Add support for ancestors from Lexigram API (refs bst-mug#17)

hpi-dhc · Jul 24, 2018 · f7309a6 · f7309a6
1 parent f7a830d
commit f7309a6
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diff --git a/src/main/java/at/medunigraz/imi/bst/lexigram/Lexigram.java b/src/main/java/at/medunigraz/imi/bst/lexigram/Lexigram.java
@@ -103,6 +103,37 @@ public static List<String> addSynonymsFromBestConceptMatch(String label) {
         return cleanUpList(keywordAndSynonyms);
     }
 
+    /**
+     * Given a string, it searches for the best matching concept and returns all its ancestors.
+     * If no match is found, an empty list is returned.
+     *
+     * @param label
+     * @return
+     */
+    public static List<String> getAncestorsFromBestConceptMatch(String label) {
+        List<String> ret = new ArrayList<>();
+
+        Optional<String> search = search(label);
+        if (!search.isPresent()) {
+            return ret;
+        }
+
+        return cleanUpList(ancestors(search.get()));
+    }
+
+    public static List<String> ancestors(String conceptId) {
+        // TODO pagination
+        JSONObject body = get(ENDPOINT + "concepts/" + conceptId + "/ancestors");
+
+        List<String> ancestors = new ArrayList<>();
+        JSONArray results = body.getJSONArray("results");
+        for(int i = 0; i < results.length(); i++) {
+            ancestors.add(cleanUpString(results.getJSONObject(i).getString("label")));
+        }
+
+        return ancestors;
+    }
+
     public static Concept concept(String conceptId) {
         /* Get info (label and synonyms) of concept */
         JSONObject body = get(ENDPOINT + "concepts/" + conceptId);

diff --git a/src/test/java/at/medunigraz/imi/bst/conceptextraction/ConceptExtractionTest.java b/src/test/java/at/medunigraz/imi/bst/conceptextraction/ConceptExtractionTest.java
@@ -14,6 +14,8 @@
 import com.mashape.unirest.http.Unirest;
 import com.mashape.unirest.http.exceptions.UnirestException;
 
+import static org.hamcrest.CoreMatchers.hasItems;
+import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.collection.IsIterableContainingInAnyOrder.containsInAnyOrder;
 
 
@@ -52,4 +54,20 @@ public void addSynonyms() {
         Assert.assertThat(Lexigram.addSynonymsFromBestConceptMatch("notfoundlabel"),
                 containsInAnyOrder("notfoundlabel"));
     }
+
+    @Test
+    public void getAncestorsFromBestConceptMatch() {
+        Assert.assertThat(Lexigram.getAncestorsFromBestConceptMatch("cholangiocarcinoma"),
+                hasItems("malignant neoplasm of digestive system",
+                        "abdominal mass",
+                        "epithelial neoplasm",
+                        "disorder of biliary tract",
+                        "neoplasm of digestive organ",
+                        "finding of biliary tract",
+                        "gastrointestinal tract finding")
+                );
+
+        Assert.assertThat(Lexigram.getAncestorsFromBestConceptMatch("notfoundlabel"),
+                empty());
+    }
 }