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V2 api inconsistencies arrays #793

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V2 api inconsistencies arrays #793

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f0da38d
Renamed base_uri to baseUri and ensured it is an array.
henrietteharmse Oct 4, 2024
8814713
Definition is now using DefinedFields and is of type array.
henrietteharmse Oct 7, 2024
837a4ce
DefinedBy is now using DefinedFields.
henrietteharmse Oct 7, 2024
3dff062
AppearsIn is now using DefinedFields.
henrietteharmse Oct 7, 2024
57b4561
DirectAncestor is now using DefinedFields and is an array.
henrietteharmse Oct 7, 2024
d3dba46
DirectParent is now using DefinedFields and is an array.
henrietteharmse Oct 7, 2024
3e60d05
ImportsFrom and exportsTo are now using DefinedFields.
henrietteharmse Oct 8, 2024
ff9b824
Renamed hasPreferredRoots to preferredRoot. Is now using DefinedField…
henrietteharmse Oct 8, 2024
5379b2c
hierarchicalParent and hierarchicalAncestor are now arrays and Define…
henrietteharmse Oct 21, 2024
e5ecfbf
Label is now an array and a DefinedField.
henrietteharmse Oct 22, 2024
98578da
Language is now an array and a DefinedField.
henrietteharmse Oct 22, 2024
270b92b
relatedTo and relatedFrom are now arrays and DefinedFields. Cleaned u…
henrietteharmse Oct 24, 2024
c89233e
synonym is now an array and DefinedField.
henrietteharmse Oct 24, 2024
6d5949e
Merge branch 'dev' of github.com:EBISPOT/ols4 into v2-api-inconsisten…
henrietteharmse Oct 24, 2024
1b0a67d
Merged with dev.
henrietteharmse Oct 24, 2024
be73bab
Improved error message.
henrietteharmse Oct 25, 2024
a1e956d
Fixed type issues.
henrietteharmse Oct 28, 2024
1621775
Added fobi.
henrietteharmse Oct 28, 2024
3e2c9de
Added BaseUri test.
henrietteharmse Nov 5, 2024
987d91f
Merged again with dev
henrietteharmse Nov 5, 2024
7fdbe90
Fixed definedBy issue and made oio available locally.
henrietteharmse Nov 6, 2024
d028624
Fixed baseUri issue.
henrietteharmse Nov 6, 2024
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18 changes: 10 additions & 8 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/SolrFieldMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
import java.util.List;
import java.util.stream.Collectors;

import static uk.ac.ebi.ols.shared.DefinedFields.*;

public class SolrFieldMapper {

// Maps OLS3 field names to the OLS4 schema
Expand Down Expand Up @@ -36,23 +38,23 @@ public static List<String> mapFieldsList(Collection<String> ols3FieldNames) {
continue;
}

if (legacyFieldName.equals("label")) {
newFields.add(prefix + "label" + suffix);
if (legacyFieldName.equals(LABEL.getText())) {
newFields.add(prefix + LABEL.getText() + suffix);
continue;
}

if (legacyFieldName.equals("synonym")) {
newFields.add(prefix + "synonym" + suffix);
if (legacyFieldName.equals(SYNONYM.getText())) {
newFields.add(prefix + SYNONYM.getText() + suffix);
continue;
}

if (legacyFieldName.equals("definition")) {
newFields.add(prefix + "definition" + suffix);
if (legacyFieldName.equals(DEFINITION.getText())) {
newFields.add(prefix + DEFINITION.getText() + suffix);
continue;
}

if (legacyFieldName.equals("description")) {
newFields.add(prefix + "definition" + suffix);
if (legacyFieldName.equals(DEFINITION.getOls3Text())) {
newFields.add(prefix + DEFINITION.getText() + suffix);
continue;
}

