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;
7 import java.util.ArrayList;
8 import java.util.Collection;
9 import java.util.HashSet;
10 import java.util.List;
13 import org.testng.Assert;
14 import org.testng.annotations.AfterMethod;
15 import org.testng.annotations.BeforeClass;
16 import org.testng.annotations.BeforeMethod;
17 import org.testng.annotations.Test;
19 import jalview.fts.api.FTSDataColumnI;
20 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
21 import jalview.fts.core.FTSRestClient;
22 import jalview.fts.core.FTSRestRequest;
23 import jalview.fts.core.FTSRestResponse;
24 import jalview.fts.service.pdb.PDBFTSRestClient;
25 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
26 import jalview.gui.JvOptionPane;
28 public class TDBeaconsFTSRestClientTest
30 @BeforeClass(alwaysRun = true)
31 public void setUpJvOptionPane()
33 JvOptionPane.setInteractiveMode(false);
34 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
37 private FTSRestClient ftsRestClient;
39 @BeforeMethod(alwaysRun = true)
40 public void setUp() throws Exception
42 ftsRestClient = new FTSRestClient()
46 public String getColumnDataConfigFileName()
48 return "/fts/tdbeacons_data_columns.txt";
52 public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
60 @AfterMethod(alwaysRun = true)
61 public void tearDown() throws Exception
66 public void getAllDefaulDisplayedDataColumns()
68 // to change when resources.tdbeacons_data_columns.txt is changed
69 Assert.assertNotNull(ftsRestClient
70 .getAllDefaultDisplayedFTSDataColumns());
71 System.out.println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
72 Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
74 Assert.assertEquals(ftsRestClient
75 .getAllDefaultDisplayedFTSDataColumns().size(), 11);
78 @Test(groups = { "Functional" })
79 public void getPrimaryKeyColumIndexTest()
81 Collection<FTSDataColumnI> wantedFields = ftsRestClient
82 .getAllDefaultDisplayedFTSDataColumns();
86 Assert.assertEquals(foundIndex, -1);
87 foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
89 Assert.assertEquals(foundIndex, 10);
90 foundIndex = ftsRestClient
91 .getPrimaryKeyColumIndex(wantedFields, true);
92 Assert.assertEquals(foundIndex, 11);
96 Assert.fail("Exception thrown while testing...");
100 @Test(groups = { "Functional" })
101 public void getDataColumnsFieldsAsCommaDelimitedString()
103 // to change when resources.tdbeacons_data_columns.txt is changed
104 Collection<FTSDataColumnI> wantedFields = ftsRestClient
105 .getAllDefaultDisplayedFTSDataColumns();
106 String actual = ftsRestClient
107 .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
108 Assert.assertEquals(actual,
109 "model_identifier,provider,model_category,uniprot_start,uniprot_end,resolution,qmean_avg_local_score,coverage,created,entry_name,model_url");
112 @Test(groups = { "Functional" })
113 public void getAllFTSDataColumns()
115 Collection<FTSDataColumnI> allFields = ftsRestClient
116 .getAllFTSDataColumns();
117 Assert.assertNotNull(allFields);
118 //System.out.println(allFields.size());
119 Assert.assertEquals(allFields.size(), 15);
122 @Test(groups = { "Functional" })
123 public void getSearchableDataColumns()
125 // to change when resources.tdbeacons_data_columns.txt is changed
126 Collection<FTSDataColumnI> searchableFields = ftsRestClient
127 .getSearchableDataColumns();
128 Assert.assertNotNull(searchableFields);
129 //System.out.println(searchableFields.size());
130 Assert.assertEquals(searchableFields.size(), 1); //only 1: uniprot accession
133 @Test(groups = { "Functional" })
134 public void getPrimaryKeyColumn()
136 // to change when resources.tdbeacons_data_columns.txt is changed
137 FTSDataColumnI expectedPKColumn;
140 expectedPKColumn = ftsRestClient
141 .getDataColumnByNameOrCode("Url");
142 Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
143 Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
145 } catch (Exception e)
148 Assert.fail("Exception thrown while testing...");
152 @Test(groups = { "Functional" })
153 public void getDataColumnByNameOrCode()
157 FTSDataColumnI foundDataCol = ftsRestClient
158 .getDataColumnByNameOrCode("uniprot_accession");
159 Assert.assertNotNull(foundDataCol);
160 Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
161 } catch (Exception e)
164 Assert.fail("Exception thrown while testing...");
168 @Test(groups = { "Functional" })
169 public void getDataColumnGroupById()
171 FTSDataColumnGroupI foundDataColGroup;
174 foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
175 Assert.assertNotNull(foundDataColGroup);
176 Assert.assertEquals(foundDataColGroup.getName(), "Quality");
177 } catch (Exception e)
183 @Test(groups = { "Functional" })
184 public void getDefaultResponsePageSize()
186 int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
187 Assert.assertEquals(defaultResSize, 100); //why 100 or 500 ? pdb is 100, uniprot 500
190 @Test(groups = { "Functional" })
191 public void getColumnMinWidthTest()
195 FTSDataColumnI foundDataCol = ftsRestClient
196 .getDataColumnByNameOrCode("uniprot_accession");
197 Assert.assertNotNull(foundDataCol);
198 int actualColMinWidth = foundDataCol.getMinWidth();
199 Assert.assertEquals(actualColMinWidth, 50);
200 } catch (Exception e)
203 Assert.fail("Exception thrown while testing...");
206 // could add test for MaxWidth & PreferedWith
208 @Test(groups = { "Functional" })
209 public void getColumnClassTest()
213 FTSDataColumnI foundDataCol = ftsRestClient
214 .getDataColumnByNameOrCode("uniprot_accession");
215 Assert.assertNotNull(foundDataCol);
216 Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
218 foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
219 Assert.assertNotNull(foundDataCol);
