test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java

   1 package jalview.fts.threedbeacons;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertTrue;
   5
   6 import java.util.ArrayList;
   7 import java.util.Collection;
   8 import java.util.HashSet;
   9 import java.util.List;
  10 import java.util.Set;
  11
  12 import org.testng.Assert;
  13 import org.testng.annotations.AfterMethod;
  14 import org.testng.annotations.BeforeClass;
  15 import org.testng.annotations.BeforeMethod;
  16 import org.testng.annotations.Test;
  17
  18 import jalview.fts.api.FTSDataColumnI;
  19 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  20 import jalview.fts.core.FTSRestClient;
  21 import jalview.fts.core.FTSRestRequest;
  22 import jalview.fts.core.FTSRestResponse;
  23 import jalview.fts.service.pdb.PDBFTSRestClient;
  24 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  25 import jalview.gui.JvOptionPane;
  26
  27 public class TDBeaconsFTSRestClientTest
  28 {
  29   @BeforeClass(alwaysRun = true)
  30   public void setUpJvOptionPane()
  31   {
  32     JvOptionPane.setInteractiveMode(false);
  33     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  34   }
  35
  36   private FTSRestClient ftsRestClient;
  37
  38   @BeforeMethod(alwaysRun = true)
  39   public void setUp() throws Exception
  40   {
  41     ftsRestClient = new FTSRestClient()
  42     {
  43
  44       @Override
  45       public String getColumnDataConfigFileName()
  46       {
  47         return "/fts/tdbeacons_data_columns.txt";
  48       }
  49
  50       @Override
  51       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  52               throws Exception
  53       {
  54         return null;
  55       }
  56     };
  57   }
  58
  59   @AfterMethod(alwaysRun = true)
  60   public void tearDown() throws Exception
  61   {
  62   }
  63
  64   @Test
  65   public void getAllDefaulDisplayedDataColumns()
  66   {
  67     // to change when resources.tdbeacons_data_columns.txt is changed
  68     Assert.assertNotNull(ftsRestClient
  69             .getAllDefaultDisplayedFTSDataColumns());
  70     System.out.println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  71     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  72             .isEmpty());
  73     Assert.assertEquals(ftsRestClient
  74             .getAllDefaultDisplayedFTSDataColumns().size(), 11);
  75   }
  76
  77   @Test(groups = { "Functional" })
  78   public void getPrimaryKeyColumIndexTest()
  79   {
  80     Collection<FTSDataColumnI> wantedFields = ftsRestClient
  81             .getAllDefaultDisplayedFTSDataColumns();
  82     int foundIndex = -1;
  83     try
  84     {
  85       Assert.assertEquals(foundIndex, -1);
  86       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  87               false);
  88       Assert.assertEquals(foundIndex, 10);
  89       foundIndex = ftsRestClient
  90               .getPrimaryKeyColumIndex(wantedFields, true);
  91       Assert.assertEquals(foundIndex, 11);
  92     } catch (Exception e)
  93     {
  94       e.printStackTrace();
  95       Assert.fail("Exception thrown while testing...");
  96     }
  97   }
  98
  99   @Test(groups = { "Functional" })
 100   public void getDataColumnsFieldsAsCommaDelimitedString()
 101   {
 102     // to change when resources.tdbeacons_data_columns.txt is changed
 103     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 104             .getAllDefaultDisplayedFTSDataColumns();
 105     String actual = ftsRestClient
 106             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 107     Assert.assertEquals(actual,
 108             "model_identifier,provider,model_category,uniprot_start,uniprot_end,resolution,qmean_avg_local_score,coverage,created,entry_name,model_url");
 109   }
 110
 111   @Test(groups = { "Functional" })
 112   public void getAllFTSDataColumns()
 113   {
 114     Collection<FTSDataColumnI> allFields = ftsRestClient
 115             .getAllFTSDataColumns();
 116     Assert.assertNotNull(allFields);
 117     //System.out.println(allFields.size());
 118     Assert.assertEquals(allFields.size(), 15);
 119   }
 120
 121   @Test(groups = { "Functional" })
 122   public void getSearchableDataColumns()
 123   {
 124     // to change when resources.tdbeacons_data_columns.txt is changed
 125     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 126             .getSearchableDataColumns();
 127     Assert.assertNotNull(searchableFields);
 128     //System.out.println(searchableFields.size());
 129     Assert.assertEquals(searchableFields.size(), 1); //only 1: uniprot accession
 130   }
 131
 132   @Test(groups = { "Functional" })
 133   public void getPrimaryKeyColumn()
 134   {
 135     // to change when resources.tdbeacons_data_columns.txt is changed
 136     FTSDataColumnI expectedPKColumn;
 137     try
 138     {
 139       expectedPKColumn = ftsRestClient
 140               .getDataColumnByNameOrCode("Url");
 141       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 142       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 143               expectedPKColumn);
 144     } catch (Exception e)
 145     {
 146       e.printStackTrace();
 147       Assert.fail("Exception thrown while testing...");
 148     }
 149   }
 150
 151   @Test(groups = { "Functional" })
 152   public void getDataColumnByNameOrCode()
 153   {
 154     try
 155     {
 156       FTSDataColumnI foundDataCol = ftsRestClient
 157               .getDataColumnByNameOrCode("uniprot_accession");
 158       Assert.assertNotNull(foundDataCol);
 159       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 160     } catch (Exception e)
 161     {
 162       e.printStackTrace();
 163       Assert.fail("Exception thrown while testing...");
 164     }
 165   }
 166
 167   @Test(groups = { "Functional" })
