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BI-1365 - Scope ontology terms to be within a program when saved over BrAPI #172

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Merged
nickpalladino merged 4 commits into from
May 26, 2022
Merged

BI-1365 - Scope ontology terms to be within a program when saved over BrAPI #172

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f3ccb50
Add program keys for creation
nickpalladino Mar 29, 2022
523d7f1
Add program keys for update
nickpalladino Mar 29, 2022
921ddb0
Added test for brapi values
nickpalladino Apr 11, 2022
a523f57
Merge branch 'develop' into feature/BI-1365
nickpalladino May 26, 2022
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16 changes: 8 additions & 8 deletions src/main/java/org/breedinginsight/daos/TraitDAO.java
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -285,7 +285,7 @@ public List<Trait> createTraitsBrAPI(List<Trait> traits, User actingUser, Progra
.referenceID(trait.getMethod().getId().toString())
.referenceSource(referenceSource);
BrAPIMethod brApiMethod = new BrAPIMethod()
.methodName(String.format("%s %s", trait.getMethod().getDescription(), trait.getMethod().getMethodClass()))
.methodName(String.format("%s %s [%s]", trait.getMethod().getDescription(), trait.getMethod().getMethodClass(), program.getKey()))
.externalReferences(List.of(methodReference))
.methodClass(trait.getMethod().getMethodClass())
.description(trait.getMethod().getDescription())
Expand All @@ -301,7 +301,7 @@ public List<Trait> createTraitsBrAPI(List<Trait> traits, User actingUser, Progra
.max(trait.getScale().getValidValueMax())
.min(trait.getScale().getValidValueMin());
BrAPIScale brApiScale = new BrAPIScale()
.scaleName(trait.getScale().getScaleName())
.scaleName(String.format("%s [%s]", trait.getScale().getScaleName(), program.getKey()))
.externalReferences(List.of(scaleReference))
.dataType(brApiTraitDataType)
.decimalPlaces(trait.getScale().getDecimalPlaces())
Expand All @@ -312,7 +312,7 @@ public List<Trait> createTraitsBrAPI(List<Trait> traits, User actingUser, Progra
.referenceID(trait.getId().toString())
.referenceSource(referenceSource);
BrAPITrait brApiTrait = new BrAPITrait()
.traitName(String.format("%s %s", trait.getEntity(), trait.getAttribute()))
.traitName(String.format("%s %s [%s]", trait.getEntity(), trait.getAttribute(), program.getKey()))
.traitDescription(trait.getTraitDescription())
.synonyms(trait.getSynonyms())
.status("active")
Expand All @@ -330,7 +330,7 @@ public List<Trait> createTraitsBrAPI(List<Trait> traits, User actingUser, Progra
.scale(brApiScale)
.trait(brApiTrait)
.externalReferences(List.of(variableReference))
.observationVariableName(trait.getObservationVariableName())
.observationVariableName(String.format("%s [%s]", trait.getObservationVariableName(), program.getKey()))
.status("active")
.language("english")
.scientist(actingUser.getName())
Expand Down Expand Up @@ -405,14 +405,14 @@ public Trait updateTraitBrAPI(Trait trait, Program program) {
BrAPIObservationVariable existingVariable = getBrAPIVariable(variablesAPI, trait.getId());

// Change method
existingVariable.getMethod().setMethodName(String.format("%s %s", trait.getMethod().getDescription(), trait.getMethod().getMethodClass()));
existingVariable.getMethod().setMethodName(String.format("%s %s [%s]", trait.getMethod().getDescription(), trait.getMethod().getMethodClass(), program.getKey()));
existingVariable.getMethod().setMethodClass(trait.getMethod().getMethodClass());
existingVariable.getMethod().setDescription(trait.getMethod().getDescription());
existingVariable.getMethod().setFormula(trait.getMethod().getFormula());

// Change scale
BrAPITraitDataType brApiTraitDataType = BrAPITraitDataType.valueOf(trait.getScale().getDataType().toString());
existingVariable.getScale().setScaleName(trait.getScale().getScaleName());
existingVariable.getScale().setScaleName(String.format("%s [%s]", trait.getScale().getScaleName(), program.getKey()));
existingVariable.getScale().setDataType(brApiTraitDataType);
existingVariable.getScale().setDecimalPlaces(trait.getScale().getDecimalPlaces());
BrAPIScaleValidValues brApiScaleValidValues = new BrAPIScaleValidValues()
Expand All @@ -422,7 +422,7 @@ public Trait updateTraitBrAPI(Trait trait, Program program) {
existingVariable.getScale().setValidValues(brApiScaleValidValues);

// Change trait
existingVariable.getTrait().setTraitName(String.format("%s %s", trait.getEntity(), trait.getAttribute()));
existingVariable.getTrait().setTraitName(String.format("%s %s [%s]", trait.getEntity(), trait.getAttribute(), program.getKey()));
existingVariable.getTrait().setTraitDescription(trait.getTraitDescription());
existingVariable.getTrait().setSynonyms(trait.getSynonyms());
existingVariable.getTrait().setEntity(trait.getProgramObservationLevel().getName());
Expand All @@ -431,7 +431,7 @@ public Trait updateTraitBrAPI(Trait trait, Program program) {
existingVariable.getTrait().setAttribute(trait.getAttribute());

