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.util.ArrayList;
   8 import java.util.Collection;
   9 import java.util.HashSet;
  10 import java.util.List;
  11 import java.util.Set;
  12
  13 import org.testng.Assert;
  14 import org.testng.annotations.AfterMethod;
  15 import org.testng.annotations.BeforeClass;
  16 import org.testng.annotations.BeforeMethod;
  17 import org.testng.annotations.Test;
  18
  19 import jalview.fts.api.FTSDataColumnI;
  20 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  21 import jalview.fts.core.FTSRestClient;
  22 import jalview.fts.core.FTSRestRequest;
  23 import jalview.fts.core.FTSRestResponse;
  24 import jalview.fts.service.pdb.PDBFTSRestClient;
  25 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  26 import jalview.gui.JvOptionPane;
  27
  28 public class TDBeaconsFTSRestClientTest
  29 {
  30   @BeforeClass(alwaysRun = true)
  31   public void setUpJvOptionPane()
  32   {
  33     JvOptionPane.setInteractiveMode(false);
  34     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  35   }
  36
  37   private FTSRestClient ftsRestClient;
  38
  39   @BeforeMethod(alwaysRun = true)
  40   public void setUp() throws Exception
  41   {
  42     ftsRestClient = new FTSRestClient()
  43     {
  44
  45       @Override
  46       public String getColumnDataConfigFileName()
  47       {
  48         return "/fts/tdbeacons_data_columns.txt";
  49       }
  50
  51       @Override
  52       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  53               throws Exception
  54       {
  55         return null;
  56       }
  57     };
  58   }
  59
  60   @AfterMethod(alwaysRun = true)
  61   public void tearDown() throws Exception
  62   {
  63   }
  64
  65   @Test
  66   public void getAllDefaulDisplayedDataColumns()
  67   {
  68     // to change when resources.tdbeacons_data_columns.txt is changed
  69     Assert.assertNotNull(ftsRestClient
  70             .getAllDefaultDisplayedFTSDataColumns());
  71     System.out.println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  72     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  73             .isEmpty());
  74     Assert.assertEquals(ftsRestClient
  75             .getAllDefaultDisplayedFTSDataColumns().size(), 11);
  76   }
  77
  78   @Test(groups = { "Functional" })
  79   public void getPrimaryKeyColumIndexTest()
  80   {
  81     Collection<FTSDataColumnI> wantedFields = ftsRestClient
  82             .getAllDefaultDisplayedFTSDataColumns();
  83     int foundIndex = -1;
  84     try
  85     {
  86       Assert.assertEquals(foundIndex, -1);
  87       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  88               false);
  89       Assert.assertEquals(foundIndex, 10);
  90       foundIndex = ftsRestClient
  91               .getPrimaryKeyColumIndex(wantedFields, true);
  92       Assert.assertEquals(foundIndex, 11);
  93     } catch (Exception e)
  94     {
  95       e.printStackTrace();
  96       Assert.fail("Exception thrown while testing...");
  97     }
  98   }
  99
 100   @Test(groups = { "Functional" })
 101   public void getDataColumnsFieldsAsCommaDelimitedString()
 102   {
 103     // to change when resources.tdbeacons_data_columns.txt is changed
 104     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 105             .getAllDefaultDisplayedFTSDataColumns();
 106     String actual = ftsRestClient
 107             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 108     Assert.assertEquals(actual,
 109             "model_identifier,provider,model_category,uniprot_start,uniprot_end,resolution,qmean_avg_local_score,coverage,created,entry_name,model_url");
 110   }
 111
 112   @Test(groups = { "Functional" })
 113   public void getAllFTSDataColumns()
 114   {
 115     Collection<FTSDataColumnI> allFields = ftsRestClient
 116             .getAllFTSDataColumns();
 117     Assert.assertNotNull(allFields);
 118     //System.out.println(allFields.size());
 119     Assert.assertEquals(allFields.size(), 15);
 120   }
 121
 122   @Test(groups = { "Functional" })
 123   public void getSearchableDataColumns()
 124   {
 125     // to change when resources.tdbeacons_data_columns.txt is changed
 126     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 127             .getSearchableDataColumns();
 128     Assert.assertNotNull(searchableFields);
 129     //System.out.println(searchableFields.size());
 130     Assert.assertEquals(searchableFields.size(), 1); //only 1: uniprot accession
 131   }
 132
 133   @Test(groups = { "Functional" })
 134   public void getPrimaryKeyColumn()
 135   {
 136     // to change when resources.tdbeacons_data_columns.txt is changed
 137     FTSDataColumnI expectedPKColumn;
 138     try
 139     {
 140       expectedPKColumn = ftsRestClient
 141               .getDataColumnByNameOrCode("Url");
