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(
  71             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  72     System.out
  73             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  74     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  75             .isEmpty());
  76     Assert.assertEquals(
  77             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
  78             13);
  79   }
  80
  81   @Test(groups = { "Functional" })
  82   public void getPrimaryKeyColumIndexTest()
  83   {
  84     Collection<FTSDataColumnI> wantedFields = ftsRestClient
  85             .getAllDefaultDisplayedFTSDataColumns();
  86     int foundIndex = -1;
  87     try
  88     {
  89       Assert.assertEquals(foundIndex, -1);
  90       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  91               false);
  92       Assert.assertEquals(foundIndex, 12);
  93       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  94               true);
  95       // 1+primary key index
  96       Assert.assertEquals(foundIndex, 13);
  97     } catch (Exception e)
  98     {
  99       e.printStackTrace();
 100       Assert.fail("Exception thrown while testing...");
 101     }
 102   }
 103
 104   @Test(groups = { "Functional" })
 105   public void getDataColumnsFieldsAsCommaDelimitedString()
 106   {
 107     // to change when resources.tdbeacons_data_columns.txt is changed
 108     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 109             .getAllDefaultDisplayedFTSDataColumns();
 110     String actual = ftsRestClient
 111             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 112     Assert.assertEquals(actual,
 113             "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url");
 114   }
 115
 116   @Test(groups = { "Functional" })
 117   public void getAllFTSDataColumns()
 118   {
 119     Collection<FTSDataColumnI> allFields = ftsRestClient
 120             .getAllFTSDataColumns();
 121     Assert.assertNotNull(allFields);
 122     // System.out.println(allFields.size());
 123     Assert.assertEquals(allFields.size(), 19);
 124   }
 125
 126   @Test(groups = { "Functional" })
 127   public void getSearchableDataColumns()
 128   {
 129     // to change when resources.tdbeacons_data_columns.txt is changed
 130     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 131             .getSearchableDataColumns();
 132     Assert.assertNotNull(searchableFields);
 133     // System.out.println(searchableFields.size());
 134     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
 135                                                      // accession
 136   }
 137
 138   @Test(groups = { "Functional" })
 139   public void getPrimaryKeyColumn()
 140   {
 141     // to change when resources.tdbeacons_data_columns.txt is changed
 142     FTSDataColumnI expectedPKColumn;
 143     try
 144     {
 145       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
 146       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 147       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 148               expectedPKColumn);
 149     } catch (Exception e)
 150     {
 151       e.printStackTrace();
 152       Assert.fail("Exception thrown while testing...");
 153     }
 154   }
 155
 156   @Test(groups = { "Functional" })
 157   public void getDataColumnByNameOrCode()
 158   {
 159     try
 160     {
 161       FTSDataColumnI foundDataCol = ftsRestClient
 162               .getDataColumnByNameOrCode("uniprot_accession");
 163       Assert.assertNotNull(foundDataCol);
 164       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 165     } catch (Exception e)
 166     {
 167       e.printStackTrace();
 168       Assert.fail("Exception thrown while testing...");
 169     }
 170   }
 171
 172   @Test(groups = { "Functional" })
 173   public void getDataColumnGroupById()
 174   {
 175     FTSDataColumnGroupI foundDataColGroup;
 176     try
 177     {
 178       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 179       Assert.assertNotNull(foundDataColGroup);
 180       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 181     } catch (Exception e)
 182     {
 183       e.printStackTrace();
 184     }
 185   }
 186
 187   @Test(groups = { "Functional" })
 188   public void getDefaultResponsePageSize()
 189   {
 190     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 191     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
 192                                               // uniprot 500
 193   }
 194
 195   @Test(groups = { "Functional" })
 196   public void getColumnMinWidthTest()
 197   {
 198     try
 199     {
 200       FTSDataColumnI foundDataCol = ftsRestClient
 201               .getDataColumnByNameOrCode("uniprot_accession");
 202       Assert.assertNotNull(foundDataCol);
 203       int actualColMinWidth = foundDataCol.getMinWidth();
 204       Assert.assertEquals(actualColMinWidth, 50);
 205     } catch (Exception e)
 206     {
 207       e.printStackTrace();
 208       Assert.fail("Exception thrown while testing...");
 209     }
 210   }
 211   // could add test for MaxWidth & PreferedWith
 212
 213   @Test(groups = { "Functional" })
 214   public void getColumnClassTest()
 215   {
 216     try
 217     {
 218       FTSDataColumnI foundDataCol = ftsRestClient
 219               .getDataColumnByNameOrCode("uniprot_accession");
 220       Assert.assertNotNull(foundDataCol);
 221       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 222               String.class);
 223       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 224       Assert.assertNotNull(foundDataCol);
 225       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 226               String.class);
 227     } catch (Exception e)
 228     {
 229       e.printStackTrace();
 230       Assert.fail("Exception thrown while testing...");
 231     }
 232   }
 233
 234   @Test(groups = { "Functional" })
 235   public void coverageForEqualsAndHashFunction()
 236   {
 237     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 238     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 239             .getSearchableDataColumns();
 240     System.out.println(searchableCols);
 241     for (FTSDataColumnI foundCol : searchableCols)
 242     {
 243       System.out.println(foundCol.toString());
 244       uniqueSet.add(foundCol);
 245       uniqueSet.add(foundCol);
 246     }
 247     Assert.assertTrue(!uniqueSet.isEmpty());
 248     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 249   }
 250
 251   @Test(groups = { "Functional" })
 252   public void getTDBIdColumIndexTest()
 253   {
 254     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 255     try
 256     {
 257       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 258               .getDataColumnByNameOrCode("Model id"));
 259       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 260               .getDataColumnByNameOrCode("uniprot_accession"));
 261       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 262               .getDataColumnByNameOrCode("Title"));
 263     } catch (Exception e)
 264     {
 265       e.printStackTrace();
 266     }
 267     try
 268     {
 269       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 270               .getPrimaryKeyColumIndex(wantedFields, true));
 271       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 272       // .getPrimaryKeyColumIndex(wantedFields, true));
 273     } catch (Exception e)
 274     {
 275       e.printStackTrace();
 276     }
 277   }
 278
 279   private static String mockRequest = "P38398.json";
 280
