1 package jalview.ws.dbsources;
3 import static org.junit.Assert.assertEquals;
4 import static org.junit.Assert.assertTrue;
5 import static org.junit.Assert.fail;
6 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
7 import jalview.ws.uimodel.PDBRestRequest;
8 import jalview.ws.uimodel.PDBRestResponse;
10 import java.io.BufferedReader;
11 import java.io.FileReader;
12 import java.io.IOException;
13 import java.util.ArrayList;
14 import java.util.Iterator;
15 import java.util.List;
17 import javax.ws.rs.core.MediaType;
19 import org.json.simple.JSONArray;
20 import org.json.simple.JSONObject;
21 import org.json.simple.parser.JSONParser;
22 import org.json.simple.parser.ParseException;
23 import org.junit.After;
24 import org.junit.Before;
25 import org.junit.Test;
27 import com.sun.jersey.api.client.Client;
28 import com.sun.jersey.api.client.ClientResponse;
29 import com.sun.jersey.api.client.WebResource;
30 import com.sun.jersey.api.client.config.ClientConfig;
31 import com.sun.jersey.api.client.config.DefaultClientConfig;
33 public class PDBRestClientTest
37 public void setUp() throws Exception
42 public void tearDown() throws Exception
47 public void executeRequestTest()
49 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
50 wantedFields.add(PDBDocField.MOLECULE_TYPE);
51 wantedFields.add(PDBDocField.PDB_ID);
52 wantedFields.add(PDBDocField.GENUS);
53 wantedFields.add(PDBDocField.GENE_NAME);
54 wantedFields.add(PDBDocField.TITLE);
56 PDBRestRequest request = new PDBRestRequest();
57 request.setAllowEmptySeq(false);
58 request.setResponseSize(100);
59 request.setFieldToSearchBy("text:");
60 request.setSearchTerm("abc");
61 request.setWantedFields(wantedFields);
63 PDBRestResponse response;
66 response = new PDBRestClient().executeRequest(request);
70 fail("Couldn't execute webservice call!");
73 assertTrue(response.getNumberOfItemsFound() > 99);
74 assertTrue(response.getSearchSummary() != null);
75 assertTrue(response.getSearchSummary().size() > 99);
79 public void getPDBDocFieldsAsCommaDelimitedStringTest()
81 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
82 wantedFields.add(PDBDocField.MOLECULE_TYPE);
83 wantedFields.add(PDBDocField.PDB_ID);
84 wantedFields.add(PDBDocField.GENUS);
85 wantedFields.add(PDBDocField.GENE_NAME);
86 wantedFields.add(PDBDocField.TITLE);
88 String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
89 String actualResult = PDBRestClient
90 .getPDBDocFieldsAsCommaDelimitedString(wantedFields);
92 assertEquals("", expectedResult, actualResult);
96 public void parsePDBJsonExceptionStringTest()
98 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
99 wantedFields.add(PDBDocField.MOLECULE_TYPE);
100 wantedFields.add(PDBDocField.PDB_ID);
101 wantedFields.add(PDBDocField.GENUS);
102 wantedFields.add(PDBDocField.GENE_NAME);
103 wantedFields.add(PDBDocField.TITLE);
105 PDBRestRequest request = new PDBRestRequest();
106 request.setAllowEmptySeq(false);
107 request.setResponseSize(100);
108 request.setFieldToSearchBy("text:");
109 request.setSearchTerm("abc");
110 request.setWantedFields(wantedFields);
112 String jsonErrorResponse = "";
115 jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
116 } catch (IOException e)
121 String parsedErrorResponse = PDBRestClient
122 .parseJsonExceptionString(jsonErrorResponse);
124 String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
126 + "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"
127 + "query: text:abc OR text:go:abc AND molecule_sequence:['' TO *]\n"
130 assertEquals(expectedErrorMsg, parsedErrorResponse);
133 @Test(expected = Exception.class)
134 public void testForExpectedRuntimeException() throws Exception
136 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
137 wantedFields.add(PDBDocField.PDB_ID);
139 PDBRestRequest request = new PDBRestRequest();
