1 package jalview.fts.threedbeacons;
3 import static org.testng.Assert.assertNull;
4 import static org.testng.AssertJUnit.assertEquals;
5 import static org.testng.AssertJUnit.assertTrue;
8 import java.nio.charset.StandardCharsets;
9 import java.util.ArrayList;
10 import java.util.Collection;
11 import java.util.HashSet;
12 import java.util.List;
15 import org.testng.Assert;
16 import org.testng.annotations.AfterMethod;
17 import org.testng.annotations.BeforeClass;
18 import org.testng.annotations.BeforeMethod;
19 import org.testng.annotations.Test;
21 import jalview.fts.api.FTSDataColumnI;
22 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
23 import jalview.fts.core.FTSRestClient;
24 import jalview.fts.core.FTSRestRequest;
25 import jalview.fts.core.FTSRestResponse;
26 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
27 import jalview.gui.JvOptionPane;
29 public class TDBeaconsFTSRestClientTest
31 @BeforeClass(alwaysRun = true)
32 public void setUpJvOptionPane()
34 JvOptionPane.setInteractiveMode(false);
35 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
38 private FTSRestClient ftsRestClient;
40 @BeforeMethod(alwaysRun = true)
41 public void setUp() throws Exception
43 ftsRestClient = new FTSRestClient()
47 public String getColumnDataConfigFileName()
49 return "/fts/tdbeacons_data_columns.txt";
53 public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
61 @AfterMethod(alwaysRun = true)
62 public void tearDown() throws Exception
67 public void getAllDefaulDisplayedDataColumns()
69 // to change when resources.tdbeacons_data_columns.txt is changed
70 Assert.assertNotNull(ftsRestClient
71 .getAllDefaultDisplayedFTSDataColumns());
72 System.out.println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
73 Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
75 Assert.assertEquals(ftsRestClient
76 .getAllDefaultDisplayedFTSDataColumns().size(), 11);
79 @Test(groups = { "Functional" })
80 public void getPrimaryKeyColumIndexTest()
82 Collection<FTSDataColumnI> wantedFields = ftsRestClient
83 .getAllDefaultDisplayedFTSDataColumns();
87 Assert.assertEquals(foundIndex, -1);
88 foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
90 Assert.assertEquals(foundIndex, 10);
91 foundIndex = ftsRestClient
92 .getPrimaryKeyColumIndex(wantedFields, true);
93 Assert.assertEquals(foundIndex, 11);
97 Assert.fail("Exception thrown while testing...");
101 @Test(groups = { "Functional" })
102 public void getDataColumnsFieldsAsCommaDelimitedString()
104 // to change when resources.tdbeacons_data_columns.txt is changed
105 Collection<FTSDataColumnI> wantedFields = ftsRestClient
106 .getAllDefaultDisplayedFTSDataColumns();
107 String actual = ftsRestClient
108 .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
109 Assert.assertEquals(actual,
110 "model_identifier,provider,model_category,uniprot_start,uniprot_end,resolution,qmean_avg_local_score,coverage,created,entry_name,model_url");
113 @Test(groups = { "Functional" })
114 public void getAllFTSDataColumns()
116 Collection<FTSDataColumnI> allFields = ftsRestClient
117 .getAllFTSDataColumns();
118 Assert.assertNotNull(allFields);
119 //System.out.println(allFields.size());
120 Assert.assertEquals(allFields.size(), 15);
123 @Test(groups = { "Functional" })
124 public void getSearchableDataColumns()
126 // to change when resources.tdbeacons_data_columns.txt is changed
127 Collection<FTSDataColumnI> searchableFields = ftsRestClient
128 .getSearchableDataColumns();
129 Assert.assertNotNull(searchableFields);
130 //System.out.println(searchableFields.size());
131 Assert.assertEquals(searchableFields.size(), 1); //only 1: uniprot accession
134 @Test(groups = { "Functional" })
135 public void getPrimaryKeyColumn()
137 // to change when resources.tdbeacons_data_columns.txt is changed
138 FTSDataColumnI expectedPKColumn;
141 expectedPKColumn = ftsRestClient
142 .getDataColumnByNameOrCode("Url");
143 Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
144 Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
146 } catch (Exception e)
149 Assert.fail("Exception thrown while testing...");
153 @Test(groups = { "Functional" })
154 public void getDataColumnByNameOrCode()
158 FTSDataColumnI foundDataCol = ftsRestClient
159 .getDataColumnByNameOrCode("uniprot_accession");
160 Assert.assertNotNull(foundDataCol);
161 Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
162 } catch (Exception e)
165 Assert.fail("Exception thrown while testing...");
169 @Test(groups = { "Functional" })
170 public void getDataColumnGroupById()
172 FTSDataColumnGroupI foundDataColGroup;
175 foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
176 Assert.assertNotNull(foundDataColGroup);
177 Assert.assertEquals(foundDataColGroup.getName(), "Quality");
178 } catch (Exception e)
184 @Test(groups = { "Functional" })
185 public void getDefaultResponsePageSize()
187 int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
188 Assert.assertEquals(defaultResSize, 100); //why 100 or 500 ? pdb is 100, uniprot 500
191 @Test(groups = { "Functional" })
192 public void getColumnMinWidthTest()
196 FTSDataColumnI foundDataCol = ftsRestClient
197 .getDataColumnByNameOrCode("uniprot_accession");
198 Assert.assertNotNull(foundDataCol);
199 int actualColMinWidth = foundDataCol.getMinWidth();
200 Assert.assertEquals(actualColMinWidth, 50);
201 } catch (Exception e)
204 Assert.fail("Exception thrown while testing...");
207 // could add test for MaxWidth & PreferedWith
209 @Test(groups = { "Functional" })
210 public void getColumnClassTest()
214 FTSDataColumnI foundDataCol = ftsRestClient
215 .getDataColumnByNameOrCode("uniprot_accession");
216 Assert.assertNotNull(foundDataCol);
217 Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
219 foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
220 Assert.assertNotNull(foundDataCol);
221 Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
223 } catch (Exception e)
226 Assert.fail("Exception thrown while testing...");
230 @Test(groups = { "Functional" })
231 public void coverageForEqualsAndHashFunction()
233 Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
234 Collection<FTSDataColumnI> searchableCols = ftsRestClient
235 .getSearchableDataColumns();
236 System.out.println(searchableCols);
