Merge pull request #827 from EBISPOT/update-api-fields

Update ontolog_purl and mailing_list fields
EBISPOT · Jan 27, 2025 · 751acf7 · 751acf7
2 parents 7e6bf8e + ff70aa1
commit 751acf7
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Showing 4 changed files with 19 additions and 6 deletions.
diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/mappers/V1OntologyMapper.java b/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/mappers/V1OntologyMapper.java
@@ -13,7 +13,7 @@
 import java.util.Map;
 import java.util.Objects;
 
-import static uk.ac.ebi.ols.shared.DefinedFields.LANGUAGE;
+import static uk.ac.ebi.ols.shared.DefinedFields.*;
 
 public class V1OntologyMapper {
 
@@ -43,12 +43,12 @@ public static V1Ontology mapOntology(JsonElement json, String lang) {
         ontology.config.description = JsonHelper.getString(localizedJson, "description");
         ontology.config.homepage = JsonHelper.getString(localizedJson, "homepage");
         ontology.config.version = JsonHelper.getString(localizedJson, "version");
-        ontology.config.mailingList = JsonHelper.getString(localizedJson, "mailing_list");
+        ontology.config.mailingList = JsonHelper.getString(localizedJson, MAILING_LIST.getText());
         ontology.config.tracker = JsonHelper.getString(localizedJson, "tracker");
         ontology.config.logo = JsonHelper.getString(localizedJson, "logo");
         ontology.config.creators = JsonHelper.getStrings(localizedJson, "creators");
         ontology.config.annotations = gson.fromJson(localizedJson.get("annotations"), Map.class);
-        ontology.config.fileLocation = JsonHelper.getString(localizedJson, "ontology_purl");
+        ontology.config.fileLocation = JsonHelper.getString(localizedJson, ONTOLOGY_PURL.getText());
         ontology.config.oboSlims = localizedJson.has("oboSlims") && localizedJson.get("oboSlims").getAsBoolean();
 
         ontology.config.labelProperty = JsonHelper.getString(localizedJson, "label_property");

diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/OntologyGraph.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/OntologyGraph.java
@@ -328,6 +328,17 @@ public void write(JsonWriter writer) throws Throwable {
                     }
 
                 }
+
+                if(configKey.equalsIgnoreCase("ontology_purl")) {
+                    // Config uses "ontology_purl" whereas rest of code base uses ONTOLOGY_PURL.getText().
+                    configKey = ONTOLOGY_PURL.getText();
+                }
+
+                if(configKey.equalsIgnoreCase("mailing_list")) {
+                    // Config uses "mailing_list" whereas rest of code base uses MAILING_LIST.getText().
+                    configKey = MAILING_LIST.getText();
+                }
+
                 // annotated as hasPreferredRoot by PreferredRootsAnnotator, no need to duplicate
                 if (configKey.equals("preferred_root_term"))
                     continue;

diff --git a/frontend/src/model/Ontology.ts b/frontend/src/model/Ontology.ts
@@ -37,13 +37,13 @@ export default class Ontology extends Thing {
     return this.properties["depicted_by"] || undefined;
   }
   getOntologyPurl(): string {
-    return this.properties["ontology_purl"];
+    return this.properties["ontologyPurl"];
   }
   getHomepage(): string {
     return this.properties["homepage"];
   }
   getMailingList(): string {
-    return this.properties["mailing_list"];
+    return this.properties["mailingList"];
   }
   getTracker(): string {
     return this.properties["tracker"];

diff --git a/ols-shared/src/main/java/uk/ac/ebi/ols/shared/DefinedFields.java b/ols-shared/src/main/java/uk/ac/ebi/ols/shared/DefinedFields.java
@@ -49,7 +49,9 @@ public enum DefinedFields {
             " in defining this class. It only considers classes in the filler position, not classes expressions in the filler position." +
             "I.e. 'liver disease' (EFO:0001421) has a relatedTo relation with 'liver' (UBERON:0002107) because " +
             "'liver disease' is a subclass of 'has_disease_location some liver'.", "array"),
-    SYNONYM("synonym", "", "The list of names that are synonyms of this entity.", "array"),;
+    SYNONYM("synonym", "", "The list of names that are synonyms of this entity.", "array"),
+    MAILING_LIST("mailingList", "", "The mailing list for the ontology.", "string"),
+    ONTOLOGY_PURL("ontologyPurl", "", "The URL of the ontology to download the ontology file.", "string");
 
     private final String text;
     private final String ols3Text;