[Echobase-commits] 01/01: Export biotic export for atlantos

This is an automated email from the git hooks/post-receive script. New commit to branch develop in repository echobase. See https://gitlab.nuiton.org/codelutin/echobase.git commit afab4f6fb127dace9cb0b97c892d185a12c23a5d Author: Julien Ruchaud <julien.ruchaud@debux.org> Date: Mon Oct 24 18:05:16 2016 +0200 Export biotic export for atlantos --- .../migration/workingDb/h2/3.911-0-atlantos.sql | 3 +- .../migration/workingDb/pg/3.911-0-atlantos.sql | 1 + echobase-domain/src/main/xmi/echobase.zargo | Bin 100253 -> 100339 bytes .../service/atlantos/xml/VocabularyExport.java | 39 ++- .../service/atlantos/xml/XmlAccousticExport.java | 4 +- .../service/atlantos/xml/XmlBioticExport.java | 306 ++++++++++++++------- .../services/service/atlantos/xml/XmlWriter.java | 2 + 7 files changed, 243 insertions(+), 112 deletions(-) diff --git a/echobase-domain/src/main/resources/migration/workingDb/h2/3.911-0-atlantos.sql b/echobase-domain/src/main/resources/migration/workingDb/h2/3.911-0-atlantos.sql index 41595e2..f7c1d6c 100644 --- a/echobase-domain/src/main/resources/migration/workingDb/h2/3.911-0-atlantos.sql +++ b/echobase-domain/src/main/resources/migration/workingDb/h2/3.911-0-atlantos.sql @@ -23,4 +23,5 @@ create table vocabularyciem (topiaId varchar(255) not null, topiaVersion bigint alter table vocabularyciem add constraint PK_VOCA primary key (topiaId); alter table vocabularyciem add constraint UK_VOCA_LABEL unique (label); -alter table mission add column country varchar(255); \ No newline at end of file +alter table mission add column country varchar(255); +alter table species add column wormscode varchar(255); \ No newline at end of file diff --git a/echobase-domain/src/main/resources/migration/workingDb/pg/3.911-0-atlantos.sql b/echobase-domain/src/main/resources/migration/workingDb/pg/3.911-0-atlantos.sql index 6abcc27..ffb7a2b 100644 --- a/echobase-domain/src/main/resources/migration/workingDb/pg/3.911-0-atlantos.sql +++ b/echobase-domain/src/main/resources/migration/workingDb/pg/3.911-0-atlantos.sql @@ -24,3 +24,4 @@ alter table vocabularyciem add constraint PK_VOCA primary key (topiaId); alter table vocabularyciem add constraint UK_VOCA_LABEL unique (label); alter table mission add column country character varying(255); +alter table species add column wormscode character varying(255); diff --git a/echobase-domain/src/main/xmi/echobase.zargo b/echobase-domain/src/main/xmi/echobase.zargo index fbdca85..d9f8c64 100644 Binary files a/echobase-domain/src/main/xmi/echobase.zargo and b/echobase-domain/src/main/xmi/echobase.zargo differ diff --git a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/VocabularyExport.java b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/VocabularyExport.java index 711a6d7..5fe9231 100644 --- a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/VocabularyExport.java +++ b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/VocabularyExport.java @@ -23,23 +23,32 @@ public class VocabularyExport implements EchoBaseService { vocabulary.put("Hull", "AC_TransducerLocation_AA"); vocabulary.put("Split", "AC_TransducerBeamType_S2"); vocabulary.put(".hac and .raw formats", "AC_StoredDataFormat_HAC"); - vocabulary.put("ER60", "AC_DataAcquisitionSoftwareName_ER60"); // À ajouter dans le voca - vocabulary.put("Movies3D", "AC_DataProcessingSoftwareName_Movies3D"); // À ajouter dans le voca - vocabulary.put("PELGAS", "AC_Survey_PELGAS"); // À ajouter dans le voca + vocabulary.put("ER60", "AC_DataAcquisitionSoftwareName_ER60"); + vocabulary.put("Movies3D", "AC_DataProcessingSoftwareName_Movies3D"); + vocabulary.put("PELGAS", "AC_Survey_PELGAS"); vocabulary.put("France", "ISO_3166_FR"); vocabulary.put("35HT", "SHIPC_35HT"); - vocabulary.put("D1", "AC_SaCategory_D1"); // À ajouter dans le voca - vocabulary.put("D2", "AC_SaCategory_D2"); // À ajouter dans le voca - vocabulary.put("D3", "AC_SaCategory_D3"); // À ajouter dans le voca - vocabulary.put("D4", "AC_SaCategory_D4"); // À ajouter dans le voca - vocabulary.put("D5", "AC_SaCategory_D5"); // À ajouter dans le voca - vocabulary.put("D6", "AC_SaCategory_D6"); // À ajouter dans le voca - vocabulary.put("D7", "AC_SaCategory_D7"); // À ajouter dans le voca - vocabulary.put("D8", "AC_SaCategory_D8"); // À ajouter dans le voca - vocabulary.put("D9", "AC_SaCategory_D9"); // À ajouter dans le voca - vocabulary.put("D10", "AC_SaCategory_D10"); // À ajouter dans le voca - vocabulary.put("D11", "AC_SaCategory_D11"); // À ajouter dans le voca - vocabulary.put("D12", "AC_SaCategory_D12"); // À ajouter dans le voca + vocabulary.put("D1", "AC_SaCategory_D1"); + vocabulary.put("D2", "AC_SaCategory_D2"); + vocabulary.put("D3", "AC_SaCategory_D3"); + vocabulary.put("D4", "AC_SaCategory_D4"); + vocabulary.put("D5", "AC_SaCategory_D5"); + vocabulary.put("D6", "AC_SaCategory_D6"); + vocabulary.put("D7", "AC_SaCategory_D7"); + vocabulary.put("D8", "AC_SaCategory_D8"); + vocabulary.put("D9", "AC_SaCategory_D9"); + vocabulary.put("D10", "AC_SaCategory_D10"); + vocabulary.put("D11", "AC_SaCategory_D11"); + vocabulary.put("D12", "AC_SaCategory_D12"); + vocabulary.put("Standard sphere, in-situ", "AC_AcquisitionMethod_SS"); + vocabulary.put("ER60", "AC_ProcessingMethod_ER60"); // À vérifier dans le voca + vocabulary.put("57x52", "Gear_57x52"); // À vérifier dans le voca + vocabulary.put("76x70", "Gear_76x70"); // À vérifier dans le voca + vocabulary.put("942OBS", "Gear_PAR"); // À vérifier dans le voca + vocabulary.put("0", "AC_CatchCategory_1"); + vocabulary.put("G", "AC_CatchCategory_2"); + vocabulary.put("P", "AC_CatchCategory_3"); + vocabulary.put("TP", "AC_CatchCategory_4"); Map<String, String> fromDB = persistenceService.getVocabulary(); vocabulary.putAll(fromDB); diff --git a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlAccousticExport.java b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlAccousticExport.java index 62ff4f4..66b229b 100644 --- a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlAccousticExport.java +++ b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlAccousticExport.java @@ -202,9 +202,9 @@ public class XmlAccousticExport implements EchoBaseService { xml.create("Date", EchoBaseCsvUtil.ISO8611_DATE_FORMATTER.format(calibration.getDate())); xml.create("AcquisitionMethod", - "IDREF", calibration.getAquisitionMethod()); + "IDREF", vocabulary.getVocabularyCode(calibration.getAquisitionMethod(), "AC_AcquisitionMethod_SS")); xml.create("ProcessingMethod", - "IDREF", calibration.getProcessingMethod()); + "IDREF", vocabulary.getVocabularyCode(calibration.getProcessingMethod(), "AC_ProcessingMethod_pmethod1")); xml.create("AccuracyEstimate", calibration.getAccuracyEstimate()); xml.create("Report", diff --git a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlBioticExport.java b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlBioticExport.java index 4d8ce25..d35f359 100644 --- a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlBioticExport.java +++ b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlBioticExport.java @@ -8,13 +8,18 @@ import fr.ifremer.echobase.entities.data.Operation; import fr.ifremer.echobase.entities.data.OperationMetadataValue; import fr.ifremer.echobase.entities.data.Sample; import fr.ifremer.echobase.entities.data.SampleData; +import fr.ifremer.echobase.entities.data.Transect; +import fr.ifremer.echobase.entities.data.Transit; import fr.ifremer.echobase.entities.data.Voyage; -import fr.ifremer.echobase.entities.references.Species; +import fr.ifremer.echobase.entities.references.SampleDataTypeImpl; import fr.ifremer.echobase.entities.references.SpeciesCategory; import fr.ifremer.echobase.services.EchoBaseService; import fr.ifremer.echobase.services.csv.EchoBaseCsvUtil; import java.io.IOException; +import java.util.ArrayList; import java.util.Collection; +import java.util.HashMap; +import java.util.Map; import javax.inject.Inject; /* @@ -55,65 +60,108 @@ public class XmlBioticExport implements EchoBaseService { "xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance", "xmlns:xsd", "http://www.w3.org/2001/XMLSchema"); - exportCruise(voyage, xml); + Collection<Transit> transits = voyage.getTransit(); + Transit transit = transits.iterator().next(); + Collection<Transect> transects = transit.getTransect(); + Transect transect = transects.iterator().next(); + + exportCruise(voyage, transect, xml); + + int index = 1; Collection<Operation> operations = voyage.getAllOperations(); for (Operation operation : operations) { - + // EXPORT HAUL - exportHaul(operation, xml); + exportHaul(operation, index++, xml); + + Map<String, Float> totalWeight = new HashMap<String, Float>(); + Map<String, Integer> totalNumber = new HashMap<String, Integer>(); + Collection<Sample> subSamples = new ArrayList<Sample>(); Collection<Sample> samples = operation.getSample(); for (Sample sample : samples) { - // EXPORT CATCH - exportCatch(sample, xml); + String name = sample.getSampleType().getName(); - Collection<SampleData> datas = sample.getSampleData(); - for (SampleData data : datas) { + if ("Total".equals(name)) { + SpeciesCategory category = sample.getSpeciesCategory(); + String code = category.getSpecies().getBaracoudaCode(); + + Float weight = totalWeight.get(code); + if (weight == null) { + weight = 0f; + } - // EXPORT BIOLOGY - exportBiology(data, xml); + Float sampleWeight = sample.getSampleWeight(); + if (sampleWeight != null) { + weight += sampleWeight; + } + totalWeight.put(code, weight); + + Integer number = totalNumber.get(code); + if (number == null) { + number = 0; + } + + Integer numberSampled = sample.getNumberSampled(); + if (numberSampled != null) { + number += numberSampled; + } + totalNumber.put(code, number); + + subSamples.add(sample); } + + if ("Subsample".equals(name)) { + subSamples.add(sample); + } + } + + for (Sample sample : subSamples) { + SpeciesCategory category = sample.getSpeciesCategory(); + String code = category.getSpecies().getBaracoudaCode(); + + Float weight = totalWeight.get(code); + Integer number = totalNumber.get(code); + + // EXPORT CATCH + exportCatch(sample, weight, number, xml); + + // EXPORT BIOLOGY: nothing we don't have the data for the moment + xml.close("Catch"); } + xml.close("Haul"); } - + xml.close("Cruise"); xml.close("Biotic"); } - public void exportCruise(Voyage voyage, XmlWriter xml) throws IOException { + public void exportCruise(Voyage voyage, Transect transect, XmlWriter xml) throws IOException { xml.open("Cruise"); xml.create("Survey", - "IDREF", "AC_Survey_HERAS"); + "IDREF", vocabulary.getVocabularyCode(voyage.getMission().getName(), "AC_Survey_PELGAS")); xml.create("Country", - "IDREF", "ISO_3166_DK"); + "IDREF", vocabulary.getVocabularyCode(voyage.getMission().getCountry(), "ISO_3166_FR")); xml.create("Platform", - "IDREF", "SHIPC_26D4"); + "IDREF", vocabulary.getVocabularyCode(transect.getVessel().getCode(), "SHIPC_35HT")); xml.create("StartDate", EchoBaseCsvUtil.ISO8611_DATE_FORMATTER.format(voyage.getStartDate())); xml.create("EndDate", EchoBaseCsvUtil.ISO8611_DATE_FORMATTER.format(voyage.getEndDate())); xml.create("Organisation", - "IDREF", "EDMO_2195"); + "IDREF", vocabulary.getVocabularyCode(voyage.getMission().getInstitution(), "EDMO_541")); xml.create("LocalID", voyage.getTopiaId()); } - public void exportHaul(Operation operation, XmlWriter xml) throws IOException { + public void exportHaul(Operation operation, int number, XmlWriter xml) throws IOException { xml.open("Haul"); - Collection<GearMetadataValue> gearMetadataValues = operation.getGearMetadataValue(); - ImmutableMap<String, GearMetadataValue> gearMetadatas = Maps.uniqueIndex(gearMetadataValues, new Function<GearMetadataValue, String>() { - @Override - public String apply(GearMetadataValue value) { - return value.getGearMetadata().getName(); - } - }); - Collection<OperationMetadataValue> operationMetadataValues = operation.getOperationMetadataValue(); ImmutableMap<String, OperationMetadataValue> operationMetadatas = Maps.uniqueIndex(operationMetadataValues, new Function<OperationMetadataValue, String>() { @Override @@ -122,100 +170,170 @@ public class