1 package jalview.ws.dbsources;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertTrue;
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.testng.Assert;
24 import org.testng.annotations.AfterMethod;
25 import org.testng.annotations.BeforeMethod;
26 import org.testng.annotations.Test;
28 import com.sun.jersey.api.client.Client;
29 import com.sun.jersey.api.client.ClientResponse;
30 import com.sun.jersey.api.client.WebResource;
31 import com.sun.jersey.api.client.config.ClientConfig;
32 import com.sun.jersey.api.client.config.DefaultClientConfig;
34 public class PDBRestClientTest
37 @BeforeMethod(alwaysRun = true)
38 public void setUp() throws Exception
43 public void tearDown() throws Exception
48 { "External", "Network" })
49 public void executeRequestTest()
51 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
52 wantedFields.add(PDBDocField.MOLECULE_TYPE);
53 wantedFields.add(PDBDocField.PDB_ID);
54 wantedFields.add(PDBDocField.GENUS);
55 wantedFields.add(PDBDocField.GENE_NAME);
56 wantedFields.add(PDBDocField.TITLE);
58 PDBRestRequest request = new PDBRestRequest();
59 request.setAllowEmptySeq(false);
60 request.setResponseSize(100);
61 request.setFieldToSearchBy("text:");
62 request.setSearchTerm("abc");
63 request.setWantedFields(wantedFields);
65 PDBRestResponse response;
68 response = new PDBRestClient().executeRequest(request);
72 Assert.fail("Couldn't execute webservice call!");
75 assertTrue(response.getNumberOfItemsFound() > 99);
76 assertTrue(response.getSearchSummary() != null);
77 assertTrue(response.getSearchSummary().size() > 99);
80 @Test(groups ={ "Functional" })
81 public void getPDBDocFieldsAsCommaDelimitedStringTest()
83 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
84 wantedFields.add(PDBDocField.MOLECULE_TYPE);
85 wantedFields.add(PDBDocField.PDB_ID);
86 wantedFields.add(PDBDocField.GENUS);
87 wantedFields.add(PDBDocField.GENE_NAME);
88 wantedFields.add(PDBDocField.TITLE);
90 String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
91 String actualResult = PDBRestClient
92 .getPDBDocFieldsAsCommaDelimitedString(wantedFields);
94 assertEquals("", expectedResult, actualResult);
98 { "External, Network" })
99 public void parsePDBJsonExceptionStringTest()
101 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
102 wantedFields.add(PDBDocField.MOLECULE_TYPE);
103 wantedFields.add(PDBDocField.PDB_ID);
104 wantedFields.add(PDBDocField.GENUS);
105 wantedFields.add(PDBDocField.GENE_NAME);
106 wantedFields.add(PDBDocField.TITLE);
108 PDBRestRequest request = new PDBRestRequest();
109 request.setAllowEmptySeq(false);
110 request.setResponseSize(100);
111 request.setFieldToSearchBy("text:");
112 request.setSearchTerm("abc");
113 request.setWantedFields(wantedFields);
115 String jsonErrorResponse = "";
118 jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
119 } catch (IOException e)
124 String parsedErrorResponse = PDBRestClient
125 .parseJsonExceptionString(jsonErrorResponse);
127 String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
129 + "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"
130 + "query: text:abc OR text:go:abc AND molecule_sequence:['' TO *]\n"
133 assertEquals(expectedErrorMsg, parsedErrorResponse);
137 { "External", "Network" }, expectedExceptions = Exception.class)
138 public void testForExpectedRuntimeException() throws Exception
140 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
141 wantedFields.add(PDBDocField.PDB_ID);
143 PDBRestRequest request = new PDBRestRequest();
144 request.setFieldToSearchBy("text:");
145 request.setSearchTerm("abc OR text:go:abc");
146 request.setWantedFields(wantedFields);
147 new PDBRestClient().executeRequest(request);
152 public void parsePDBJsonResponseTest()
154 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
155 wantedFields.add(PDBDocField.MOLECULE_TYPE);
156 wantedFields.add(PDBDocField.PDB_ID);
157 wantedFields.add(PDBDocField.GENUS);
158 wantedFields.add(PDBDocField.GENE_NAME);
159 wantedFields.add(PDBDocField.TITLE);
161 PDBRestRequest request = new PDBRestRequest();
162 request.setAllowEmptySeq(false);
163 request.setWantedFields(wantedFields);
165 String jsonString = "";
168 jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
169 } catch (IOException e)
173 PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
174 jsonString, request);
175 assertTrue(response.getSearchSummary() != null);
176 assertTrue(response.getNumberOfItemsFound() == 931);
177 assertTrue(response.getSearchSummary().size() == 14);
180 @Test(groups ={ "Functional" })
181 public void getPDBIdColumIndexTest()
183 List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
184 wantedFields.add(PDBDocField.MOLECULE_TYPE);
185 wantedFields.add(PDBDocField.GENUS);
186 wantedFields.add(PDBDocField.GENE_NAME);
187 wantedFields.add(PDBDocField.TITLE);
188 wantedFields.add(PDBDocField.PDB_ID);
189 assertEquals(5, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
190 assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
195 public void externalServiceIntegrationTest()
197 ClientConfig clientConfig = new DefaultClientConfig();
198 Client client = Client.create(clientConfig);
200 // Build request parameters for the REST Request
201 WebResource webResource = client
202 .resource(PDBRestClient.PDB_SEARCH_ENDPOINT)
203 .queryParam("wt", "json").queryParam("rows", String.valueOf(1))
204 .queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
206 // Execute the REST request
207 ClientResponse clientResponse = webResource.accept(
208 MediaType.APPLICATION_JSON).get(ClientResponse.class);
210 // Get the JSON string from the response object
211 String pdbJsonResponseString = clientResponse.getEntity(String.class);
213 // Check the response status and report exception if one occurs
214 if (clientResponse.getStatus() != 200)
216 Assert.fail("Webservice call failed!!!");
222 JSONParser jsonParser = new JSONParser();
223 JSONObject jsonObj = (JSONObject) jsonParser
224 .parse(pdbJsonResponseString);
225 JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
226 String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
227 .get("QTime").toString();
228 String numFound = pdbResponse.get("numFound").toString();
229 JSONArray docs = (JSONArray) pdbResponse.get("docs");
230 Iterator<JSONObject> docIter = docs.iterator();
232 assertTrue("Couldn't Retrieve 'response' object",
233 pdbResponse != null);
234 assertTrue("Couldn't Retrieve 'QTime' value", queryTime != null);
235 assertTrue("Couldn't Retrieve 'numFound' value", numFound != null);
236 assertTrue("Couldn't Retrieve 'docs' object", docs != null
237 || !docIter.hasNext());
239 JSONObject pdbJsonDoc = docIter.next();
241 for (PDBDocField field : PDBDocField.values())
243 if (field == PDBDocField.ALL)
247 if (pdbJsonDoc.get(field.getCode()) == null)
249 // System.out.println(">>>\t" + field.getCode());
250 assertTrue(field.getClass()
251 + " has been removed from PDB doc Entity",
252 !pdbJsonResponseString.contains(field.getCode()));
255 } catch (ParseException e)
257 Assert.fail(">>> Test failed due to exception while parsing pdb response json !!!");
263 public String readJsonStringFromFile(String filePath) throws IOException
266 BufferedReader br = new BufferedReader(new FileReader(filePath));
269 StringBuilder sb = new StringBuilder();
270 String line = br.readLine();
275 sb.append(System.lineSeparator());
276 line = br.readLine();
278 fileContent = sb.toString();