Expand Down
1 change: 1 addition & 0 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1PreferredRootTermAssembler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import org.springframework.web.util.UriUtils;
import uk.ac.ebi.spot.ols.model.v1.V1Related;
import uk.ac.ebi.spot.ols.model.v1.V1Term;
import static uk.ac.ebi.ols.shared.DefinedFields.*;

import java.util.Collection;
import java.util.HashSet;
Expand Down
29 changes: 16 additions & 13 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java
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Expand Up @@ -130,7 +130,7 @@ public void search(
solrQuery.set("defType", "edismax");
solrQuery.setQuery(query.toLowerCase());
// Specify the query fields with boosting
String[] fields = {"label_s^5", "synonym_s^3", "short_form_s^2", "obo_id_s^2", "iri_s", "annotations_trimmed"};
String[] fields = {LABEL.getText()+"_s^5", SYNONYM.getText()+"_s^3", "short_form_s^2", "obo_id_s^2", "iri_s", "annotations_trimmed"};
solrQuery.set("qf", String.join(" ", SolrFieldMapper.mapFieldsList(List.of(fields))));
// Boost exact phrase matches in label and synonym fields
solrQuery.set("pf", "lowercase_label^10 lowercase_synonym^5");
Expand All @@ -142,7 +142,7 @@ public void search(
solrQuery.set("defType", "edismax");
solrQuery.setQuery(query);

String[] fields = {"label^5", "synonym^3", "definition", "short_form^2", "obo_id^2", "iri", "annotations_trimmed"};
String[] fields = {LABEL.getText()+"^5", SYNONYM.getText()+"^3", DEFINITION.getText(), "short_form^2", "obo_id^2", "iri", "annotations_trimmed"};

solrQuery.set("qf", String.join(" ", SolrFieldMapper.mapFieldsList(List.of(fields))));

Expand Down Expand Up @@ -206,9 +206,10 @@ public void search(
.collect(Collectors.joining(" OR "));

if (inclusive) {
solrQuery.addFilterQuery("filter( iri: (" + result + ")) filter(hierarchicalAncestor: (" + result + "))");
solrQuery.addFilterQuery("filter( iri: (" + result + ")) filter(" + HIERARCHICAL_ANCESTOR.getText()+
": (" + result + "))");
} else {
solrQuery.addFilterQuery("hierarchicalAncestor: (" + result + ")");
solrQuery.addFilterQuery(HIERARCHICAL_ANCESTOR.getText() + ": (" + result + ")");
}

}
Expand All @@ -219,9 +220,10 @@ public void search(
.collect(Collectors.joining(" OR "));

if (inclusive) {
solrQuery.addFilterQuery("filter( iri: (" + result + ")) filter(hierarchicalAncestor: (" + result + "))");
solrQuery.addFilterQuery("filter( iri: (" + result + ")) filter("+ HIERARCHICAL_ANCESTOR.getText()+
": (" + result + "))");
} else {
solrQuery.addFilterQuery("hierarchicalAncestor: (" + result + ")");
solrQuery.addFilterQuery(HIERARCHICAL_ANCESTOR.getText()+": (" + result + ")");
}
}

