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.datamodel.Sequence;
  43 import jalview.fts.api.FTSData;
  44 import jalview.fts.api.FTSDataColumnI;
  45 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  46 import jalview.fts.core.FTSRestClient;
  47 import jalview.fts.core.FTSRestRequest;
  48 import jalview.fts.core.FTSRestResponse;
  49 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  50 import jalview.fts.service.threedbeacons.TDB_FTSData;
  51 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  52 import jalview.gui.JvOptionPane;
  53 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  54 import jalview.gui.structurechooser.TDBResultAnalyser;
  55 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  56
  57 public class TDBeaconsFTSRestClientTest
  58 {
  59   @BeforeClass(alwaysRun = true)
  60   public void setUpJvOptionPane()
  61   {
  62     JvOptionPane.setInteractiveMode(false);
  63     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  64   }
  65
  66   private FTSRestClient ftsRestClient;
  67
  68   @BeforeMethod(alwaysRun = true)
  69   public void setUp() throws Exception
  70   {
  71     ftsRestClient = new FTSRestClient()
  72     {
  73
  74       @Override
  75       public String getColumnDataConfigFileName()
  76       {
  77         return "/fts/tdbeacons_data_columns.txt";
  78       }
  79
  80       @Override
  81       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  82               throws Exception
  83       {
  84         return null;
  85       }
  86     };
  87   }
  88
  89   @AfterMethod(alwaysRun = true)
  90   public void tearDown() throws Exception
  91   {
  92   }
  93
  94   @Test
  95   public void getAllDefaulDisplayedDataColumns()
  96   {
  97     // to change when resources.tdbeacons_data_columns.txt is changed
  98     Assert.assertNotNull(
  99             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
 100     System.out
 101             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
 102     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
 103             .isEmpty());
 104     Assert.assertEquals(
 105             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
 106             15);
 107   }
 108
 109   @Test(groups = { "Functional" })
 110   public void getPrimaryKeyColumIndexTest()
 111   {
 112     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 113             .getAllDefaultDisplayedFTSDataColumns();
 114     int foundIndex = -1;
 115     try
 116     {
 117       Assert.assertEquals(foundIndex, -1);
 118       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
 119               false);
 120       Assert.assertEquals(foundIndex, 12);
 121       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
 122               true);
 123       // 1+primary key index
 124       Assert.assertEquals(foundIndex, 13);
 125     } catch (Exception e)
 126     {
 127       e.printStackTrace();
 128       Assert.fail("Exception thrown while testing...");
 129     }
 130   }
 131
 132   @Test(groups = { "Functional" })
 133   public void getDataColumnsFieldsAsCommaDelimitedString()
 134   {
 135     // to change when resources.tdbeacons_data_columns.txt is changed
 136     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 137             .getAllDefaultDisplayedFTSDataColumns();
 138     String actual = ftsRestClient
 139             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 140     Assert.assertEquals(actual,
 141             "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");
 142   }
 143
 144   @Test(groups = { "Functional" })
 145   public void getAllFTSDataColumns()
 146   {
 147     Collection<FTSDataColumnI> allFields = ftsRestClient
 148             .getAllFTSDataColumns();
 149     Assert.assertNotNull(allFields);
 150     // System.out.println(allFields.size());
 151     Assert.assertEquals(allFields.size(), 20);
 152   }
 153
 154   @Test(groups = { "Functional" })
 155   public void getSearchableDataColumns()
 156   {
 157     // to change when resources.tdbeacons_data_columns.txt is changed
 158     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 159             .getSearchableDataColumns();
 160     Assert.assertNotNull(searchableFields);
 161     // System.out.println(searchableFields.size());
 162     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
 163                                                      // accession
 164   }
 165
 166   @Test(groups = { "Functional" })
 167   public void getPrimaryKeyColumn()
 168   {
 169     // to change when resources.tdbeacons_data_columns.txt is changed
 170     FTSDataColumnI expectedPKColumn;
 171     try
 172     {
 173       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
 174       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 175       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 176               expectedPKColumn);
 177     } catch (Exception e)
 178     {
 179       e.printStackTrace();
 180       Assert.fail("Exception thrown while testing...");
 181     }
 182   }
 183
 184   @Test(groups = { "Functional" })
 185   public void getDataColumnByNameOrCode()
 186   {
 187     try
 188     {
 189       FTSDataColumnI foundDataCol = ftsRestClient
 190               .getDataColumnByNameOrCode("uniprot_accession");
 191       Assert.assertNotNull(foundDataCol);
 192       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 193     } catch (Exception e)
 194     {
 195       e.printStackTrace();
 196       Assert.fail("Exception thrown while testing...");
 197     }
 198   }
 199
 200   @Test(groups = { "Functional" })
