null && !options.isEmpty()) { |
| - jvmOptions = (String[]) ArrayUtils.addAll(jvmOptions, options.split("\\s+")); |
| - } |
| - |
| - // java -Doms_prj=. -cp "dist/AgES.jar" oms3.CLI -l OFF -r "projects/sfir30/simulation/sfir30.sim" |
| - return Binaries.getResourceOMSDSL( |
| - dsl, // the dsl file to run |
| - jvmOptions, // jvm options |
| - ws, // workspace dir |
| - Arrays.asList(res.getFile(ID_AGES_JAR)), // the ages jar file |
| - param.getString(KEY_LOGLEVEL, "INFO"), // The log level |
| - LOG); // This session logger |
| - } |
| - |
| - private static final int FILE = 0; |
| - private static final int TABLE = 1; |
| - private static final int COLUMN = 2; |
| - |
| - /** |
| - * |
| - * @param d |
| - * @param workspace |
| - * @param start |
| - * @param end |
| - * @return |
| - * @throws IOException |
| - */ |
| - public static double[] getData(String d, File workspace, |
| - String start, String end) throws IOException { |
| - if (d == null) { |
| - throw new IllegalArgumentException("Missing data property: " + d); |
| - } |
| - String[] parts = DataIO.parseCsvFilename(d); |
| - if (parts.length != 3) { |
| - throw new IllegalArgumentException("invalid: " + d + " expected:: <file>/<table>/<column>"); |
| - } |
| - |
| -// System.out.println(Arrays.toString(parts)); |
| - CSTable t = DataIO.table(new File(workspace, parts[FILE]), parts[TABLE]); |
| - |
| - Date startDate = Conversions.convert(start, Date.class); |
| - Date endDate = Conversions.convert(end, Date.class); |
| + Date startDate = Conversions.convert(start, Date.class); |
| + Date endDate = Conversions.convert(end, Date.class); |
| |
| // System.out.println(startDate); |
| // System.out.println(endDate); |
| - double[] vals = DataIO.getColumnDoubleValuesInterval(startDate, endDate, t, |
| - parts[COLUMN], DataIO.DAILY); |
| + double[] vals = DataIO.getColumnDoubleValuesInterval(startDate, endDate, t, |
| + parts[COLUMN], DataIO.DAILY); |
| |
| - return vals; |
| - } |
| + return vals; |
| + } |
| |
| // static void d() throws IOException { |
| // CSProperties pr = DataIO.properties(new File("/od/projects/csip-all/csip-oms/tmp/data/main_params.csv"), "Parameter"); |
| @@ -287,11 +360,12 @@ |
| // System.out.println("\"" + string + "\","); |
| // } |
| // } |
| - public static void main(String[] args) throws IOException { |
| - // small test |
| - double[] d = getData("obs_data02_14.csv/obs/orun[1]", new File("/tmp"), "2002-01-18", "2002-02-18"); |
| - System.out.println(Arrays.toString(d)); |
| + |
| + public static void main(String[] args) throws IOException { |
| + // small test |
| + double[] d = getData("obs_data02_14.csv/obs/orun[1]", new File("/tmp"), "2002-01-18", "2002-02-18"); |
| + System.out.println(Arrays.toString(d)); |
| // d(); |
| - } |
| + } |
| |
| } |