220 Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
222 } catch (Exception e)
225 Assert.fail("Exception thrown while testing...");
229 @Test(groups = { "Functional" })
230 public void coverageForEqualsAndHashFunction()
232 Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
233 Collection<FTSDataColumnI> searchableCols = ftsRestClient
234 .getSearchableDataColumns();
235 System.out.println(searchableCols);
236 for (FTSDataColumnI foundCol : searchableCols)
238 System.out.println(foundCol.toString());
239 uniqueSet.add(foundCol);
240 uniqueSet.add(foundCol);
242 Assert.assertTrue(!uniqueSet.isEmpty());
243 //Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
246 @Test(groups = { "Functional" })
247 public void getTDBIdColumIndexTest()
249 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
252 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
253 .getDataColumnByNameOrCode("Model id"));
254 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
255 .getDataColumnByNameOrCode("uniprot_accession"));
256 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
257 .getDataColumnByNameOrCode("entry name"));
258 } catch (Exception e)
264 assertEquals(4, TDBeaconsFTSRestClient.getInstance()
265 .getPrimaryKeyColumIndex(wantedFields, true));
266 // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
267 // .getPrimaryKeyColumIndex(wantedFields, true));
268 } catch (Exception e)
274 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\":\"612f67c86ba77a10ab6f34ec\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-01\",\"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\":\"612f67c86ba77a10ab6f34f0\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-01\",\"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\"}]}";
276 public static void setMock() {
277 FTSRestClient.createMockFTSRestClient((FTSRestClient)TDBeaconsFTSRestClient.getInstance(),"P38398.json", mockResponse);
279 @Test(groups= {"Functional"})
280 public void testMockTDBRequest()
284 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
287 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
288 .getDataColumnByNameOrCode("Model Id"));
289 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
290 .getDataColumnByNameOrCode("model_url"));
291 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
292 .getDataColumnByNameOrCode("provider"));
293 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
294 .getDataColumnByNameOrCode("model_category"));
295 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
296 .getDataColumnByNameOrCode("qmean_avg_local_score"));
297 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
298 .getDataColumnByNameOrCode("uniprot_start"));
299 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
300 .getDataColumnByNameOrCode("uniprot_end"));
301 } catch (Exception e1)
303 e1.printStackTrace();
305 System.out.println("wantedFields >>" + wantedFields);
307 FTSRestRequest request = new FTSRestRequest();
308 FTSRestResponse response;
310 request.setResponseSize(100);
311 request.setFieldToSearchBy("");
312 request.setWantedFields(wantedFields);
313 // check 404 behaviour
314 request.setSearchTerm("P00000.json");
318 response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
320 assertNull(response);
321 } catch (Exception e)
324 Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
327 // check 200 behaviour
328 request.setSearchTerm("P38398.json");
329 System.out.println("request : " + request.getFieldToSearchBy());
330 //System.out.println(request.toString());
334 response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
335 } catch (Exception e)
338 Assert.fail("Couldn't execute webservice call!");
341 assertTrue(response.getSearchSummary() != null);
342 assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
343 System.out.println("Search summary : \n" + response.getSearchSummary());
345 //System.out.println(response.getSearchSummary().size());
348 @Test(groups = { "External", "Network" })
349 public void executeRequestTest()
351 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
354 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
355 .getDataColumnByNameOrCode("Model Id"));
356 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
357 .getDataColumnByNameOrCode("model_url"));
358 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
359 .getDataColumnByNameOrCode("provider"));
360 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
361 .getDataColumnByNameOrCode("model_category"));
362 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
363 .getDataColumnByNameOrCode("qmean_avg_local_score"));
364 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
365 .getDataColumnByNameOrCode("uniprot_start"));
366 wantedFields.add(TDBeaconsFTSRestClient.getInstance()
367 .getDataColumnByNameOrCode("uniprot_end"));
368 } catch (Exception e1)
370 e1.printStackTrace();
372 System.out.println("wantedFields >>" + wantedFields);
374 FTSRestRequest request = new FTSRestRequest();
375 request.setResponseSize(100);
376 request.setFieldToSearchBy("");
377 request.setSearchTerm("P01318.json");
378 request.setWantedFields(wantedFields);
379 System.out.println("request : " + request.getFieldToSearchBy());
380 //System.out.println(request.toString());
382 FTSRestResponse response;
385 response = TDBeaconsFTSRestClient.getInstance().executeRequest(request);
386 } catch (Exception e)
389 Assert.fail("Couldn't execute webservice call!");
392 assertTrue(response.getSearchSummary() != null);
393 assertTrue(response.getNumberOfItemsFound() > 3); //4 atm
394 System.out.println("Search summary : \n" + response.getSearchSummary());
395 //System.out.println(response.getSearchSummary().size());