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.io.IOException;
   8 import java.net.URL;
   9 import java.nio.charset.StandardCharsets;
  10 import java.util.ArrayList;
  11 import java.util.Collection;
  12 import java.util.HashSet;
  13 import java.util.List;
  14 import java.util.Set;
  15
  16 import org.testng.Assert;
  17 import org.testng.annotations.AfterMethod;
  18 import org.testng.annotations.BeforeClass;
  19 import org.testng.annotations.BeforeMethod;
  20 import org.testng.annotations.Test;
  21
  22 import jalview.fts.api.FTSDataColumnI;
  23 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  24 import jalview.fts.core.FTSRestClient;
  25 import jalview.fts.core.FTSRestRequest;
  26 import jalview.fts.core.FTSRestResponse;
  27 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  28 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  29 import jalview.gui.JvOptionPane;
  30
  31 public class TDBeaconsFTSRestClientTest
  32 {
  33   @BeforeClass(alwaysRun = true)
  34   public void setUpJvOptionPane()
  35   {
  36     JvOptionPane.setInteractiveMode(false);
  37     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  38   }
  39
  40   private FTSRestClient ftsRestClient;
  41
  42   @BeforeMethod(alwaysRun = true)
  43   public void setUp() throws Exception
  44   {
  45     ftsRestClient = new FTSRestClient()
  46     {
  47
  48       @Override
  49       public String getColumnDataConfigFileName()
  50       {
  51         return "/fts/tdbeacons_data_columns.txt";
  52       }
  53
  54       @Override
  55       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  56               throws Exception
  57       {
  58         return null;
  59       }
  60     };
  61   }
  62
  63   @AfterMethod(alwaysRun = true)
  64   public void tearDown() throws Exception
  65   {
  66   }
  67
  68   @Test
  69   public void getAllDefaulDisplayedDataColumns()
  70   {
  71     // to change when resources.tdbeacons_data_columns.txt is changed
  72     Assert.assertNotNull(
  73             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  74     System.out
  75             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  76     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  77             .isEmpty());
  78     Assert.assertEquals(
  79             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
  80             14);
  81   }
  82
  83   @Test(groups = { "Functional" })
  84   public void getPrimaryKeyColumIndexTest()
  85   {
  86     Collection<FTSDataColumnI> wantedFields = ftsRestClient
  87             .getAllDefaultDisplayedFTSDataColumns();
  88     int foundIndex = -1;
  89     try
  90     {
  91       Assert.assertEquals(foundIndex, -1);
  92       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  93               false);
  94       Assert.assertEquals(foundIndex, 12);
  95       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  96               true);
  97       // 1+primary key index
  98       Assert.assertEquals(foundIndex, 13);
  99     } catch (Exception e)
 100     {
 101       e.printStackTrace();
 102       Assert.fail("Exception thrown while testing...");
 103     }
 104   }
 105
 106   @Test(groups = { "Functional" })
 107   public void getDataColumnsFieldsAsCommaDelimitedString()
 108   {
 109     // to change when resources.tdbeacons_data_columns.txt is changed
 110     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 111             .getAllDefaultDisplayedFTSDataColumns();
 112     String actual = ftsRestClient
 113             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 114     Assert.assertEquals(actual,
 115             "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_page_url");
 116   }
 117
 118   @Test(groups = { "Functional" })
 119   public void getAllFTSDataColumns()
 120   {
 121     Collection<FTSDataColumnI> allFields = ftsRestClient
 122             .getAllFTSDataColumns();
 123     Assert.assertNotNull(allFields);
 124     // System.out.println(allFields.size());
 125     Assert.assertEquals(allFields.size(), 19);
 126   }
 127
 128   @Test(groups = { "Functional" })
 129   public void getSearchableDataColumns()
 130   {
 131     // to change when resources.tdbeacons_data_columns.txt is changed
 132     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 133             .getSearchableDataColumns();
 134     Assert.assertNotNull(searchableFields);
 135     // System.out.println(searchableFields.size());
 136     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
 137                                                      // accession
 138   }
 139
 140   @Test(groups = { "Functional" })
 141   public void getPrimaryKeyColumn()
 142   {
 143     // to change when resources.tdbeacons_data_columns.txt is changed
 144     FTSDataColumnI expectedPKColumn;
 145     try
 146     {
 147       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
 148       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 149       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 150               expectedPKColumn);
 151     } catch (Exception e)
 152     {
 153       e.printStackTrace();
 154       Assert.fail("Exception thrown while testing...");
 155     }
 156   }
 157
 158   @Test(groups = { "Functional" })
 159   public void getDataColumnByNameOrCode()
 160   {
 161     try
 162     {
 163       FTSDataColumnI foundDataCol = ftsRestClient
 164               .getDataColumnByNameOrCode("uniprot_accession");
 165       Assert.assertNotNull(foundDataCol);
 166       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 167     } catch (Exception e)
