test/jalview/fts/service/pdb/PDBFTSRestClientTest.java

   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
  30 import java.io.BufferedReader;
  31 import java.io.FileReader;
  32 import java.io.IOException;
  33 import java.util.ArrayList;
  34 import java.util.Iterator;
  35 import java.util.List;
  36
  37 import javax.ws.rs.core.MediaType;
  38
  39 import org.json.simple.JSONArray;
  40 import org.json.simple.JSONObject;
  41 import org.json.simple.parser.JSONParser;
  42 import org.json.simple.parser.ParseException;
  43 import org.testng.Assert;
  44 import org.testng.annotations.AfterMethod;
  45 import org.testng.annotations.BeforeMethod;
  46 import org.testng.annotations.Test;
  47
  48 import com.sun.jersey.api.client.Client;
  49 import com.sun.jersey.api.client.ClientResponse;
  50 import com.sun.jersey.api.client.WebResource;
  51 import com.sun.jersey.api.client.config.ClientConfig;
  52 import com.sun.jersey.api.client.config.DefaultClientConfig;
  53
  54 public class PDBFTSRestClientTest
  55 {
  56
  57   @BeforeMethod(alwaysRun = true)
  58   public void setUp() throws Exception
  59   {
  60   }
  61
  62   @AfterMethod
  63   public void tearDown() throws Exception
  64   {
  65   }
  66
  67   @Test(groups = { "External", "Network" })
  68   public void executeRequestTest()
  69   {
  70     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
  71     try
  72     {
  73       wantedFields.add(PDBFTSRestClient.getInstance()
  74               .getDataColumnByNameOrCode("molecule_type"));
  75       wantedFields
  76 .add(PDBFTSRestClient.getInstance()
  77               .getDataColumnByNameOrCode("pdb_id"));
  78       wantedFields.add(PDBFTSRestClient.getInstance()
  79               .getDataColumnByNameOrCode("genus"));
  80       wantedFields
  81 .add(PDBFTSRestClient.getInstance()
  82               .getDataColumnByNameOrCode("gene_name"));
  83       wantedFields.add(PDBFTSRestClient.getInstance()
  84               .getDataColumnByNameOrCode("title"));
  85     } catch (Exception e1)
  86     {
  87       e1.printStackTrace();
  88     }
  89
  90     FTSRestRequest request = new FTSRestRequest();
  91     request.setAllowEmptySeq(false);
  92     request.setResponseSize(100);
  93     request.setFieldToSearchBy("text:");
  94     request.setSearchTerm("abc");
  95     request.setWantedFields(wantedFields);
  96
  97     FTSRestResponse response;
  98     try
  99     {
 100       response = PDBFTSRestClient.getInstance().executeRequest(request);
 101     } catch (Exception e)
 102     {
 103       e.printStackTrace();
 104       Assert.fail("Couldn't execute webservice call!");
 105       return;
 106     }
 107     assertTrue(response.getNumberOfItemsFound() > 99);
 108     assertTrue(response.getSearchSummary() != null);
 109     assertTrue(response.getSearchSummary().size() > 99);
 110   }
 111
 112   @Test(groups = { "Functional" })
 113   public void getPDBDocFieldsAsCommaDelimitedStringTest()
 114   {
 115     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 116     try
 117     {
 118       wantedFields.add(PDBFTSRestClient.getInstance()
 119               .getDataColumnByNameOrCode("molecule_type"));
 120       wantedFields
 121 .add(PDBFTSRestClient.getInstance()
 122               .getDataColumnByNameOrCode("pdb_id"));
 123       wantedFields.add(PDBFTSRestClient.getInstance()
 124               .getDataColumnByNameOrCode("genus"));
 125       wantedFields
 126 .add(PDBFTSRestClient.getInstance()
 127               .getDataColumnByNameOrCode("gene_name"));
 128       wantedFields.add(PDBFTSRestClient.getInstance()
 129               .getDataColumnByNameOrCode("title"));
 130     } catch (Exception e)
 131     {
 132       e.printStackTrace();
 133     }
 134
 135     String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
 136     String actualResult = PDBFTSRestClient.getInstance()
 137             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 138
 139     assertEquals("", expectedResult, actualResult);
 140   }
 141
 142   @Test(groups = { "External, Network" })
 143   public void parsePDBJsonExceptionStringTest()
 144   {
 145     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 146     try
 147     {
 148       wantedFields.add(PDBFTSRestClient.getInstance()
 149               .getDataColumnByNameOrCode("molecule_type"));
