2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.fts.threedbeacons;
23 import static org.testng.Assert.assertNull;
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertTrue;
27 import java.io.IOException;
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;
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;
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;
51 public class TDBeaconsFTSRestClientTest
53 @BeforeClass(alwaysRun = true)
54 public void setUpJvOptionPane()
56 JvOptionPane.setInteractiveMode(false);
57 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
60 private FTSRestClient ftsRestClient;
62 @BeforeMethod(alwaysRun = true)
63 public void setUp() throws Exception
65 ftsRestClient = new FTSRestClient()
69 public String getColumnDataConfigFileName()
71 return "/fts/tdbeacons_data_columns.txt";
75 public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
83 @AfterMethod(alwaysRun = true)
84 public void tearDown() throws Exception
89 public void getAllDefaulDisplayedDataColumns()
91 // to change when resources.tdbeacons_data_columns.txt is changed
93 ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
95 .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
96 Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
99 ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
103 @Test(groups = { "Functional" })
104 public void getPrimaryKeyColumIndexTest()
106 Collection<FTSDataColumnI> wantedFields = ftsRestClient
107 .getAllDefaultDisplayedFTSDataColumns();
111 Assert.assertEquals(foundIndex, -1);
112 foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
114 Assert.assertEquals(foundIndex, 12);
115 foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
117 // 1+primary key index
118 Assert.assertEquals(foundIndex, 13);
119 } catch (Exception e)
122 Assert.fail("Exception thrown while testing...");
126 @Test(groups = { "Functional" })
127 public void getDataColumnsFieldsAsCommaDelimitedString()
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");
138 @Test(groups = { "Functional" })
139 public void getAllFTSDataColumns()
141 Collection<FTSDataColumnI> allFields = ftsRestClient
142 .getAllFTSDataColumns();
143 Assert.assertNotNull(allFields);
144 // System.out.println(allFields.size());
145 Assert.assertEquals(allFields.size(), 20);
148 @Test(groups = { "Functional" })
149 public void getSearchableDataColumns()
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
160 @Test(groups = { "Functional" })
161 public void getPrimaryKeyColumn()
163 // to change when resources.tdbeacons_data_columns.txt is changed
164 FTSDataColumnI expectedPKColumn;
167 expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
168 Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
169 Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
171 } catch (Exception e)
174 Assert.fail("Exception thrown while testing...");
178 @Test(groups = { "Functional" })
179 public void getDataColumnByNameOrCode()
183 FTSDataColumnI foundDataCol = ftsRestClient
184 .getDataColumnByNameOrCode("uniprot_accession");
185 Assert.assertNotNull(foundDataCol);
186 Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
187 } catch (Exception e)
190 Assert.fail("Exception thrown while testing...");
194 @Test(groups = { "Functional" })
195 public void getDataColumnGroupById()
197 FTSDataColumnGroupI foundDataColGroup;
200 foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
201 Assert.assertNotNull(foundDataColGroup);
202 Assert.assertEquals(foundDataColGroup.getName(), "Quality");
203 } catch (Exception e)
209 @Test(groups = { "Functional" })
210 public void getDefaultResponsePageSize()
212 int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
213 Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
217 @Test(groups = { "Functional" })
218 public void getColumnMinWidthTest()
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)
230 Assert.fail("Exception thrown while testing...");
233 // could add test for MaxWidth & PreferedWith
235 @Test(groups = { "Functional" })
236 public void getColumnClassTest()
240 FTSDataColumnI foundDataCol = ftsRestClient
241 .getDataColumnByNameOrCode("uniprot_accession");
242 Assert.assertNotNull(foundDataCol);
243 Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
245 foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
246 Assert.assertNotNull(foundDataCol);
247 Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
249 } catch (Exception e)
252 Assert.fail("Exception thrown while testing...");
256 @Test(groups = { "Functional" })
257 public void coverageForEqualsAndHashFunction()
259 Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
260 Collection<FTSDataColumnI> searchableCols = ftsRestClient
261 .getSearchableDataColumns();
262 System.out.println(searchableCols);
263 for (FTSDataColumnI foundCol : searchableCols)
265 System.out.println(foundCol.toString());
266 uniqueSet.add(foundCol);
267 uniqueSet.add(foundCol);
269 Assert.assertTrue(!uniqueSet.isEmpty());
270 // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
273 @Test(groups = { "Functional" })
274 public void getTDBIdColumIndexTest()
276 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
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)
291 assertEquals(4, TDBeaconsFTSRestClient.getInstance()
292 .getPrimaryKeyColumIndex(wantedFields, true));
293 // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
294 // .getPrimaryKeyColumIndex(wantedFields, true));
295 } catch (Exception e)
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 } };
305 private static void setMockData()
309 mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
310 "test/jalview/fts/threedbeacons/p01308_tdb_resp.txt");
311 } catch (IOException e)
313 Assert.fail("Couldn't read mock response data", e);
317 public static void setMock()
320 FTSRestClient.createMockFTSRestClient(
321 (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
324 private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
326 private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
329 * check that the mock request and response are the same as the response from
330 * a live 3D-beacons endpoint
332 * Note - servers often have rapidly changing ids / URIs so this might fail,
333 * but the overall structure will remain.
337 @Test(groups = { "Network", "Integration" })
338 public void verifyMockTDBRequest() throws Exception
341 for (String[] otherMock : mocks)
343 verifyMockTDBRequest(otherMock[0], otherMock[1]);
347 private void verifyMockTDBRequest(String mockRequest,
348 String _mockResponse) throws Exception
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());
356 @Test(groups = { "Functional" })
357 public void testMockTDBRequest()
361 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
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)
380 e1.printStackTrace();
382 System.out.println("wantedFields >>" + wantedFields);
384 FTSRestRequest request = new FTSRestRequest();
385 FTSRestResponse response;
387 request.setResponseSize(100);
388 request.setFieldToSearchBy("");
389 request.setWantedFields(wantedFields);
390 // check 404 behaviour
391 request.setSearchTerm("P00000.json");
395 response = TDBeaconsFTSRestClient.getInstance()
396 .executeRequest(request);
398 assertNull(response);
399 } catch (Exception e)
402 Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
405 // check 200 behaviour
406 request.setSearchTerm("P38398.json");
407 System.out.println("request : " + request.getFieldToSearchBy());
408 // System.out.println(request.toString());
412 response = TDBeaconsFTSRestClient.getInstance()
413 .executeRequest(request);
414 } catch (Exception e)
417 Assert.fail("Couldn't execute webservice call!");
420 assertTrue(response.getSearchSummary() != null);
421 assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
422 System.out.println("Search summary : \n" + response.getSearchSummary());
424 // System.out.println(response.getSearchSummary().size());
427 @Test(groups = { "External", "Network" })
428 public void executeRequestTest()
430 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
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)
449 e1.printStackTrace();
451 System.out.println("wantedFields >>" + wantedFields);
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());
461 FTSRestResponse response;
464 response = TDBeaconsFTSRestClient.getInstance()
465 .executeRequest(request);
466 } catch (Exception e)
469 Assert.fail("Couldn't execute webservice call!");
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());