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Merged
timparsons merged 2 commits into from
Jul 24, 2023
Merged

BI-1842 - Append existing exp with observations isn't working #273

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2aca53d
[BI-1842] loosening the validation of observations to not throw an er…
timparsons Jul 18, 2023
efefd46
[BI-1842] Handling more cases of uploading new data when there's exis…
timparsons Jul 20, 2023
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38 changes: 32 additions & 6 deletions ...inginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@

import java.math.BigInteger;
import java.time.LocalDateTime;
import java.time.OffsetDateTime;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.function.Supplier;
Expand Down Expand Up @@ -303,8 +304,15 @@ public BrAPIObservation constructBrAPIObservation(
String value,
String variableName,
String seasonDbId,
BrAPIObservationUnit obsUnit
) {
BrAPIObservationUnit obsUnit,
boolean commit,
Program program,
User user,
String referenceSource,
UUID trialID,
UUID studyID,
UUID obsUnitID,
UUID id) {
BrAPIObservation observation = new BrAPIObservation();
observation.setGermplasmName(getGermplasmName());
if (getEnv() != null) {
Expand All @@ -320,11 +328,21 @@ public BrAPIObservation constructBrAPIObservation(
season.setSeasonDbId(seasonDbId);
observation.setSeason(season);

if(commit) {
Map<String, Object> createdBy = new HashMap<>();
createdBy.put(BrAPIAdditionalInfoFields.CREATED_BY_USER_ID, user.getId());
createdBy.put(BrAPIAdditionalInfoFields.CREATED_BY_USER_NAME, user.getName());
observation.putAdditionalInfoItem(BrAPIAdditionalInfoFields.CREATED_BY, createdBy);
observation.putAdditionalInfoItem(BrAPIAdditionalInfoFields.CREATED_DATE, DateTimeFormatter.ISO_OFFSET_DATE_TIME.format(OffsetDateTime.now()));

observation.setExternalReferences(getObservationExternalReferences(program, referenceSource, trialID, studyID, obsUnitID, id));
}

return observation;
}

private List<BrAPIExternalReference> getBrAPIExternalReferences(
Program program, String referenceSourceBaseName, UUID trialId, UUID studyId, UUID obsUnitId) {
Program program, String referenceSourceBaseName, UUID trialId, UUID studyId, UUID obsUnitId, UUID observationId) {
List<BrAPIExternalReference> refs = new ArrayList<>();

addReference(refs, program.getId(), referenceSourceBaseName, ExternalReferenceSource.PROGRAMS);
Expand All @@ -337,23 +355,31 @@ private List<BrAPIExternalReference> getBrAPIExternalReferences(
if (obsUnitId != null) {
addReference(refs, obsUnitId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATION_UNITS);
}
if (observationId != null) {
addReference(refs, observationId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATIONS);
}

return refs;
}

private List<BrAPIExternalReference> getTrialExternalReferences(
Program program, String referenceSourceBaseName, UUID trialId) {
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, null, null);
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, null, null, null);
}

private List<BrAPIExternalReference> getStudyExternalReferences(
Program program, String referenceSourceBaseName, UUID trialId, UUID studyId) {
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, null);
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, null, null);
}

private List<BrAPIExternalReference> getObsUnitExternalReferences(
Program program, String referenceSourceBaseName, UUID trialId, UUID studyId, UUID obsUnitId) {
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, obsUnitId);
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, obsUnitId, null);
}

private List<BrAPIExternalReference> getObservationExternalReferences(
Program program, String referenceSourceBaseName, UUID trialId, UUID studyId, UUID obsUnitId, UUID observationId) {
return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, obsUnitId, observationId);
}


Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/breedinginsight/brapps/importer/services/ExternalReferenceSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ public enum ExternalReferenceSource {
STUDIES("studies"),
OBSERVATION_UNITS("observationunits"),
DATASET("dataset"),
LISTS("lists");
LISTS("lists"),
OBSERVATIONS("observations");

private String name;

Expand Down
24 changes: 18 additions & 6 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -388,9 +388,8 @@ private void prepareDataForValidation(List<BrAPIImport> importRows, List<Column<
mappedImportRow.setObservationUnit(this.observationUnitByNameNoScope.get(createObservationUnitKey(importRow)));

// loop over phenotype column observation data for current row
List<PendingImportObject<BrAPIObservation>> observations = mappedImportRow.getObservations();
for (Column<?> column : phenotypeCols) {
List<PendingImportObject<BrAPIObservation>> observations = mappedImportRow.getObservations();

