test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.fts.threedbeacons;
  22
  23 import static org.testng.Assert.assertNull;
  24 import static org.testng.AssertJUnit.assertEquals;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import java.io.IOException;
  28 import java.net.URL;
  29 import java.nio.charset.StandardCharsets;
  30 import java.util.ArrayList;
  31 import java.util.Collection;
  32 import java.util.HashSet;
  33 import java.util.List;
  34 import java.util.Set;
  35
  36 import org.testng.Assert;
  37 import org.testng.annotations.AfterMethod;
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.BeforeMethod;
  40 import org.testng.annotations.Test;
  41
  42 import jalview.fts.api.FTSDataColumnI;
  43 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  44 import jalview.fts.core.FTSRestClient;
  45 import jalview.fts.core.FTSRestRequest;
  46 import jalview.fts.core.FTSRestResponse;
  47 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  48 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  49 import jalview.gui.JvOptionPane;
  50
  51 public class TDBeaconsFTSRestClientTest
  52 {
  53   @BeforeClass(alwaysRun = true)
  54   public void setUpJvOptionPane()
  55   {
  56     JvOptionPane.setInteractiveMode(false);
  57     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  58   }
  59
  60   private FTSRestClient ftsRestClient;
  61
  62   @BeforeMethod(alwaysRun = true)
  63   public void setUp() throws Exception
  64   {
  65     ftsRestClient = new FTSRestClient()
  66     {
  67
  68       @Override
  69       public String getColumnDataConfigFileName()
  70       {
  71         return "/fts/tdbeacons_data_columns.txt";
  72       }
  73
  74       @Override
  75       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  76               throws Exception
  77       {
  78         return null;
  79       }
  80     };
  81   }
  82
  83   @AfterMethod(alwaysRun = true)
  84   public void tearDown() throws Exception
  85   {
  86   }
  87
  88   @Test
  89   public void getAllDefaulDisplayedDataColumns()
  90   {
  91     // to change when resources.tdbeacons_data_columns.txt is changed
  92     Assert.assertNotNull(
  93             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  94     System.out
  95             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  96     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  97             .isEmpty());
  98     Assert.assertEquals(
  99             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
 100             15);
 101   }
 102
 103   @Test(groups = { "Functional" })
 104   public void getPrimaryKeyColumIndexTest()
 105   {
 106     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 107             .getAllDefaultDisplayedFTSDataColumns();
 108     int foundIndex = -1;
 109     try
 110     {
 111       Assert.assertEquals(foundIndex, -1);
 112       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
 113               false);
 114       Assert.assertEquals(foundIndex, 12);
 115       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
 116               true);
 117       // 1+primary key index
 118       Assert.assertEquals(foundIndex, 13);
 119     } catch (Exception e)
 120     {
 121       e.printStackTrace();
 122       Assert.fail("Exception thrown while testing...");
 123     }
 124   }
 125
 126   @Test(groups = { "Functional" })
 127   public void getDataColumnsFieldsAsCommaDelimitedString()
 128   {
 129     // to change when resources.tdbeacons_data_columns.txt is changed
 130     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 131             .getAllDefaultDisplayedFTSDataColumns();
 132     String actual = ftsRestClient
 133             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 134     Assert.assertEquals(actual,
 135             "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_format,model_page_url");
 136   }
 137
 138   @Test(groups = { "Functional" })
 139   public void getAllFTSDataColumns()
 140   {
 141     Collection<FTSDataColumnI> allFields = ftsRestClient
 142             .getAllFTSDataColumns();
 143     Assert.assertNotNull(allFields);
 144     // System.out.println(allFields.size());
 145     Assert.assertEquals(allFields.size(), 20);
 146   }
 147
 148   @Test(groups = { "Functional" })
 149   public void getSearchableDataColumns()
 150   {
 151     // to change when resources.tdbeacons_data_columns.txt is changed
 152     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 153             .getSearchableDataColumns();
 154     Assert.assertNotNull(searchableFields);
 155     // System.out.println(searchableFields.size());
 156     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
 157                                                      // accession
 158   }
 159
 160   @Test(groups = { "Functional" })
 161   public void getPrimaryKeyColumn()
 162   {
 163     // to change when resources.tdbeacons_data_columns.txt is changed
 164     FTSDataColumnI expectedPKColumn;
 165     try
 166     {
 167       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
 168       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 169       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 170               expectedPKColumn);
 171     } catch (Exception e)
 172     {
 173       e.printStackTrace();
 174       Assert.fail("Exception thrown while testing...");
 175     }
 176   }
 177
 178   @Test(groups = { "Functional" })
 179   public void getDataColumnByNameOrCode()
 180   {
 181     try
 182     {
 183       FTSDataColumnI foundDataCol = ftsRestClient