 168   public void getDataColumnGroupById()
 169   {
 170     FTSDataColumnGroupI foundDataColGroup;
 171     try
 172     {
 173       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 174       Assert.assertNotNull(foundDataColGroup);
 175       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 176     } catch (Exception e)
 177     {
 178       e.printStackTrace();
 179     }
 180   }
 181
 182   @Test(groups = { "Functional" })
 183   public void getDefaultResponsePageSize()
 184   {
 185     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 186     Assert.assertEquals(defaultResSize, 100); //why 100 or 500 ? pdb is 100, uniprot 500
 187   }
 188
 189   @Test(groups = { "Functional" })
 190   public void getColumnMinWidthTest()
 191   {
 192     try
 193     {
 194       FTSDataColumnI foundDataCol = ftsRestClient
 195               .getDataColumnByNameOrCode("uniprot_accession");
 196       Assert.assertNotNull(foundDataCol);
 197       int actualColMinWidth = foundDataCol.getMinWidth();
 198       Assert.assertEquals(actualColMinWidth, 50);
 199     } catch (Exception e)
 200     {
 201       e.printStackTrace();
 202       Assert.fail("Exception thrown while testing...");
 203     }
 204   }
 205   // could add test for MaxWidth & PreferedWith
 206
 207   @Test(groups = { "Functional" })
 208   public void getColumnClassTest()
 209   {
 210     try
 211     {
 212       FTSDataColumnI foundDataCol = ftsRestClient
 213               .getDataColumnByNameOrCode("uniprot_accession");
 214       Assert.assertNotNull(foundDataCol);
 215       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 216               String.class);
 217       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 218       Assert.assertNotNull(foundDataCol);
 219       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 220               String.class);
 221     } catch (Exception e)
 222     {
 223       e.printStackTrace();
 224       Assert.fail("Exception thrown while testing...");
 225     }
 226   }
 227
 228   @Test(groups = { "Functional" })
 229   public void coverageForEqualsAndHashFunction()
 230   {
 231     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 232     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 233             .getSearchableDataColumns();
 234     System.out.println(searchableCols);
 235     for (FTSDataColumnI foundCol : searchableCols)
 236     {
 237       System.out.println(foundCol.toString());
 238       uniqueSet.add(foundCol);
 239       uniqueSet.add(foundCol);
 240     }
 241     Assert.assertTrue(!uniqueSet.isEmpty());
 242     //Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 243   }
 244
 245   @Test(groups = { "Functional" })
 246   public void getTDBIdColumIndexTest()
 247   {
 248     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 249     try
 250     {
 251       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 252               .getDataColumnByNameOrCode("Model id"));
 253       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 254               .getDataColumnByNameOrCode("uniprot_accession"));
 255       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 256               .getDataColumnByNameOrCode("entry name"));
 257     } catch (Exception e)
 258     {
 259       e.printStackTrace();
 260     }
 261     try
 262     {
 263       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 264               .getPrimaryKeyColumIndex(wantedFields, true));
 265 //      assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 266 //              .getPrimaryKeyColumIndex(wantedFields, true));
 267     } catch (Exception e)
 268     {
 269       e.printStackTrace();
 270     }
 271   }
 272
 273
 274   @Test(groups = { "External", "Network" })
 275   public void executeRequestTest()
 276   {
 277     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 278     try
 279     {
 280       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 281               .getDataColumnByNameOrCode("Model Id"));
 282       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 283               .getDataColumnByNameOrCode("model_url"));
 284       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 285               .getDataColumnByNameOrCode("provider"));
 286       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 287               .getDataColumnByNameOrCode("model_category"));
 288       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 289               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 290       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 291               .getDataColumnByNameOrCode("uniprot_start"));
 292       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 293               .getDataColumnByNameOrCode("uniprot_end"));
 294     } catch (Exception e1)
 295     {
 296       e1.printStackTrace();
 297     }
 298     System.out.println("wantedFields >>" + wantedFields);
 299
 300     FTSRestRequest request = new FTSRestRequest();
 301     request.setResponseSize(100);
 302     request.setFieldToSearchBy("");
 303     request.setSearchTerm("P01318.json");
 304     request.setWantedFields(wantedFields);
 305     System.out.println("request : " + request.getFieldToSearchBy());
 306     //System.out.println(request.toString());
 307
 308     FTSRestResponse response;
 309     try
 310     {
 311       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 312     } catch (Exception e)
 313     {
 314       e.printStackTrace();
 315       Assert.fail("Couldn't execute webservice call!");
 316       return;
 317     }
 318     assertTrue(response.getSearchSummary() != null);
 319     assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
 320     System.out.println("Search summary : \n" + response.getSearchSummary());
 321     //System.out.println(response.getSearchSummary().size());
 322   }
 323 }