Merge branch 'Luke' into 'master'

Added preprocessor for FINNCEREAL model.

See merge request !1

src/main/java/no/nibio/vips/logic/scheduling/model/preprocessor/FinnCerealModelsPreprocessor.java

+package no.nibio.vips.logic.scheduling.model.preprocessor;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import no.nibio.vips.entity.ModelConfiguration;
+import no.nibio.vips.entity.WeatherObservation;
+import no.nibio.vips.logic.entity.ForecastConfiguration;
+import no.nibio.vips.logic.entity.PointOfInterestWeatherStation;
+import no.nibio.vips.logic.scheduling.model.ModelRunPreprocessor;
+import no.nibio.vips.logic.scheduling.model.PreprocessorException;
+import no.nibio.vips.model.ConfigValidationException;
+import no.nibio.vips.util.WeatherElements;
+import no.nibio.vips.util.WeatherObservationListException;
+import no.nibio.vips.util.WeatherUtil;
+import no.nibio.vips.util.weather.WeatherDataSourceException;
+import no.nibio.vips.util.weather.WeatherDataSourceUtil;
+
+public class FinnCerealModelsPreprocessor extends ModelRunPreprocessor {
+
+	public static final String SOWING_DATE ="FINNCEREAL_FIELD_SOWING_DATE";
+	public static final String PREVIOUS_CROP ="FINNCEREAL_PREVIOUS_CROP";
+	public static final String TILLAGE ="FINNCEREAL_TILLAGE_METHOD";
+	public static final String SUSCEPTIBILITY ="FINNCEREAL_CROP_SUSCEPTIBILITY";
+	public static final String MODEL ="FINNCEREAL_MODEL_NAME";
+
+	/**
+	 * This method implementation is based on the DOWNCASTModelPreprocessor implemention of getModelCOnfiguration.
+	 */
+	@Override
+	public ModelConfiguration getModelConfiguration(ForecastConfiguration configuration) throws PreprocessorException {
+		ModelConfiguration config = new ModelConfiguration();
+        PointOfInterestWeatherStation weatherStation =  (PointOfInterestWeatherStation) configuration.getWeatherStationPointOfInterestId();
+        WeatherDataSourceUtil wdsUtil = new WeatherDataSourceUtil();
+        WeatherUtil wUtil = new WeatherUtil();
+        
+        List<WeatherObservation> observations;
+        Date sowingDate = null;
+        SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
+        
+        try {
+        	sowingDate = format.parse(configuration.getForecastModelConfigurationValue(SOWING_DATE));
+            observations = wdsUtil.getWeatherObservations(
+                    weatherStation,
+                    WeatherObservation.LOG_INTERVAL_ID_1H,
+                    new String[]{
+                        WeatherElements.WIND_SPEED_2M,
+                        WeatherElements.WIND_SPEED_10MIN_2M,
+                        WeatherElements.RELATIVE_HUMIDITY_MEAN,
+                        WeatherElements.PRECIPITATION, 
+                        WeatherElements.TEMPERATURE_MEAN 
+                    },
+                    sowingDate,
+                    configuration.getDateEndInTimeZone());
+            observations = wUtil.checkForAndFixHourlyTimeSeriesHoles(observations);
+			List<WeatherObservation> temperature = observations.stream().filter(t -> t.getElementMeasurementTypeId().equals(WeatherElements.TEMPERATURE_MEAN))
+					.collect(Collectors.toList());
+			List<WeatherObservation> rainfall = observations.stream().filter(t -> t.getElementMeasurementTypeId().equals(WeatherElements.PRECIPITATION))
+					.collect(Collectors.toList());
+			List<WeatherObservation> rh = observations.stream().filter(t -> t.getElementMeasurementTypeId().equals(WeatherElements.RELATIVE_HUMIDITY_MEAN))
+					.collect(Collectors.toList());
+			List<WeatherObservation> windSpeedAll = observations.stream().filter(t -> t.getElementMeasurementTypeId().equals(WeatherElements.WIND_SPEED_2M))
+					.collect(Collectors.toList());
+			if(windSpeedAll.isEmpty()) {
+				windSpeedAll = observations.stream().filter(t -> t.getElementMeasurementTypeId().equals(WeatherElements.WIND_SPEED_10MIN_2M))
+						.collect(Collectors.toList());
+			}
+	        config.setModelId(this.getModelId());
+	        config.setConfigParameter("timeZone", weatherStation.getTimeZone());
+	        config.setConfigParameter("temperature", temperature);
+	        config.setConfigParameter("rainfall", rainfall);
+	        config.setConfigParameter("rh", rh);
+	        config.setConfigParameter("windspeed", windSpeedAll);
+	        config.setConfigParameter("precedingCrop", configuration.getForecastModelConfigurationValue(PREVIOUS_CROP));
+	        config.setConfigParameter("tillageMethod", configuration.getForecastModelConfigurationValue(TILLAGE));
+	        config.setConfigParameter("diseaseSusceptibility", configuration.getForecastModelConfigurationValue(SUSCEPTIBILITY));
+	        config.setConfigParameter("model", configuration.getForecastModelConfigurationValue(MODEL));
+        } catch (WeatherDataSourceException | WeatherObservationListException | ParseException ex ) {
+            throw new PreprocessorException(ex.getMessage());
+        }
+        return config;
+	}
+
+	@Override
+	public String getModelId() {
+		return "FINNCEREAL";
+	}
+
+}

