X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fcore%2FFTSRestClient.java;h=0bca0709c34b00663c302f8f74cad2dabcd7dc89;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=f611d5b43367df8ddb2e26e6dc0d1087a7b823d7;hpb=e3a91c662873d6b6e6f86b6b596f578a16e23779;p=jalview.git

diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index f611d5b..0bca070 100644
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -1,16 +1,42 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.fts.core;
 
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
-import jalview.fts.api.FTSRestClientI;
+import java.util.Locale;
 
 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.HashMap;
 import java.util.Objects;
 
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
+import jalview.fts.api.FTSRestClientI;
+
 /**
  * Base class providing implementation for common methods defined in
  * FTSRestClientI
@@ -21,13 +47,13 @@ import java.util.Objects;
  */
 public abstract class FTSRestClient implements FTSRestClientI
 {
-  protected Collection<FTSDataColumnI> dataColumns = new ArrayList<FTSDataColumnI>();
+  protected Collection<FTSDataColumnI> dataColumns = new ArrayList<>();
 
-  protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<FTSDataColumnGroupI>();
+  protected Collection<FTSDataColumnGroupI> dataColumnGroups = new ArrayList<>();
 
-  protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<FTSDataColumnI>();
+  protected Collection<FTSDataColumnI> searchableDataColumns = new ArrayList<>();
 
-  protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<FTSDataColumnI>();
+  protected Collection<FTSDataColumnI> defaulDisplayedDataColumns = new ArrayList<>();
 
   protected FTSDataColumnI primaryKeyColumn;
 
@@ -35,6 +61,8 @@ public abstract class FTSRestClient implements FTSRestClientI
 
   private int defaultResponsePageSize = 100;
 
+  protected HashMap<String,String> mockQueries = null;
+
   protected FTSRestClient()
   {
 
@@ -43,7 +71,10 @@ 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)
@@ -57,8 +88,8 @@ public abstract class FTSRestClient implements FTSRestClientI
             {
               primaryKeyColumnCode = lineData[1];
             }
-            if (lineData[0]
-                    .equalsIgnoreCase("_data_column.default_response_page_size"))
+            if (lineData[0].equalsIgnoreCase(
+                    "_data_column.default_response_page_size"))
             {
               defaultResponsePageSize = Integer.valueOf(lineData[1]);
             }
@@ -127,25 +158,74 @@ 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
-              public Class<?> getDataColumnClass()
+              public DataTypeI getDataType()
               {
-                String classString = lineData[2];
-                classString = classString.toUpperCase();
-                switch (classString)
+                final String[] dataTypeString = lineData[2].split("\\|");
+                final String classString = dataTypeString[0].toUpperCase(Locale.ROOT);
+
+                return new DataTypeI()
                 {
-                case "INT":
-                case "INTEGER":
-                  return Integer.class;
-                case "DOUBLE":
-                  return Double.class;
-                case "STRING":
-                default:
-                  return String.class;
-                }
+
+                  @Override
+                  public boolean isFormtted()
+                  {
+                    if (dataTypeString.length > 1
+                            && dataTypeString[1] != null)
+                    {
+                      switch (dataTypeString[1].toUpperCase(Locale.ROOT))
+                      {
+                      case "T":
+                      case "TRUE":
+                        return true;
+                      case "F":
+                      case "False":
+                      default:
+                        return false;
+                      }
+                    }
+                    return false;
+                  }
+
+                  @Override
+                  public int getSignificantFigures()
+                  {
+                    if (dataTypeString.length > 2
+                            && dataTypeString[2] != null)
+                    {
+                      return Integer.valueOf(dataTypeString[2]);
+                    }
+                    return 0;
+                  }
+
+                  @Override
+                  public Class getDataTypeClass()
+                  {
+                    switch (classString)
+                    {
+                    case "INT":
+                    case "INTEGER":
+                      return Integer.class;
+                    case "DOUBLE":
+                      return Double.class;
+                    case "STRING":
+                    default:
+                      return String.class;
+                    }
+                  }
+                };
+
               }
 
