test/jalview/ws/dbsources/PDBRestClientTest.java

   1 package jalview.ws.dbsources;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertTrue;
   5 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
   6 import jalview.ws.uimodel.PDBRestRequest;
   7 import jalview.ws.uimodel.PDBRestResponse;
   8
   9 import java.io.BufferedReader;
  10 import java.io.FileReader;
  11 import java.io.IOException;
  12 import java.util.ArrayList;
  13 import java.util.List;
  14
  15 import org.junit.After;
  16 import org.junit.Before;
  17 import org.junit.Test;
  18
  19 public class PDBRestClientTest
  20 {
  21
  22   @Before
  23   public void setUp() throws Exception
  24   {
  25   }
  26
  27   @After
  28   public void tearDown() throws Exception
  29   {
  30   }
  31
  32   @Test
  33   public void executeRequestTest()
  34   {
  35     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  36     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  37     wantedFields.add(PDBDocField.PDB_ID);
  38     wantedFields.add(PDBDocField.GENUS);
  39     wantedFields.add(PDBDocField.GENE_NAME);
  40     wantedFields.add(PDBDocField.TITLE);
  41
  42     PDBRestRequest request = new PDBRestRequest();
  43     request.setAllowEmptySeq(false);
  44     request.setResponseSize(100);
  45     request.setFieldToSearchBy("text:");
  46     request.setSearchTerm("abc");
  47     request.setWantedFields(wantedFields);
  48
  49     PDBRestResponse response = new PDBRestClient().executeRequest(request);
  50     assertTrue(response.getNumberOfItemsFound() > 99);
  51     assertTrue(response.getSearchSummary() != null);
  52     assertTrue(response.getSearchSummary().size() > 99);
  53   }
  54
  55   @Test
  56   public void getPDBDocFieldsAsCommaDelimitedStringTest()
  57   {
  58     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  59     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  60     wantedFields.add(PDBDocField.PDB_ID);
  61     wantedFields.add(PDBDocField.GENUS);
  62     wantedFields.add(PDBDocField.GENE_NAME);
  63     wantedFields.add(PDBDocField.TITLE);
  64     assertEquals("molecule_type,pdb_id,genus,gene_name,title",
  65             PDBRestClient
  66                     .getPDBDocFieldsAsCommaDelimitedString(wantedFields));
  67   }
  68
  69   @Test
  70   public void parsePDBJsonExceptionStringTest()
  71   {
  72     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  73     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  74     wantedFields.add(PDBDocField.PDB_ID);
  75     wantedFields.add(PDBDocField.GENUS);
  76     wantedFields.add(PDBDocField.GENE_NAME);
  77     wantedFields.add(PDBDocField.TITLE);
  78
  79     PDBRestRequest request = new PDBRestRequest();
  80     request.setAllowEmptySeq(false);
  81     request.setResponseSize(100);
  82     request.setFieldToSearchBy("text:");
  83     request.setSearchTerm("abc");
  84     request.setWantedFields(wantedFields);
  85
  86     String jsonErrorResponse = "";
  87     try
  88     {
  89       jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
  90     } catch (IOException e)
  91     {
  92       e.printStackTrace();
  93     }
  94
  95     String parsedErrorResponse = PDBRestClient
  96             .parseJsonExceptionString(jsonErrorResponse);
  97     String expectedErrorMsg = "org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.{\"q\":\"text:abc OR text:go:abc AND molecule_sequence:['' TO *]\",\"fl\":\"pdb_id\",\"sort\":\"\",\"rows\":\"100\",\"wt\":\"json\"}";
  98
  99     assertEquals(expectedErrorMsg, parsedErrorResponse);
 100   }
 101
 102   @Test(expected = RuntimeException.class)
 103   public void testForExpectedRuntimeException()
 104   {
 105     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 106     wantedFields.add(PDBDocField.PDB_ID);
 107
 108     PDBRestRequest request = new PDBRestRequest();
 109     request.setFieldToSearchBy("text:");
 110     request.setSearchTerm("abc OR text:go:abc");
 111     request.setWantedFields(wantedFields);
 112     new PDBRestClient().executeRequest(request);
 113   }
 114
 115   @Test
 116   public void parsePDBJsonResponseTest()
 117   {
 118     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 119     wantedFields.add(PDBDocField.MOLECULE_TYPE);
 120     wantedFields.add(PDBDocField.PDB_ID);
 121     wantedFields.add(PDBDocField.GENUS);
 122     wantedFields.add(PDBDocField.GENE_NAME);
 123     wantedFields.add(PDBDocField.TITLE);
 124
 125     PDBRestRequest request = new PDBRestRequest();
 126     request.setAllowEmptySeq(false);
 127     request.setWantedFields(wantedFields);
 128
 129     String jsonString = "";
 130     try
 131     {
 132       jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
 133     } catch (IOException e)
 134     {
 135       e.printStackTrace();
 136     }
 137     PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
 138             jsonString, request);
 139     assertTrue(response.getSearchSummary() != null);
 140     assertTrue(response.getNumberOfItemsFound() == 931);
 141     assertTrue(response.getSearchSummary().size() == 14);
 142   }
 143
 144   @Test
 145   public void getPDBIdColumIndexTest()
 146   {
 147     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 148     wantedFields.add(PDBDocField.MOLECULE_TYPE);
 149     wantedFields.add(PDBDocField.GENUS);
 150     wantedFields.add(PDBDocField.GENE_NAME);
 151     wantedFields.add(PDBDocField.TITLE);
 152     wantedFields.add(PDBDocField.PDB_ID);
 153     assertEquals(5, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
 154     assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
 155   }
 156
 157   public String readJsonStringFromFile(String filePath) throws IOException
 158   {
 159     String fileContent;
 160     BufferedReader br = new BufferedReader(new FileReader(filePath));
 161     try
 162     {
 163       StringBuilder sb = new StringBuilder();
 164       String line = br.readLine();
 165
 166       while (line != null)
 167       {
 168         sb.append(line);
 169         sb.append(System.lineSeparator());
 170         line = br.readLine();
 171         }
 172       fileContent = sb.toString();
 173     } finally
 174     {
 175       br.close();
 176     }
 177     return fileContent;
 178   }
 179
 180
 181 }