Expand Down Expand Up @@ -281,8 +283,8 @@ public void search(
fieldList.add("id");
fieldList.add("iri");
fieldList.add("ontology_name");
fieldList.add("label");
fieldList.add("description");
fieldList.add(LABEL.getText());
fieldList.add(DEFINITION.getOls3Text());
fieldList.add("short_form");
fieldList.add("obo_id");
fieldList.add("type");
Expand All @@ -292,13 +294,14 @@ public void search(
if (fieldList.contains("id")) outDoc.put("id", JsonHelper.getString(json, "id"));
if (fieldList.contains("iri")) outDoc.put("iri", JsonHelper.getString(json, "iri"));
if (fieldList.contains("ontology_name")) outDoc.put("ontology_name", JsonHelper.getString(json, "ontologyId"));
if (fieldList.contains("label")) {
var label = outDoc.put("label", JsonHelper.getString(json, "label"));
if (fieldList.contains(LABEL.getText())) {
var label = outDoc.put(LABEL.getText(), JsonHelper.getString(json, LABEL.getText()));
if(label!=null) {
outDoc.put("label", label);
outDoc.put(LABEL.getText(), label);
}
}
if (fieldList.contains("description")) outDoc.put("description", JsonHelper.getStrings(json, "definition"));
if (fieldList.contains(DEFINITION.getOls3Text())) outDoc.put(DEFINITION.getOls3Text(),
JsonHelper.getStrings(json, DEFINITION.getText()));
if (fieldList.contains("short_form")) outDoc.put("short_form", JsonHelper.getString(json, "shortForm"));
if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getString(json, "curie"));
if (fieldList.contains(IS_DEFINING_ONTOLOGY.getOls3Text())) outDoc.put(IS_DEFINING_ONTOLOGY.getOls3Text(),
Expand All @@ -307,7 +310,7 @@ public void search(
if (fieldList.contains("type")) {
outDoc.put("type", JsonHelper.getType(json, "type"));
}
if (fieldList.contains("synonym")) outDoc.put("synonym", JsonHelper.getStrings(json, "synonym"));
if (fieldList.contains(SYNONYM.getText())) outDoc.put(SYNONYM.getText(), JsonHelper.getStrings(json, SYNONYM.getText()));
if (fieldList.contains("ontology_prefix")) outDoc.put("ontology_prefix", JsonHelper.getString(json, "ontologyPreferredPrefix"));
if (fieldList.contains("subset")) outDoc.put("subset", JsonHelper.getStrings(json, "http://www.geneontology.org/formats/oboInOwl#inSubset"));
if (fieldList.contains("ontology_iri")) outDoc.put("ontology_iri", JsonHelper.getStrings(json, "ontologyIri").get(0));
Expand Down
25 changes: 13 additions & 12 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java
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Expand Up @@ -97,7 +97,7 @@ public void select(
}
solrQuery.setQuery(query);
solrQuery.set("defType", "edismax");
solrQuery.set("qf", "label whitespace_edge_label synonym whitespace_edge_synonym shortForm whitespace_edge_shortForm curie iri");
solrQuery.set("qf", LABEL.getText()+" whitespace_edge_label synonym whitespace_edge_synonym shortForm whitespace_edge_shortForm curie iri");
solrQuery.set("bq", "type:ontology^10.0 " +
IS_DEFINING_ONTOLOGY.getText() +":true^100.0 str_label:\"" + queryLc + "\"^1000 edge_label:\"" +
queryLc + "\"^500 str_synonym:\"" + queryLc + "\" edge_synonym:\"" + queryLc + "\"^100");
Expand Down Expand Up @@ -129,14 +129,14 @@ public void select(
String result = childrenOf.stream()
.map(addQuotes)
.collect(Collectors.joining(" OR "));
solrQuery.addFilterQuery("directAncestor: (" + result + ")");
solrQuery.addFilterQuery(DIRECT_ANCESTOR.getText() + ": (" + result + ")");
}

if (allChildrenOf != null) {
String result = allChildrenOf.stream()
.map(addQuotes)
.collect(Collectors.joining(" OR "));
solrQuery.addFilterQuery("hierarchicalAncestor: (" + result + ")");
solrQuery.addFilterQuery(HIERARCHICAL_ANCESTOR.getText() + ": (" + result + ")");
}

solrQuery.addFilterQuery(IS_OBSOLETE.getText() + ":" + queryObsoletes);
Expand All @@ -146,9 +146,9 @@ public void select(
solrQuery.add("hl.simple.pre", "<b>");
solrQuery.add("hl.simple.post", "</b>");
solrQuery.addHighlightField("whitespace_edge_label");
solrQuery.addHighlightField("label");
solrQuery.addHighlightField(LABEL.getText());
solrQuery.addHighlightField("whitespace_edge_synonym");
solrQuery.addHighlightField("synonym");
solrQuery.addHighlightField(SYNONYM.getText());

logger.debug("select: ()", solrQuery.toQueryString());

