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.Collections;
  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 final static String ENSEMBL_REST = "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://" + ENSEMBL_REST + "/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
 104   public enum EnsemblSeqType
 105   {
 106     GENOMIC("genomic"), CDS("cds"), TRANSCRIPT("cds"), PROTEIN("protein"), CDNA(
 107             "cdna");
 108
 109     private String type;
 110
 111     EnsemblSeqType(String t)
 112     {
 113       type = t;
 114     }
 115
 116     public String getType()
 117     {
 118       return type;
 119     }
 120   }
 121
 122   /**
 123    * reolve request type as an argument for sequence and features queries
 124    *
 125    * @param type
 126    */
 127   public List<NameValuePair> getObjectTypeArg(EnsemblSeqType type)
 128   {
 129     NameValuePair nameValue = new BasicNameValuePair("type", type.getType());
 130     return Collections.singletonList(nameValue);
 131   }
 132
 133   /**
 134    * return a reader to a Fasta response from the Ensembl sequence endpoint
 135    *
 136    * @param returnType
 137    * @param ids
 138    * @return
 139    * @throws IOException
 140    */
 141   public FileParse getSequenceReader(EnsemblSeqType returnType,
 142           List<String> ids) throws IOException
 143   {
 144
 145     // adapted From the rest.ensembl.org documentation for sequence_id
 146
 147     String urls = "http://" + ENSEMBL_REST + "/sequence/id";
 148     List<NameValuePair> vals = getObjectTypeArg(returnType);
 149     boolean f = true;
 150     for (NameValuePair nvp : vals)
 151     {
 152       if (f)
 153       {
 154         f = false;
 155         urls += "?";
 156       }
 157       else
 158       {
 159         urls += "&";
 160       }
 161       urls += nvp.getName() + "=" + nvp.getValue();
 162     }
 163
 164     URL url = new URL(urls);
 165
 166     URLConnection connection = url.openConnection();
 167     HttpURLConnection httpConnection = (HttpURLConnection) connection;
 168
 169     httpConnection.setRequestMethod("POST");
 170     httpConnection.setRequestProperty("Content-Type", "application/json");
 171     httpConnection.setRequestProperty("Accept", "text/x-fasta");
 172     byte[] thepostbody;
 173     {
 174       StringBuilder postBody = new StringBuilder();
 175       postBody.append("{\"ids\":[");
 176       boolean first = true;
 177       for (String id : ids)
 178       {
 179         if (first)
 180         {
 181           first = false;
 182         }
 183         else
 184         {
 185           postBody.append(",");
 186         }
 187         postBody.append("\"");
 188         postBody.append(id.trim());
 189         postBody.append("\"");
 190       }
 191       postBody.append("]}");
 192       thepostbody = postBody.toString().getBytes();
 193     }
 194     httpConnection.setRequestProperty("Content-Length",
 195             Integer.toString(thepostbody.length));
 196     httpConnection.setUseCaches(false);
 197     httpConnection.setDoInput(true);
 198     httpConnection.setDoOutput(true);
 199
 200     DataOutputStream wr = new DataOutputStream(
 201             httpConnection.getOutputStream());
 202     wr.write(thepostbody);
 203     wr.flush();
 204     wr.close();
 205
 206     InputStream response = connection.getInputStream();
 207     int responseCode = httpConnection.getResponseCode();
 208
 209     if (responseCode != 200)
 210     {
 211       throw new RuntimeException(
 212               "Response code was not 200. Detected response was "
 213                       + responseCode);
 214     }
 215
 216     BufferedReader reader = null;
 217     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
 218     FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
 219     return fp;
 220   }
 221
 222 }