Skip to content

[BI-1930] trait names are case sensitive #300

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
davedrp merged 2 commits into from
Oct 20, 2023
Merged

[BI-1930] trait names are case sensitive #300

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
84cce7d
[BI-1930] made observationvariable validations with ontologies case-i…
davedrp Oct 9, 2023
f318dbb
[BI-1930] Fixed bug with sorting observation variables.
davedrp Oct 13, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion src/main/java/org/breedinginsight/brapps/importer/services/FileMappingUtil.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
package org.breedinginsight.brapps.importer.services;

import io.reactivex.functions.Function;
import org.apache.commons.collections4.map.CaseInsensitiveMap;
import org.apache.commons.lang3.tuple.MutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.breedinginsight.brapps.importer.model.config.MappedImportRelation;
Expand Down Expand Up @@ -76,7 +77,7 @@ public List<Pair<Integer, String>> findFileRelationships(Table data, List<Mapped
}

public <T> List<T> sortByField(List<String> sortedFields, List<T> unsortedItems, Function<T, String> fieldGetter) {
HashMap<String, Integer> sortOrder = new HashMap<>();
CaseInsensitiveMap<String, Integer> sortOrder = new CaseInsensitiveMap<>();
for (int i = 0; i < sortedFields.size(); i++) {
sortOrder.put(sortedFields.get(i), i);
}
Expand Down
22 changes: 12 additions & 10 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.collections4.map.CaseInsensitiveMap;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.*;
Expand All @@ -41,7 +42,6 @@
import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
import org.breedinginsight.brapps.importer.daos.*;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.brapps.importer.model.base.AdditionalInfo;
import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
import org.breedinginsight.brapps.importer.model.imports.PendingImport;
import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
Expand Down Expand Up @@ -70,12 +70,9 @@
import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeParseException;
import java.util.*;
import java.util.function.Function;
import java.util.function.Supplier;
import java.util.stream.Collectors;

import static org.breedinginsight.brapps.importer.services.FileMappingUtil.EXPERIMENT_TEMPLATE_NAME;

@Slf4j
@Prototype
public class ExperimentProcessor implements Processor {
Expand Down Expand Up @@ -444,10 +441,11 @@ private List<Trait> verifyTraits(UUID programId, List<Column<?>> phenotypeCols,

private List<Trait> fetchFileTraits(UUID programId, Collection<String> varNames) {
try {
Collection<String> upperCaseVarNames = varNames.stream().map(String::toUpperCase).collect(Collectors.toList());
List<Trait> traits = ontologyService.getTraitsByProgramId(programId, true);
// filter out just traits specified in file
return traits.stream()
.filter(e -> varNames.contains(e.getObservationVariableName()))
.filter(e -> upperCaseVarNames.contains(e.getObservationVariableName().toUpperCase()))
.collect(Collectors.toList());
} catch (DoesNotExistException e) {
log.error(e.getMessage(), e);
Expand Down Expand Up @@ -547,8 +545,10 @@ private ValidationErrors validateFields(List<BrAPIImport> importRows, Validation
List<Column<?>> phenotypeCols, boolean commit) throws MissingRequiredInfoException, ApiException {
//fetching any existing observations for any OUs in the import
Map<String, BrAPIObservation> existingObsByObsHash = fetchExistingObservations(referencedTraits, program);
Map<String, Trait> colVarMap = referencedTraits.stream().collect(Collectors.toMap(Trait::getObservationVariableName, Function.identity()));

CaseInsensitiveMap<String, Trait> colVarMap = new CaseInsensitiveMap<>();
for ( Trait trait: referencedTraits) {
colVarMap.put(trait.getObservationVariableName(),trait);
}
Set<String> uniqueStudyAndObsUnit = new HashSet<>();
for (int rowNum = 0; rowNum < importRows.size(); rowNum++) {
ExperimentObservation importRow = (ExperimentObservation) importRows.get(rowNum);
Expand Down Expand Up @@ -619,7 +619,7 @@ private Map<String, BrAPIObservation> fetchExistingObservations(List<Trait> refe
.collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue));
}

private void validateObservations(ValidationErrors validationErrors, int rowNum, ExperimentObservation importRow, List<Column<?>> phenotypeCols, Map<String, Trait> colVarMap, Map<String, BrAPIObservation> existingObservations) {
private void validateObservations(ValidationErrors validationErrors, int rowNum, ExperimentObservation importRow, List<Column<?>> phenotypeCols, CaseInsensitiveMap<String, Trait> colVarMap, Map<String, BrAPIObservation> existingObservations) {
phenotypeCols.forEach(phenoCol -> {
var importHash = getImportObservationHash(importRow, phenoCol.name());
if(existingObservations.containsKey(importHash) && StringUtils.isNotBlank(phenoCol.getString(rowNum)) && !existingObservations.get(importHash).getValue().equals(phenoCol.getString(rowNum))) {
Expand Down Expand Up @@ -969,8 +969,10 @@ private void updateObservationDependencyValues(Program program) {

// Update ObservationVariable DbIds
List<Trait> traits = getTraitList(program);
Map<String, Trait> traitMap = traits.stream().collect(Collectors.toMap(TraitEntity::getObservationVariableName, Function.identity()));

CaseInsensitiveMap<String, Trait> traitMap = new CaseInsensitiveMap<>();
for ( Trait trait: traits) {
traitMap.put(trait.getObservationVariableName(),trait);
}
for (PendingImportObject<BrAPIObservation> observation : this.observationByHash.values()) {
String observationVariableName = observation.getBrAPIObject().getObservationVariableName();
if (observationVariableName != null && traitMap.containsKey(observationVariableName)) {
Expand Down