 142       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 143       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 144               expectedPKColumn);
 145     } catch (Exception e)
 146     {
 147       e.printStackTrace();
 148       Assert.fail("Exception thrown while testing...");
 149     }
 150   }
 151
 152   @Test(groups = { "Functional" })
 153   public void getDataColumnByNameOrCode()
 154   {
 155     try
 156     {
 157       FTSDataColumnI foundDataCol = ftsRestClient
 158               .getDataColumnByNameOrCode("uniprot_accession");
 159       Assert.assertNotNull(foundDataCol);
 160       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 161     } catch (Exception e)
 162     {
 163       e.printStackTrace();
 164       Assert.fail("Exception thrown while testing...");
 165     }
 166   }
 167
 168   @Test(groups = { "Functional" })
 169   public void getDataColumnGroupById()
 170   {
 171     FTSDataColumnGroupI foundDataColGroup;
 172     try
 173     {
 174       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 175       Assert.assertNotNull(foundDataColGroup);
 176       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 177     } catch (Exception e)
 178     {
 179       e.printStackTrace();
 180     }
 181   }
 182
 183   @Test(groups = { "Functional" })
 184   public void getDefaultResponsePageSize()
 185   {
 186     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 187     Assert.assertEquals(defaultResSize, 100); //why 100 or 500 ? pdb is 100, uniprot 500
 188   }
 189
 190   @Test(groups = { "Functional" })
 191   public void getColumnMinWidthTest()
 192   {
 193     try
 194     {
 195       FTSDataColumnI foundDataCol = ftsRestClient
 196               .getDataColumnByNameOrCode("uniprot_accession");
 197       Assert.assertNotNull(foundDataCol);
 198       int actualColMinWidth = foundDataCol.getMinWidth();
 199       Assert.assertEquals(actualColMinWidth, 50);
 200     } catch (Exception e)
 201     {
 202       e.printStackTrace();
 203       Assert.fail("Exception thrown while testing...");
 204     }
 205   }
 206   // could add test for MaxWidth & PreferedWith
 207
 208   @Test(groups = { "Functional" })
 209   public void getColumnClassTest()
 210   {
 211     try
 212     {
 213       FTSDataColumnI foundDataCol = ftsRestClient
 214               .getDataColumnByNameOrCode("uniprot_accession");
 215       Assert.assertNotNull(foundDataCol);
 216       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 217               String.class);
 218       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 219       Assert.assertNotNull(foundDataCol);
 220       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 221               String.class);
 222     } catch (Exception e)
 223     {
 224       e.printStackTrace();
 225       Assert.fail("Exception thrown while testing...");
 226     }
 227   }
 228
 229   @Test(groups = { "Functional" })
 230   public void coverageForEqualsAndHashFunction()
 231   {
 232     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 233     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 234             .getSearchableDataColumns();
 235     System.out.println(searchableCols);
 236     for (FTSDataColumnI foundCol : searchableCols)
 237     {
 238       System.out.println(foundCol.toString());
 239       uniqueSet.add(foundCol);
 240       uniqueSet.add(foundCol);
 241     }
 242     Assert.assertTrue(!uniqueSet.isEmpty());
 243     //Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 244   }
 245
 246   @Test(groups = { "Functional" })
 247   public void getTDBIdColumIndexTest()
 248   {
 249     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 250     try
 251     {
 252       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 253               .getDataColumnByNameOrCode("Model id"));
 254       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 255               .getDataColumnByNameOrCode("uniprot_accession"));
 256       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 257               .getDataColumnByNameOrCode("entry name"));
 258     } catch (Exception e)
 259     {
 260       e.printStackTrace();
 261     }
 262     try
 263     {
 264       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 265               .getPrimaryKeyColumIndex(wantedFields, true));
 266 //      assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 267 //              .getPrimaryKeyColumIndex(wantedFields, true));
 268     } catch (Exception e)
 269     {
 270       e.printStackTrace();
 271     }
 272   }
 273
 274   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\":\"612f67c86ba77a10ab6f34ec\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-01\",\"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\":\"612f67c86ba77a10ab6f34f0\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-01\",\"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\"}]}";
 275
 276   public static void setMock() {
