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BI-2127 Position Information missing from exp download file #356

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Merged
davedrp merged 5 commits into from
May 22, 2024
Merged

BI-2127 Position Information missing from exp download file #356

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e7e46b7
[BI-2127] return Lat, Long, Elevation, and RTK
davedrp May 13, 2024
1a909b6
[BI-2127] protect against nulls
davedrp May 13, 2024
5a2100c
[BI-2127] protect against a double beign NaN (not yet set) before con…
davedrp May 14, 2024
4bcc841
Merge branch 'develop' into bug/BI-2127
davedrp May 17, 2024
2e41d4c
[BI-2127] made code more readable
davedrp May 17, 2024
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49 changes: 46 additions & 3 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
package org.breedinginsight.brapi.v2.services;

import com.github.filosganga.geogson.model.Coordinates;
import com.github.filosganga.geogson.model.positions.SinglePosition;
import com.google.gson.JsonObject;
import io.micronaut.context.annotation.Property;
import io.micronaut.http.MediaType;
import io.micronaut.http.server.exceptions.InternalServerException;
Expand Down Expand Up @@ -465,6 +468,26 @@ private Map<String, Object> createExportRow(
row.put(ExperimentObservation.Columns.EXP_TYPE, experiment.getAdditionalInfo().getAsJsonObject().get(BrAPIAdditionalInfoFields.EXPERIMENT_TYPE).getAsString());
row.put(ExperimentObservation.Columns.ENV, Utilities.removeProgramKeyAndUnknownAdditionalData(study.getStudyName(), program.getKey()));
row.put(ExperimentObservation.Columns.ENV_LOCATION, Utilities.removeProgramKey(study.getLocationName(), program.getKey()));

// Lat, Long, Elevation
Coordinates coordinates = extractCoordinates(ou);
Optional.ofNullable(coordinates)
.map(c -> doubleToString(c.getLat()))
.ifPresent(lat -> row.put(ExperimentObservation.Columns.LAT, lat));
Optional.ofNullable(coordinates)
.map(c -> doubleToString(c.getLon()))
.ifPresent(lon -> row.put(ExperimentObservation.Columns.LONG, lon));
Optional.ofNullable(coordinates)
.map(c -> doubleToString(c.getAlt()))
.ifPresent(elevation -> row.put(ExperimentObservation.Columns.ELEVATION, elevation));

// RTK
JsonObject additionalInfo = ou.getAdditionalInfo();
String rtk = ( additionalInfo==null || additionalInfo.get(BrAPIAdditionalInfoFields.RTK) ==null )
? null
: additionalInfo.get(BrAPIAdditionalInfoFields.RTK).getAsString();
row.put(ExperimentObservation.Columns.RTK, rtk);

BrAPISeason season = seasonDAO.getSeasonById(study.getSeasons().get(0), program.getId());
row.put(ExperimentObservation.Columns.ENV_YEAR, season.getYear());
row.put(ExperimentObservation.Columns.EXP_UNIT_ID, Utilities.removeProgramKeyAndUnknownAdditionalData(ou.getObservationUnitName(), program.getKey()));
Expand All @@ -484,11 +507,13 @@ private Map<String, Object> createExportRow(
.findFirst();
blockLevel.ifPresent(brAPIObservationUnitLevelRelationship ->
row.put(ExperimentObservation.Columns.BLOCK_NUM, Integer.parseInt(brAPIObservationUnitLevelRelationship.getLevelCode())));
if (ou.getObservationUnitPosition() != null && ou.getObservationUnitPosition().getPositionCoordinateX() != null &&
ou.getObservationUnitPosition().getPositionCoordinateY() != null) {

//Row and Column
if ( ou.getObservationUnitPosition() != null ) {
Comment on lines +510 to +512
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@mlm483 mlm483 May 15, 2024

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Is it allowed to upload a file that has row but not column data or vice versa? I think this change makes sense regardless.

row.put(ExperimentObservation.Columns.ROW, ou.getObservationUnitPosition().getPositionCoordinateX());
row.put(ExperimentObservation.Columns.COLUMN, ou.getObservationUnitPosition().getPositionCoordinateY());
}

if (ou.getTreatments() != null && !ou.getTreatments().isEmpty()) {
row.put(ExperimentObservation.Columns.TREATMENT_FACTORS, ou.getTreatments().get(0).getFactor());
} else {
Expand All @@ -499,7 +524,25 @@ private Map<String, Object> createExportRow(
return row;
}


private String doubleToString(double val){
return Double.isNaN(val) ? null : String.valueOf( val );
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@mlm483 mlm483 May 15, 2024

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Nice.

}
private Coordinates extractCoordinates(BrAPIObservationUnit ou){
Coordinates coordinates = null;
if ( ou.getObservationUnitPosition()!=null
&& ou.getObservationUnitPosition().getGeoCoordinates()!=null
&& ou.getObservationUnitPosition().getGeoCoordinates().getGeometry()!=null
&& ou.getObservationUnitPosition().getGeoCoordinates().getGeometry().positions()!=null
)
{
Object o = ou.getObservationUnitPosition().getGeoCoordinates().getGeometry().positions();
if (o instanceof SinglePosition){
SinglePosition sp = (SinglePosition)o;
coordinates= sp.coordinates();
}
}
return coordinates;
}

private void addObsVarColumns(
List<Column> columns,
Expand Down