JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks
[jalview.git] / test / jalview / fts / threedbeacons / TDBeaconsFTSRestClientTest.java
1 package jalview.fts.threedbeacons;
2
3 import static org.testng.Assert.assertNull;
4 import static org.testng.AssertJUnit.assertEquals;
5 import static org.testng.AssertJUnit.assertTrue;
6
7 import java.net.URL;
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;
13 import java.util.Set;
14
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;
20
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;
28
29 public class TDBeaconsFTSRestClientTest
30 {
31   @BeforeClass(alwaysRun = true)
32   public void setUpJvOptionPane()
33   {
34     JvOptionPane.setInteractiveMode(false);
35     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
36   }
37
38   private FTSRestClient ftsRestClient;
39
40   @BeforeMethod(alwaysRun = true)
41   public void setUp() throws Exception
42   {
43     ftsRestClient = new FTSRestClient()
44     {
45
46       @Override
47       public String getColumnDataConfigFileName()
48       {
49         return "/fts/tdbeacons_data_columns.txt";
50       }
51
52       @Override
53       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
54               throws Exception
55       {
56         return null;
57       }
58     };
59   }
60
61   @AfterMethod(alwaysRun = true)
62   public void tearDown() throws Exception
63   {
64   }
65
66   @Test
67   public void getAllDefaulDisplayedDataColumns()
68   {
69     // to change when resources.tdbeacons_data_columns.txt is changed
70     Assert.assertNotNull(
71             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
72     System.out
73             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
74     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
75             .isEmpty());
76     Assert.assertEquals(
77             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
78             13);
79   }
80
81   @Test(groups = { "Functional" })
82   public void getPrimaryKeyColumIndexTest()
83   {
84     Collection<FTSDataColumnI> wantedFields = ftsRestClient
85             .getAllDefaultDisplayedFTSDataColumns();
86     int foundIndex = -1;
87     try
88     {
89       Assert.assertEquals(foundIndex, -1);
90       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
91               false);
92       Assert.assertEquals(foundIndex, 12);
93       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
94               true);
95       // 1+primary key index
96       Assert.assertEquals(foundIndex, 13);
97     } catch (Exception e)
98     {
99       e.printStackTrace();
100       Assert.fail("Exception thrown while testing...");
101     }
102   }
103
104   @Test(groups = { "Functional" })
105   public void getDataColumnsFieldsAsCommaDelimitedString()
106   {
107     // to change when resources.tdbeacons_data_columns.txt is changed
108     Collection<FTSDataColumnI> wantedFields = ftsRestClient
109             .getAllDefaultDisplayedFTSDataColumns();
110     String actual = ftsRestClient
111             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
112     Assert.assertEquals(actual,
113             "uniprot_start,uniprot_end,provider,model_identifier,model_category,model_title,resolution,confidence_avg_local_score,confidence_type,confidence_version,coverage,created,model_url");
114   }
115
116   @Test(groups = { "Functional" })
117   public void getAllFTSDataColumns()
118   {
119     Collection<FTSDataColumnI> allFields = ftsRestClient
120             .getAllFTSDataColumns();
121     Assert.assertNotNull(allFields);
122     // System.out.println(allFields.size());
123     Assert.assertEquals(allFields.size(), 19);
124   }
125
126   @Test(groups = { "Functional" })
127   public void getSearchableDataColumns()
128   {
129     // to change when resources.tdbeacons_data_columns.txt is changed
130     Collection<FTSDataColumnI> searchableFields = ftsRestClient
131             .getSearchableDataColumns();
132     Assert.assertNotNull(searchableFields);
133     // System.out.println(searchableFields.size());
134     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
135                                                      // accession
136   }
137
138   @Test(groups = { "Functional" })
139   public void getPrimaryKeyColumn()
140   {
141     // to change when resources.tdbeacons_data_columns.txt is changed
142     FTSDataColumnI expectedPKColumn;
143     try
144     {
145       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
146       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
147       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
148               expectedPKColumn);
149     } catch (Exception e)
150     {
151       e.printStackTrace();
152       Assert.fail("Exception thrown while testing...");
153     }
154   }
155
156   @Test(groups = { "Functional" })
157   public void getDataColumnByNameOrCode()
158   {
159     try
160     {
161       FTSDataColumnI foundDataCol = ftsRestClient
162               .getDataColumnByNameOrCode("uniprot_accession");
163       Assert.assertNotNull(foundDataCol);
164       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
165     } catch (Exception e)
166     {
167       e.printStackTrace();
168       Assert.fail("Exception thrown while testing...");
169     }
170   }
171
172   @Test(groups = { "Functional" })
173   public void getDataColumnGroupById()
174   {
175     FTSDataColumnGroupI foundDataColGroup;
176     try
177     {
178       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
179       Assert.assertNotNull(foundDataColGroup);
180       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
181     } catch (Exception e)
182     {
183       e.printStackTrace();
184     }
185   }
186
187   @Test(groups = { "Functional" })
188   public void getDefaultResponsePageSize()
189   {
190     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
191     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
192                                               // uniprot 500
193   }
194
195   @Test(groups = { "Functional" })
