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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.fts.service.pdb

File PDBFTSRestClientTest.java

 

Code metrics

8
134
11
1
377
311
25
0.19
12.18
11
2.27

Classes

Class Line # Actions
PDBFTSRestClientTest 56 134 25 126
0.176470617.6%
 

Contributing tests

This file is covered by 2 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.fts.service.pdb;
22   
23    import static org.testng.AssertJUnit.assertEquals;
24    import static org.testng.AssertJUnit.assertTrue;
25   
26    import jalview.fts.api.FTSDataColumnI;
27    import jalview.fts.core.FTSRestRequest;
28    import jalview.fts.core.FTSRestResponse;
29    import jalview.gui.JvOptionPane;
30   
31    import java.io.BufferedReader;
32    import java.io.FileReader;
33    import java.io.IOException;
34    import java.util.ArrayList;
35    import java.util.Iterator;
36    import java.util.List;
37   
38    import javax.ws.rs.core.MediaType;
39   
40    import org.json.simple.JSONArray;
41    import org.json.simple.JSONObject;
42    import org.json.simple.parser.JSONParser;
43    import org.json.simple.parser.ParseException;
44    import org.testng.Assert;
45    import org.testng.annotations.AfterMethod;
46    import org.testng.annotations.BeforeClass;
47    import org.testng.annotations.BeforeMethod;
48    import org.testng.annotations.Test;
49   
50    import com.sun.jersey.api.client.Client;
51    import com.sun.jersey.api.client.ClientResponse;
52    import com.sun.jersey.api.client.WebResource;
53    import com.sun.jersey.api.client.config.ClientConfig;
54    import com.sun.jersey.api.client.config.DefaultClientConfig;
55   
 
56    public class PDBFTSRestClientTest
57    {
58   
 
59  1 toggle @BeforeClass(alwaysRun = true)
60    public void setUpJvOptionPane()
61    {
62  1 JvOptionPane.setInteractiveMode(false);
63  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64    }
65   
 
66  2 toggle @BeforeMethod(alwaysRun = true)
67    public void setUp() throws Exception
68    {
69    }
70   
 
71  2 toggle @AfterMethod(alwaysRun = true)
72    public void tearDown() throws Exception
73    {
74    }
75   
 
76  0 toggle @Test(groups = { "External", "Network" })
77    public void executeRequestTest()
78    {
79  0 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
80  0 try
81    {
82  0 wantedFields.add(PDBFTSRestClient.getInstance()
83    .getDataColumnByNameOrCode("molecule_type"));
84  0 wantedFields.add(PDBFTSRestClient.getInstance()
85    .getDataColumnByNameOrCode("pdb_id"));
86  0 wantedFields.add(PDBFTSRestClient.getInstance()
87    .getDataColumnByNameOrCode("genus"));
88  0 wantedFields.add(PDBFTSRestClient.getInstance()
89    .getDataColumnByNameOrCode("gene_name"));
90  0 wantedFields.add(PDBFTSRestClient.getInstance()
91    .getDataColumnByNameOrCode("title"));
92    } catch (Exception e1)
93    {
94  0 e1.printStackTrace();
95    }
96   
97  0 FTSRestRequest request = new FTSRestRequest();
98  0 request.setAllowEmptySeq(false);
99  0 request.setResponseSize(100);
100  0 request.setFieldToSearchBy("text:");
101  0 request.setSearchTerm("abc");
102  0 request.setWantedFields(wantedFields);
103   
104  0 FTSRestResponse response;
105  0 try
106    {
107  0 response = PDBFTSRestClient.getInstance().executeRequest(request);
108    } catch (Exception e)
109    {
110  0 e.printStackTrace();
111  0 Assert.fail("Couldn't execute webservice call!");
112  0 return;
113    }
114  0 assertTrue(response.getNumberOfItemsFound() > 99);
115  0 assertTrue(response.getSearchSummary() != null);
116  0 assertTrue(response.getSearchSummary().size() > 99);
117    }
118   
 
119  1 toggle @Test(groups = { "Functional" })
120    public void getPDBDocFieldsAsCommaDelimitedStringTest()
121    {
122  1 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
123  1 try
124    {
125  1 wantedFields.add(PDBFTSRestClient.getInstance()
126    .getDataColumnByNameOrCode("molecule_type"));
127  1 wantedFields.add(PDBFTSRestClient.getInstance()
128    .getDataColumnByNameOrCode("pdb_id"));
129  1 wantedFields.add(PDBFTSRestClient.getInstance()
130    .getDataColumnByNameOrCode("genus"));
131  1 wantedFields.add(PDBFTSRestClient.getInstance()
132    .getDataColumnByNameOrCode("gene_name"));
133  1 wantedFields.add(PDBFTSRestClient.getInstance()
134    .getDataColumnByNameOrCode("title"));
135    } catch (Exception e)
136    {
137  0 e.printStackTrace();
138    }
139   
140  1 String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
141  1 String actualResult = PDBFTSRestClient.getInstance()
142    .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
143   
144  1 assertEquals("", expectedResult, actualResult);
145    }
146   
 