 277     FTSRestClient.createMockFTSRestClient((FTSRestClient)TDBeaconsFTSRestClient.getInstance(),"P38398.json", mockResponse);
 278   }
 279   @Test(groups= {"Functional"})
 280   public void testMockTDBRequest()
 281   {
 282
 283     setMock();
 284     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 285     try
 286     {
 287       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 288               .getDataColumnByNameOrCode("Model Id"));
 289       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 290               .getDataColumnByNameOrCode("model_url"));
 291       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 292               .getDataColumnByNameOrCode("provider"));
 293       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 294               .getDataColumnByNameOrCode("model_category"));
 295       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 296               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 297       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 298               .getDataColumnByNameOrCode("uniprot_start"));
 299       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 300               .getDataColumnByNameOrCode("uniprot_end"));
 301     } catch (Exception e1)
 302     {
 303       e1.printStackTrace();
 304     }
 305     System.out.println("wantedFields >>" + wantedFields);
 306
 307     FTSRestRequest request = new FTSRestRequest();
 308     FTSRestResponse response;
 309
 310     request.setResponseSize(100);
 311     request.setFieldToSearchBy("");
 312     request.setWantedFields(wantedFields);
 313     // check 404 behaviour
 314     request.setSearchTerm("P00000.json");
 315
 316
 317     try {
 318       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 319
 320       assertNull(response);
 321     } catch (Exception e)
 322     {
 323       e.printStackTrace();
 324       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 325     }
 326
 327     // check 200 behaviour
 328     request.setSearchTerm("P38398.json");
 329     System.out.println("request : " + request.getFieldToSearchBy());
 330     //System.out.println(request.toString());
 331
 332     try
 333     {
 334       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 335     } catch (Exception e)
 336     {
 337       e.printStackTrace();
 338       Assert.fail("Couldn't execute webservice call!");
 339       return;
 340     }
 341     assertTrue(response.getSearchSummary() != null);
 342     assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
 343     System.out.println("Search summary : \n" + response.getSearchSummary());
 344
 345     //System.out.println(response.getSearchSummary().size());
 346   }
 347
 348   @Test(groups = { "External", "Network" })
 349   public void executeRequestTest()
 350   {
 351     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 352     try
 353     {
 354       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 355               .getDataColumnByNameOrCode("Model Id"));
 356       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 357               .getDataColumnByNameOrCode("model_url"));
 358       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 359               .getDataColumnByNameOrCode("provider"));
 360       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 361               .getDataColumnByNameOrCode("model_category"));
 362       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 363               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 364       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 365               .getDataColumnByNameOrCode("uniprot_start"));
 366       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 367               .getDataColumnByNameOrCode("uniprot_end"));
 368     } catch (Exception e1)
 369     {
 370       e1.printStackTrace();
 371     }
 372     System.out.println("wantedFields >>" + wantedFields);
 373
 374     FTSRestRequest request = new FTSRestRequest();
 375     request.setResponseSize(100);
 376     request.setFieldToSearchBy("");
 377     request.setSearchTerm("P01318.json");
 378     request.setWantedFields(wantedFields);
 379     System.out.println("request : " + request.getFieldToSearchBy());
 380     //System.out.println(request.toString());
 381
 382     FTSRestResponse response;
 383     try
 384     {
 385       response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
 386     } catch (Exception e)
 387     {
 388       e.printStackTrace();
 389       Assert.fail("Couldn't execute webservice call!");
 390       return;
 391     }
 392     assertTrue(response.getSearchSummary() != null);
 393     assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
 394     System.out.println("Search summary : \n" + response.getSearchSummary());
 395     //System.out.println(response.getSearchSummary().size());
 396   }
 397 }