XmlBioticExport implements EchoBaseService { } }); + String gearCode = operation.getGear().getGearCode(); + OperationMetadataValue meanWaterDepthMeta = operationMetadatas.get("MeanWaterDepth"); + float meanWaterDepth = Float.parseFloat(meanWaterDepthMeta.getDataValue()); + + float minTrawlDepth; + float maxTrawlDepth; + + String depthStratum = operation.getDepthStratum().getId(); + if (depthStratum.equals("SURF")) { + minTrawlDepth = 0; + maxTrawlDepth = 30; + + } else { + minTrawlDepth = meanWaterDepth; + maxTrawlDepth = minTrawlDepth; + + switch (gearCode) { + case "76x70": + minTrawlDepth -= 20; + break; + case "57x52": + minTrawlDepth -= 15; + break; + case "942OBS": + minTrawlDepth -= 30; + break; + } + } + + Float startLatitude = operation.getGearShootingStartLatitude(); + Float startLongitude = operation.getGearShootingStartLongitude(); + Float endLatitude = operation.getGearShootingEndLatitude(); + Float endLongitude = operation.getGearShootingEndLongitude(); + + int distance = (int) (Math.sqrt(Math.pow(startLatitude - startLatitude, 2) + Math.pow(endLongitude - startLongitude, 2)) * 60 * 1852); + + int netopening = 0; + switch (gearCode) { + case "76x70": + netopening = 20; + break; + case "57x52": + netopening = 15; + break; + case "942OBS": + netopening = 30; + break; + } + xml.create("Gear", - "IDREF", operation.getTopiaId()); - xml.create("Number"); - xml.create("StationName"); + "IDREF", vocabulary.getVocabularyCode(gearCode, "Gear_PAR")); + xml.create("Number", + number); + xml.create("StationName", + operation.getId()); xml.create("StartTime", EchoBaseCsvUtil.ISO8611_DATE_FORMATTER.format(operation.getGearShootingStartTime())); xml.create("Duration", (int)((operation.getGearShootingEndTime().getTime() - operation.getGearShootingStartTime().getTime()) / (1000 * 60))); xml.create("Validity", - "IDREF", ""); - xml.create("StartLatitude", - operation.getGearShootingStartLatitude()); - xml.create("StartLongitude", - operation.getGearShootingStartLongitude()); - xml.create("StopLatitude", - operation.getGearShootingEndLatitude()); - xml.create("StopLongitude", - operation.getGearShootingEndLongitude()); - xml.create("StatisticalRectangle"); - xml.create("MinTrawlDepth"); - xml.create("MaxTrawlDepth"); - xml.create("BottomDepth"); - xml.create("Distance"); - xml.create("Netopening"); - xml.create("CodendMesh"); - xml.create("SweepLength"); - xml.create("GearExceptions", - "IDREF", ""); - xml.create("DoorType", - "IDREF", ""); - xml.create("WarpLength"); - xml.create("WarpDiameter"); - xml.create("WarpDensity"); - xml.create("DoorSurface"); - xml.create("DoorWeight"); - xml.create("DoorSpread"); - xml.create("WingSpread"); - xml.create("Buoyancy"); - xml.create("KiteArea"); - xml.create("GroundRopeWeight"); - xml.create("Rigging"); - xml.create("Tickler"); - xml.create("HydrographicStationID"); - xml.create("TowDirection"); - xml.create("SpeedGround"); - xml.create("SpeedWater"); - xml.create("WindDirection"); - xml.create("WindSpeed"); - xml.create("SwellDirection"); - xml.create("SwellHeight"); - xml.create("LogDistance"); + "IDREF", "AC_HaulValidity_V"); + xml.create("StartLatitude", startLatitude); + xml.create("StartLongitude", startLongitude); + xml.create("StopLatitude", endLatitude); + xml.create("StopLongitude", endLongitude); +// xml.create("StatisticalRectangle"); + xml.create("MinTrawlDepth", + minTrawlDepth); + xml.create("MaxTrawlDepth", + maxTrawlDepth); + xml.create("BottomDepth", + meanWaterDepth); + xml.create("Distance", + distance); + xml.create("Netopening", + netopening); +// xml.create("CodendMesh"); +// xml.create("SweepLength"); +// xml.create("GearExceptions", +// "IDREF", ""); +// xml.create("DoorType", +// "IDREF", ""); +// xml.create("WarpLength"); +// xml.create("WarpDiameter"); +// xml.create("WarpDensity"); +// xml.create("DoorSurface"); +// xml.create("DoorWeight"); +// xml.create("DoorSpread"); +// xml.create("WingSpread"); +// xml.create("Buoyancy"); +// xml.create("KiteArea"); +// xml.create("GroundRopeWeight"); +// xml.create("Rigging"); +// xml.create("Tickler"); +// xml.create("HydrographicStationID"); +// xml.create("TowDirection"); +// xml.create("SpeedGround"); +// xml.create("SpeedWater"); +// xml.create("WindDirection"); +// xml.create("WindSpeed"); +// xml.create("SwellDirection"); +// xml.create("SwellHeight"); +// xml.create("LogDistance"); } - public