JAL-1563 JAL-2091 Added generic pagination for FTS Service, pagination for PDB FTS...

[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 f611d5b..2f24a01 100644 (file)
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -3,10 +3,12 @@ package jalview.fts.core;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
 import jalview.fts.api.FTSRestClientI;
+import jalview.util.MessageManager;
 
 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 +45,10 @@ 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)
@@ -127,7 +132,14 @@ public abstract class FTSRestClient implements FTSRestClientI
               @Override
               public String getCode()
               {
-                return lineData[1];
+                return lineData[1].split("\\|")[0];
+              }
+
+              @Override
+              public String getAltCode()
+              {
+                return lineData[1].split("\\|").length > 1 ? lineData[1]
+                        .split("\\|")[1] : getCode();
               }
 
               @Override
@@ -291,31 +303,6 @@ public abstract class FTSRestClient implements FTSRestClientI
     return result;
   }
 
-  /**
-   * Takes a collection of FTSDataColumnI and converts its 'code' values into a
-   * tab delimited string.
-   * 
-   * @param dataColumnFields
-   *          the collection of FTSDataColumnI to process
-   * @return the generated comma delimited string from the supplied
-   *         FTSDataColumnI collection
-   */
-  public String getDataColumnsFieldsAsTabDelimitedString(
-          Collection<FTSDataColumnI> dataColumnFields)
-  {
-    String result = "";
-    if (dataColumnFields != null && !dataColumnFields.isEmpty())
-    {
-      StringBuilder returnedFields = new StringBuilder();
-      for (FTSDataColumnI field : dataColumnFields)
-      {
-        returnedFields.append("\t").append(field.getName());
-      }
-      returnedFields.deleteCharAt(0);
-      result = returnedFields.toString();
-    }
-    return result;
-  }
 
   @Override
   public Collection<FTSDataColumnI> getAllFTSDataColumns()
@@ -397,6 +384,42 @@ public abstract class FTSRestClient implements FTSRestClientI
     throw new Exception("Couldn't find data column group with id : " + id);
   }
 
+  public String getMessageByHTTPStatusCode(int code, String service)
+  {
+    String message = "";
+    switch (code)
+    {
+    case 400:
+      message = MessageManager
+              .getString("exception.bad_request");
+      break;
+      
+    case 410:
+      message = MessageManager.formatMessage(
+              "exception.fts_rest_service_no_longer_available", service);
+      break;
+    case 403:
+    case 404:
+      message = MessageManager.getString("exception.resource_not_be_found");
+      break;
+    case 408:
+    case 409:
+    case 500:
+    case 501:
+    case 502:
+    case 504:
+    case 505:
+      message = MessageManager.getString("exception.fts_server_error");
+      break;
+    case 503:
+      message = MessageManager.getString("exception.service_not_available");
+      break;
+    default:
+      break;
+    }
+    return message;
+  }
+
   protected String getResourceFile(String fileName)
   {
     String result = "";
@@ -414,6 +437,10 @@ public abstract class FTSRestClient implements FTSRestClientI
   @Override
   public int getDefaultResponsePageSize()
   {
+    if (dataColumns == null || dataColumns.isEmpty())
+    {
+      parseDataColumnsConfigFile();
+    }
     return defaultResponsePageSize;
   }