 150       wantedFields
 151 .add(PDBFTSRestClient.getInstance()
 152               .getDataColumnByNameOrCode("pdb_id"));
 153       wantedFields.add(PDBFTSRestClient.getInstance()
 154               .getDataColumnByNameOrCode("genus"));
 155       wantedFields
 156 .add(PDBFTSRestClient.getInstance()
 157               .getDataColumnByNameOrCode("gene_name"));
 158       wantedFields.add(PDBFTSRestClient.getInstance()
 159               .getDataColumnByNameOrCode("title"));
 160     } catch (Exception e1)
 161     {
 162       e1.printStackTrace();
 163     }
 164
 165     FTSRestRequest request = new FTSRestRequest();
 166     request.setAllowEmptySeq(false);
 167     request.setResponseSize(100);
 168     request.setFieldToSearchBy("text:");
 169     request.setSearchTerm("abc");
 170     request.setWantedFields(wantedFields);
 171
 172     String jsonErrorResponse = "";
 173     try
 174     {
 175       jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
 176     } catch (IOException e)
 177     {
 178       e.printStackTrace();
 179     }
 180
 181     String parsedErrorResponse = PDBFTSRestClient
 182             .parseJsonExceptionString(jsonErrorResponse);
 183
 184     String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
 185             + "Status: 400\n"
 186             + "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"
 187             + "query: text:abc OR text:go:abc AND molecule_sequence:['' TO *]\n"
 188             + "fl: pdb_id\n";
 189
 190     assertEquals(expectedErrorMsg, parsedErrorResponse);
 191   }
 192
 193   @Test(
 194     groups = { "External", "Network" },
 195     expectedExceptions = Exception.class)
 196   public void testForExpectedRuntimeException() throws Exception
 197   {
 198     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 199     wantedFields.add(PDBFTSRestClient.getInstance()
 200             .getDataColumnByNameOrCode("pdb_id"));
 201
 202     FTSRestRequest request = new FTSRestRequest();
 203     request.setFieldToSearchBy("text:");
 204     request.setSearchTerm("abc OR text:go:abc");
 205     request.setWantedFields(wantedFields);
 206     PDBFTSRestClient.getInstance().executeRequest(request);
 207   }
 208
 209   @Test(groups = { "External" })
 210   public void parsePDBJsonResponseTest()
 211   {
 212     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 213     try
 214     {
 215       wantedFields.add(PDBFTSRestClient.getInstance()
 216               .getDataColumnByNameOrCode("molecule_type"));
 217       wantedFields
 218 .add(PDBFTSRestClient.getInstance()
 219               .getDataColumnByNameOrCode("pdb_id"));
 220       wantedFields.add(PDBFTSRestClient.getInstance()
 221               .getDataColumnByNameOrCode("genus"));
 222       wantedFields
 223 .add(PDBFTSRestClient.getInstance()
 224               .getDataColumnByNameOrCode("gene_name"));
 225       wantedFields.add(PDBFTSRestClient.getInstance()
 226               .getDataColumnByNameOrCode("title"));
 227     } catch (Exception e1)
 228     {
 229       e1.printStackTrace();
 230     }
 231
 232     FTSRestRequest request = new FTSRestRequest();
 233     request.setAllowEmptySeq(false);
 234     request.setWantedFields(wantedFields);
 235
 236     String jsonString = "";
 237     try
 238     {
 239       jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
 240     } catch (IOException e)
 241     {
 242       e.printStackTrace();
 243     }
 244     FTSRestResponse response = PDBFTSRestClient.parsePDBJsonResponse(
 245             jsonString, request);
 246     assertTrue(response.getSearchSummary() != null);
 247     assertTrue(response.getNumberOfItemsFound() == 931);
 248     assertTrue(response.getSearchSummary().size() == 14);
 249   }
 250
 251   @Test(groups = { "Functional" })
 252   public void getPDBIdColumIndexTest()
 253   {
 254     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 255     try
 256     {
 257       wantedFields.add(PDBFTSRestClient.getInstance()
 258               .getDataColumnByNameOrCode("molecule_type"));
 259       wantedFields.add(PDBFTSRestClient.getInstance()
 260               .getDataColumnByNameOrCode("genus"));
 261       wantedFields
 262 .add(PDBFTSRestClient.getInstance()
 263               .getDataColumnByNameOrCode("gene_name"));
