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Merged
dmeidlin merged 1 commit into from
Aug 15, 2024
Merged

BI-2134 GeoGson Type Adapter Bug #389

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32 changes: 10 additions & 22 deletions ...g/breedinginsight/brapps/importer/services/processors/experiment/ExperimentUtilities.java
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Expand Up @@ -17,52 +17,40 @@

package org.breedinginsight.brapps.importer.services.processors.experiment;

import com.github.filosganga.geogson.gson.GeometryAdapterFactory;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonObject;
import com.google.gson.JsonSyntaxException;
import io.micronaut.http.HttpStatus;
import io.micronaut.http.exceptions.HttpStatusException;
import io.reactivex.functions.Function;
import org.apache.commons.collections4.map.CaseInsensitiveMap;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIStudy;
import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
import org.breedinginsight.brapps.importer.model.response.ImportObjectState;
import org.breedinginsight.brapps.importer.model.response.PendingImportObject;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.model.AppendOverwriteMiddlewareContext;
import org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.exceptions.UnprocessableEntityException;

import javax.inject.Singleton;
import java.util.*;
import java.util.stream.Collectors;

import com.google.gson.JsonObject;
import io.micronaut.http.HttpStatus;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.collections4.map.CaseInsensitiveMap;
import org.apache.commons.lang3.StringUtils;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIStudy;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.brapi.v2.model.pheno.BrAPIObservation;
import org.brapi.v2.model.pheno.BrAPIScaleValidValuesCategories;
import org.breedinginsight.api.model.v1.response.ValidationError;
import org.breedinginsight.api.model.v1.response.ValidationErrors;
import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
import org.breedinginsight.brapps.importer.model.response.ImportObjectState;
import org.breedinginsight.brapps.importer.model.response.PendingImportObject;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.model.AppendOverwriteMiddlewareContext;
import org.breedinginsight.brapps.importer.services.processors.experiment.create.model.PendingData;
import org.breedinginsight.brapps.importer.services.processors.experiment.create.model.ProcessedPhenotypeData;
import org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Scale;
import org.breedinginsight.model.Trait;
import tech.tablesaw.columns.Column;

import javax.inject.Singleton;
import java.math.BigDecimal;
import java.time.OffsetDateTime;
import java.time.format.DateTimeFormatter;
Expand All @@ -88,7 +76,7 @@ public class ExperimentUtilities {
Gson gson;

public ExperimentUtilities() {
this.gson = new Gson();
this.gson = new GsonBuilder().registerTypeAdapterFactory(new GeometryAdapterFactory()).create();
}

/**
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4 changes: 3 additions & 1 deletion ...importer/services/processors/experiment/appendoverwrite/factory/data/OverwrittenData.java
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Expand Up @@ -17,7 +17,9 @@

package org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.factory.data;

import com.github.filosganga.geogson.gson.GeometryAdapterFactory;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import io.micronaut.context.annotation.Prototype;
Expand Down Expand Up @@ -91,7 +93,7 @@ public OverwrittenData(boolean canOverwrite,
this.program = program;
this.fieldValidator = fieldValidator;
this.observationService = observationService;
this.gson = new Gson();
this.gson = new GsonBuilder().registerTypeAdapterFactory(new GeometryAdapterFactory()).create();
}

@Override
Expand Down
10 changes: 6 additions & 4 deletions ...services/processors/experiment/appendoverwrite/middleware/process/ImportTableProcess.java
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Expand Up @@ -17,7 +17,9 @@

package org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.middleware.process;

import com.github.filosganga.geogson.gson.GeometryAdapterFactory;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import io.micronaut.context.annotation.Property;
import io.micronaut.context.annotation.Prototype;
import lombok.extern.slf4j.Slf4j;
Expand All @@ -44,11 +46,11 @@
import org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.factory.data.VisitedObservationData;
import org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.model.AppendOverwriteMiddleware;
import org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.model.AppendOverwriteMiddlewareContext;
import org.breedinginsight.brapps.importer.services.processors.experiment.validator.field.FieldValidator;
import org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.model.MiddlewareException;
import org.breedinginsight.brapps.importer.services.processors.experiment.service.ObservationService;
import org.breedinginsight.brapps.importer.services.processors.experiment.service.ObservationVariableService;
import org.breedinginsight.brapps.importer.services.processors.experiment.service.StudyService;
import org.breedinginsight.brapps.importer.services.processors.experiment.validator.field.FieldValidator;
import org.breedinginsight.dao.db.tables.pojos.TraitEntity;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Trait;
Expand All @@ -60,12 +62,12 @@
import tech.tablesaw.columns.Column;

import javax.inject.Inject;
import java.time.OffsetDateTime;
import java.util.*;
import java.util.stream.Collectors;

import static org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants.*;
import static org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants.ErrMessage.MULTIPLE_EXP_TITLES;
import static org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants.TIMESTAMP_PREFIX;
import static org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants.TIMESTAMP_REGEX;

@Slf4j
@Prototype
Expand Down Expand Up @@ -96,7 +98,7 @@ public ImportTableProcess(StudyService studyService,
this.brAPIObservationDAO = brAPIObservationDAO;
this.observationService = observationService;
this.experimentUtil = experimentUtil;
this.gson = new Gson();
this.gson = new GsonBuilder().registerTypeAdapterFactory(new GeometryAdapterFactory()).create();
this.fieldValidator = fieldValidator;
this.statistic = statistic;
this.processedDataFactory = processedDataFactory;
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/org/breedinginsight/model/delta/DeltaEntity.java
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@@ -1,6 +1,8 @@
package org.breedinginsight.model.delta;

import com.github.filosganga.geogson.gson.GeometryAdapterFactory;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import lombok.NonNull;

public abstract class DeltaEntity<T> {
Expand All @@ -13,7 +15,7 @@ public abstract class DeltaEntity<T> {
// Note: do not use @Inject, DeltaEntity<T> are always constructed by DeltaEntityFactory.
protected DeltaEntity(@NonNull T entity) {
this.entity = entity;
this.gson = new Gson();
this.gson = new GsonBuilder().registerTypeAdapterFactory(new GeometryAdapterFactory()).create();
}

protected T getEntity() {
Expand Down