Move Lexigram API key to properties (fixes #17)

This ease key manipulation and allow injection via environment variable, which can be used not to skip tests during CI.
bst-mug · Jul 24, 2018 · 6828282 · 6828282
1 parent 41744c0
commit 6828282
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Showing 5 changed files with 13 additions and 42 deletions.
diff --git a/src/main/java/at/medunigraz/imi/bst/config/TrecConfig.java b/src/main/java/at/medunigraz/imi/bst/config/TrecConfig.java
@@ -19,7 +19,7 @@ public final class TrecConfig {
     public static final int ELASTIC_PORT = getInteger("ELASTIC_PORT");
     public static final String ELASTIC_CLUSTER = getString("ELASTIC_CLUSTER");
 
-
+    public static final String LEXIGRAM_APIKEY = getString("LEXIGRAM_APIKEY");
 
 
     /* DATA - MEDLINE */

diff --git a/src/main/java/at/medunigraz/imi/bst/lexigram/Lexigram.java b/src/main/java/at/medunigraz/imi/bst/lexigram/Lexigram.java
@@ -1,10 +1,10 @@
 package at.medunigraz.imi.bst.lexigram;
 
+import at.medunigraz.imi.bst.config.TrecConfig;
 import com.mashape.unirest.http.HttpResponse;
 import com.mashape.unirest.http.JsonNode;
 import com.mashape.unirest.http.Unirest;
 import com.mashape.unirest.http.exceptions.UnirestException;
-import org.apache.commons.io.FileUtils;
 import org.json.JSONArray;
 import org.json.JSONObject;
 
@@ -19,20 +19,6 @@ public class Lexigram {
 
     private static final String ENDPOINT = "https://api.lexigram.io/v1/lexigraph/";
 
-    static String API_KEY_FILE = "src/main/resources/apikey.txt";
-    static String API_KEY;
-
-    static {
-        File apiFile = new File(API_KEY_FILE);
-
-        try {
-            API_KEY = FileUtils.readFileToString(apiFile, "UTF-8").replace("\n", "");
-        } catch (IOException e) {
-            System.out.print("Please place your Lexigram API key in the following file: " + API_KEY_FILE);
-            e.printStackTrace();
-        }
-    }
-
     private static class Cache {
         private static final String FILENAME = "cache/lexigram.ser";
         private static HashMap<String, String> CALLS = new HashMap<>();
@@ -206,12 +192,16 @@ private static JSONObject get(String url) {
             HttpResponse<JsonNode> response = null;
             try {
                 response = Unirest.get(url)
-                        .header("authorization", "Bearer " + API_KEY)
+                        .header("authorization", "Bearer " + TrecConfig.LEXIGRAM_APIKEY)
                         .asJson();
             } catch (UnirestException e) {
                 throw new RuntimeException(e);
             }
 
+            if (response.getStatus() == 401) {
+                throw new RuntimeException("Unauthorized access to Lexigram API. Place your key in the file trec-pm.properties.");
+            }
+
             JSONObject body = new JSONObject(response.getBody());
             String firstArrayObject = body.getJSONArray("array").getJSONObject(0).toString();
 

diff --git a/src/main/resources/config.properties b/src/main/resources/config.properties
@@ -5,4 +5,5 @@ ELASTIC_BA_INDEX=${elastic.ba.index}
 ELASTIC_BA_MEDLINE_TYPE=${elastic.ba.medline.type}
 ELASTIC_BA_EXTRA_TYPE=${elastic.ba.extra.type}
 ELASTIC_CT_INDEX=${elastic.ct.index}
-ELASTIC_CT_TYPE=${elastic.ct.type}
+ELASTIC_CT_TYPE=${elastic.ct.type}
+LEXIGRAM_APIKEY=${lexigram.apikey}
diff --git a/src/test/java/at/medunigraz/imi/bst/conceptextraction/ConceptExtractionTest.java b/src/test/java/at/medunigraz/imi/bst/conceptextraction/ConceptExtractionTest.java
@@ -1,40 +1,19 @@
 package at.medunigraz.imi.bst.conceptextraction;
 
-import java.io.File;
-import java.io.IOException;
-
+import at.medunigraz.imi.bst.config.TrecConfig;
 import at.medunigraz.imi.bst.lexigram.Lexigram;
-import org.apache.commons.io.FileUtils;
-import org.json.JSONArray;
-import org.json.JSONObject;
 import org.junit.*;
 
-import com.mashape.unirest.http.HttpResponse;
-import com.mashape.unirest.http.JsonNode;
-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;
 
 
 public class ConceptExtractionTest {
 
-    String API_KEY_FILE = "src/main/resources/apikey.txt";
-    String API_KEY;
-
     @Before
     public void SetUp() {
-        File apiFile = new File(API_KEY_FILE);
-        Assume.assumeTrue(apiFile.exists());
-
-        try {
-            API_KEY = FileUtils.readFileToString(apiFile, "UTF-8").replace("\n", "");
-        } catch (IOException e) {
-            System.out.print("Please place your Lexigram API key in the following file: " + API_KEY_FILE);
-            e.printStackTrace();
-        }
+        Assume.assumeFalse(TrecConfig.LEXIGRAM_APIKEY.equalsIgnoreCase("secret")); // placeholder key
     }
 
     @Test

diff --git a/trec-pm.properties b/trec-pm.properties
@@ -5,4 +5,5 @@ elastic.ba.index=trec
 elastic.ba.medline.type=medline
 elastic.ba.extra.type=extra
 elastic.ct.index=clinicaltrials
-elastic.ct.type=clinicaltrials
+elastic.ct.type=clinicaltrials
+lexigram.apikey=secret