 201   public void getDataColumnGroupById()
 202   {
 203     FTSDataColumnGroupI foundDataColGroup;
 204     try
 205     {
 206       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 207       Assert.assertNotNull(foundDataColGroup);
 208       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 209     } catch (Exception e)
 210     {
 211       e.printStackTrace();
 212     }
 213   }
 214
 215   @Test(groups = { "Functional" })
 216   public void getDefaultResponsePageSize()
 217   {
 218     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 219     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
 220                                               // uniprot 500
 221   }
 222
 223   @Test(groups = { "Functional" })
 224   public void getColumnMinWidthTest()
 225   {
 226     try
 227     {
 228       FTSDataColumnI foundDataCol = ftsRestClient
 229               .getDataColumnByNameOrCode("uniprot_accession");
 230       Assert.assertNotNull(foundDataCol);
 231       int actualColMinWidth = foundDataCol.getMinWidth();
 232       Assert.assertEquals(actualColMinWidth, 50);
 233     } catch (Exception e)
 234     {
 235       e.printStackTrace();
 236       Assert.fail("Exception thrown while testing...");
 237     }
 238   }
 239   // could add test for MaxWidth & PreferedWith
 240
 241   @Test(groups = { "Functional" })
 242   public void getColumnClassTest()
 243   {
 244     try
 245     {
 246       FTSDataColumnI foundDataCol = ftsRestClient
 247               .getDataColumnByNameOrCode("uniprot_accession");
 248       Assert.assertNotNull(foundDataCol);
 249       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 250               String.class);
 251       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 252       Assert.assertNotNull(foundDataCol);
 253       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 254               String.class);
 255     } catch (Exception e)
 256     {
 257       e.printStackTrace();
 258       Assert.fail("Exception thrown while testing...");
 259     }
 260   }
 261
 262   @Test(groups = { "Functional" })
 263   public void coverageForEqualsAndHashFunction()
 264   {
 265     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 266     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 267             .getSearchableDataColumns();
 268     System.out.println(searchableCols);
 269     for (FTSDataColumnI foundCol : searchableCols)
 270     {
 271       System.out.println(foundCol.toString());
 272       uniqueSet.add(foundCol);
 273       uniqueSet.add(foundCol);
 274     }
 275     Assert.assertTrue(!uniqueSet.isEmpty());
 276     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 277   }
 278
 279   @Test(groups = { "Functional" })
 280   public void getTDBIdColumIndexTest()
 281   {
 282     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 283     try
 284     {
 285       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 286               .getDataColumnByNameOrCode("Model id"));
 287       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 288               .getDataColumnByNameOrCode("uniprot_accession"));
 289       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 290               .getDataColumnByNameOrCode("Title"));
 291     } catch (Exception e)
 292     {
 293       e.printStackTrace();
 294     }
 295     try
 296     {
 297       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 298               .getPrimaryKeyColumIndex(wantedFields, true));
 299       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 300       // .getPrimaryKeyColumIndex(wantedFields, true));
 301     } catch (Exception e)
 302     {
 303       e.printStackTrace();
 304     }
 305   }
 306
 307   private static String[][] mocks = { { "P38398.json", null },
 308       { "P01308.json", null },
 309       { "P0DTD1.json", null },
 310       { "P27787.json", null },
 311       { "Q99814.json", null }
 312
 313       // , { "P0DTD3.json", "{}" } actually results in 404, but {} is in body
 314   };
 315
 316   private static void setMockData()
 317   {
 318     try
 319     {
 320       mocks[0][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 321               "test/jalview/fts/threedbeacons/p38398_tdb_fts_query_resp.txt");
 322
 323       mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 324               "test/jalview/fts/threedbeacons/p01308_tdb_fts_query_resp.txt");
 325
 326       mocks[2][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 327               "test/jalview/fts/threedbeacons/p0dtd1_tdb_fts_query_resp.txt");
 328
 329       mocks[3][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 330               "test/jalview/fts/threedbeacons/p27787_tdb_fts_query_resp.txt");
 331       mocks[4][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 332               "test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt");
 333
 334     } catch (IOException e)
 335     {
 336       Assert.fail("Couldn't read mock response data", e);
 337     }
 338   }
 339
 340   public static void setMock()
 341   {
 342     setMockData();
 343     FTSRestClient.createMockFTSRestClient(
 344             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
 345   }
 346
 347   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 348
 349   private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 350
 351   /**
 352    * check that the mock request and response are the same as the response from
 353    * a live 3D-beacons endpoint
 354    *
 355    * Note - servers often have rapidly changing ids / URIs so this might fail,
 356    * but the overall structure will remain.