// Change variable
existingVariable.setObservationVariableName(trait.getObservationVariableName());
existingVariable.setObservationVariableName(String.format("%s [%s]", trait.getObservationVariableName(), program.getKey()));
existingVariable.setDefaultValue(trait.getDefaultValue());
existingVariable.setSynonyms(trait.getSynonyms());
if (trait.getActive() == null || trait.getActive()){
Expand Down
112 changes: 112 additions & 0 deletions src/test/java/org/breedinginsight/api/v1/controller/TraitControllerIntegrationTest.java
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
import lombok.SneakyThrows;
import org.brapi.client.v2.ApiResponse;
import org.brapi.client.v2.BrAPIClient;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.client.v2.model.queryParams.phenotype.VariableQueryParams;
import org.brapi.client.v2.modules.phenotype.ObservationVariablesApi;
import org.brapi.client.v2.modules.phenotype.ObservationsApi;
Expand All @@ -41,6 +42,7 @@
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationVariableListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationVariableListResponseResult;
import org.breedinginsight.BrAPITest;
import org.breedinginsight.TestUtils;
import org.breedinginsight.api.model.v1.request.ProgramRequest;
Expand Down Expand Up @@ -360,6 +362,116 @@ public void postTraitsMultiple() {
validTraits = traits;
}

@Test
@SneakyThrows
@Order(4)
public void checkBrapiValues() {

Trait trait1 = new Trait();
trait1.setTraitDescription("trait 1 description");
trait1.setEntity("entity1");
trait1.setObservationVariableName("Test Brapi");
trait1.setProgramObservationLevel(ProgramObservationLevel.builder().name("Plant").build());
Scale scale1 = new Scale();
scale1.setScaleName("Test Scale");
scale1.setDataType(DataType.TEXT);
Method method1 = new Method();
trait1.setScale(scale1);
trait1.setMethod(method1);

// Set the brapi properties
setBrAPIProperties(trait1);

// set the synonyms
trait1.setSynonyms(List.of("Test Trait", "test1", "test2"));

// Set the tags
trait1.setTags(List.of("leaf trait"));

List<Trait> traits = List.of(trait1);

// Call endpoint
Flowable<HttpResponse<String>> call = client.exchange(
POST("/programs/" + validProgram.getId() + "/traits", traits)
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
);
HttpResponse<String> res = call.blockingFirst();
assertEquals(HttpStatus.OK, res.getStatus());

JsonObject result = JsonParser.parseString(res.getBody().get()).getAsJsonObject().getAsJsonObject("result");
JsonArray data = result.getAsJsonArray("data");

for (JsonElement traitJson: data) {
JsonObject trait = (JsonObject) traitJson;
String traitName = trait.get("observationVariableName").getAsString();
if (traitName.equals(trait1.getObservationVariableName())) {
trait1.setId(UUID.fromString(trait.get("id").getAsString()));
}
}

String validProgramKey = validProgram.getKey();
BrAPIObservationVariable variable = getBrapiVariable(trait1.getObservationVariableName(), "Test Program");

assertEquals(String.format("%s [%s]", trait1.getObservationVariableName(), validProgramKey),
variable.getObservationVariableName(), "Unexpected observation variable name");
String methodName = String.format("%s %s", trait1.getMethod().getDescription(), trait1.getMethod().getMethodClass());
assertEquals(String.format("%s [%s]", methodName, validProgramKey),
variable.getMethod().getMethodName(), "Unexpected method name");
assertEquals(String.format("%s [%s]", trait1.getScale().getScaleName(), validProgramKey),
variable.getScale().getScaleName(), "Unexpected scale name");
String traitName = String.format("%s %s", trait1.getEntity(), trait1.getAttribute());
assertEquals(String.format("%s [%s]", traitName, validProgramKey),
variable.getTrait().getTraitName(), "Unexpected trait name");

// update
trait1.getMethod().setMethodClass("Observation");
trait1.getMethod().setDescription("Updated description");
trait1.setEntity("Updated entity");
trait1.setAttribute("Updated attribute");
trait1.setObservationVariableName("Updated name");
trait1.getScale().setScaleName("Updated Scale");

Flowable<HttpResponse<String>> call2 = client.exchange(
PUT("/programs/" + validProgram.getId() + "/traits", traits)
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
);
HttpResponse<String> response2 = call2.blockingFirst();
assertEquals(HttpStatus.OK, response2.getStatus());

variable = getBrapiVariable(trait1.getObservationVariableName(), "Test Program");

assertEquals(String.format("%s [%s]", trait1.getObservationVariableName(), validProgramKey),
variable.getObservationVariableName(), "Unexpected observation variable name");
methodName = String.format("%s %s", trait1.getMethod().getDescription(), trait1.getMethod().getMethodClass());
assertEquals(String.format("%s [%s]", methodName, validProgramKey),
variable.getMethod().getMethodName(), "Unexpected method name");
assertEquals(String.format("%s [%s]", trait1.getScale().getScaleName(), validProgramKey),
variable.getScale().getScaleName(), "Unexpected scale name");
traitName = String.format("%s %s", trait1.getEntity(), trait1.getAttribute());
assertEquals(String.format("%s [%s]", traitName, validProgramKey),
variable.getTrait().getTraitName(), "Unexpected trait name");

}

private BrAPIObservationVariable getBrapiVariable(String variableName, String programName) throws ApiException {
BrAPIClient client2 = new BrAPIClient(getProperties().get("brapi.server.pheno-url"));
ObservationVariablesApi variablesApi = new ObservationVariablesApi(client2);
VariableQueryParams queryParams = new VariableQueryParams();
ApiResponse<BrAPIObservationVariableListResponse> response = variablesApi.variablesGet(queryParams);

BrAPIObservationVariableListResponse variableResponse = response.getBody();
BrAPIObservationVariableListResponseResult result = variableResponse.getResult();
List<BrAPIObservationVariable> variables = result.getData();

Optional<BrAPIObservationVariable> searchResult = variables.stream().filter(
variable -> variable.getObservationVariableName().contains(variableName)
&& variable.getInstitution().equals(programName)).findFirst();

return searchResult.orElseThrow();
}

@Test
@SneakyThrows
@Order(4)
Expand Down