test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java

   1 package jalview.fts.threedbeacons;
   2
   3 import static org.testng.Assert.assertNull;
   4 import static org.testng.AssertJUnit.assertEquals;
   5 import static org.testng.AssertJUnit.assertTrue;
   6
   7 import java.net.URL;
   8 import java.nio.charset.StandardCharsets;
   9 import java.util.ArrayList;
  10 import java.util.Collection;
  11 import java.util.HashSet;
  12 import java.util.List;
  13 import java.util.Set;
  14
  15 import org.testng.Assert;
  16 import org.testng.annotations.AfterMethod;
  17 import org.testng.annotations.BeforeClass;
  18 import org.testng.annotations.BeforeMethod;
  19 import org.testng.annotations.Test;
  20
  21 import jalview.fts.api.FTSDataColumnI;
  22 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  23 import jalview.fts.core.FTSRestClient;
  24 import jalview.fts.core.FTSRestRequest;
  25 import jalview.fts.core.FTSRestResponse;
  26 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  27 import jalview.gui.JvOptionPane;
  28
  29 public class TDBeaconsFTSRestClientTest
  30 {
  31   @BeforeClass(alwaysRun = true)
  32   public void setUpJvOptionPane()
  33   {
  34     JvOptionPane.setInteractiveMode(false);
  35     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  36   }
  37
  38   private FTSRestClient ftsRestClient;
  39
  40   @BeforeMethod(alwaysRun = true)
  41   public void setUp() throws Exception
  42   {
  43     ftsRestClient = new FTSRestClient()
  44     {
  45
  46       @Override
  47       public String getColumnDataConfigFileName()
  48       {
  49         return "/fts/tdbeacons_data_columns.txt";
  50       }
  51
  52       @Override
  53       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  54               throws Exception
  55       {
  56         return null;
  57       }
  58     };
  59   }
  60
  61   @AfterMethod(alwaysRun = true)
  62   public void tearDown() throws Exception
  63   {
  64   }
  65
  66   @Test
  67   public void getAllDefaulDisplayedDataColumns()
  68   {
  69     // to change when resources.tdbeacons_data_columns.txt is changed
  70     Assert.assertNotNull(ftsRestClient
  71             .getAllDefaultDisplayedFTSDataColumns());
  72     System.out.println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  73     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  74             .isEmpty());
  75     Assert.assertEquals(ftsRestClient
  76             .getAllDefaultDisplayedFTSDataColumns().size(), 11);
  77   }
  78
  79   @Test(groups = { "Functional" })
  80   public void getPrimaryKeyColumIndexTest()
  81   {
  82     Collection<FTSDataColumnI> wantedFields = ftsRestClient
  83             .getAllDefaultDisplayedFTSDataColumns();
  84     int foundIndex = -1;
  85     try
  86     {
  87       Assert.assertEquals(foundIndex, -1);
  88       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  89               false);
  90       Assert.assertEquals(foundIndex, 10);
  91       foundIndex = ftsRestClient
  92               .getPrimaryKeyColumIndex(wantedFields, true);
  93       Assert.assertEquals(foundIndex, 11);
  94     } catch (Exception e)
  95     {
  96       e.printStackTrace();
  97       Assert.fail("Exception thrown while testing...");
  98     }
  99   }
 100
 101   @Test(groups = { "Functional" })
 102   public void getDataColumnsFieldsAsCommaDelimitedString()
 103   {
 104     // to change when resources.tdbeacons_data_columns.txt is changed
 105     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 106             .getAllDefaultDisplayedFTSDataColumns();
 107     String actual = ftsRestClient
 108             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 109     Assert.assertEquals(actual,
 110             "model_identifier,provider,model_category,uniprot_start,uniprot_end,resolution,qmean_avg_local_score,coverage,created,entry_name,model_url");
 111   }
 112
 113   @Test(groups = { "Functional" })
 114   public void getAllFTSDataColumns()
 115   {
 116     Collection<FTSDataColumnI> allFields = ftsRestClient
 117             .getAllFTSDataColumns();
 118     Assert.assertNotNull(allFields);
 119     //System.out.println(allFields.size());
 120     Assert.assertEquals(allFields.size(), 15);
 121   }
 122
 123   @Test(groups = { "Functional" })
 124   public void getSearchableDataColumns()
 125   {
 126     // to change when resources.tdbeacons_data_columns.txt is changed
 127     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 128             .getSearchableDataColumns();
 129     Assert.assertNotNull(searchableFields);
 130     //System.out.println(searchableFields.size());
 131     Assert.assertEquals(searchableFields.size(), 1); //only 1: uniprot accession
 132   }
 133
 134   @Test(groups = { "Functional" })
 135   public void getPrimaryKeyColumn()
 136   {
 137     // to change when resources.tdbeacons_data_columns.txt is changed
 138     FTSDataColumnI expectedPKColumn;
 139     try
 140     {
 141       expectedPKColumn = ftsRestClient
 142               .getDataColumnByNameOrCode("Url");
 143       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 144       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 145               expectedPKColumn);
 146     } catch (Exception e)
 147     {
 148       e.printStackTrace();