237 for (FTSDataColumnI foundCol : searchableCols)
239 System.out.println(foundCol.toString());
240 uniqueSet.add(foundCol);
241 uniqueSet.add(foundCol);
243 Assert.assertTrue(!uniqueSet.isEmpty());
244 //Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
247 @Test(groups = { "Functional" })
248 public void getTDBIdColumIndexTest()
250 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
253 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
254 .getDataColumnByNameOrCode("Model id"));
255 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
256 .getDataColumnByNameOrCode("uniprot_accession"));
257 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
258 .getDataColumnByNameOrCode("entry name"));
259 } catch (Exception e)
265 assertEquals(4, TDBeaconsFTSRestClient.getInstance()
266 .getPrimaryKeyColumIndex(wantedFields, true));
267 // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
268 // .getPrimaryKeyColumIndex(wantedFields, true));
269 } catch (Exception e)
275 private static String mockRequest = "P38398.json";
277 private static String mockResponse = "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"6138930b772bfbf9fe34f912\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-08\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"qmean_version\":\"4.2.0\",\"qmean_avg_local_score\":0.776,\"model_url\":\"https://beta.swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\"},{\"model_identifier\":\"6138930b772bfbf9fe34f916\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-08\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"qmean_version\":\"4.2.0\",\"qmean_avg_local_score\":0.655,\"model_url\":\"https://beta.swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"Deep learning\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\"}]}";
279 public static void setMock()
281 FTSRestClient.createMockFTSRestClient(
282 (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
283 mockRequest, mockResponse);
286 private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
289 * check that the mock request and response are the same as the response from
290 * a live 3D-beacons endpoint
294 @Test(groups = { "Network", "Integration" })
295 public void verifyMockTDBRequest() throws Exception
297 URL tdb_req = new URL(dev_url + mockRequest);
298 byte[] resp = tdb_req.openStream().readAllBytes();
299 String tresp = new String(resp, StandardCharsets.UTF_8);
300 assertEquals(mockResponse.trim(), tresp.trim());
303 @Test(groups = { "Functional" })
304 public void testMockTDBRequest()
308 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
311 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
312 .getDataColumnByNameOrCode("Model Id"));
313 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
314 .getDataColumnByNameOrCode("model_url"));
315 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
316 .getDataColumnByNameOrCode("provider"));
317 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
318 .getDataColumnByNameOrCode("model_category"));
319 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
320 .getDataColumnByNameOrCode("qmean_avg_local_score"));
321 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
322 .getDataColumnByNameOrCode("uniprot_start"));
323 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
324 .getDataColumnByNameOrCode("uniprot_end"));
325 } catch (Exception e1)
327 e1.printStackTrace();
329 System.out.println("wantedFields >>" + wantedFields);
331 FTSRestRequest request = new FTSRestRequest();
332 FTSRestResponse response;
334 request.setResponseSize(100);
335 request.setFieldToSearchBy("");
336 request.setWantedFields(wantedFields);
337 // check 404 behaviour
338 request.setSearchTerm("P00000.json");
342 response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
344 assertNull(response);
345 } catch (Exception e)
348 Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
351 // check 200 behaviour
352 request.setSearchTerm("P38398.json");
353 System.out.println("request : " + request.getFieldToSearchBy());
354 //System.out.println(request.toString());
358 response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
359 } catch (Exception e)
362 Assert.fail("Couldn't execute webservice call!");
365 assertTrue(response.getSearchSummary() != null);
366 assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
367 System.out.println("Search summary : \n" + response.getSearchSummary());
369 //System.out.println(response.getSearchSummary().size());
372 @Test(groups = { "External", "Network" })
373 public void executeRequestTest()
375 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
378 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
379 .getDataColumnByNameOrCode("Model Id"));
380 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
381 .getDataColumnByNameOrCode("model_url"));
382 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
383 .getDataColumnByNameOrCode("provider"));
384 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
385 .getDataColumnByNameOrCode("model_category"));
386 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
387 .getDataColumnByNameOrCode("qmean_avg_local_score"));
388 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
389 .getDataColumnByNameOrCode("uniprot_start"));
390 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
391 .getDataColumnByNameOrCode("uniprot_end"));
392 } catch (Exception e1)
394 e1.printStackTrace();
396 System.out.println("wantedFields >>" + wantedFields);
398 FTSRestRequest request = new FTSRestRequest();
399 request.setResponseSize(100);
400 request.setFieldToSearchBy("");
401 request.setSearchTerm("P01318.json");
402 request.setWantedFields(wantedFields);
403 System.out.println("request : " + request.getFieldToSearchBy());
404 //System.out.println(request.toString());
406 FTSRestResponse response;
409 response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
410 } catch (Exception e)
413 Assert.fail("Couldn't execute webservice call!");
416 assertTrue(response.getSearchSummary() != null);
417 assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
418 System.out.println("Search summary : \n" + response.getSearchSummary());
419 //System.out.println(response.getSearchSummary().size());