Merge pull request #697 from EBISPOT/fix-693

Fix for #693.
EBISPOT · Jul 11, 2024 · e5c4a2e · e5c4a2e
2 parents 56a60e3 + 829f40c
commit e5c4a2e
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Showing 4 changed files with 82 additions and 5 deletions.
diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java
@@ -81,6 +81,8 @@ public void search(
             @RequestParam(value = "lang", defaultValue = "en") String lang,
             HttpServletResponse response
     ) throws IOException, SolrServerException {
+        System.out.println("fieldList 1 = " + fieldList);
+        System.out.println("type = " + types);
 
         final SolrQuery solrQuery = new SolrQuery(); // 1
 
@@ -206,15 +208,15 @@ public void search(
 		 * Fix: End
 		 */
         solrQuery.add("wt", format);
+        System.out.println("fieldList 2 = " + fieldList);
 
-
-        System.out.println(solrQuery.jsonStr());
+        System.out.println("solrQuery=" + solrQuery.jsonStr());
 
         QueryResponse qr = solrClient.dispatchSearch(solrQuery, "ols4_entities");
 
         List<Object> docs = new ArrayList<>();
         for(SolrDocument res : qr.getResults()) {
-
+            System.out.println("res = " + res.toString());
             String _json = (String)res.get("_json");
             if(_json == null) {
                 throw new RuntimeException("_json was null");
@@ -256,7 +258,9 @@ public void search(
             if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getString(json, "curie"));
             if (fieldList.contains("is_defining_ontology")) outDoc.put("is_defining_ontology",
                     JsonHelper.getString(json, "isDefiningOntology") != null && JsonHelper.getString(json, "isDefiningOntology").equals("true"));
-            if (fieldList.contains("type")) outDoc.put("type", "class");
+            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("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"));

diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java b/backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SelectController.java
@@ -161,7 +161,9 @@ public void select(
             if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getString(json, "curie"));
             if (fieldList.contains("is_defining_ontology")) outDoc.put("is_defining_ontology",
                     JsonHelper.getString(json, "isDefiningOntology") != null && JsonHelper.getString(json, "isDefiningOntology").equals("true"));
-            if (fieldList.contains("type")) outDoc.put("type", "class");
+            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("ontology_prefix")) outDoc.put("ontology_prefix", JsonHelper.getString(json, "ontologyPreferredPrefix"));
 

diff --git a/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/JsonHelper.java b/backend/src/main/java/uk/ac/ebi/spot/ols/repository/v1/JsonHelper.java
@@ -64,6 +64,18 @@ public static List<String> getStrings(JsonObject json, String predicate) {
         return getValues(json, predicate).stream().map(JsonHelper::objectToString).collect(Collectors.toList());
     }
 
+    /**
+     * This methi
+     * @param json
+     * @param predicate
+     * @return
+     */
+    public static String getType(JsonObject json, String predicate){
+        List<String> types = getValues(json, predicate).stream().map(JsonHelper::objectToString).collect(Collectors.toList());
+        types.remove("entity");
+        return types.get(0);
+    }
+
     public static List<JsonObject> getObjects(JsonObject json, String predicate) {
         return getValues(json, predicate).stream().map(v -> v.getAsJsonObject()).collect(Collectors.toList());
     }

diff --git a/dataload/configs/gaz.json b/dataload/configs/gaz.json
@@ -0,0 +1,59 @@
+{
+  "ontologies": [
+    {
+      "activity_status": "inactive",
+      "build": {
+        "method": "archive",
+        "path": "archive",
+        "source_url": "http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/*zip*/archive.zip"
+      },
+      "contact": {
+        "email": "lschriml@som.umaryland.edu",
+        "github": "lschriml",
+        "label": "Lynn Schriml",
+        "orcid": "0000-0001-8910-9851"
+      },
+      "description": "A gazetteer constructed on ontological principles",
+      "homepage": "http://environmentontology.github.io/gaz/",
+      "id": "gaz",
+      "preferredPrefix": "GAZ",
+      "layout": "ontology_detail",
+      "license": {
+        "label": "CC0 1.0",
+        "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/cc-zero.png",
+        "url": "https://creativecommons.org/publicdomain/zero/1.0/"
+      },
+      "mailing_list": "https://groups.google.com/forum/#!forum/obo-gazetteer",
+      "ontology_purl": "http://purl.obolibrary.org/obo/gaz.owl",
+      "products": [
+        {
+          "id": "gaz.owl",
+          "ontology_purl": "http://purl.obolibrary.org/obo/gaz.owl"
+        },
+        {
+          "id": "gaz.obo",
+          "ontology_purl": "http://purl.obolibrary.org/obo/gaz.obo"
+        }
+      ],
+      "repository": "https://github.com/EnvironmentOntology/gaz",
+      "title": "Gazetteer",
+      "tracker": "https://github.com/EnvironmentOntology/gaz/issues",
+      "hierarchical_property":[
+        "http://purl.obolibrary.org/obo/BFO_0000050",
+        "http://purl.obolibrary.org/obo/RO_0001025",
+        "http://purl.obolibrary.org/obo/RO_0002151",
+        "http://purl.obolibrary.org/obo/RO_0002376",
+        "http://purl.obolibrary.org/obo/RO_0002377",
+        "http://purl.obolibrary.org/obo/UBREL_0000001",
+        "http://purl.obolibrary.org/obo/RO_0002219",
+        "http://purl.obolibrary.org/obo/RO_0002379",
+        "http://purl.obolibrary.org/obo/RO_0002378",
+        "http://purl.obolibrary.org/obo/RO_0002090",
+        "http://purl.obolibrary.org/obo/TEMP#proper_partof",
+        "http://purl.obolibrary.org/obo/TEMP#overlapped_by",
+        "http://purl.obolibrary.org/obo/RO_0002131",
+        "http://purl.obolibrary.org/obo/RO_0002220"
+      ]
+    }
+  ]
+}