147  0 toggle @Test(groups = { "External, Network" })
148    public void parsePDBJsonExceptionStringTest()
149    {
150  0 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
151  0 try
152    {
153  0 wantedFields.add(PDBFTSRestClient.getInstance()
154    .getDataColumnByNameOrCode("molecule_type"));
155  0 wantedFields.add(PDBFTSRestClient.getInstance()
156    .getDataColumnByNameOrCode("pdb_id"));
157  0 wantedFields.add(PDBFTSRestClient.getInstance()
158    .getDataColumnByNameOrCode("genus"));
159  0 wantedFields.add(PDBFTSRestClient.getInstance()
160    .getDataColumnByNameOrCode("gene_name"));
161  0 wantedFields.add(PDBFTSRestClient.getInstance()
162    .getDataColumnByNameOrCode("title"));
163    } catch (Exception e1)
164    {
165  0 e1.printStackTrace();
166    }
167   
168  0 FTSRestRequest request = new FTSRestRequest();
169  0 request.setAllowEmptySeq(false);
170  0 request.setResponseSize(100);
171  0 request.setFieldToSearchBy("text:");
172  0 request.setSearchTerm("abc");
173  0 request.setWantedFields(wantedFields);
174   
175  0 String jsonErrorResponse = "";
176  0 try
177    {
178  0 jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
179    } catch (IOException e)
180    {
181  0 e.printStackTrace();
182    }
183   
184  0 String parsedErrorResponse = PDBFTSRestClient
185    .parseJsonExceptionString(jsonErrorResponse);
186   
187  0 String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
188    + "Status: 400\n"
189    + "Message: org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.\n"
190    + "query: text:abc OR text:go:abc AND molecule_sequence:['' TO *]\n"
191    + "fl: pdb_id\n";
192   
193  0 assertEquals(expectedErrorMsg, parsedErrorResponse);
194    }
195   
 
196  0 toggle @Test(groups = { "External" }, expectedExceptions = Exception.class)
197    public void testForExpectedRuntimeException() throws Exception
198    {
199  0 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
200  0 wantedFields.add(PDBFTSRestClient.getInstance()
201    .getDataColumnByNameOrCode("pdb_id"));
202   
203  0 FTSRestRequest request = new FTSRestRequest();
204  0 request.setFieldToSearchBy("text:");
205  0 request.setSearchTerm("abc OR text:go:abc");
206  0 request.setWantedFields(wantedFields);
207  0 PDBFTSRestClient.getInstance().executeRequest(request);
208    }
209   
210    // JBP: Is this actually external ? Looks like it is mocked
 
211  0 toggle @Test(groups = { "External" })
212    public void parsePDBJsonResponseTest()
213    {
214  0 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
215  0 try
216    {
217  0 wantedFields.add(PDBFTSRestClient.getInstance()
218    .getDataColumnByNameOrCode("molecule_type"));
219  0 wantedFields.add(PDBFTSRestClient.getInstance()
220    .getDataColumnByNameOrCode("pdb_id"));
221  0 wantedFields.add(PDBFTSRestClient.getInstance()
222    .getDataColumnByNameOrCode("genus"));
223  0 wantedFields.add(PDBFTSRestClient.getInstance()
224    .getDataColumnByNameOrCode("gene_name"));
225  0 wantedFields.add(PDBFTSRestClient.getInstance()
226    .getDataColumnByNameOrCode("title"));
227    } catch (Exception e1)
228    {
229  0 e1.printStackTrace();
230    }
231   
232  0 FTSRestRequest request = new FTSRestRequest();
233  0 request.setAllowEmptySeq(false);
234  0 request.setWantedFields(wantedFields);
235   
236  0 String jsonString = "";
237  0 try
238    {
239  0 jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
240    } catch (IOException e)
241    {
242  0 e.printStackTrace();
243    }
244  0 FTSRestResponse response = PDBFTSRestClient.parsePDBJsonResponse(
245    jsonString, request);
246  0 assertTrue(response.getSearchSummary() != null);
247  0 assertTrue(response.getNumberOfItemsFound() == 931);
248  0 assertTrue(response.getSearchSummary().size() == 14);
249    }
250   
 
