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
  65     String expectedResult = "molecule_type,pdb_id,genus,gene_name,title";
  66     String actualResult = PDBRestClient
  67             .getPDBDocFieldsAsCommaDelimitedString(wantedFields);
  68
  69     assertEquals("", expectedResult, actualResult);
  70   }
  71
  72   @Test
  73   public void parsePDBJsonExceptionStringTest()
  74   {
  75     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  76     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  77     wantedFields.add(PDBDocField.PDB_ID);
  78     wantedFields.add(PDBDocField.GENUS);
  79     wantedFields.add(PDBDocField.GENE_NAME);
  80     wantedFields.add(PDBDocField.TITLE);
  81
  82     PDBRestRequest request = new PDBRestRequest();
  83     request.setAllowEmptySeq(false);
  84     request.setResponseSize(100);
  85     request.setFieldToSearchBy("text:");
  86     request.setSearchTerm("abc");
  87     request.setWantedFields(wantedFields);
  88
  89     String jsonErrorResponse = "";
  90     try
  91     {
  92       jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
  93     } catch (IOException e)
  94     {
  95       e.printStackTrace();
  96     }
  97
  98     String parsedErrorResponse = PDBRestClient
  99             .parseJsonExceptionString(jsonErrorResponse);
 100
 101     String expectedErrorMsg = "\n============= PDB Rest Client RunTime error =============\n"
 102             + "Status: 400\n"
 103             + "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"
 104             + "query: text:abc OR text:go:abc AND molecule_sequence:['' TO *]\n"
 105             + "fl: pdb_id\n";
 106
 107     assertEquals(expectedErrorMsg, parsedErrorResponse);
 108   }
 109
 110   @Test(expected = RuntimeException.class)
 111   public void testForExpectedRuntimeException()
 112   {
 113     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 114     wantedFields.add(PDBDocField.PDB_ID);
 115
 116     PDBRestRequest request = new PDBRestRequest();
 117     request.setFieldToSearchBy("text:");
 118     request.setSearchTerm("abc OR text:go:abc");
 119     request.setWantedFields(wantedFields);
 120     new PDBRestClient().executeRequest(request);
 121   }
 122
 123   @Test
 124   public void parsePDBJsonResponseTest()
 125   {
 126     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 127     wantedFields.add(PDBDocField.MOLECULE_TYPE);
 128     wantedFields.add(PDBDocField.PDB_ID);
 129     wantedFields.add(PDBDocField.GENUS);
 130     wantedFields.add(PDBDocField.GENE_NAME);
 131     wantedFields.add(PDBDocField.TITLE);
 132
 133     PDBRestRequest request = new PDBRestRequest();
 134     request.setAllowEmptySeq(false);
 135     request.setWantedFields(wantedFields);
 136
 137     String jsonString = "";
 138     try
 139     {
 140       jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
 141     } catch (IOException e)
 142     {
 143       e.printStackTrace();
 144     }
 145     PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
 146             jsonString, request);
 147     assertTrue(response.getSearchSummary() != null);
 148     assertTrue(response.getNumberOfItemsFound() == 931);
 149     assertTrue(response.getSearchSummary().size() == 14);
 150   }
 151
 152   @Test
 153   public void getPDBIdColumIndexTest()
 154   {
 155     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
 156     wantedFields.add(PDBDocField.MOLECULE_TYPE);
 157     wantedFields.add(PDBDocField.GENUS);
 158     wantedFields.add(PDBDocField.GENE_NAME);
 159     wantedFields.add(PDBDocField.TITLE);
 160     wantedFields.add(PDBDocField.PDB_ID);
 161     assertEquals(5, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
 162     assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
 163   }
 164
 165   public String readJsonStringFromFile(String filePath) throws IOException
 166   {
 167     String fileContent;
 168     BufferedReader br = new BufferedReader(new FileReader(filePath));
 169     try
 170     {
 171       StringBuilder sb = new StringBuilder();
 172       String line = br.readLine();
 173
 174       while (line != null)
 175       {
 176         sb.append(line);
 177         sb.append(System.lineSeparator());
 178         line = br.readLine();
 179         }
 180       fileContent = sb.toString();
 181     } finally
 182     {
 183       br.close();
 184     }
 185     return fileContent;
 186   }
 187
 188
 189 }