use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.
the class StatementAnnotationBuilder method buildAnnotationList.
public List<T> buildAnnotationList(String isoformName, List<Statement> flatStatements) {
List<T> annotations = new ArrayList<>();
Map<String, List<Statement>> flatStatementsByAnnotationHash = flatStatements.stream().collect(Collectors.groupingBy(rs -> rs.getValue(StatementField.ANNOTATION_ID)));
flatStatementsByAnnotationHash.forEach((key, statements) -> {
T annotation = get();
Statement firstStatement = statements.get(0);
annotation.setAnnotationHash(firstStatement.getValue(StatementField.ANNOTATION_ID));
// annotation.setAnnotationName(firstStatement.getValue(StatementField.ANNOTATION_NAME));
AnnotationCategory category = AnnotationCategory.getDecamelizedAnnotationTypeName(StringUtils.camelToKebabCase(firstStatement.getValue(StatementField.ANNOTATION_CATEGORY)));
annotation.setAnnotationCategory(category);
if (category.equals(AnnotationCategory.VARIANT) || category.equals(AnnotationCategory.MUTAGENESIS)) {
setVariantAttributes(annotation, firstStatement);
}
setIsoformTargeting(annotation, firstStatement);
setIsoformName(annotation, isoformName);
annotation.setDescription(firstStatement.getValue(StatementField.ANNOT_DESCRIPTION));
String cvTermAccession = firstStatement.getValue(StatementField.ANNOT_CV_TERM_ACCESSION);
// Set the evidences if not Mammalian phenotype or Protein Property https://issues.isb-sib.ch/browse/BIOEDITOR-466
if (!ANNOT_CATEGORIES_WITHOUT_EVIDENCES.contains(category)) {
annotation.setEvidences(buildAnnotationEvidences(statements));
// TODO Remove this when you are able to do XREFs
if (((annotation.getEvidences() == null) || ((annotation.getEvidences().isEmpty()))) && (category.equals(AnnotationCategory.VARIANT) || category.equals(AnnotationCategory.MUTAGENESIS))) {
// All variants from BED are GOLD, and this is a special case when we don't have evidences for VDs.
annotation.setQualityQualifier("GOLD");
} else {
annotation.setQualityQualifier(AnnotationUtils.computeAnnotationQualityBasedOnEvidences(annotation.getEvidences()).name());
}
} else {
// Case of Protein propert and mammalian phenotypes
annotation.setEvidences(new ArrayList<AnnotationEvidence>());
boolean foundGold = statements.stream().anyMatch(s -> s.getValue(StatementField.EVIDENCE_QUALITY).equalsIgnoreCase("GOLD"));
if (foundGold) {
annotation.setQualityQualifier("GOLD");
} else {
annotation.setQualityQualifier("SILVER");
}
}
if (cvTermAccession != null && !cvTermAccession.isEmpty()) {
annotation.setCvTermAccessionCode(cvTermAccession);
CvTerm cvTerm = terminologyService.findCvTermByAccession(cvTermAccession);
if (cvTerm != null) {
annotation.setCvTermName(cvTerm.getName());
annotation.setCvApiName(cvTerm.getOntology());
annotation.setCvTermDescription(cvTerm.getDescription());
if (category.equals(AnnotationCategory.PROTEIN_PROPERTY)) {
// according to https://issues.isb-sib.ch/browse/BIOEDITOR-466
annotation.setDescription(cvTerm.getDescription());
} else if (category.equals(AnnotationCategory.MAMMALIAN_PHENOTYPE)) {
annotation.setDescription("Relative to modification-effect annotations");
}
} else {
LOGGER.error("cv term was expected to be found " + cvTermAccession);
annotation.setCvTermName(firstStatement.getValue(StatementField.ANNOT_CV_TERM_NAME));
annotation.setCvApiName(firstStatement.getValue(StatementField.ANNOT_CV_TERM_TERMINOLOGY));
}
}
annotation.setAnnotationHash(firstStatement.getValue(StatementField.ANNOTATION_ID));
annotation.setAnnotationName(firstStatement.getValue(StatementField.ANNOTATION_NAME));
// Check this with PAM (does it need to be a human readable stuff)
// Does it need a name?