140 request.setFieldToSearchBy("text:");
141 request.setSearchTerm("abc OR text:go:abc");
142 request.setWantedFields(wantedFields);
143 new PDBRestClient().executeRequest(request);
147 public void parsePDBJsonResponseTest()
149 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
150 wantedFields.add(PDBDocField.MOLECULE_TYPE);
151 wantedFields.add(PDBDocField.PDB_ID);
152 wantedFields.add(PDBDocField.GENUS);
153 wantedFields.add(PDBDocField.GENE_NAME);
154 wantedFields.add(PDBDocField.TITLE);
156 PDBRestRequest request = new PDBRestRequest();
157 request.setAllowEmptySeq(false);
158 request.setWantedFields(wantedFields);
160 String jsonString = "";
163 jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
164 } catch (IOException e)
168 PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
169 jsonString, request);
170 assertTrue(response.getSearchSummary() != null);
171 assertTrue(response.getNumberOfItemsFound() == 931);
172 assertTrue(response.getSearchSummary().size() == 14);
176 public void getPDBIdColumIndexTest()
178 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
179 wantedFields.add(PDBDocField.MOLECULE_TYPE);
180 wantedFields.add(PDBDocField.GENUS);
181 wantedFields.add(PDBDocField.GENE_NAME);
182 wantedFields.add(PDBDocField.TITLE);
183 wantedFields.add(PDBDocField.PDB_ID);
184 assertEquals(5, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
185 assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
189 public void externalServiceIntegrationTest()
191 ClientConfig clientConfig = new DefaultClientConfig();
192 Client client = Client.create(clientConfig);
194 // Build request parameters for the REST Request
195 WebResource webResource = client
196 .resource(PDBRestClient.PDB_SEARCH_ENDPOINT)
197 .queryParam("wt", "json").queryParam("rows", String.valueOf(1))
198 .queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
200 // Execute the REST request
201 ClientResponse clientResponse = webResource.accept(
202 MediaType.APPLICATION_JSON).get(ClientResponse.class);
204 // Get the JSON string from the response object
205 String pdbJsonResponseString = clientResponse.getEntity(String.class);
207 // Check the response status and report exception if one occurs
208 if (clientResponse.getStatus() != 200)
210 fail("Webservice call failed!!!");
216 JSONParser jsonParser = new JSONParser();
217 JSONObject jsonObj = (JSONObject) jsonParser
218 .parse(pdbJsonResponseString);
219 JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
220 String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
221 .get("QTime").toString();
222 String numFound = pdbResponse.get("numFound").toString();
223 JSONArray docs = (JSONArray) pdbResponse.get("docs");
224 Iterator<JSONObject> docIter = docs.iterator();
226 assertTrue("Couldn't Retrieve 'response' object",
227 pdbResponse != null);
228 assertTrue("Couldn't Retrieve 'QTime' value", queryTime != null);
229 assertTrue("Couldn't Retrieve 'numFound' value", numFound != null);
230 assertTrue("Couldn't Retrieve 'docs' object", docs != null
231 || !docIter.hasNext());
233 JSONObject pdbJsonDoc = docIter.next();
235 for (PDBDocField field : PDBDocField.values())
237 if (field == PDBDocField.ALL)
241 if (pdbJsonDoc.get(field.getCode()) == null)
243 // System.out.println(">>>\t" + field.getCode());
244 assertTrue(field.getClass()
245 + " has been removed from PDB doc Entity",
246 !pdbJsonResponseString.contains(field.getCode()));
249 } catch (ParseException e)
251 fail(">>> Test failed due to exception while parsing pdb response json !!!");
257 public String readJsonStringFromFile(String filePath) throws IOException
260 BufferedReader br = new BufferedReader(new FileReader(filePath));
263 StringBuilder sb = new StringBuilder();
264 String line = br.readLine();
269 sb.append(System.lineSeparator());
270 line = br.readLine();
272 fileContent = sb.toString();