test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.fts.threedbeacons;
  22
  23 import static org.testng.Assert.assertNull;
  24 import static org.testng.AssertJUnit.assertEquals;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import java.io.IOException;
  28 import java.net.URL;
  29 import java.nio.charset.StandardCharsets;
  30 import java.util.ArrayList;
  31 import java.util.Collection;
  32 import java.util.HashSet;
  33 import java.util.List;
  34 import java.util.Set;
  35
  36 import org.testng.Assert;
  37 import org.testng.annotations.AfterMethod;
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.BeforeMethod;
  40 import org.testng.annotations.Test;
  41
  42 import jalview.fts.api.FTSDataColumnI;
  43 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  44 import jalview.fts.core.FTSRestClient;
  45 import jalview.fts.core.FTSRestRequest;
  46 import jalview.fts.core.FTSRestResponse;
  47 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  48 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  49 import jalview.gui.JvOptionPane;
  50
  51 public class TDBeaconsFTSRestClientTest
  52 {
  53   @BeforeClass(alwaysRun = true)
  54   public void setUpJvOptionPane()
  55   {
  56     JvOptionPane.setInteractiveMode(false);
  57     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  58   }
  59
  60   private FTSRestClient ftsRestClient;
  61
  62   @BeforeMethod(alwaysRun = true)
  63   public void setUp() throws Exception
  64   {
  65     ftsRestClient = new FTSRestClient()
  66     {
  67
  68       @Override
  69       public String getColumnDataConfigFileName()
  70       {
  71         return "/fts/tdbeacons_data_columns.txt";
  72       }
  73
  74       @Override
  75       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  76               throws Exception
  77       {
  78         return null;
  79       }
  80     };
  81   }
  82
  83   @AfterMethod(alwaysRun = true)
  84   public void tearDown() throws Exception
  85   {
  86   }
  87
  88   @Test
  89   public void getAllDefaulDisplayedDataColumns()
  90   {
  91     // to change when resources.tdbeacons_data_columns.txt is changed
  92     Assert.assertNotNull(
  93             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  94     System.out
  95             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  96     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  97             .isEmpty());
  98     Assert.assertEquals(
  99             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
 100             15);
 101   }
 102
 103   @Test(groups = { "Functional" })
 104   public void getPrimaryKeyColumIndexTest()
 105   {
 106     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 107             .getAllDefaultDisplayedFTSDataColumns();
 108     int foundIndex = -1;
 109     try
 110     {
 111       Assert.assertEquals(foundIndex, -1);
 112       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
 113               false);
 114       Assert.assertEquals(foundIndex, 12);
 115       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
 116               true);
 117       // 1+primary key index
 118       Assert.assertEquals(foundIndex, 13);
 119     } catch (Exception e)
 120     {
 121       e.printStackTrace();
 122       Assert.fail("Exception thrown while testing...");
 123     }
 124   }
 125
 126   @Test(groups = { "Functional" })
 127   public void getDataColumnsFieldsAsCommaDelimitedString()
 128   {
 129     // to change when resources.tdbeacons_data_columns.txt is changed
 130     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 131             .getAllDefaultDisplayedFTSDataColumns();
 132     String actual = ftsRestClient
 133             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 134     Assert.assertEquals(actual,
 135             "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url,model_format,model_page_url");
 136   }
 137
 138   @Test(groups = { "Functional" })
 139   public void getAllFTSDataColumns()
 140   {
 141     Collection<FTSDataColumnI> allFields = ftsRestClient
 142             .getAllFTSDataColumns();
 143     Assert.assertNotNull(allFields);
 144     // System.out.println(allFields.size());
 145     Assert.assertEquals(allFields.size(), 20);
 146   }
 147
 148   @Test(groups = { "Functional" })
 149   public void getSearchableDataColumns()
 150   {
 151     // to change when resources.tdbeacons_data_columns.txt is changed
 152     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 153             .getSearchableDataColumns();
 154     Assert.assertNotNull(searchableFields);
 155     // System.out.println(searchableFields.size());
 156     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
 157                                                      // accession
 158   }
 159
 160   @Test(groups = { "Functional" })
 161   public void getPrimaryKeyColumn()
 162   {
 163     // to change when resources.tdbeacons_data_columns.txt is changed
 164     FTSDataColumnI expectedPKColumn;
 165     try
 166     {
 167       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
 168       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 169       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 170               expectedPKColumn);
 171     } catch (Exception e)
 172     {
 173       e.printStackTrace();
 174       Assert.fail("Exception thrown while testing...");
 175     }
 176   }
 177
 178   @Test(groups = { "Functional" })
 179   public void getDataColumnByNameOrCode()
 180   {
 181     try
 182     {
 183       FTSDataColumnI foundDataCol = ftsRestClient