 264       wantedFields.add(PDBFTSRestClient.getInstance()
 265               .getDataColumnByNameOrCode("title"));
 266       wantedFields
 267 .add(PDBFTSRestClient.getInstance()
 268               .getDataColumnByNameOrCode("pdb_id"));
 269     } catch (Exception e)
 270     {
 271       e.printStackTrace();
 272     }
 273     try
 274     {
 275       assertEquals(5,
 276  PDBFTSRestClient.getInstance()
 277               .getPrimaryKeyColumIndex(wantedFields, true));
 278       assertEquals(4,
 279  PDBFTSRestClient.getInstance()
 280               .getPrimaryKeyColumIndex(wantedFields, false));
 281     } catch (Exception e)
 282     {
 283       // TODO Auto-generated catch block
 284       e.printStackTrace();
 285     }
 286   }
 287
 288   @Test(groups = { "External" })
 289   public void externalServiceIntegrationTest()
 290   {
 291     ClientConfig clientConfig = new DefaultClientConfig();
 292     Client client = Client.create(clientConfig);
 293
 294     // Build request parameters for the REST Request
 295     WebResource webResource = client
 296             .resource(PDBFTSRestClient.PDB_SEARCH_ENDPOINT)
 297             .queryParam("wt", "json").queryParam("rows", String.valueOf(1))
 298             .queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
 299
 300     // Execute the REST request
 301     ClientResponse clientResponse = webResource.accept(
 302             MediaType.APPLICATION_JSON).get(ClientResponse.class);
 303
 304     // Get the JSON string from the response object
 305     String pdbJsonResponseString = clientResponse.getEntity(String.class);
 306
 307     // Check the response status and report exception if one occurs
 308     if (clientResponse.getStatus() != 200)
 309     {
 310       Assert.fail("Webservice call failed!!!");
 311     }
 312     else
 313     {
 314       try
 315       {
 316         JSONParser jsonParser = new JSONParser();
 317         JSONObject jsonObj = (JSONObject) jsonParser
 318                 .parse(pdbJsonResponseString);
 319         JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
 320         String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
 321                 .get("QTime").toString();
 322         String numFound = pdbResponse.get("numFound").toString();
 323         JSONArray docs = (JSONArray) pdbResponse.get("docs");
 324         Iterator<JSONObject> docIter = docs.iterator();
 325
 326         assertTrue("Couldn't Retrieve 'response' object",
 327                 pdbResponse != null);
 328         assertTrue("Couldn't Retrieve 'QTime' value", queryTime != null);
 329         assertTrue("Couldn't Retrieve 'numFound' value", numFound != null);
 330         assertTrue("Couldn't Retrieve 'docs' object", docs != null
 331                 || !docIter.hasNext());
 332
 333         JSONObject pdbJsonDoc = docIter.next();
 334
 335         for (FTSDataColumnI field : PDBFTSRestClient.getInstance()
 336                 .getAllFTSDataColumns())
 337         {
 338           if (field.getName().equalsIgnoreCase("ALL"))
 339           {
 340             continue;
 341           }
 342           if (pdbJsonDoc.get(field.getCode()) == null)
 343           {
 344             // System.out.println(">>>\t" + field.getCode());
 345             assertTrue(field.getCode()
 346                     + " has been removed from PDB doc Entity",
 347                     !pdbJsonResponseString.contains(field.getCode()));
 348           }
 349         }
 350       } catch (ParseException e)
 351       {
 352         Assert.fail(">>>  Test failed due to exception while parsing pdb response json !!!");
 353         e.printStackTrace();
 354       }
 355     }
 356   }
 357
 358   public String readJsonStringFromFile(String filePath) throws IOException
 359   {
 360     String fileContent;
 361     BufferedReader br = new BufferedReader(new FileReader(filePath));
 362     try
 363     {
 364       StringBuilder sb = new StringBuilder();
 365       String line = br.readLine();
 366
 367       while (line != null)
 368       {
 369         sb.append(line);
 370         sb.append(System.lineSeparator());
 371         line = br.readLine();
 372       }
 373       fileContent = sb.toString();
 374     } finally
 375     {
 376       br.close();
 377     }
 378     return fileContent;
 379   }
 380
 381 }