 149       Assert.fail("Exception thrown while testing...");
 150     }
 151   }
 152
 153   @Test(groups = { "Functional" })
 154   public void getDataColumnByNameOrCode()
 155   {
 156     try
 157     {
 158       FTSDataColumnI foundDataCol = ftsRestClient
 159               .getDataColumnByNameOrCode("uniprot_accession");
 160       Assert.assertNotNull(foundDataCol);
 161       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 162     } catch (Exception e)
 163     {
 164       e.printStackTrace();
 165       Assert.fail("Exception thrown while testing...");
 166     }
 167   }
 168
 169   @Test(groups = { "Functional" })
 170   public void getDataColumnGroupById()
 171   {
 172     FTSDataColumnGroupI foundDataColGroup;
 173     try
 174     {
 175       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 176       Assert.assertNotNull(foundDataColGroup);
 177       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 178     } catch (Exception e)
 179     {
 180       e.printStackTrace();
 181     }
 182   }
 183
 184   @Test(groups = { "Functional" })
 185   public void getDefaultResponsePageSize()
 186   {
 187     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 188     Assert.assertEquals(defaultResSize, 100); //why 100 or 500 ? pdb is 100, uniprot 500
 189   }
 190
 191   @Test(groups = { "Functional" })
 192   public void getColumnMinWidthTest()
 193   {
 194     try
 195     {
 196       FTSDataColumnI foundDataCol = ftsRestClient
 197               .getDataColumnByNameOrCode("uniprot_accession");
 198       Assert.assertNotNull(foundDataCol);
 199       int actualColMinWidth = foundDataCol.getMinWidth();
 200       Assert.assertEquals(actualColMinWidth, 50);
 201     } catch (Exception e)
 202     {
 203       e.printStackTrace();
 204       Assert.fail("Exception thrown while testing...");
 205     }
 206   }
 207   // could add test for MaxWidth & PreferedWith
 208
 209   @Test(groups = { "Functional" })
 210   public void getColumnClassTest()
 211   {
 212     try
 213     {
 214       FTSDataColumnI foundDataCol = ftsRestClient
 215               .getDataColumnByNameOrCode("uniprot_accession");
 216       Assert.assertNotNull(foundDataCol);
 217       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 218               String.class);
 219       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 220       Assert.assertNotNull(foundDataCol);
 221       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 222               String.class);
 223     } catch (Exception e)
 224     {
 225       e.printStackTrace();
 226       Assert.fail("Exception thrown while testing...");
 227     }
 228   }
 229
 230   @Test(groups = { "Functional" })
 231   public void coverageForEqualsAndHashFunction()
 232   {
 233     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 234     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 235             .getSearchableDataColumns();
 236     System.out.println(searchableCols);
 237     for (FTSDataColumnI foundCol : searchableCols)
 238     {
 239       System.out.println(foundCol.toString());
 240       uniqueSet.add(foundCol);
 241       uniqueSet.add(foundCol);
 242     }
 243     Assert.assertTrue(!uniqueSet.isEmpty());
 244     //Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 245   }
 246
 247   @Test(groups = { "Functional" })
 248   public void getTDBIdColumIndexTest()
 249   {
 250     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 251     try
 252     {
 253       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 254               .getDataColumnByNameOrCode("Model id"));
 255       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 256               .getDataColumnByNameOrCode("uniprot_accession"));
 257       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 258               .getDataColumnByNameOrCode("entry name"));
 259     } catch (Exception e)
 260     {
 261       e.printStackTrace();
 262     }
 263     try
 264     {
 265       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 266               .getPrimaryKeyColumIndex(wantedFields, true));
 267 //      assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 268 //              .getPrimaryKeyColumIndex(wantedFields, true));
 269     } catch (Exception e)
 270     {
 271       e.printStackTrace();
 272     }
 273   }
 274
 275   private static String mockRequest = "P38398.json";
 276
 277   private static String mockResponse = "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"6138930b772bfbf9fe34f912\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-08\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"qmean_version\":\"4.2.0\",\"qmean_avg_local_score\":0.776,\"model_url\":\"https://beta.swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\"},{\"model_identifier\":\"6138930b772bfbf9fe34f916\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-08\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"qmean_version\":\"4.2.0\",\"qmean_avg_local_score\":0.655,\"model_url\":\"https://beta.swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"Deep learning\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\"}]}";
 278
 279   public static void setMock()
 280   {
 281     FTSRestClient.createMockFTSRestClient(
 282             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
 283             mockRequest, mockResponse);
 284   }