 184               .getDataColumnByNameOrCode("uniprot_accession");
 185       Assert.assertNotNull(foundDataCol);
 186       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 187     } catch (Exception e)
 188     {
 189       e.printStackTrace();
 190       Assert.fail("Exception thrown while testing...");
 191     }
 192   }
 193
 194   @Test(groups = { "Functional" })
 195   public void getDataColumnGroupById()
 196   {
 197     FTSDataColumnGroupI foundDataColGroup;
 198     try
 199     {
 200       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 201       Assert.assertNotNull(foundDataColGroup);
 202       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 203     } catch (Exception e)
 204     {
 205       e.printStackTrace();
 206     }
 207   }
 208
 209   @Test(groups = { "Functional" })
 210   public void getDefaultResponsePageSize()
 211   {
 212     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 213     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
 214                                               // uniprot 500
 215   }
 216
 217   @Test(groups = { "Functional" })
 218   public void getColumnMinWidthTest()
 219   {
 220     try
 221     {
 222       FTSDataColumnI foundDataCol = ftsRestClient
 223               .getDataColumnByNameOrCode("uniprot_accession");
 224       Assert.assertNotNull(foundDataCol);
 225       int actualColMinWidth = foundDataCol.getMinWidth();
 226       Assert.assertEquals(actualColMinWidth, 50);
 227     } catch (Exception e)
 228     {
 229       e.printStackTrace();
 230       Assert.fail("Exception thrown while testing...");
 231     }
 232   }
 233   // could add test for MaxWidth & PreferedWith
 234
 235   @Test(groups = { "Functional" })
 236   public void getColumnClassTest()
 237   {
 238     try
 239     {
 240       FTSDataColumnI foundDataCol = ftsRestClient
 241               .getDataColumnByNameOrCode("uniprot_accession");
 242       Assert.assertNotNull(foundDataCol);
 243       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 244               String.class);
 245       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 246       Assert.assertNotNull(foundDataCol);
 247       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 248               String.class);
 249     } catch (Exception e)
 250     {
 251       e.printStackTrace();
 252       Assert.fail("Exception thrown while testing...");
 253     }
 254   }
 255
 256   @Test(groups = { "Functional" })
 257   public void coverageForEqualsAndHashFunction()
 258   {
 259     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 260     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 261             .getSearchableDataColumns();
 262     System.out.println(searchableCols);
 263     for (FTSDataColumnI foundCol : searchableCols)
 264     {
 265       System.out.println(foundCol.toString());
 266       uniqueSet.add(foundCol);
 267       uniqueSet.add(foundCol);
 268     }
 269     Assert.assertTrue(!uniqueSet.isEmpty());
 270     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 271   }
 272
 273   @Test(groups = { "Functional" })
 274   public void getTDBIdColumIndexTest()
 275   {
 276     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 277     try
 278     {
 279       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 280               .getDataColumnByNameOrCode("Model id"));
 281       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 282               .getDataColumnByNameOrCode("uniprot_accession"));
 283       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 284               .getDataColumnByNameOrCode("Title"));
 285     } catch (Exception e)
 286     {
 287       e.printStackTrace();
 288     }
 289     try
 290     {
 291       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 292               .getPrimaryKeyColumIndex(wantedFields, true));
 293       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 294       // .getPrimaryKeyColumIndex(wantedFields, true));
 295     } catch (Exception e)
 296     {
 297       e.printStackTrace();
 298     }
 299   }
 300
 301   private static String[][] mocks = { { "P38398.json", null },
 302       { "P01308.json", null },
 303       { "P0DTD1.json", null }
 304
 305       // , { "P0DTD3.json", "{}" } actually results in 404, but {} is in body
 306   };
 307
 308   private static void setMockData()
 309   {
 310     try
 311     {
 312       mocks[0][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 313               "test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt");
 314
 315       mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 316               "test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt");
 317
 318       mocks[2][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 319               "test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt");
 320
 321     } catch (IOException e)
 322     {
 323       Assert.fail("Couldn't read mock response data", e);
 324     }
 325   }
 326
 327   public static void setMock()
 328   {
 329     setMockData();
 330     FTSRestClient.createMockFTSRestClient(
 331             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
 332   }
 333
 334   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 335
 336   private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 337
 338   /**
 339    * check that the mock request and response are the same as the response from
 340    * a live 3D-beacons endpoint
 341    *
 342    * Note - servers often have rapidly changing ids / URIs so this might fail,
 343    * but the overall structure will remain.