196   public void getColumnMinWidthTest()
197   {
198     try
199     {
200       FTSDataColumnI foundDataCol = ftsRestClient
201               .getDataColumnByNameOrCode("uniprot_accession");
202       Assert.assertNotNull(foundDataCol);
203       int actualColMinWidth = foundDataCol.getMinWidth();
204       Assert.assertEquals(actualColMinWidth, 50);
205     } catch (Exception e)
206     {
207       e.printStackTrace();
208       Assert.fail("Exception thrown while testing...");
209     }
210   }
211   // could add test for MaxWidth & PreferedWith
212
213   @Test(groups = { "Functional" })
214   public void getColumnClassTest()
215   {
216     try
217     {
218       FTSDataColumnI foundDataCol = ftsRestClient
219               .getDataColumnByNameOrCode("uniprot_accession");
220       Assert.assertNotNull(foundDataCol);
221       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
222               String.class);
223       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
224       Assert.assertNotNull(foundDataCol);
225       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
226               String.class);
227     } catch (Exception e)
228     {
229       e.printStackTrace();
230       Assert.fail("Exception thrown while testing...");
231     }
232   }
233
234   @Test(groups = { "Functional" })
235   public void coverageForEqualsAndHashFunction()
236   {
237     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
238     Collection<FTSDataColumnI> searchableCols = ftsRestClient
239             .getSearchableDataColumns();
240     System.out.println(searchableCols);
241     for (FTSDataColumnI foundCol : searchableCols)
242     {
243       System.out.println(foundCol.toString());
244       uniqueSet.add(foundCol);
245       uniqueSet.add(foundCol);
246     }
247     Assert.assertTrue(!uniqueSet.isEmpty());
248     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
249   }
250
251   @Test(groups = { "Functional" })
252   public void getTDBIdColumIndexTest()
253   {
254     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
255     try
256     {
257       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
258               .getDataColumnByNameOrCode("Model id"));
259       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
260               .getDataColumnByNameOrCode("uniprot_accession"));
261       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
262               .getDataColumnByNameOrCode("Title"));
263     } catch (Exception e)
264     {
265       e.printStackTrace();
266     }
267     try
268     {
269       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
270               .getPrimaryKeyColumIndex(wantedFields, true));
271       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
272       // .getPrimaryKeyColumIndex(wantedFields, true));
273     } catch (Exception e)
274     {
275       e.printStackTrace();
276     }
277   }
278
279   private static String[][] mocks = { { "P38398.json",
280       "{\"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 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281       { "P01308.json",
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_end\":110,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P01308-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P01308\"},{\"model_identifier\":\"2400\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2018-11-11\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE25_fit1_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE25\"},{\"model_identifier\":\"2396\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2018-11-11\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE25_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE25\"},{\"model_identifier\":\"2452\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEV5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEV5\"},{\"model_identifier\":\"2453\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEV5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEV5\"},{\"model_identifier\":\"2456\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEW5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEW5\"},{\"model_identifier\":\"2457\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEW5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEW5\"},{\"model_identifier\":\"2459\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEX5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEX5\"},{\"model_identifier\":\"2460\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEX5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEX5\"},{\"model_identifier\":\"2462\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEY5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEY5\"},{\"model_identifier\":\"2463\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEY5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEY5\"},{\"model_identifier\":\"2465\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEZ5_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEZ5\"},{\"model_identifier\":\"2467\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDEZ5_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDEZ5\"},{\"model_identifier\":\"2469\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE26_fit2_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE26\"},{\"model_identifier\":\"2470\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2019-04-07\",\"uniprot_start\":25,\"uniprot_end\":609,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDE26_fit3_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDE26\"},{\"model_identifier\":\"4420\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJY3_fit1_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJY3\"},{\"model_identifier\":\"4421\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJY3_fit1_model2.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJY3\"},{\"model_identifier\":\"4422\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJZ3_fit1_model1.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJZ3\"},{\"model_identifier\":\"4423\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"SASBDB\",\"created\":\"2020-12-18\",\"uniprot_start\":25,\"uniprot_end\":110,\"model_url\":\"https://www.sasbdb.org/media/pdb_file/SASDJZ3_fit1_model2.pdb\",\"model_format\":\"PDB\",\"model_page_url\":\"https://www.sasbdb.org/data/SASDJZ3\"}]}" } };