 168     {
 169       e.printStackTrace();
 170       Assert.fail("Exception thrown while testing...");
 171     }
 172   }
 173
 174   @Test(groups = { "Functional" })
 175   public void getDataColumnGroupById()
 176   {
 177     FTSDataColumnGroupI foundDataColGroup;
 178     try
 179     {
 180       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 181       Assert.assertNotNull(foundDataColGroup);
 182       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 183     } catch (Exception e)
 184     {
 185       e.printStackTrace();
 186     }
 187   }
 188
 189   @Test(groups = { "Functional" })
 190   public void getDefaultResponsePageSize()
 191   {
 192     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 193     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
 194                                               // uniprot 500
 195   }
 196
 197   @Test(groups = { "Functional" })
 198   public void getColumnMinWidthTest()
 199   {
 200     try
 201     {
 202       FTSDataColumnI foundDataCol = ftsRestClient
 203               .getDataColumnByNameOrCode("uniprot_accession");
 204       Assert.assertNotNull(foundDataCol);
 205       int actualColMinWidth = foundDataCol.getMinWidth();
 206       Assert.assertEquals(actualColMinWidth, 50);
 207     } catch (Exception e)
 208     {
 209       e.printStackTrace();
 210       Assert.fail("Exception thrown while testing...");
 211     }
 212   }
 213   // could add test for MaxWidth & PreferedWith
 214
 215   @Test(groups = { "Functional" })
 216   public void getColumnClassTest()
 217   {
 218     try
 219     {
 220       FTSDataColumnI foundDataCol = ftsRestClient
 221               .getDataColumnByNameOrCode("uniprot_accession");
 222       Assert.assertNotNull(foundDataCol);
 223       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 224               String.class);
 225       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 226       Assert.assertNotNull(foundDataCol);
 227       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 228               String.class);
 229     } catch (Exception e)
 230     {
 231       e.printStackTrace();
 232       Assert.fail("Exception thrown while testing...");
 233     }
 234   }
 235
 236   @Test(groups = { "Functional" })
 237   public void coverageForEqualsAndHashFunction()
 238   {
 239     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 240     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 241             .getSearchableDataColumns();
 242     System.out.println(searchableCols);
 243     for (FTSDataColumnI foundCol : searchableCols)
 244     {
 245       System.out.println(foundCol.toString());
 246       uniqueSet.add(foundCol);
 247       uniqueSet.add(foundCol);
 248     }
 249     Assert.assertTrue(!uniqueSet.isEmpty());
 250     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 251   }
 252
 253   @Test(groups = { "Functional" })
 254   public void getTDBIdColumIndexTest()
 255   {
 256     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 257     try
 258     {
 259       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 260               .getDataColumnByNameOrCode("Model id"));
 261       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 262               .getDataColumnByNameOrCode("uniprot_accession"));
 263       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 264               .getDataColumnByNameOrCode("Title"));
 265     } catch (Exception e)
 266     {
 267       e.printStackTrace();
 268     }
 269     try
 270     {
 271       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 272               .getPrimaryKeyColumIndex(wantedFields, true));
 273       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 274       // .getPrimaryKeyColumIndex(wantedFields, true));
 275     } catch (Exception e)
 276     {
 277       e.printStackTrace();
 278     }
 279   }
 280
 281   private static String[][] mocks = { { "P38398.json",
 282       "{\"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\":\"614833627ca5054bb52d2f3f\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-20\",\"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\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?provider=swissmodelrange=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"614833627ca5054bb52d2f43\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-09-20\",\"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\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?provider=swissmodelrange=1-103&template=1jm7.1.A\",\"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\"}]}" },
 283       { "P01308.json",null}};
 284
 285   private static void setMockData()
 286   {
 287     try
 288     {
 289       mocks[1][1]= PDBFTSRestClientTest.readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_tdb_resp.txt");
 290     } catch (IOException e)
 291     {
 292       Assert.fail("Couldn't read mock response data",e);
 293     }
 294   }
 295
 296   public static void setMock()
 297   {
 298     setMockData();
 299     FTSRestClient.createMockFTSRestClient(
 300             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
 301             mocks);
 302   }
 303
 304   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 305   private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 306
 307   /**
 308    * check that the mock request and response are the same as the response from
 309    * a live 3D-beacons endpoint
 310    *
 311    * Note - servers often have rapidly changing ids / URIs so this might fail, but the overall structure will remain.