251  1 toggle @Test(groups = { "Functional" })
252    public void getPDBIdColumIndexTest()
253    {
254  1 List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
255  1 try
256    {
257  1 wantedFields.add(PDBFTSRestClient.getInstance()
258    .getDataColumnByNameOrCode("molecule_type"));
259  1 wantedFields.add(PDBFTSRestClient.getInstance()
260    .getDataColumnByNameOrCode("genus"));
261  1 wantedFields.add(PDBFTSRestClient.getInstance()
262    .getDataColumnByNameOrCode("gene_name"));
263  1 wantedFields.add(PDBFTSRestClient.getInstance()
264    .getDataColumnByNameOrCode("title"));
265  1 wantedFields.add(PDBFTSRestClient.getInstance()
266    .getDataColumnByNameOrCode("pdb_id"));
267    } catch (Exception e)
268    {
269  0 e.printStackTrace();
270    }
271  1 try
272    {
273  1 assertEquals(5, PDBFTSRestClient.getInstance()
274    .getPrimaryKeyColumIndex(wantedFields, true));
275  1 assertEquals(4, PDBFTSRestClient.getInstance()
276    .getPrimaryKeyColumIndex(wantedFields, false));
277    } catch (Exception e)
278    {
279    // TODO Auto-generated catch block
280  0 e.printStackTrace();
281    }
282    }
283   
 
284  0 toggle @Test(groups = { "External" })
285    public void externalServiceIntegrationTest()
286    {
287  0 ClientConfig clientConfig = new DefaultClientConfig();
288  0 Client client = Client.create(clientConfig);
289   
290    // Build request parameters for the REST Request
291  0 WebResource webResource = client
292    .resource(PDBFTSRestClient.PDB_SEARCH_ENDPOINT)
293    .queryParam("wt", "json").queryParam("rows", String.valueOf(1))
294    .queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
295   
296    // Execute the REST request
297  0 ClientResponse clientResponse = webResource.accept(
298    MediaType.APPLICATION_JSON).get(ClientResponse.class);
299   
300    // Get the JSON string from the response object
301  0 String pdbJsonResponseString = clientResponse.getEntity(String.class);
302   
303    // Check the response status and report exception if one occurs
304  0 if (clientResponse.getStatus() != 200)
305    {
306  0 Assert.fail("Webservice call failed!!!");
307    }
308    else
309    {
310  0 try
311    {
312  0 JSONParser jsonParser = new JSONParser();
313  0 JSONObject jsonObj = (JSONObject) jsonParser
314    .parse(pdbJsonResponseString);
315  0 JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
316  0 String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
317    .get("QTime").toString();
318  0 String numFound = pdbResponse.get("numFound").toString();
319  0 JSONArray docs = (JSONArray) pdbResponse.get("docs");
320  0 Iterator<JSONObject> docIter = docs.iterator();
321   
322  0 assertTrue("Couldn't Retrieve 'response' object",
323    pdbResponse != null);
324  0 assertTrue("Couldn't Retrieve 'QTime' value", queryTime != null);
325  0 assertTrue("Couldn't Retrieve 'numFound' value", numFound != null);
326  0 assertTrue("Couldn't Retrieve 'docs' object", docs != null
327    || !docIter.hasNext());
328   
329  0 JSONObject pdbJsonDoc = docIter.next();
330   
331  0 for (FTSDataColumnI field : PDBFTSRestClient.getInstance()
332    .getAllFTSDataColumns())
333    {
334  0 if (field.getName().equalsIgnoreCase("ALL"))
335    {
336  0 continue;
337    }
338  0 if (pdbJsonDoc.get(field.getCode()) == null)
339    {
340    // System.out.println(">>>\t" + field.getCode());
341  0 assertTrue(field.getCode()
342    + " has been removed from PDB doc Entity",
343    !pdbJsonResponseString.contains(field.getCode()));
344    }
345    }
346    } catch (ParseException e)
347    {
348  0 Assert.fail(">>> Test failed due to exception while parsing pdb response json !!!");
349  0 e.printStackTrace();
350    }
351    }
352    }
353   
 
354  0 toggle public String readJsonStringFromFile(String filePath) throws IOException
355    {
356  0 String fileContent;
357  0 BufferedReader br = new BufferedReader(new FileReader(filePath));
358  0 try
359    {
360  0 StringBuilder sb = new StringBuilder();
361  0 String line = br.readLine();
362   
363  0 while (line != null)
364    {
365  0 sb.append(line);
366  0 sb.append(System.lineSeparator());
367  0 line = br.readLine();
368    }
369  0 fileContent = sb.toString();
370    } finally
371    {
372  0 br.close();
373    }
374  0 return fileContent;
375    }
376   
377    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.