annotation.setUniqueName(firstStatement.getValue(StatementField.ANNOTATION_ID));
String bioObjectAnnotationHash = firstStatement.getValue(StatementField.OBJECT_ANNOTATION_IDS);
String bioObjectAccession = firstStatement.getValue(StatementField.BIOLOGICAL_OBJECT_ACCESSION);
String bot = firstStatement.getValue(StatementField.BIOLOGICAL_OBJECT_TYPE);
if ((bioObjectAnnotationHash != null) && (bioObjectAnnotationHash.length() > 0) || (bioObjectAccession != null && (bioObjectAccession.length() > 0))) {
BioObject bioObject;
if (AnnotationCategory.BINARY_INTERACTION.equals(annotation.getAPICategory())) {
if (bioObjectAccession.startsWith("NX_") && BioType.PROTEIN.name().equalsIgnoreCase(bot)) {
// note that if we handle BioType.PROTEIN_ISOFORM in the future, we should
// add the property isoformName as well, see how it's done in BinaryInteraction2Annotation.newBioObject()
bioObject = BioObject.internal(BioType.PROTEIN);
// // TODO: REMOVE THIS HACK WHEN ISSUE https://issues.isb-sib.ch/browse/NEXTPROT-1513 will be fixed
// // NX_P62158 was split in 3 accessions: NX_P0DP23/CALM1, NX_P0DP24/CALM2 and NX_P0DP25/CALM3
// // BEGIN DIRTY HACK
/*
if (bioObjectAccession.equals("NX_P62158")) {
switch (isoformName) {
case "NX_P35499":
bioObjectAccession = "NX_P0DP23";
break;
case "NX_Q99250":
bioObjectAccession = "NX_P0DP23";
break;
case "NX_Q9UQD0":
bioObjectAccession = "NX_P0DP23";
break;
case "NX_Q9Y5Y9":
bioObjectAccession = "NX_P0DP23";
break;
}
}
*/
// /// END OF HACK
bioObject.setAccession(bioObjectAccession);
bioObject.putPropertyNameValue("geneName", firstStatement.getValue(StatementField.BIOLOGICAL_OBJECT_NAME));
String proteinName = mainNamesService.findIsoformOrEntryMainName(bioObjectAccession).orElseThrow(() -> new NextProtException("Cannot create a binary interaction with " + isoformName + ": unknown protein accession " + bioObject.getAccession())).getName();
bioObject.putPropertyNameValue("proteinName", proteinName);
bioObject.putPropertyNameValue("url", "https://www.nextprot.org/entry/" + bioObjectAccession + "/interactions");
} else {
throw new NextProtException("Binary Interaction only expects to be a nextprot entry NX_ and found " + bioObjectAccession + " with type " + bot);
}
} else if (AnnotationCategory.PHENOTYPIC_VARIATION.equals(annotation.getAPICategory())) {
bioObject = BioObject.internal(BioType.ENTRY_ANNOTATION);
bioObject.setAnnotationHash(bioObjectAnnotationHash);
} else {
throw new NextProtException("Category not expected for bioobject " + annotation.getAPICategory());
}
annotation.setBioObject(bioObject);
}
annotations.add(annotation);
});
return annotations;
}
use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.
the class AnnotationUtils method convertRelativeEvidenceToExternalChemicalBioObject.
private static List<AnnotationEvidence> convertRelativeEvidenceToExternalChemicalBioObject(Annotation annot) {
List<AnnotationEvidence> toRemove = new ArrayList<>();
for (AnnotationEvidence evi : annot.getEvidences()) {
if ("relative".equals(evi.getResourceAssociationType())) {
annot.setBioObject(newExternalChemicalBioObject(evi));
toRemove.add(evi);
}
}
return toRemove;
}
use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.
the class AnnotationUtils method filterAnnotationsByCategory.
/**
* Filter annotation by its category
* @param withChildren if true, annotations having a category which is a child of annotationCategory are included in the list
* @return a list of annotations
*/
public static List<Annotation> filterAnnotationsByCategory(List<Annotation> annotations, AnnotationCategory annotationCategory, boolean withChildren, boolean goldOnly) {
if (annotations == null)
return null;
List<Annotation> filteredAnnotations = annotations.stream().filter((a) -> {
boolean categoryMatch = (annotationCategory == null) || ((a.getAPICategory() == annotationCategory) || (withChildren && a.getAPICategory().isChildOf(annotationCategory)));
boolean qualityMatch = true;
if (goldOnly) {
qualityMatch = "GOLD".equalsIgnoreCase(a.getQualityQualifier());
}
return categoryMatch && qualityMatch;
}).collect(Collectors.toList());
if (goldOnly) {
for (Annotation a : filteredAnnotations) {
List<AnnotationEvidence> evidences = a.getEvidences();
List<AnnotationEvidence> goldEvidences = evidences.stream().filter(e -> "GOLD".equalsIgnoreCase(e.getQualityQualifier()) || (e.getQualityQualifier() == null) || e.getQualityQualifier().isEmpty()).collect(Collectors.toList());
// TODO check if this mutable annotation is not breaken in eh cache!!
a.setEvidences(goldEvidences);
}
}
if (annotationCategory == AnnotationCategory.PHENOTYPIC_VARIATION) {
Collections.sort(filteredAnnotations, AnnotationComparators.newPhenotypicVariationComparator(EntryUtils.getHashAnnotationMap(annotations)));
} else {
Collections.sort(filteredAnnotations, AnnotationComparators.newComparator(annotationCategory));
}
return filteredAnnotations;
}
use of org.nextprot.api.core.domain.annotation.AnnotationEvidence in project nextprot-api by calipho-sib.
the class EntryPartExporterImpl method collectRows.
/*
protected List<Row> sortRows(List<Row> rows, Comparator<Row> comparator) {
return rows.stream().sorted(comparator).collect(Collectors.toList());
}
*/
private void collectRows(List<Row> rows, Entry entry, Annotation annotation) {
for (AnnotationEvidence evidence : annotation.getEvidences()) {
Row row = new Row(headerList.size());
setRowValue(row, ENTRY_ACCESSION, entry.getUniqueName());
setRowValue(row, CATEGORY, StringUtils.camelToKebabCase(annotation.getApiTypeName()));
setRowValue(row, TERM_ACCESSION, annotation.getCvTermAccessionCode());
setRowValue(row, TERM_NAME, annotation.getCvTermName());
setRowValue(row, ECO_ACCESSION, evidence.getEvidenceCodeAC());
setRowValue(row, ECO_NAME, evidence.getEvidenceCodeName());
setRowValue(row, QUALITY, evidence.getQualityQualifier());
setRowValue(row, NEGATIVE, String.valueOf(evidence.isNegativeEvidence()));
setRowValue(row, EXPRESSION_LEVEL, evidence.getExpressionLevel());
setRowValue(row, SOURCE, evidence.getAssignedBy());
setRowValue(row, URL, entry.getXref(evidence.getResourceId()).map(DbXref::getResolvedUrl).orElse("null"));
setExperimentalContextRowValues(row, entry, evidence);
rows.add(row);
}
}
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