JAL-2071 improvement to get column data files as InputStream

[jalview.git] / src / jalview / fts / core / FTSRestClient.java

diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index eeb7ec6..0605fef 100644 (file)
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -5,8 +5,9 @@ import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
 import jalview.fts.api.FTSRestClientI;
 
 import java.io.BufferedReader;
-import java.io.FileReader;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Objects;
@@ -43,7 +44,10 @@ public abstract class FTSRestClient implements FTSRestClientI
   public void parseDataColumnsConfigFile()
   {
     String fileName = getColumnDataConfigFileName();
-    try (BufferedReader br = new BufferedReader(new FileReader(fileName)))
+    
+    InputStream in = getClass().getResourceAsStream(fileName); 
+    
+    try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
     {
       String line;
       while ((line = br.readLine()) != null)
@@ -239,6 +243,13 @@ public abstract class FTSRestClient implements FTSRestClientI
           e.printStackTrace();
         }
       }
+      try
+      {
+        this.primaryKeyColumn = getDataColumnByNameOrCode(primaryKeyColumnCode);
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     } catch (IOException e)
     {
       e.printStackTrace();
@@ -344,6 +355,11 @@ public abstract class FTSRestClient implements FTSRestClientI
   @Override
   public FTSDataColumnI getPrimaryKeyColumn()
   {
+    if (defaulDisplayedDataColumns == null
+            || defaulDisplayedDataColumns.isEmpty())
+    {
+      parseDataColumnsConfigFile();
+    }
     return primaryKeyColumn;
   }
 
@@ -387,11 +403,10 @@ public abstract class FTSRestClient implements FTSRestClientI
 
   protected String getResourceFile(String fileName)
   {
-    ClassLoader classLoader = getClass().getClassLoader();
     String result = "";
     try
     {
-      result = classLoader.getResource(fileName).getFile();
+      result = getClass().getResource(fileName).getFile();
     } catch (Exception e)
     {
       e.printStackTrace();