 312    *
 313    * @throws Exception
 314    */
 315   @Test(groups = { "Network", "Integration" })
 316   public void verifyMockTDBRequest() throws Exception
 317   {
 318     setMockData();
 319     for (String[] otherMock:mocks)
 320     {
 321     verifyMockTDBRequest(otherMock[0],otherMock[1]);
 322     }
 323   }
 324   private void verifyMockTDBRequest(String mockRequest, String _mockResponse) throws Exception
 325   {
 326     URL tdb_req = new URL(prod_url + mockRequest);
 327     byte[] resp = tdb_req.openStream().readAllBytes();
 328     String tresp = new String(resp, StandardCharsets.UTF_8);
 329     assertEquals(_mockResponse.trim(), tresp.trim());
 330   }
 331
 332   @Test(groups = { "Functional" })
 333   public void testMockTDBRequest()
 334   {
 335
 336     setMock();
 337     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 338     try
 339     {
 340       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 341               .getDataColumnByNameOrCode("Model Id"));
 342       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 343               .getDataColumnByNameOrCode("model_url"));
 344       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 345               .getDataColumnByNameOrCode("provider"));
 346       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 347               .getDataColumnByNameOrCode("model_category"));
 348       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 349               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 350       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 351               .getDataColumnByNameOrCode("uniprot_start"));
 352       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 353               .getDataColumnByNameOrCode("uniprot_end"));
 354     } catch (Exception e1)
 355     {
 356       e1.printStackTrace();
 357     }
 358     System.out.println("wantedFields >>" + wantedFields);
 359
 360     FTSRestRequest request = new FTSRestRequest();
 361     FTSRestResponse response;
 362
 363     request.setResponseSize(100);
 364     request.setFieldToSearchBy("");
 365     request.setWantedFields(wantedFields);
 366     // check 404 behaviour
 367     request.setSearchTerm("P00000.json");
 368
 369     try
 370     {
 371       response = TDBeaconsFTSRestClient.getInstance()
 372               .executeRequest(request);
 373
 374       assertNull(response);
 375     } catch (Exception e)
 376     {
 377       e.printStackTrace();
 378       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 379     }
 380
 381     // check 200 behaviour
 382     request.setSearchTerm("P38398.json");
 383     System.out.println("request : " + request.getFieldToSearchBy());
 384     // System.out.println(request.toString());
 385
 386     try
 387     {
 388       response = TDBeaconsFTSRestClient.getInstance()
 389               .executeRequest(request);
 390     } catch (Exception e)
 391     {
 392       e.printStackTrace();
 393       Assert.fail("Couldn't execute webservice call!");
 394       return;
 395     }
 396     assertTrue(response.getSearchSummary() != null);
 397     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 398     System.out.println("Search summary : \n" + response.getSearchSummary());
 399
 400     // System.out.println(response.getSearchSummary().size());
 401   }
 402
 403   @Test(groups = { "External", "Network" })
 404   public void executeRequestTest()
 405   {
 406     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 407     try
 408     {
 409       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 410               .getDataColumnByNameOrCode("Model Id"));
 411       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 412               .getDataColumnByNameOrCode("model_url"));
 413       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 414               .getDataColumnByNameOrCode("provider"));
 415       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 416               .getDataColumnByNameOrCode("model_category"));
 417       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 418               .getDataColumnByNameOrCode("confidence_avg_local_score"));
 419       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 420               .getDataColumnByNameOrCode("uniprot_start"));
 421       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 422               .getDataColumnByNameOrCode("uniprot_end"));
 423     } catch (Exception e1)
 424     {
 425       e1.printStackTrace();
 426     }
 427     System.out.println("wantedFields >>" + wantedFields);
 428
 429     FTSRestRequest request = new FTSRestRequest();
 430     request.setResponseSize(100);
 431     request.setFieldToSearchBy("");
 432     request.setSearchTerm("P01318.json");
 433     request.setWantedFields(wantedFields);
 434     System.out.println("request : " + request.getFieldToSearchBy());
 435     // System.out.println(request.toString());
 436
 437     FTSRestResponse response;
 438     try
 439     {
 440       response = TDBeaconsFTSRestClient.getInstance()
 441               .executeRequest(request);
 442     } catch (Exception e)
 443     {
 444       e.printStackTrace();
 445       Assert.fail("Couldn't execute webservice call!");
 446       return;
 447     }
 448     assertTrue(response.getSearchSummary() != null);
 449     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 450     System.out.println("Search summary : \n" + response.getSearchSummary());
 451     // System.out.println(response.getSearchSummary().size());
 452   }
 453 }