// if value was blank won't be entry in map for this observation
observations.add(this.observationByHash.get(getImportObservationHash(importRow, getVariableNameFromColumn(column))));
}
Expand Down Expand Up @@ -516,7 +515,7 @@ private void initNewBrapiData(List<BrAPIImport> importRows, List<Column<?>> phen
}
//column.name() gets phenotype name
String seasonDbId = this.yearToSeasonDbId(importRow.getEnvYear(), program.getId());
fetchOrCreateObservationPIO(importRow, column.name(), column.getString(rowNum), dateTimeValue, commit, seasonDbId, obsUnitPIO);
fetchOrCreateObservationPIO(program, user, importRow, column.name(), column.getString(rowNum), dateTimeValue, commit, seasonDbId, obsUnitPIO);
}
}
}
Expand Down Expand Up @@ -618,12 +617,18 @@ private Map<String, BrAPIObservation> fetchExistingObservations(List<Trait> refe

private void validateObservations(ValidationErrors validationErrors, int rowNum, ExperimentObservation importRow, List<Column<?>> phenotypeCols, Map<String, Trait> colVarMap, Map<String, BrAPIObservation> existingObservations) {
phenotypeCols.forEach(phenoCol -> {
if(existingObservations.containsKey(getImportObservationHash(importRow, phenoCol.name()))) {
var importHash = getImportObservationHash(importRow, phenoCol.name());
if(existingObservations.containsKey(importHash) && StringUtils.isNotBlank(phenoCol.getString(rowNum)) && !existingObservations.get(importHash).getValue().equals(phenoCol.getString(rowNum))) {
addRowError(
phenoCol.name(),
String.format("Value already exists for ObsUnitId: %s, Phenotype: %s", importRow.getObsUnitID(), phenoCol.name()),
validationErrors, rowNum
);
} else if(existingObservations.containsKey(importHash) && (StringUtils.isBlank(phenoCol.getString(rowNum)) || existingObservations.get(importHash).getValue().equals(phenoCol.getString(rowNum)))) {
BrAPIObservation existingObs = existingObservations.get(importHash);
existingObs.setObservationVariableName(phenoCol.name());
observationByHash.get(importHash).setState(ImportObjectState.EXISTING);
observationByHash.get(importHash).setBrAPIObject(existingObs);
} else {
validateObservationValue(colVarMap.get(phenoCol.name()), phenoCol.getString(rowNum), phenoCol.name(), validationErrors, rowNum);

Expand Down Expand Up @@ -808,7 +813,9 @@ private PendingImportObject<BrAPIObservationUnit> fetchOrCreateObsUnitPIO(Progra
}


private PendingImportObject<BrAPIObservation> fetchOrCreateObservationPIO(ExperimentObservation importRow,
private PendingImportObject<BrAPIObservation> fetchOrCreateObservationPIO(Program program,
User user,
ExperimentObservation importRow,
String variableName,
String value,
String timeStampValue,
Expand All @@ -820,7 +827,12 @@ private PendingImportObject<BrAPIObservation> fetchOrCreateObservationPIO(Experi
if (this.observationByHash.containsKey(key)) {
pio = observationByHash.get(key);
} else {
BrAPIObservation newObservation = importRow.constructBrAPIObservation(value, variableName, seasonDbId, obsUnitPIO.getBrAPIObject());
PendingImportObject<BrAPITrial> trialPIO = this.trialByNameNoScope.get(importRow.getExpTitle());
UUID trialID = trialPIO.getId();
PendingImportObject<BrAPIStudy> studyPIO = this.studyByNameNoScope.get(importRow.getEnv());
UUID studyID = studyPIO.getId();
UUID id = UUID.randomUUID();
BrAPIObservation newObservation = importRow.constructBrAPIObservation(value, variableName, seasonDbId, obsUnitPIO.getBrAPIObject(), commit, program, user, BRAPI_REFERENCE_SOURCE, trialID, studyID, obsUnitPIO.getId(), id);
//NOTE: Can't parse invalid timestamp value, so have to skip if invalid.
// Validation error should be thrown for offending value, but that doesn't happen until later downstream
if (timeStampValue != null && !timeStampValue.isBlank() && (validDateValue(timeStampValue) || validDateTimeValue(timeStampValue))) {
Expand Down
152 changes: 152 additions & 0 deletions src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -863,6 +863,158 @@ public void importSecondExpAfterFirstExpWithObs() {
assertRowSaved(newExpB, program, traits);
}