void exportCatch(Sample sample, XmlWriter xml) throws IOException { + public void exportCatch(Sample sample, Float weight, Integer number, XmlWriter xml) throws IOException { xml.open("Catch"); - SpeciesCategory category = sample.getSpeciesCategory(); - boolean hasCategory = category != null; - - boolean hasSpecies = false; - Species species = null; - if (hasCategory) { - species = category.getSpecies(); - hasSpecies = species != null; + Map<String, String> sampleDataValues = new HashMap<String, String>(); + Collection<SampleData> datas = sample.getSampleData(); + for (SampleData data : datas) { + + String name = data.getSampleDataType().getName(); + Float value = data.getDataValue(); + String label = data.getDataLabel(); + + if (SampleDataTypeImpl.LTCM0_5.equals(name) + || SampleDataTypeImpl.L_TCM_1.equals(name)) { + + sampleDataValues.put(SampleDataTypeImpl.NUMBER_AT_LENGTH, String.valueOf(value)); + sampleDataValues.put(name, label); + sampleDataValues.put("LengthClass", label); + + } else { + sampleDataValues.put(name, String.valueOf(value)); + } } + SpeciesCategory category = sample.getSpeciesCategory(); + xml.create("DataType", "IDREF", "AC_CatchDataType_R"); xml.create("SpeciesCode", - "IDREF", hasSpecies ? species.getBaracoudaCode() : null); + "IDREF", "SpecWoRMS_" + category.getSpecies().getWormsCode()); xml.create("SpeciesValidity", - "IDREF", ""); + "IDREF", "AC_SpeciesValidity_1"); xml.create("SpeciesTotalNumber", - sample.getNumberSampled()); + number); xml.create("WeightUnit", "IDREF", "AC_WeightUnit_kg"); xml.create("SpeciesTotalWeight", - sample.getSampleWeight()); + weight.intValue()); + xml.create("SpeciesCategory", - "IDREF", hasSpecies ? species.getTaxonCode() : null); - xml.create("SpeciesSex", - "IDREF", hasCategory ? category.getSexCategoryLabel() : null); - xml.create("CategoryWeight"); - xml.create("SubsampledNumber"); - xml.create("SubsamplingFactor"); - xml.create("SubsampleWeight"); + "IDREF", vocabulary.getVocabularyCode(category.getSizeCategoryLabel(), "AC_CatchCategory_1")); +// xml.create("SpeciesSex"); +// xml.create("CategoryWeight"); + xml.create("SubsampledNumber", + sample.getNumberSampled()); + xml.create("SubsamplingFactor", + weight / sample.getSampleWeight()); + xml.create("SubsampleWeight", + sample.getSampleWeight()); + xml.create("LengthCode", - "IDREF", "AC_LengthCode_mm"); + "IDREF", sampleDataValues.containsKey(SampleDataTypeImpl.LTCM0_5) ? "AC_LengthCode_halfcm" : "AC_LengthCode_cm"); xml.create("LengthClass", - hasCategory ? category.getLengthClass() : null); + sampleDataValues.get("LengthClass")); xml.create("LengthType", "IDREF", "AC_LengthMeasurementType_1"); - xml.create("NumberAtLength"); - xml.create("WeightAtLength"); + xml.create("NumberAtLength", + sampleDataValues.get(SampleDataTypeImpl.NUMBER_AT_LENGTH)); + xml.create("WeightAtLength", + sampleDataValues.get(SampleDataTypeImpl.WEIGHT_AT_LENGTHKG)); } public void exportBiology(SampleData data, XmlWriter xml) throws IOException { diff --git a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlWriter.java b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlWriter.java index b368b0d..6ce3845 100644 --- a/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlWriter.java +++ b/echobase-services/src/main/java/fr/ifremer/echobase/services/service/atlantos/xml/XmlWriter.java @@ -63,6 +63,8 @@ public class XmlWriter { Object innerValue = attributes[attributes.length - 1]; if (innerValue != null) { this.writer.append(">" + innerValue); + } else { + this.writer.append(">"); } this.writer.append("</" + tag + ">\n"); } else { -- To stop receiving notification emails like this one, please contact codelutin.com SCM administrator <admin+scm@codelutin.com>.