               @Override
@@ -206,12 +286,12 @@ public abstract class FTSRestClient implements FTSRestClientI
                         this.getGroup());
               }
 
-
               @Override
               public boolean equals(Object otherObject)
               {
                 FTSDataColumnI that = (FTSDataColumnI) otherObject;
-                return this.getCode().equals(that.getCode())
+                return otherObject == null ? false
+                        : this.getCode().equals(that.getCode())
                         && this.getName().equals(that.getName())
                         && this.getGroup().equals(that.getGroup());
               }
@@ -241,7 +321,8 @@ public abstract class FTSRestClient implements FTSRestClientI
       }
       try
       {
-        this.primaryKeyColumn = getDataColumnByNameOrCode(primaryKeyColumnCode);
+        this.primaryKeyColumn = getDataColumnByNameOrCode(
+                primaryKeyColumnCode);
       } catch (Exception e)
       {
         e.printStackTrace();
@@ -291,32 +372,6 @@ 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()
   {
@@ -338,7 +393,7 @@ public abstract class FTSRestClient implements FTSRestClientI
   }
 
   @Override
-  public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns()
+  public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns()
   {
     if (defaulDisplayedDataColumns == null
             || defaulDisplayedDataColumns.isEmpty())
@@ -375,8 +430,18 @@ public abstract class FTSRestClient implements FTSRestClientI
         return column;
       }
     }
-    throw new Exception("Couldn't find data column with name : "
-            + nameOrCode);
+    throw new Exception(
+            "Couldn't find data column with name : " + nameOrCode);
+  }
+
+  /**
+   * 
+   * @param instance
+   * @param mocks {{working query, working response}, ...}
+   */
+  public static void createMockFTSRestClient(FTSRestClient instance,String[][] mocks)
+  {
+    instance.setMock(mocks);
   }
 
   @Override
@@ -397,6 +462,46 @@ public abstract class FTSRestClient implements FTSRestClientI
     throw new Exception("Couldn't find data column group with id : " + id);
   }
 
+  public static String getMessageByHTTPStatusCode(int code, String service)
+  {
+    String message = "";
+    switch (code)
+    {
+    case 400:
+      message = "Bad request. There is a problem with your input.";
+      break;
+
+    case 410:
+      message = service + " rest services no longer available!";
+      break;
+    case 403:
+    case 404:
+      message = "The requested resource could not be found";
+      break;
+    case 408:
+    case 409:
+    case 500:
+    case 501:
+    case 502:
+    case 504:
+    case 505:
+      message = "There seems to be an error from the " + service
+              + " server";
+      break;
+    case 503:
+      message = "Service not available. The server is being updated, try again later.";
+      break;
+    default:
+      break;
+    }
+    return String.valueOf(code) + " " + message;
+  }
+
+  public static void unMock(FTSRestClient instance)
+  {
+    instance.mockQueries=null;
+  }
+
   protected String getResourceFile(String fileName)
   {
     String result = "";
@@ -414,7 +519,44 @@ public abstract class FTSRestClient implements FTSRestClientI
   @Override
   public int getDefaultResponsePageSize()
   {
+    if (dataColumns == null || dataColumns.isEmpty())
+    {
+      parseDataColumnsConfigFile();
+    }
     return defaultResponsePageSize;
   }
 
+  protected void setMock(String[][] mocks)
+  {
+    if (mocks==null) {
+      mockQueries=null;
+      return;
+    }
+    mockQueries=new HashMap<String,String>();
+    for (String[] mock:mocks)
+    {
+      mockQueries.put(mock[0],mock[1]);
+    }
+  }
+
+  protected boolean isMocked()
+  {
+    return mockQueries!=null;
+  }
+
+  @Override
+  public String[] getPreferencesColumnsFor(PreferenceSource source)
+  {
+    String[] columnNames = null;
+    switch (source)
+    {
+    case SEARCH_SUMMARY:
+      columnNames = new String[] { "", "Display", "Group" };
+      break;
+    default:
+      // non structure sources don't return any other kind of preferences columns
+      break;
+    }
+    return columnNames;
+  }
 }