 357    *
 358    * @throws Exception
 359    */
 360   @Test(groups = { "Network", "Integration" })
 361   public void verifyMockTDBRequest() throws Exception
 362   {
 363     setMockData();
 364     for (String[] otherMock : mocks)
 365     {
 366       verifyMockTDBRequest(otherMock[0], otherMock[1]);
 367     }
 368   }
 369
 370   private void verifyMockTDBRequest(String mockRequest,
 371           String _mockResponse) throws Exception
 372   {
 373     URL tdb_req = new URL(prod_url + mockRequest);
 374     byte[] resp = tdb_req.openStream().readAllBytes();
 375     String tresp = new String(resp, StandardCharsets.UTF_8);
 376     // this simple test fails for responses containing multi-chain structures -
 377     // since chain order in the json elements is arbitrary and varies between
 378     // queries.
 379     assertEquals(_mockResponse.trim(), tresp.trim());
 380   }
 381
 382   @Test(groups = { "Functional" })
 383   public void testMockTDBRequest()
 384   {
 385
 386     setMock();
 387     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 388     try
 389     {
 390       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 391               .getDataColumnByNameOrCode("Model Id"));
 392       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 393               .getDataColumnByNameOrCode("model_url"));
 394       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 395               .getDataColumnByNameOrCode("provider"));
 396       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 397               .getDataColumnByNameOrCode("model_category"));
 398       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 399               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 400       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 401               .getDataColumnByNameOrCode("uniprot_start"));
 402       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 403               .getDataColumnByNameOrCode("uniprot_end"));
 404     } catch (Exception e1)
 405     {
 406       e1.printStackTrace();
 407     }
 408     System.out.println("wantedFields >>" + wantedFields);
 409
 410     FTSRestRequest request = new FTSRestRequest();
 411     FTSRestResponse response;
 412
 413     request.setResponseSize(100);
 414     request.setFieldToSearchBy("");
 415     request.setWantedFields(wantedFields);
 416     // check 404 behaviour
 417     request.setSearchTerm("P00000.json");
 418
 419     try
 420     {
 421       response = TDBeaconsFTSRestClient.getInstance()
 422               .executeRequest(request);
 423
 424       assertNull(response);
 425     } catch (Exception e)
 426     {
 427       e.printStackTrace();
 428       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 429     }
 430
 431     // check 200 behaviour
 432     request.setSearchTerm("P38398.json");
 433     System.out.println("request : " + request.getFieldToSearchBy());
 434     // System.out.println(request.toString());
 435
 436     try
 437     {
 438       response = TDBeaconsFTSRestClient.getInstance()
 439               .executeRequest(request);
 440     } catch (Exception e)
 441     {
 442       e.printStackTrace();
 443       Assert.fail("Couldn't execute webservice call!");
 444       return;
 445     }
 446     assertTrue(response.getSearchSummary() != null);
 447     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 448     System.out.println("Search summary : \n" + response.getSearchSummary());
 449
 450     // System.out.println(response.getSearchSummary().size());
 451   }
 452
 453   @Test(groups = { "External", "Network" })
 454   public void executeRequestTest()
 455   {
 456     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 457     try
 458     {
 459       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 460               .getDataColumnByNameOrCode("Model Id"));
 461       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 462               .getDataColumnByNameOrCode("model_url"));
 463       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 464               .getDataColumnByNameOrCode("provider"));
 465       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 466               .getDataColumnByNameOrCode("model_category"));
 467       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 468               .getDataColumnByNameOrCode("confidence_avg_local_score"));
 469       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 470               .getDataColumnByNameOrCode("uniprot_start"));
 471       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 472               .getDataColumnByNameOrCode("uniprot_end"));
 473     } catch (Exception e1)
 474     {
 475       e1.printStackTrace();
 476     }
 477     System.out.println("wantedFields >>" + wantedFields);
 478
 479     FTSRestRequest request = new FTSRestRequest();
 480     request.setResponseSize(100);
 481     request.setFieldToSearchBy("");
 482     request.setSearchTerm("P01318.json");
 483     request.setWantedFields(wantedFields);
 484     System.out.println("request : " + request.getFieldToSearchBy());
 485     // System.out.println(request.toString());
 486
 487     FTSRestResponse response;
 488     try
 489     {
 490       response = TDBeaconsFTSRestClient.getInstance()
 491               .executeRequest(request);
 492     } catch (Exception e)
 493     {
 494       e.printStackTrace();
 495       Assert.fail("Couldn't execute webservice call!");
 496       return;
 497     }
 498     assertTrue(response.getSearchSummary() != null);
 499     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 500     System.out.println("Search summary : \n" + response.getSearchSummary());
 501     // System.out.println(response.getSearchSummary().size());
 502   }
 503
 504 }