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[BI-873] Remove crosses from the germplasm importer #86

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Merged
ctucker3 merged 5 commits into from
May 13, 2021
Merged

[BI-873] Remove crosses from the germplasm importer #86

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8f89499
update brapi image
May 4, 2021
1df8a98
fix import post method
May 4, 2021
7f5492a
remove cross from germplasm import
May 4, 2021
54c4dc0
add program id to germplasm for germplasm import
May 5, 2021
b5a41cc
PR changes to germplasm import
May 10, 2021
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2 changes: 1 addition & 1 deletion docker-compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ services:
aliases:
- dbserver
brapi-server:
image: breedinginsight/brapi-java-server:v2.0-3
image: breedinginsight/brapi-java-server:v2.0-4
container_name: brapi-server
depends_on:
- bidb
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2 changes: 0 additions & 2 deletions src/main/java/org/breedinginsight/brapps/importer/daos/BrAPIGermplasmDAO.java
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Expand Up @@ -48,8 +48,6 @@ public BrAPIGermplasmDAO(BrAPIProvider brAPIProvider) {
public List<BrAPIGermplasm> getGermplasmByName(List<String> germplasmNames, BrAPIProgram brAPIProgram) throws ApiException {
BrAPIGermplasmSearchRequest germplasmSearch = new BrAPIGermplasmSearchRequest();
germplasmSearch.germplasmNames(germplasmNames);
// Germplasm doesn't have program attached. Do species as next best thing
germplasmSearch.setCommonCropNames(List.of(brAPIProgram.getCommonCropName()));
germplasmSearch.setPageSize(BrAPIDAOUtil.RESULTS_PER_QUERY);
GermplasmApi api = brAPIProvider.getGermplasmApi(BrAPIClientType.CORE);
return BrAPIDAOUtil.search(
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35 changes: 27 additions & 8 deletions src/main/java/org/breedinginsight/brapps/importer/model/base/Germplasm.java
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Expand Up @@ -21,12 +21,11 @@
import lombok.NoArgsConstructor;
import lombok.Setter;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIProgram;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.breedinginsight.brapps.importer.model.config.ImportFieldMetadata;
import org.breedinginsight.brapps.importer.model.config.ImportMappingRequired;
import org.breedinginsight.brapps.importer.model.config.ImportFieldTypeEnum;
import org.breedinginsight.brapps.importer.model.config.ImportFieldType;
import org.breedinginsight.brapps.importer.model.config.*;

import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
Expand All @@ -38,11 +37,27 @@
description = "A germplasm object corresponds to a non-physical entity and is used to track a unique genetic composition. This is commonly used for populations.")
public class Germplasm implements BrAPIObject {

public static final String GERMPLASM_NAME_TARGET = "germplasmName";

@ImportFieldType(type= ImportFieldTypeEnum.TEXT)
@ImportMappingRequired
@ImportFieldMetadata(id="germplasmName", name="Germplasm Name", description = "Name of germplasm")
private String germplasmName;

@ImportFieldType(type= ImportFieldTypeEnum.RELATIONSHIP)
@ImportFieldRelations(relations = {
@ImportFieldRelation(type = ImportRelationType.DB_LOOKUP, importFields = {GERMPLASM_NAME_TARGET}),
})
@ImportFieldMetadata(id="femaleParent", name="Female Parent", description = "The female parent of the germplasm.")
private MappedImportRelation femaleParent;

@ImportFieldType(type= ImportFieldTypeEnum.RELATIONSHIP)
@ImportFieldRelations(relations = {
@ImportFieldRelation(type = ImportRelationType.DB_LOOKUP, importFields = {GERMPLASM_NAME_TARGET}),
})
@ImportFieldMetadata(id="maleParent", name="Male Parent", description = "The male parent of the germplasm. Can be left blank for self crosses.")
private MappedImportRelation maleParent;

@ImportFieldType(type= ImportFieldTypeEnum.TEXT)
@ImportFieldMetadata(id="germplasmPUI", name="Germplasm Permanent Unique Identifier", description = "The Permanent Unique Identifier which represents a germplasm from the source or donor.")
private String germplasmPUI;
Expand Down Expand Up @@ -78,7 +93,6 @@ public BrAPIGermplasm constructBrAPIGermplasm() {
germplasm.setGermplasmName(getGermplasmName());
germplasm.setGermplasmPUI(getGermplasmPUI());
germplasm.setAccessionNumber(getAccessionNumber());
germplasm.setAccessionNumber(getAccessionNumber());
germplasm.setCollection(getCollection());
//TODO: Need to check that the acquisition date it in date format
//brAPIGermplasm.setAcquisitionDate(pedigreeImport.getGermplasm().getAcquisitionDate());
Expand All @@ -99,10 +113,15 @@ public BrAPIGermplasm constructBrAPIGermplasm() {
return germplasm;
}

public BrAPIGermplasm constructBrAPIGermplasm(String species) {
public BrAPIGermplasm constructBrAPIGermplasm(BrAPIProgram brAPIProgram) {
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@nickpalladino nickpalladino May 10, 2021

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Not here but in the constructBrAPIGermplasm without parameters, getting an error for germplasm.setAccessionNumber(getAccessionNumber()); and also duplicated.

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@ctucker3 ctucker3 May 10, 2021

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Spoke with Nick, the error is his IntelliJ environment because github actions builds it fine. I removed the duplicate.

BrAPIGermplasm germplasm = constructBrAPIGermplasm();
germplasm.setSpecies(species);
germplasm.setCommonCropName(species);
germplasm.setCommonCropName(brAPIProgram.getCommonCropName());

// Set programId in additionalInfo
Map<String, String> additionalInfo = germplasm.getAdditionalInfo() != null ? germplasm.getAdditionalInfo() : new HashMap<>();
additionalInfo.put("programId", brAPIProgram.getProgramDbId());
germplasm.setAdditionalInfo(additionalInfo);

return germplasm;
}

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