 281   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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t29\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxb\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jnx\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxa\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0h\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0k\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1n5o\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxc\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxd\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2u\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k15\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxe\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k16\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ofb\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3coj\"},{\"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\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7lyb\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y18\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4jlu\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4u4a\"},{\"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\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/2ing\"},{\"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\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7jzv\"},{\"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\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"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\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"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\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"613a3ff37621f8e40b0713bb\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-09\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"613a3ff37621f8e40b0713bf\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-09\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"confidence_type\":\"QMEANDisCo\"},{\"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\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}";
 282
 283   public static void setMock()
 284   {
 285     FTSRestClient.createMockFTSRestClient(
 286             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
 287             mockRequest, mockResponse);
 288   }
 289
 290   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 291
 292   /**
 293    * check that the mock request and response are the same as the response from
 294    * a live 3D-beacons endpoint
 295    *
 296    * @throws Exception
 297    */
 298   @Test(groups = { "Network", "Integration" })
 299   public void verifyMockTDBRequest() throws Exception
 300   {
 301     URL tdb_req = new URL(dev_url + mockRequest);
 302     byte[] resp = tdb_req.openStream().readAllBytes();
 303     String tresp = new String(resp, StandardCharsets.UTF_8);
 304     assertEquals(mockResponse.trim(), tresp.trim());
 305   }
 306
 307   @Test(groups = { "Functional" })
 308   public void testMockTDBRequest()
 309   {
 310
 311     setMock();
 312     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 313     try
 314     {
 315       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 316               .getDataColumnByNameOrCode("Model Id"));
 317       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 318               .getDataColumnByNameOrCode("model_url"));
 319       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 320               .getDataColumnByNameOrCode("provider"));
 321       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 322               .getDataColumnByNameOrCode("model_category"));
 323       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 324               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 325       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 326               .getDataColumnByNameOrCode("uniprot_start"));
 327       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 328               .getDataColumnByNameOrCode("uniprot_end"));
 329     } catch (Exception e1)
 330     {
 331       e1.printStackTrace();
 332     }
 333     System.out.println("wantedFields >>" + wantedFields);
 334
 335     FTSRestRequest request = new FTSRestRequest();
 336     FTSRestResponse response;
 337
 338     request.setResponseSize(100);
 339     request.setFieldToSearchBy("");
 340     request.setWantedFields(wantedFields);
 341     // check 404 behaviour
 342     request.setSearchTerm("P00000.json");
 343
 344     try
 345     {
 346       response = TDBeaconsFTSRestClient.getInstance()
 347               .executeRequest(request);
 348
 349       assertNull(response);
 350     } catch (Exception e)
 351     {
 352       e.printStackTrace();
 353       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 354     }
 355
 356     // check 200 behaviour
 357     request.setSearchTerm("P38398.json");
 358     System.out.println("request : " + request.getFieldToSearchBy());
 359     // System.out.println(request.toString());
 360
 361     try
 362     {
 363       response = TDBeaconsFTSRestClient.getInstance()
 364               .executeRequest(request);
 365     } catch (Exception e)
 366     {
 367       e.printStackTrace();
 368       Assert.fail("Couldn't execute webservice call!");
 369       return;
 370     }
 371     assertTrue(response.getSearchSummary() != null);
 372     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 373     System.out.println("Search summary : \n" + response.getSearchSummary());
 374
 375     // System.out.println(response.getSearchSummary().size());
 376   }
 377
 378   @Test(groups = { "External", "Network" })
 379   public void executeRequestTest()
 380   {
 381     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 382     try
 383     {
 384       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 385               .getDataColumnByNameOrCode("Model Id"));
 386       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 387               .getDataColumnByNameOrCode("model_url"));
 388       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 389               .getDataColumnByNameOrCode("provider"));
 390       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 391               .getDataColumnByNameOrCode("model_category"));
 392       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 393               .getDataColumnByNameOrCode("confidence_avg_local_score"));
 394       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 395               .getDataColumnByNameOrCode("uniprot_start"));
 396       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 397               .getDataColumnByNameOrCode("uniprot_end"));
 398     } catch (Exception e1)
 399     {
 400       e1.printStackTrace();
 401     }
 402     System.out.println("wantedFields >>" + wantedFields);
 403
 404     FTSRestRequest request = new FTSRestRequest();
 405     request.setResponseSize(100);
 406     request.setFieldToSearchBy("");
 407     request.setSearchTerm("P01318.json");
 408     request.setWantedFields(wantedFields);
 409     System.out.println("request : " + request.getFieldToSearchBy());
 410     // System.out.println(request.toString());
 411
 412     FTSRestResponse response;
 413     try
 414     {
 415       response = TDBeaconsFTSRestClient.getInstance()
 416               .executeRequest(request);
 417     } catch (Exception e)
 418     {
 419       e.printStackTrace();
 420       Assert.fail("Couldn't execute webservice call!");
 421       return;
 422     }
 423     assertTrue(response.getSearchSummary() != null);
 424     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 425     System.out.println("Search summary : \n" + response.getSearchSummary());
 426     // System.out.println(response.getSearchSummary().size());
 427   }
 428 }