Expand All @@ -175,10 +175,10 @@ public void select(
fieldList.add("iri");
fieldList.add("short_form");
fieldList.add("obo_id");
fieldList.add("label");
fieldList.add(LABEL.getText());
fieldList.add("ontology_name");
fieldList.add("ontology_prefix");
fieldList.add("description");
fieldList.add(DEFINITION.getOls3Text());
fieldList.add("type");
}

Expand All @@ -187,8 +187,9 @@ public void select(
if (fieldList.contains("id")) outDoc.put("id", res.get("id").toString().replace('+', ':'));
if (fieldList.contains("iri")) outDoc.put("iri", JsonHelper.getString(json, "iri"));
if (fieldList.contains("ontology_name")) outDoc.put("ontology_name", JsonHelper.getString(json, "ontologyId"));
if (fieldList.contains("label")) outDoc.put("label", JsonHelper.getString(json, "label"));
if (fieldList.contains("description")) outDoc.put("description", JsonHelper.getStrings(json, "definition"));
if (fieldList.contains(LABEL.getText())) outDoc.put(LABEL.getText(), JsonHelper.getString(json, LABEL.getText()));
if (fieldList.contains(DEFINITION.getOls3Text())) outDoc.put(DEFINITION.getOls3Text(),
JsonHelper.getStrings(json, DEFINITION.getText()));
if (fieldList.contains("short_form")) outDoc.put("short_form", JsonHelper.getString(json, "shortForm"));
if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getString(json, "curie"));
if (fieldList.contains(IS_DEFINING_ONTOLOGY.getOls3Text())) outDoc.put(IS_DEFINING_ONTOLOGY.getOls3Text(),
Expand All @@ -197,7 +198,7 @@ public void select(
if (fieldList.contains("type")) {
outDoc.put("type", JsonHelper.getType(json, "type"));
}
if (fieldList.contains("synonym")) outDoc.put("synonym", JsonHelper.getStrings(json, "synonym"));
if (fieldList.contains(SYNONYM.getText())) outDoc.put(SYNONYM.getText(), JsonHelper.getStrings(json, SYNONYM.getText()));
if (fieldList.contains("ontology_prefix")) outDoc.put("ontology_prefix", JsonHelper.getString(json, "ontologyPreferredPrefix"));

docs.add(outDoc);
Expand Down Expand Up @@ -228,9 +229,9 @@ public void select(
Map<String,Object> resHighlight = new LinkedHashMap<>();
for(var fieldName : highlight.keySet()) {
if(fieldName.equals("whitespace_edge_label")) {
resHighlight.put("label_autosuggest", highlight.get(fieldName));
resHighlight.put(LABEL.getText()+"_autosuggest", highlight.get(fieldName));
} else if(fieldName.equals("whitespace_edge_synonym")) {
resHighlight.put("synonym_autosuggest", highlight.get(fieldName));
resHighlight.put(SYNONYM.getText()+"_autosuggest", highlight.get(fieldName));
} else {
resHighlight.put(fieldName, highlight.get(fieldName));
}
Expand Down
10 changes: 6 additions & 4 deletions backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SuggestController.java
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Expand Up @@ -26,6 +26,8 @@
import java.nio.charset.StandardCharsets;
import java.util.*;

import static uk.ac.ebi.ols.shared.DefinedFields.*;

@Tag(name = "Suggest Controller")
@RestController
public class V1SuggestController {
Expand Down Expand Up @@ -55,9 +57,9 @@ public void suggest(

solrQuery.setQuery(query);
solrQuery.set("defType", "edismax");
solrQuery.set("qf", "label^10 edge_label^2 whitespace_edge_label^1");
solrQuery.set("qf", LABEL.getText()+"^10 edge_label^2 whitespace_edge_label^1");
solrQuery.set("wt", "json");
solrQuery.setFields("label");
solrQuery.setFields(LABEL.getText());

solrQuery.setSort("score", SolrQuery.ORDER.desc);