283
284   public static void setMock()
285   {
286     FTSRestClient.createMockFTSRestClient(
287             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
288             mocks);
289   }
290
291   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
292
293   /**
294    * check that the mock request and response are the same as the response from
295    * a live 3D-beacons endpoint
296    * 
297    * @throws Exception
298    */
299   @Test(groups = { "Network", "Integration" })
300   public void verifyMockTDBRequest() throws Exception
301   {
302     for (String[] otherMock:mocks)
303     {
304     verifyMockTDBRequest(otherMock[0],otherMock[1]);
305     }
306   }
307   private void verifyMockTDBRequest(String mockRequest, String _mockResponse) throws Exception
308   {
309     URL tdb_req = new URL(dev_url + mockRequest);
310     byte[] resp = tdb_req.openStream().readAllBytes();
311     String tresp = new String(resp, StandardCharsets.UTF_8);
312     assertEquals(_mockResponse.trim(), tresp.trim());
313   }
314
315   @Test(groups = { "Functional" })
316   public void testMockTDBRequest()
317   {
318
319     setMock();
320     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
321     try
322     {
323       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
324               .getDataColumnByNameOrCode("Model Id"));
325       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
326               .getDataColumnByNameOrCode("model_url"));
327       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
328               .getDataColumnByNameOrCode("provider"));
329       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
330               .getDataColumnByNameOrCode("model_category"));
331       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
332               .getDataColumnByNameOrCode("qmean_avg_local_score"));
333       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
334               .getDataColumnByNameOrCode("uniprot_start"));
335       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
336               .getDataColumnByNameOrCode("uniprot_end"));
337     } catch (Exception e1)
338     {
339       e1.printStackTrace();
340     }
341     System.out.println("wantedFields >>" + wantedFields);
342
343     FTSRestRequest request = new FTSRestRequest();
344     FTSRestResponse response;
345
346     request.setResponseSize(100);
347     request.setFieldToSearchBy("");
348     request.setWantedFields(wantedFields);
349     // check 404 behaviour
350     request.setSearchTerm("P00000.json");
351
352     try
353     {
354       response = TDBeaconsFTSRestClient.getInstance()
355               .executeRequest(request);
356
357       assertNull(response);
358     } catch (Exception e)
359     {
360       e.printStackTrace();
361       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
362     }
363
364     // check 200 behaviour
365     request.setSearchTerm("P38398.json");
366     System.out.println("request : " + request.getFieldToSearchBy());
367     // System.out.println(request.toString());
368
369     try
370     {
371       response = TDBeaconsFTSRestClient.getInstance()
372               .executeRequest(request);
373     } catch (Exception e)
374     {
375       e.printStackTrace();
376       Assert.fail("Couldn't execute webservice call!");
377       return;
378     }
379     assertTrue(response.getSearchSummary() != null);
380     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
381     System.out.println("Search summary : \n" + response.getSearchSummary());
382
383     // System.out.println(response.getSearchSummary().size());
384   }
385
386   @Test(groups = { "External", "Network" })
387   public void executeRequestTest()
388   {
389     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
390     try
391     {
392       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
393               .getDataColumnByNameOrCode("Model Id"));
394       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
395               .getDataColumnByNameOrCode("model_url"));
396       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
397               .getDataColumnByNameOrCode("provider"));
398       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
399               .getDataColumnByNameOrCode("model_category"));
400       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
401               .getDataColumnByNameOrCode("confidence_avg_local_score"));
402       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
403               .getDataColumnByNameOrCode("uniprot_start"));
404       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
405               .getDataColumnByNameOrCode("uniprot_end"));
406     } catch (Exception e1)
407     {
408       e1.printStackTrace();
409     }
410     System.out.println("wantedFields >>" + wantedFields);
411
412     FTSRestRequest request = new FTSRestRequest();
413     request.setResponseSize(100);
414     request.setFieldToSearchBy("");
415     request.setSearchTerm("P01318.json");
416     request.setWantedFields(wantedFields);
417     System.out.println("request : " + request.getFieldToSearchBy());
418     // System.out.println(request.toString());
419
420     FTSRestResponse response;
421     try
422     {
423       response = TDBeaconsFTSRestClient.getInstance()
424               .executeRequest(request);
425     } catch (Exception e)
426     {
427       e.printStackTrace();
428       Assert.fail("Couldn't execute webservice call!");
429       return;
430     }
431     assertTrue(response.getSearchSummary() != null);
432     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
433     System.out.println("Search summary : \n" + response.getSearchSummary());
434     // System.out.println(response.getSearchSummary().size());
435   }
436 }