Merge dev into stable

README.md

@@ -407,7 +407,7 @@ new expected output:
 
         git add -A testcases_expected_output
 
-8. Commit the updates to testcases to a branch with suffix `-testcases`.
+8. Commit the updates to testcases to a branch with suffix `-testcases` and message "TESTCASES updated".
 9. Now continue with API testing.
 
 ### Testing API
@@ -440,7 +440,7 @@ the old `testcases_expected_output_api` and replace with new expected output:
 
         git add -A testcases_expected_output_api
 
-16. Commit the API tests to a branch with suffix `-api-tests`.
+16. Commit the API tests to a branch with suffix `-api-tests` and message "API-TESTS updated".
 
 17. You can stop the OLS4 backend with "Ctrl-C", and Solr and Neo4J with:
 

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/SolrFieldMapper.java

@@ -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
@@ -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;
             }
 

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1PreferredRootTermAssembler.java

@@ -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;

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java

@@ -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");
@@ -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))));
 
@@ -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 + ")");
             }
 
         }
@@ -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 + ")");
             }
         }
 
@@ -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");
@@ -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(),
@@ -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));

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java

@@ -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");
@@ -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);
@@ -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());
 
@@ -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");
             }
 
@@ -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(),
@@ -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);
@@ -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));
                 }

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SuggestController.java

@@ -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 {
@@ -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);
 
@@ -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");
 
 
@@ -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);
         }

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1AncestorsJsTreeBuilder.java

@@ -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);
 

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1ChildrenJsTreeBuilder.java

@@ -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<>();

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1GraphRepository.java

@@ -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;
 
@@ -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());
@@ -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;

backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/V1JsTreeRepository.java

@@ -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;
 
@@ -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;
 
@@ -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;