 344    *
 345    * @throws Exception
 346    */
 347   @Test(groups = { "Network", "Integration" })
 348   public void verifyMockTDBRequest() throws Exception
 349   {
 350     setMockData();
 351     for (String[] otherMock : mocks)
 352     {
 353       verifyMockTDBRequest(otherMock[0], otherMock[1]);
 354     }
 355   }
 356
 357   private void verifyMockTDBRequest(String mockRequest,
 358           String _mockResponse) throws Exception
 359   {
 360     URL tdb_req = new URL(prod_url + mockRequest);
 361     byte[] resp = tdb_req.openStream().readAllBytes();
 362     String tresp = new String(resp, StandardCharsets.UTF_8);
 363     assertEquals(_mockResponse.trim(), tresp.trim());
 364   }
 365
 366   @Test(groups = { "Functional" })
 367   public void testMockTDBRequest()
 368   {
 369
 370     setMock();
 371     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 372     try
 373     {
 374       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 375               .getDataColumnByNameOrCode("Model Id"));
 376       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 377               .getDataColumnByNameOrCode("model_url"));
 378       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 379               .getDataColumnByNameOrCode("provider"));
 380       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 381               .getDataColumnByNameOrCode("model_category"));
 382       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 383               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 384       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 385               .getDataColumnByNameOrCode("uniprot_start"));
 386       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 387               .getDataColumnByNameOrCode("uniprot_end"));
 388     } catch (Exception e1)
 389     {
 390       e1.printStackTrace();
 391     }
 392     System.out.println("wantedFields >>" + wantedFields);
 393
 394     FTSRestRequest request = new FTSRestRequest();
 395     FTSRestResponse response;
 396
 397     request.setResponseSize(100);
 398     request.setFieldToSearchBy("");
 399     request.setWantedFields(wantedFields);
 400     // check 404 behaviour
 401     request.setSearchTerm("P00000.json");
 402
 403     try
 404     {
 405       response = TDBeaconsFTSRestClient.getInstance()
 406               .executeRequest(request);
 407
 408       assertNull(response);
 409     } catch (Exception e)
 410     {
 411       e.printStackTrace();
 412       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 413     }
 414
 415     // check 200 behaviour
 416     request.setSearchTerm("P38398.json");
 417     System.out.println("request : " + request.getFieldToSearchBy());
 418     // System.out.println(request.toString());
 419
 420     try
 421     {
 422       response = TDBeaconsFTSRestClient.getInstance()
 423               .executeRequest(request);
 424     } catch (Exception e)
 425     {
 426       e.printStackTrace();
 427       Assert.fail("Couldn't execute webservice call!");
 428       return;
 429     }
 430     assertTrue(response.getSearchSummary() != null);
 431     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 432     System.out.println("Search summary : \n" + response.getSearchSummary());
 433
 434     // System.out.println(response.getSearchSummary().size());
 435   }
 436
 437   @Test(groups = { "External", "Network" })
 438   public void executeRequestTest()
 439   {
 440     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 441     try
 442     {
 443       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 444               .getDataColumnByNameOrCode("Model Id"));
 445       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 446               .getDataColumnByNameOrCode("model_url"));
 447       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 448               .getDataColumnByNameOrCode("provider"));
 449       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 450               .getDataColumnByNameOrCode("model_category"));
 451       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 452               .getDataColumnByNameOrCode("confidence_avg_local_score"));
 453       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 454               .getDataColumnByNameOrCode("uniprot_start"));
 455       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 456               .getDataColumnByNameOrCode("uniprot_end"));
 457     } catch (Exception e1)
 458     {
 459       e1.printStackTrace();
 460     }
 461     System.out.println("wantedFields >>" + wantedFields);
 462
 463     FTSRestRequest request = new FTSRestRequest();
 464     request.setResponseSize(100);
 465     request.setFieldToSearchBy("");
 466     request.setSearchTerm("P01318.json");
 467     request.setWantedFields(wantedFields);
 468     System.out.println("request : " + request.getFieldToSearchBy());
 469     // System.out.println(request.toString());
 470
 471     FTSRestResponse response;
 472     try
 473     {
 474       response = TDBeaconsFTSRestClient.getInstance()
 475               .executeRequest(request);
 476     } catch (Exception e)
 477     {
 478       e.printStackTrace();
 479       Assert.fail("Couldn't execute webservice call!");
 480       return;
 481     }
 482     assertTrue(response.getSearchSummary() != null);
 483     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 484     System.out.println("Search summary : \n" + response.getSearchSummary());
 485     // System.out.println(response.getSearchSummary().size());
 486   }
 487 }