Expand All @@ -73,7 +75,7 @@ public void suggest(
solrQuery.setStart(start);
solrQuery.setRows(rows);
solrQuery.add("group", "true");
solrQuery.add("group.field", "label");
solrQuery.add("group.field", LABEL.getText());
solrQuery.add("group.main", "true");


Expand All @@ -90,7 +92,7 @@ public void suggest(
for(SolrDocument res : qr.getResults()) {
Map<String,Object> outDoc = new HashMap<>();

outDoc.put("autosuggest", res.get("label"));
outDoc.put("autosuggest", res.get(LABEL.getText()));

docs.add(outDoc);
}
Expand Down
2 changes: 1 addition & 1 deletion backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1AncestorsJsTreeBuilder.java
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Expand Up @@ -80,7 +80,7 @@ private void createJsTreeEntries(List<Map<String,Object>> jstree, JsonObject ent
}

jstreeEntry.put("iri", entityIri);
jstreeEntry.put("text", JsonHelper.getString(entity, "label"));
jstreeEntry.put("text", JsonHelper.getString(entity, LABEL.getText()));

Collection<String> childIris = entityIriToChildIris.get(entityIri);

Expand Down
4 changes: 2 additions & 2 deletions backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1ChildrenJsTreeBuilder.java
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Expand Up @@ -32,11 +32,11 @@ List<Map<String,Object>> buildJsTree() {
jstreeEntry.put("id", base64Encode(thisEntityJsTreeIdDecoded + ";" + child.getAsJsonObject().get("iri").getAsString()));
jstreeEntry.put("parent", base64Encode(thisEntityJsTreeIdDecoded));
jstreeEntry.put("iri", JsonHelper.getString(child.getAsJsonObject(), "iri"));
jstreeEntry.put("text", JsonHelper.getString(child.getAsJsonObject(), "label"));
jstreeEntry.put("text", JsonHelper.getString(child.getAsJsonObject(), LABEL.getText()));
jstreeEntry.put("state", Map.of("opened", false));
jstreeEntry.put("children",
JsonHelper.getString(child.getAsJsonObject(), HAS_DIRECT_CHILDREN.getText()).equals("true")
|| JsonHelper.getString(child.getAsJsonObject(), "hasHierarchicalChildren").equals("true")
|| JsonHelper.getString(child.getAsJsonObject(), HAS_HIERARCHICAL_CHILDREN.getText()).equals("true")
);

Map<String,Object> attrObj = new LinkedHashMap<>();
Expand Down
8 changes: 5 additions & 3 deletions backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1GraphRepository.java
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Expand Up @@ -12,6 +12,8 @@
import uk.ac.ebi.spot.ols.repository.transforms.RemoveLiteralDatatypesTransform;
import uk.ac.ebi.spot.ols.service.Neo4jClient;

import static uk.ac.ebi.ols.shared.DefinedFields.*;

import java.util.*;
import java.util.stream.Collectors;

Expand Down Expand Up @@ -76,13 +78,13 @@ private Map<String, Object> getGraphForEntity(String iri, String type, String ne
for(String referencedIri : linkedEntities.keySet()) {
JsonObject reference = linkedEntities.getAsJsonObject(referencedIri);
if(!iriToLabel.containsKey(referencedIri))
iriToLabel.put(referencedIri, JsonHelper.getString(reference, "label"));
iriToLabel.put(referencedIri, JsonHelper.getString(reference, LABEL.getText()));
}
}

Map<String, Object> nodeRes = new LinkedHashMap<>();
nodeRes.put("iri", JsonHelper.getString(ontologyNodeObject, "iri"));
nodeRes.put("label", JsonHelper.getString(ontologyNodeObject, "label"));
nodeRes.put(LABEL.getText(), JsonHelper.getString(ontologyNodeObject, LABEL.getText()));
return nodeRes;