 285
 286   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 287
 288   /**
 289    * check that the mock request and response are the same as the response from
 290    * a live 3D-beacons endpoint
 291    *
 292    * @throws Exception
 293    */
 294   @Test(groups = { "Network", "Integration" })
 295   public void verifyMockTDBRequest() throws Exception
 296   {
 297     URL tdb_req = new URL(dev_url + mockRequest);
 298     byte[] resp = tdb_req.openStream().readAllBytes();
 299     String tresp = new String(resp, StandardCharsets.UTF_8);
 300     assertEquals(mockResponse.trim(), tresp.trim());
 301   }
 302
 303   @Test(groups = { "Functional" })
 304   public void testMockTDBRequest()
 305   {
 306
 307     setMock();
 308     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 309     try
 310     {
 311       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 312               .getDataColumnByNameOrCode("Model Id"));
 313       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 314               .getDataColumnByNameOrCode("model_url"));
 315       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 316               .getDataColumnByNameOrCode("provider"));
 317       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 318               .getDataColumnByNameOrCode("model_category"));
 319       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 320               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 321       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 322               .getDataColumnByNameOrCode("uniprot_start"));
 323       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 324               .getDataColumnByNameOrCode("uniprot_end"));
 325     } catch (Exception e1)
 326     {
 327       e1.printStackTrace();
 328     }
 329     System.out.println("wantedFields >>" + wantedFields);
 330
 331     FTSRestRequest request = new FTSRestRequest();
 332     FTSRestResponse response;
 333
 334     request.setResponseSize(100);
 335     request.setFieldToSearchBy("");
 336     request.setWantedFields(wantedFields);
 337     // check 404 behaviour
 338     request.setSearchTerm("P00000.json");
 339
 340
 341     try {
 342       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 343
 344       assertNull(response);
 345     } catch (Exception e)
 346     {
 347       e.printStackTrace();
 348       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 349     }
 350
 351     // check 200 behaviour
 352     request.setSearchTerm("P38398.json");
 353     System.out.println("request : " + request.getFieldToSearchBy());
 354     //System.out.println(request.toString());
 355
 356     try
 357     {
 358       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 359     } catch (Exception e)
 360     {
 361       e.printStackTrace();
 362       Assert.fail("Couldn't execute webservice call!");
 363       return;
 364     }
 365     assertTrue(response.getSearchSummary() != null);
 366     assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
 367     System.out.println("Search summary : \n" + response.getSearchSummary());
 368
 369     //System.out.println(response.getSearchSummary().size());
 370   }
 371
 372   @Test(groups = { "External", "Network" })
 373   public void executeRequestTest()
 374   {
 375     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 376     try
 377     {
 378       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 379               .getDataColumnByNameOrCode("Model Id"));
 380       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 381               .getDataColumnByNameOrCode("model_url"));
 382       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 383               .getDataColumnByNameOrCode("provider"));
 384       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 385               .getDataColumnByNameOrCode("model_category"));
 386       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 387               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 388       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 389               .getDataColumnByNameOrCode("uniprot_start"));
 390       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 391               .getDataColumnByNameOrCode("uniprot_end"));
 392     } catch (Exception e1)
 393     {
 394       e1.printStackTrace();
 395     }
 396     System.out.println("wantedFields >>" + wantedFields);
 397
 398     FTSRestRequest request = new FTSRestRequest();
 399     request.setResponseSize(100);
 400     request.setFieldToSearchBy("");
 401     request.setSearchTerm("P01318.json");
 402     request.setWantedFields(wantedFields);
 403     System.out.println("request : " + request.getFieldToSearchBy());
 404     //System.out.println(request.toString());
 405
 406     FTSRestResponse response;
 407     try
 408     {
 409       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 410     } catch (Exception e)
 411     {
 412       e.printStackTrace();
 413       Assert.fail("Couldn't execute webservice call!");
 414       return;
 415     }
 416     assertTrue(response.getSearchSummary() != null);
 417     assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
 418     System.out.println("Search summary : \n" + response.getSearchSummary());
 419     //System.out.println(response.getSearchSummary().size());
 420   }
 421 }