/*
Scenario:
- an experiment was created with observations
- do a second upload with additional observations for the experiment
- verify the second set of observations get uploaded successfully
*/
@ParameterizedTest
@ValueSource(booleans = {true, false})
@SneakyThrows
public void importNewObsAfterFirstExpWithObs(boolean commit) {
List<Trait> traits = createTraits(2);
Program program = createProgram("Exp with additional Uploads "+(commit ? "C" : "P"), "EXAU"+(commit ? "C" : "P"), "EXAU"+(commit ? "C" : "P"), BRAPI_REFERENCE_SOURCE, createGermplasm(1), traits);
Map<String, Object> newExp = new HashMap<>();
newExp.put(Columns.GERMPLASM_GID, "1");
newExp.put(Columns.TEST_CHECK, "T");
newExp.put(Columns.EXP_TITLE, "Test Exp");
newExp.put(Columns.EXP_UNIT, "Plot");
newExp.put(Columns.EXP_TYPE, "Phenotyping");
newExp.put(Columns.ENV, "New Env");
newExp.put(Columns.ENV_LOCATION, "Location A");
newExp.put(Columns.ENV_YEAR, "2023");
newExp.put(Columns.EXP_UNIT_ID, "a-1");
newExp.put(Columns.REP_NUM, "1");
newExp.put(Columns.BLOCK_NUM, "1");
newExp.put(Columns.ROW, "1");
newExp.put(Columns.COLUMN, "1");
newExp.put(traits.get(0).getObservationVariableName(), "1");

importTestUtils.uploadAndFetch(writeDataToFile(List.of(newExp), traits), null, true, client, program, mappingId);

BrAPITrial brAPITrial = brAPITrialDAO.getTrialsByName(List.of(Utilities.appendProgramKey((String)newExp.get(Columns.EXP_TITLE), program.getKey())), program).get(0);
Optional<BrAPIExternalReference> trialIdXref = Utilities.getExternalReference(brAPITrial.getExternalReferences(), String.format("%s/%s", BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.TRIALS.getName()));
assertTrue(trialIdXref.isPresent());
BrAPIStudy brAPIStudy = brAPIStudyDAO.getStudiesByExperimentID(UUID.fromString(trialIdXref.get().getReferenceID()), program).get(0);

BrAPIObservationUnit ou = ouDAO.getObservationUnitsForStudyDbId(brAPIStudy.getStudyDbId(), program).get(0);
Optional<BrAPIExternalReference> ouIdXref = Utilities.getExternalReference(ou.getExternalReferences(), String.format("%s/%s", BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.OBSERVATION_UNITS.getName()));
assertTrue(ouIdXref.isPresent());

Map<String, Object> newObservation = new HashMap<>();
newObservation.put(Columns.GERMPLASM_GID, "1");
newObservation.put(Columns.TEST_CHECK, "T");
newObservation.put(Columns.EXP_TITLE, "Test Exp");
newObservation.put(Columns.EXP_UNIT, "Plot");
newObservation.put(Columns.EXP_TYPE, "Phenotyping");
newObservation.put(Columns.ENV, "New Env");
newObservation.put(Columns.ENV_LOCATION, "Location A");
newObservation.put(Columns.ENV_YEAR, "2023");
newObservation.put(Columns.EXP_UNIT_ID, "a-1");
newObservation.put(Columns.REP_NUM, "1");
newObservation.put(Columns.BLOCK_NUM, "1");
newObservation.put(Columns.ROW, "1");
newObservation.put(Columns.COLUMN, "1");
newObservation.put(Columns.OBS_UNIT_ID, ouIdXref.get().getReferenceID());
newObservation.put(traits.get(0).getObservationVariableName(), "1");
newObservation.put(traits.get(1).getObservationVariableName(), "2");

JsonObject result = importTestUtils.uploadAndFetch(writeDataToFile(List.of(newObservation), traits), null, commit, client, program, mappingId);

JsonArray previewRows = result.get("preview").getAsJsonObject().get("rows").getAsJsonArray();
assertEquals(1, previewRows.size());
JsonObject row = previewRows.get(0).getAsJsonObject();

assertEquals("EXISTING", row.getAsJsonObject("trial").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("location").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("study").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("observationUnit").get("state").getAsString());
if(commit) {
assertRowSaved(newObservation, program, traits);
} else {
assertValidPreviewRow(newObservation, row, program, traits);
}
}

