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       { "P27787.json", null }
 305
 306       // , { "P0DTD3.json", "{}" } actually results in 404, but {} is in body
 307   };
 308
 309   private static void setMockData()
 310   {
 311     try
 312     {
 313       mocks[0][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 314               "test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt");
 315
 316       mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 317               "test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt");
 318
 319       mocks[2][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 320               "test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt");
 321
 322       mocks[3][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 323               "test/jalview/fts/threedbeacons/p27787_tdb_fts_query_resp.txt");
 324
 325     } catch (IOException e)
 326     {
 327       Assert.fail("Couldn't read mock response data", e);
 328     }
 329   }
 330
 331   public static void setMock()
 332   {
 333     setMockData();
 334     FTSRestClient.createMockFTSRestClient(
 335             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
 336   }
 337
 338   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 339
 340   private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 341
 342   /**
 343    * check that the mock request and response are the same as the response from
 344    * a live 3D-beacons endpoint
 345    *
 346    * Note - servers often have rapidly changing ids / URIs so this might fail,
 347    * but the overall structure will remain.
 348    *
 349    * @throws Exception
 350    */
 351   @Test(groups = { "Network", "Integration" })
 352   public void verifyMockTDBRequest() throws Exception
 353   {
 354     setMockData();
 355     for (String[] otherMock : mocks)
 356     {
 357       verifyMockTDBRequest(otherMock[0], otherMock[1]);
 358     }
 359   }
 360
 361   private void verifyMockTDBRequest(String mockRequest,
 362           String _mockResponse) throws Exception
 363   {
 364     URL tdb_req = new URL(prod_url + mockRequest);
 365     byte[] resp = tdb_req.openStream().readAllBytes();
 366     String tresp = new String(resp, StandardCharsets.UTF_8);
 367     // this simple test fails for responses containing multi-chain structures -
 368     // since chain order in the json elements is arbitrary and varies between
 369     // queries.
 370     assertEquals(_mockResponse.trim(), tresp.trim());
 371   }
 372
 373   @Test(groups = { "Functional" })
 374   public void testMockTDBRequest()
 375   {
 376
 377     setMock();
 378     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 379     try
 380     {
 381       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 382               .getDataColumnByNameOrCode("Model Id"));
 383       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 384               .getDataColumnByNameOrCode("model_url"));
 385       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 386               .getDataColumnByNameOrCode("provider"));
 387       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 388               .getDataColumnByNameOrCode("model_category"));
 389       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 390               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 391       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 392               .getDataColumnByNameOrCode("uniprot_start"));
 393       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 394               .getDataColumnByNameOrCode("uniprot_end"));
 395     } catch (Exception e1)
 396     {
 397       e1.printStackTrace();
 398     }
 399     System.out.println("wantedFields >>" + wantedFields);
 400
 401     FTSRestRequest request = new FTSRestRequest();
 402     FTSRestResponse response;
 403
 404     request.setResponseSize(100);
 405     request.setFieldToSearchBy("");
 406     request.setWantedFields(wantedFields);
 407     // check 404 behaviour
 408     request.setSearchTerm("P00000.json");
 409
 410     try
 411     {
 412       response = TDBeaconsFTSRestClient.getInstance()
 413               .executeRequest(request);
 414
 415       assertNull(response);
 416     } catch (Exception e)
 417     {
 418       e.printStackTrace();
 419       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 420     }
 421
 422     // check 200 behaviour
 423     request.setSearchTerm("P38398.json");
 424     System.out.println("request : " + request.getFieldToSearchBy());
 425     // System.out.println(request.toString());
 426
 427     try
 428     {
 429       response = TDBeaconsFTSRestClient.getInstance()
 430               .executeRequest(request);
 431     } catch (Exception e)
 432     {
 433       e.printStackTrace();
 434       Assert.fail("Couldn't execute webservice call!");
 435       return;
 436     }
 437     assertTrue(response.getSearchSummary() != null);
 438     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 439     System.out.println("Search summary : \n" + response.getSearchSummary());
 440
 441     // System.out.println(response.getSearchSummary().size());
 442   }
 443
 444   @Test(groups = { "External", "Network" })
 445   public void executeRequestTest()
 446   {
 447     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 448     try
 449     {
 450       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 451               .getDataColumnByNameOrCode("Model Id"));
 452       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 453               .getDataColumnByNameOrCode("model_url"));
 454       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 455               .getDataColumnByNameOrCode("provider"));
 456       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 457               .getDataColumnByNameOrCode("model_category"));
 458       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 459               .getDataColumnByNameOrCode("confidence_avg_local_score"));
 460       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 461               .getDataColumnByNameOrCode("uniprot_start"));
 462       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 463               .getDataColumnByNameOrCode("uniprot_end"));
 464     } catch (Exception e1)
 465     {
 466       e1.printStackTrace();
 467     }
 468     System.out.println("wantedFields >>" + wantedFields);
 469
 470     FTSRestRequest request = new FTSRestRequest();
 471     request.setResponseSize(100);
 472     request.setFieldToSearchBy("");
 473     request.setSearchTerm("P01318.json");
 474     request.setWantedFields(wantedFields);
 475     System.out.println("request : " + request.getFieldToSearchBy());
 476     // System.out.println(request.toString());
 477
 478     FTSRestResponse response;
 479     try
 480     {
 481       response = TDBeaconsFTSRestClient.getInstance()
 482               .executeRequest(request);
 483     } catch (Exception e)
 484     {
 485       e.printStackTrace();
 486       Assert.fail("Couldn't execute webservice call!");
 487       return;
 488     }
 489     assertTrue(response.getSearchSummary() != null);
 490     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 491     System.out.println("Search summary : \n" + response.getSearchSummary());
 492     // System.out.println(response.getSearchSummary().size());
 493   }
 494 }