}).collect(Collectors.toList());
Expand All @@ -107,7 +109,7 @@ private Map<String, Object> getGraphForEntity(String iri, String type, String ne
if(propertyLabel == null)
propertyLabel = "is a";

edgeRes.put("label", propertyLabel);
edgeRes.put(LABEL.getText(), propertyLabel);
edgeRes.put("uri", uri);

return edgeRes;
Expand Down
6 changes: 4 additions & 2 deletions backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1JsTreeRepository.java
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Expand Up @@ -7,6 +7,8 @@
import uk.ac.ebi.spot.ols.repository.neo4j.OlsNeo4jClient;
import uk.ac.ebi.spot.ols.repository.transforms.LocalizationTransform;

import static uk.ac.ebi.ols.shared.DefinedFields.*;

import java.util.*;
import java.util.stream.Collectors;

Expand All @@ -30,7 +32,7 @@ public List<Map<String,Object>> getJsTreeForIndividual(String iri, String ontolo

private List<Map<String,Object>> getJsTreeForEntity(String iri, String type, String neo4jType, String ontologyId, String lang) {

List<String> parentRelationIRIs = List.of("directParent");
List<String> parentRelationIRIs = List.of(DIRECT_PARENT.getText());

String thisEntityId = ontologyId + "+" + type + "+" + iri;

Expand Down Expand Up @@ -59,7 +61,7 @@ public List<Map<String,Object>> getJsTreeChildrenForIndividual(String individual

private List<Map<String,Object>> getJsTreeChildrenForEntity(String iri, String jstreeId, String type, String neo4jType, String ontologyId, String lang) {

List<String> parentRelationIRIs = List.of("directParent");
List<String> parentRelationIRIs = List.of(DIRECT_PARENT.getText());

String thisEntityId = ontologyId + "+" + type + "+" + iri;

Expand Down
12 changes: 8 additions & 4 deletions backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1PropertyRepository.java
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Expand Up @@ -30,22 +30,26 @@ public class V1PropertyRepository {
V1OntologyRepository ontologyRepository;

public Page<V1Property> getParents(String ontologyId, String iri, String lang, Pageable pageable) {
return neo4jClient.traverseOutgoingEdges("OntologyProperty", ontologyId + "+property+" + iri, Arrays.asList("directParent"), Map.of(), pageable)
return neo4jClient.traverseOutgoingEdges("OntologyProperty", ontologyId + "+property+" + iri,
Arrays.asList(DIRECT_PARENT.getText()), Map.of(), pageable)
.map(record -> V1PropertyMapper.mapProperty(record, lang));
}

public Page<V1Property> getChildren(String ontologyId, String iri, String lang, Pageable pageable) {
return this.neo4jClient.traverseIncomingEdges("OntologyProperty", ontologyId + "+property+" + iri, Arrays.asList("directParent"), Map.of(), pageable)
return this.neo4jClient.traverseIncomingEdges("OntologyProperty", ontologyId + "+property+" + iri,
Arrays.asList(DIRECT_PARENT.getText()), Map.of(), pageable)
.map(record -> V1PropertyMapper.mapProperty(record, lang));
}

public Page<V1Property> getDescendants(String ontologyId, String iri, String lang, Pageable pageable) {
return this.neo4jClient.recursivelyTraverseIncomingEdges("OntologyProperty", ontologyId + "+property+" + iri, Arrays.asList("directParent"), Map.of(), pageable)
return this.neo4jClient.recursivelyTraverseIncomingEdges("OntologyProperty", ontologyId + "+property+" + iri,
Arrays.asList(DIRECT_PARENT.getText()), Map.of(), pageable)
.map(record -> V1PropertyMapper.mapProperty(record, lang));
}

public Page<V1Property> getAncestors(String ontologyId, String iri, String lang, Pageable pageable) {
return neo4jClient.recursivelyTraverseOutgoingEdges("OntologyProperty", ontologyId + "+property+" + iri, Arrays.asList("directParent"), Map.of(), pageable)
return neo4jClient.recursivelyTraverseOutgoingEdges("OntologyProperty", ontologyId + "+property+" + iri,
Arrays.asList(DIRECT_PARENT.getText()), Map.of(), pageable)
.map(record -> V1PropertyMapper.mapProperty(record, lang));
}

Expand Down
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