/*
Scenario:
- an experiment was created with observations
- do a second upload with additional observations for the experiment. Make sure the original observations are blank values
- verify the second set of observations get uploaded successfully
*/
@ParameterizedTest
@ValueSource(booleans = {true, false})
@SneakyThrows
public void importNewObsAfterFirstExpWithObs_blank(boolean commit) {
List<Trait> traits = createTraits(2);
Program program = createProgram("Exp with additional Uploads (blank) "+(commit ? "C" : "P"), "EXAUB"+(commit ? "C" : "P"), "EXAUB"+(commit ? "C" : "P"), BRAPI_REFERENCE_SOURCE, createGermplasm(1), traits);
Map<String, Object> newExp = new HashMap<>();
newExp.put(Columns.GERMPLASM_GID, "1");
newExp.put(Columns.TEST_CHECK, "T");
newExp.put(Columns.EXP_TITLE, "Test Exp");
newExp.put(Columns.EXP_UNIT, "Plot");
newExp.put(Columns.EXP_TYPE, "Phenotyping");
newExp.put(Columns.ENV, "New Env");
newExp.put(Columns.ENV_LOCATION, "Location A");
newExp.put(Columns.ENV_YEAR, "2023");
newExp.put(Columns.EXP_UNIT_ID, "a-1");
newExp.put(Columns.REP_NUM, "1");
newExp.put(Columns.BLOCK_NUM, "1");
newExp.put(Columns.ROW, "1");
newExp.put(Columns.COLUMN, "1");
newExp.put(traits.get(0).getObservationVariableName(), "1");

importTestUtils.uploadAndFetch(writeDataToFile(List.of(newExp), traits), null, true, client, program, mappingId);

BrAPITrial brAPITrial = brAPITrialDAO.getTrialsByName(List.of(Utilities.appendProgramKey((String)newExp.get(Columns.EXP_TITLE), program.getKey())), program).get(0);
Optional<BrAPIExternalReference> trialIdXref = Utilities.getExternalReference(brAPITrial.getExternalReferences(), String.format("%s/%s", BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.TRIALS.getName()));
assertTrue(trialIdXref.isPresent());
BrAPIStudy brAPIStudy = brAPIStudyDAO.getStudiesByExperimentID(UUID.fromString(trialIdXref.get().getReferenceID()), program).get(0);

BrAPIObservationUnit ou = ouDAO.getObservationUnitsForStudyDbId(brAPIStudy.getStudyDbId(), program).get(0);
Optional<BrAPIExternalReference> ouIdXref = Utilities.getExternalReference(ou.getExternalReferences(), String.format("%s/%s", BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.OBSERVATION_UNITS.getName()));
assertTrue(ouIdXref.isPresent());

assertRowSaved(newExp, program, traits);

Map<String, Object> newObservation = new HashMap<>();
newObservation.put(Columns.GERMPLASM_GID, "1");
newObservation.put(Columns.TEST_CHECK, "T");
newObservation.put(Columns.EXP_TITLE, "Test Exp");
newObservation.put(Columns.EXP_UNIT, "Plot");
newObservation.put(Columns.EXP_TYPE, "Phenotyping");
newObservation.put(Columns.ENV, "New Env");
newObservation.put(Columns.ENV_LOCATION, "Location A");
newObservation.put(Columns.ENV_YEAR, "2023");
newObservation.put(Columns.EXP_UNIT_ID, "a-1");
newObservation.put(Columns.REP_NUM, "1");
newObservation.put(Columns.BLOCK_NUM, "1");
newObservation.put(Columns.ROW, "1");
newObservation.put(Columns.COLUMN, "1");
newObservation.put(Columns.OBS_UNIT_ID, ouIdXref.get().getReferenceID());
newObservation.put(traits.get(0).getObservationVariableName(), "");
newObservation.put(traits.get(1).getObservationVariableName(), "2");

JsonObject result = importTestUtils.uploadAndFetch(writeDataToFile(List.of(newObservation), traits), null, commit, client, program, mappingId);

JsonArray previewRows = result.get("preview").getAsJsonObject().get("rows").getAsJsonArray();
assertEquals(1, previewRows.size());
JsonObject row = previewRows.get(0).getAsJsonObject();

assertEquals("EXISTING", row.getAsJsonObject("trial").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("location").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("study").get("state").getAsString());
assertEquals("EXISTING", row.getAsJsonObject("observationUnit").get("state").getAsString());

newObservation.put(traits.get(0).getObservationVariableName(), "1");
if(commit) {
assertRowSaved(newObservation, program, traits);
} else {
assertValidPreviewRow(newObservation, row, program, traits);
}
}

private Map<String, Object> assertRowSaved(Map<String, Object> expected, Program program, List<Trait> traits) throws ApiException {
Map<String, Object> ret = new HashMap<>();

Expand Down