 184               .getDataColumnByNameOrCode("uniprot_accession");
 185       Assert.assertNotNull(foundDataCol);
 186       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 187     } catch (Exception e)
 188     {
 189       e.printStackTrace();
 190       Assert.fail("Exception thrown while testing...");
 191     }
 192   }
 193
 194   @Test(groups = { "Functional" })
 195   public void getDataColumnGroupById()
 196   {
 197     FTSDataColumnGroupI foundDataColGroup;
 198     try
 199     {
 200       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 201       Assert.assertNotNull(foundDataColGroup);
 202       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 203     } catch (Exception e)
 204     {
 205       e.printStackTrace();
 206     }
 207   }
 208
 209   @Test(groups = { "Functional" })
 210   public void getDefaultResponsePageSize()
 211   {
 212     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 213     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
 214                                               // uniprot 500
 215   }
 216
 217   @Test(groups = { "Functional" })
 218   public void getColumnMinWidthTest()
 219   {
 220     try
 221     {
 222       FTSDataColumnI foundDataCol = ftsRestClient
 223               .getDataColumnByNameOrCode("uniprot_accession");
 224       Assert.assertNotNull(foundDataCol);
 225       int actualColMinWidth = foundDataCol.getMinWidth();
 226       Assert.assertEquals(actualColMinWidth, 50);
 227     } catch (Exception e)
 228     {
 229       e.printStackTrace();
 230       Assert.fail("Exception thrown while testing...");
 231     }
 232   }
 233   // could add test for MaxWidth & PreferedWith
 234
 235   @Test(groups = { "Functional" })
 236   public void getColumnClassTest()
 237   {
 238     try
 239     {
 240       FTSDataColumnI foundDataCol = ftsRestClient
 241               .getDataColumnByNameOrCode("uniprot_accession");
 242       Assert.assertNotNull(foundDataCol);
 243       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 244               String.class);
 245       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 246       Assert.assertNotNull(foundDataCol);
 247       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 248               String.class);
 249     } catch (Exception e)
 250     {
 251       e.printStackTrace();
 252       Assert.fail("Exception thrown while testing...");
 253     }
 254   }
 255
 256   @Test(groups = { "Functional" })
 257   public void coverageForEqualsAndHashFunction()
 258   {
 259     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 260     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 261             .getSearchableDataColumns();
 262     System.out.println(searchableCols);
 263     for (FTSDataColumnI foundCol : searchableCols)
 264     {
 265       System.out.println(foundCol.toString());
 266       uniqueSet.add(foundCol);
 267       uniqueSet.add(foundCol);
 268     }
 269     Assert.assertTrue(!uniqueSet.isEmpty());
 270     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 271   }
 272
 273   @Test(groups = { "Functional" })
 274   public void getTDBIdColumIndexTest()
 275   {
 276     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 277     try
 278     {
 279       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 280               .getDataColumnByNameOrCode("Model id"));
 281       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 282               .getDataColumnByNameOrCode("uniprot_accession"));
 283       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 284               .getDataColumnByNameOrCode("Title"));
 285     } catch (Exception e)
 286     {
 287       e.printStackTrace();
 288     }
 289     try
 290     {
 291       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 292               .getPrimaryKeyColumIndex(wantedFields, true));
 293       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 294       // .getPrimaryKeyColumIndex(wantedFields, true));
 295     } catch (Exception e)
 296     {
 297       e.printStackTrace();
 298     }
 299   }
 300
 301   private static String[][] mocks = { { "P38398.json",
 302       "{\"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\":\"P38398_1646-1859:6g2i.1.K\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"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?range=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"P38398_1-103:1jm7.1.A\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"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?range=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\"}]}" },
 303       { "P01308.json", null } };
 304
 305   private static void setMockData()
 306   {
 307     try
 308     {
 309       mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
 310               "test/jalview/fts/threedbeacons/p01308_tdb_resp.txt");
 311     } catch (IOException e)
 312     {
 313       Assert.fail("Couldn't read mock response data", e);
 314     }
 315   }
 316
 317   public static void setMock()
 318   {
 319     setMockData();
 320     FTSRestClient.createMockFTSRestClient(
 321             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
 322   }
 323
 324   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 325
 326   private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 327
 328   /**
 329    * check that the mock request and response are the same as the response from
 330    * a live 3D-beacons endpoint
 331    *
 332    * Note - servers often have rapidly changing ids / URIs so this might fail,
 333    * but the overall structure will remain.
