src/jalview/ext/ensembl/SeqFetcher.java

   1 package jalview.ext.ensembl;
   2
   3 import jalview.io.FileParse;
   4
   5 import java.io.BufferedReader;
   6 import java.io.DataOutputStream;
   7 import java.io.IOException;
   8 import java.io.InputStream;
   9 import java.io.InputStreamReader;
  10 import java.net.HttpURLConnection;
  11 import java.net.URL;
  12 import java.net.URLConnection;
  13 import java.util.Arrays;
  14 import java.util.List;
  15
  16 import org.apache.http.NameValuePair;
  17 import org.apache.http.message.BasicNameValuePair;
  18
  19 public class SeqFetcher
  20 {
  21   private static String ensemblRest = "rest.ensembl.org";
  22
  23   private static boolean ensemblRestavailable = false;
  24
  25   private static long lastCheck = -1;
  26
  27   public boolean isEnsemblAvailable()
  28   {
  29     if (isTesting || !ensemblRestavailable
  30             || System.currentTimeMillis() - lastCheck > 10000)
  31     {
  32       checkEnsembl();
  33       lastCheck = System.currentTimeMillis();
  34     }
  35     return ensemblRestavailable;
  36   }
  37
  38   private boolean isTesting, testEnsemblStatus;
  39
  40   /**
  41    * @return the isTesting
  42    */
  43   public boolean isTesting()
  44   {
  45     return isTesting;
  46   }
  47
  48   /**
  49    * @param isTesting
  50    *          the isTesting to set
  51    */
  52   public void setTesting(boolean isTesting)
  53   {
  54     this.isTesting = isTesting;
  55   }
  56
  57   /**
  58    * @return the testEnsemblStatus
  59    */
  60   public boolean isTestEnsemblStatus()
  61   {
  62     return testEnsemblStatus;
  63   }
  64
  65   /**
  66    * @param testEnsemblStatus
  67    *          the testEnsemblStatus to set
  68    */
  69   public void setTestEnsemblStatus(boolean testEnsemblStatus)
  70   {
  71     this.testEnsemblStatus = testEnsemblStatus;
  72   }
  73
  74   private void checkEnsembl()
  75   {
  76     if (isTesting)
  77     {
  78       ensemblRestavailable = testEnsemblStatus;
  79       return;
  80     }
  81     try
  82     {
  83       URL ping = new URL("http://" + ensemblRest + "/info/ping");
  84       HttpURLConnection conn = (HttpURLConnection) (ping.openConnection());
  85       if (conn.getResponseCode() >= 200 && conn.getResponseCode() < 300)
  86       {
  87         ensemblRestavailable = true;
  88         return;
  89       }
  90     } catch (Error err)
  91     {
  92       err.printStackTrace();
  93     } catch (Exception exx)
  94     {
  95       exx.printStackTrace();
  96     }
  97     ensemblRestavailable = false;
  98   }
  99
 100   public SeqFetcher()
 101   {
 102
 103     // TODO Auto-generated constructor stub
 104   }
 105
 106   public enum EnsemblSeqType
 107   {
 108     GENOMIC, CDS, TRANSCRIPT, PROTEIN, CDNA;
 109   }
 110
 111   /**
 112    * reolve request type as an argument for sequence and features queries
 113    *
 114    * @param type
 115    */
 116   public List<NameValuePair> getObjectTypeArg(EnsemblSeqType type)
 117   {
 118     String arg;
 119     switch (type)
 120     {
 121     case CDS:
 122       arg = "cds";
 123       break;
 124     case TRANSCRIPT:
 125       arg = "cds";
 126       break;
 127     case CDNA:
 128       arg = "CDNA";
 129       break;
 130     case PROTEIN:
 131       arg = "protein";
 132       break;
 133     case GENOMIC:
 134     default:
 135       arg = "genomic";
 136     }
 137     return Arrays.asList(new NameValuePair[]
 138     { new BasicNameValuePair("type", arg) });
 139   }
 140
 141   /**
 142    * return a reader to a Fasta response from the Ensembl sequence endpoint
 143    *
 144    * @param returnType
 145    * @param ids
 146    * @return
 147    * @throws IOException
 148    */
 149   public FileParse getSequenceReader(EnsemblSeqType returnType,
 150           List<String> ids) throws IOException
 151   {
 152
 153     // adapted From the rest.ensembl.org documentation for sequence_id
 154
 155     String urls = "http://" + ensemblRest + "/sequence/id";
 156     List<NameValuePair> vals = getObjectTypeArg(returnType);
 157     boolean f = true;
 158     for (NameValuePair nvp : vals)
 159     {
 160       if (f)
 161       {
 162         f = false;
 163         urls += "?";
 164       }
 165       else
 166       {
 167         urls += "&";
 168       }
 169       urls += nvp.getName() + "=" + nvp.getValue();
 170     }
 171
 172     URL url = new URL(urls);
 173
 174     URLConnection connection = url.openConnection();
 175     HttpURLConnection httpConnection = (HttpURLConnection) connection;
 176
 177     httpConnection.setRequestMethod("POST");
 178     httpConnection.setRequestProperty("Content-Type", "application/json");
 179     httpConnection.setRequestProperty("Accept", "text/x-fasta");
 180     byte[] thepostbody;
 181     {
 182       StringBuilder postBody = new StringBuilder();
 183       postBody.append("{\"ids\":[");
 184       boolean first = true;
 185       for (String id : ids)
 186       {
 187         if (first)
 188         {
 189           first = false;
 190         }
 191         else
 192         {
 193           postBody.append(",");
 194         }
 195         postBody.append("\"");
 196         postBody.append(id.trim());
 197         postBody.append("\"");
 198       }
 199       postBody.append("]}");
 200       thepostbody = postBody.toString().getBytes();
 201     }
 202     httpConnection.setRequestProperty("Content-Length",
 203             Integer.toString(thepostbody.length));
 204     httpConnection.setUseCaches(false);
 205     httpConnection.setDoInput(true);
 206     httpConnection.setDoOutput(true);
 207
 208     DataOutputStream wr = new DataOutputStream(
 209             httpConnection.getOutputStream());
 210     wr.write(thepostbody);
 211     wr.flush();
 212     wr.close();
 213
 214     InputStream response = connection.getInputStream();
 215     int responseCode = httpConnection.getResponseCode();
 216
 217     if (responseCode != 200)
 218     {
 219       throw new RuntimeException(
 220               "Response code was not 200. Detected response was "
 221                       + responseCode);
 222     }
 223
 224     BufferedReader reader = null;
 225     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
 226     FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
 227     return fp;
 228   }
 229
 230 }