src/main/webapp/formdefinitions/models/FINNCEREAL.json

+{
+    "_licensenbte": [
+        "Copyright (c) 2014 NIBIO <http://www.nibio.nb/>. ",
+        "",
+        "This file is part of VIPSLogic. ",
+        "VIPSLogic is free software: you can redistribute it and/or modify ",
+        "it under the terms of the NIBIO Open Source License as published by ",
+        "NIBIO, either version 1 of the License, or (at your option) any ",
+        "later version. ",
+        "",
+        "VIPSLogic 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 ",
+        "NIBIO Open Source License for more details. ",
+        "",
+        "You should have received a copy of the NIBIO Open Source License ",
+        "along with VIPSLogic.  If nbt, see <http://www.nibio.nb/licenses/>. "
+    ],
+    "_comment" : "Sowing date, previous crop, tillage method, and current crop disease susceptibility for the specific field",
+    "fields": [
+         {
+            "name" : "modelName",
+            "dataType" : "STRING",
+            "fieldType" : "SELECT_SINGLE",
+            "required" : true,
+			"options": [
+				{"value":"PyrenophoraTeres", "label":{"en":"Net Blotch","nb":"?","fi":"Verkkolaikku"}, "selected":"true"},
+				{"value":"DrechsleraTriticiRepentis", "label":{"en":"Tan Spot","nb":"","fi":"Ruskolaikku"}},
+				{"value":"StagonosporaNodorum", "label":{"en" : "Stagonspora spot", "nb":"?", "fi":"Pistelaikku"}}
+			]
+        },
+        {
+            "name" : "fieldSowingDate",
+            "dataType" : "DATE",
+            "dateFormat" : "yyyy-MM-dd",
+            "required" : true
+        },
+        {
+            "name" : "previousCrop",
+            "dataType" : "STRING",
+            "fieldType" : "SELECT_SINGLE",
+            "required" : true,
+			"options": [
+				{"value":"Wheat", "label":{"en":"Wheat","nb":"Hvete","fi":"Vehn"}, "selected":"true"},
+				{"value":"Barley", "label":{"en":"Barley","nb":"Barley","fi":"Kaura"}},
+				{"value":"Oats", "label":{"en" : "Oats", "nb":"?", "fi":"Ohra"}},
+				{"value":"Grass", "label":{"en" : "Grass", "nb":"?","fi":"Hein"}},
+				{"value":"Rapeseed", "label":{"en" : "Turnip rape", "nb":"?","fi":"Rypsi"}},
+				{"value":"SugarBeet", "label":{"en" : "Sugar beet", "nb":"?","fi":"Sokerijuurikas"}},
+				{"value":"Legumes", "label":{"en" : "Legumes", "nb":"?","fi":"Herneet"}}
+			]
+        },
+        {
+            "name" : "tillageMethod",
+            "dataType" : "STRING",
+            "fieldType" : "SELECT_SINGLE",
+            "required" : true,
+			"options": [
+				{"value":"Intensive", "label":{"en":"Ploughing","nb":"?","fi":"Kynt"}, "selected":"true"},
+				{"value":"Reduced", "label":{"en":"Reduced tillage","nb":"?","fi":"Kevytmuokkaus"}},
+				{"value":"nbne", "label":{"en" : "Direct seeding", "nb":"?","fi":"Suorakylv"}}
+			]
+        },
+        {
+            "name" : "cropSusceptibility",
+            "dataType" : "STRING",
+            "fieldType" : "SELECT_SINGLE",
+            "required" : true,
+			"options": [
+				{"value":"nbrmal", "label":{"en":"nbrmal","nb":"?", "fi":"normaali"}, "selected":"true"},
+				{"value":"Resistant", "label":{"en":"Resistant","nb":"?","fi":"Resistentti"}},
+				{"value":"Sensitive", "label":{"en" : "Susceptible", "nb":"?", "fi":"Haavoittuva"}}
+			]
+        }
+                
+    ]
+}
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