 334    *
 335    * @throws Exception
 336    */
 337   @Test(groups = { "Network", "Integration" })
 338   public void verifyMockTDBRequest() throws Exception
 339   {
 340     setMockData();
 341     for (String[] otherMock : mocks)
 342     {
 343       verifyMockTDBRequest(otherMock[0], otherMock[1]);
 344     }
 345   }
 346
 347   private void verifyMockTDBRequest(String mockRequest,
 348           String _mockResponse) throws Exception
 349   {
 350     URL tdb_req = new URL(prod_url + mockRequest);
 351     byte[] resp = tdb_req.openStream().readAllBytes();
 352     String tresp = new String(resp, StandardCharsets.UTF_8);
 353     assertEquals(_mockResponse.trim(), tresp.trim());
 354   }
 355
 356   @Test(groups = { "Functional" })
 357   public void testMockTDBRequest()
 358   {
 359
 360     setMock();
 361     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 362     try
 363     {
 364       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 365               .getDataColumnByNameOrCode("Model Id"));
 366       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 367               .getDataColumnByNameOrCode("model_url"));
 368       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 369               .getDataColumnByNameOrCode("provider"));
 370       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 371               .getDataColumnByNameOrCode("model_category"));
 372       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 373               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 374       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 375               .getDataColumnByNameOrCode("uniprot_start"));
 376       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 377               .getDataColumnByNameOrCode("uniprot_end"));
 378     } catch (Exception e1)
 379     {
 380       e1.printStackTrace();
 381     }
 382     System.out.println("wantedFields >>" + wantedFields);
 383
 384     FTSRestRequest request = new FTSRestRequest();
 385     FTSRestResponse response;
 386
 387     request.setResponseSize(100);
 388     request.setFieldToSearchBy("");
 389     request.setWantedFields(wantedFields);
 390     // check 404 behaviour
 391     request.setSearchTerm("P00000.json");
 392
 393     try
 394     {
 395       response = TDBeaconsFTSRestClient.getInstance()
 396               .executeRequest(request);
 397
 398       assertNull(response);
 399     } catch (Exception e)
 400     {
 401       e.printStackTrace();
 402       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 403     }
 404
 405     // check 200 behaviour
 406     request.setSearchTerm("P38398.json");
 407     System.out.println("request : " + request.getFieldToSearchBy());
 408     // System.out.println(request.toString());
 409
 410     try
 411     {
 412       response = TDBeaconsFTSRestClient.getInstance()
 413               .executeRequest(request);
 414     } catch (Exception e)
 415     {
 416       e.printStackTrace();
 417       Assert.fail("Couldn't execute webservice call!");
 418       return;
 419     }
 420     assertTrue(response.getSearchSummary() != null);
 421     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 422     System.out.println("Search summary : \n" + response.getSearchSummary());
 423
 424     // System.out.println(response.getSearchSummary().size());
 425   }
 426
 427   @Test(groups = { "External", "Network" })
 428   public void executeRequestTest()
 429   {
 430     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 431     try
 432     {
 433       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 434               .getDataColumnByNameOrCode("Model Id"));
 435       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 436               .getDataColumnByNameOrCode("model_url"));
 437       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 438               .getDataColumnByNameOrCode("provider"));
 439       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 440               .getDataColumnByNameOrCode("model_category"));
 441       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 442               .getDataColumnByNameOrCode("confidence_avg_local_score"));
 443       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 444               .getDataColumnByNameOrCode("uniprot_start"));
 445       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 446               .getDataColumnByNameOrCode("uniprot_end"));
 447     } catch (Exception e1)
 448     {
 449       e1.printStackTrace();
 450     }
 451     System.out.println("wantedFields >>" + wantedFields);
 452
 453     FTSRestRequest request = new FTSRestRequest();
 454     request.setResponseSize(100);
 455     request.setFieldToSearchBy("");
 456     request.setSearchTerm("P01318.json");
 457     request.setWantedFields(wantedFields);
 458     System.out.println("request : " + request.getFieldToSearchBy());
 459     // System.out.println(request.toString());
 460
 461     FTSRestResponse response;
 462     try
 463     {
 464       response = TDBeaconsFTSRestClient.getInstance()
 465               .executeRequest(request);
 466     } catch (Exception e)
 467     {
 468       e.printStackTrace();
 469       Assert.fail("Couldn't execute webservice call!");
 470       return;
 471     }
 472     assertTrue(response.getSearchSummary() != null);
 473     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 474     System.out.println("Search summary : \n" + response.getSearchSummary());
 475     // System.out.println(response.getSearchSummary().size());
 476   }
 477 }