private String addNewInteraction(String fingerprint, BiologicalInteraction interaction)
     throws SQLException {
   String sql =
       String.format(
           "INSERT IGNORE INTO interaction (fingerprint) VALUES (%s)",
           SqlUtil.toSqlVarchar(fingerprint));
   if (1 != DBUtil.update(sql)) {
     System.out.println("SQL update failed? " + sql);
   }
   String interaction_id = DBUtil.querySingle("SELECT LAST_INSERT_ID()");
   Iterator<BiologicalEntity> iter = interaction.getEntityIterator();
   StringBuffer sb =
       new StringBuffer(
           "INSERT IGNORE INTO interaction_pool (interaction_id, gene_id, entity_src_table, role) VALUES ");
   while (iter.hasNext()) {
     BiologicalEntity entity = iter.next();
     sb.append("(")
         .append(interaction_id)
         .append(", ")
         .append(SqlUtil.toSqlVarchar(entity.getId()))
         .append(", '")
         .append(srcTableLookup.get(entity.getId_src()))
         .append("', '")
         .append(entity.getRole())
         .append("')");
     if (iter.hasNext()) sb.append(", ");
   }
   if (DBUtil.update(sb.toString()) != interaction.getEnvolvedEntityCount()) {
     System.out.println("SQL update failed? " + sb);
   }
   return interaction_id;
 }
Ejemplo n.º 2
0
 public void login(HttpServletRequest request, HttpServletResponse response) throws IOException {
   String username = request.getParameter("username");
   String password = request.getParameter("password");
   if (username == null) {
     response.sendRedirect("index.html");
     return;
   }
   String sql =
       "SELECT id FROM curator WHERE name="
           + SqlUtil.toSqlVarchar(username)
           + " AND passwd=PASSWORD("
           + SqlUtil.toSqlVarchar(password)
           + ")";
   String id = DBUtil.querySingle(sql);
   if (id == null) {
     response.sendRedirect("index.html");
     return;
   }
   Cookie cookie = new Cookie("username", username);
   if (request.getParameter("remember_me") != null
       && request.getParameter("remember_me").equals("on")) {
     cookie.setMaxAge(86400 * 365);
   } else {
     cookie.setMaxAge(-1);
   }
   response.addCookie(cookie);
   cookie = new Cookie("userid", id);
   if (request.getParameter("remember_me") != null
       && request.getParameter("remember_me").equals("on")) {
     cookie.setMaxAge(86400 * 365);
   } else {
     cookie.setMaxAge(-1);
   }
   response.addCookie(cookie);
 }
  public void flush() throws SQLException {
    InteractionFingerprinter fingerprinter = new InteractionFingerprinter();
    for (BiologicalInteraction interaction : interactions) {
      String fingerprint = fingerprinter.getFingerprint(interaction);
      String sql =
          String.format(
              "SELECT interaction_id FROM interaction WHERE fingerprint=%s",
              SqlUtil.toSqlVarchar(fingerprint));
      String id = DBUtil.querySingle(sql);

      if (id == null) {
        id = addNewInteraction(fingerprint, interaction);
      }

      interaction.setInteractionId(Integer.valueOf(id));
    }
    System.out.println("Evidences count: " + evidences.size());
    for (Evidence evidence : evidences) {
      String sql =
          "INSERT INTO evidence SET "
              + "interaction_id="
              + evidence.getInteraction().getInteractionId()
              + ", "
              + "negative=0, "
              + "directed="
              + (evidence.getInteraction().isDirected() ? 1 : 0)
              + ", "
              + "interaction_type='"
              + evidence.getInteraction().getInteractionType()
              + "', "
              + "source='"
              + evidence.getDataSource()
              + "', "
              + "macro_id='"
              + evidence.getMacroId()
              + "', "
              + "micro_id='"
              + evidence.getMicroId()
              + "', "
              + "confidence=100, "
              + "evidence_text="
              + SqlUtil.toSqlVarchar(evidence.getEvidenceText())
              + ", "
              + "curator=0";
      DBUtil.update(sql);
    }
  }
Ejemplo n.º 4
0
 private String guessProtein(String name) {
   String sql = "SELECT pname FROM proteinGene WHERE gene='" + name + "'";
   String s = DBUtil.querySingle(sql);
   if (s != null) {
     return s;
   }
   return null;
 }
Ejemplo n.º 5
0
 private String guessOther(String key) {
   String sql = "SELECT gene_id FROM other_entity WHERE name='" + key + "'";
   String s = DBUtil.querySingle(sql);
   if (s != null) {
     return s;
   }
   return null;
 }
Ejemplo n.º 6
0
 private BiologicalEntity guessEntity(String key) {
   String sql;
   if (key.endsWith("_HUMAN")) {
     sql = "SELECT * FROM proteinGene WHERE pname='" + key + "'";
     HashMap<String, String> line = DBUtil.fillFirstRow(sql);
     if (line != null) {
       BiologicalEntity be = new BiologicalEntity();
       be.setId(line.get("geneid"));
       be.setId_src(BiologicalEntity.ENTREZ);
       be.setType(BiologicalEntity.GENE);
       be.setName(key); // line.get("pname"));
       return be;
     }
   }
   sql = "SELECT geneid FROM gene WHERE symbol='" + key + "' AND taxid=9606";
   String s = DBUtil.querySingle(sql);
   if (s != null) {
     BiologicalEntity be = new BiologicalEntity();
     be.setId(s);
     be.setName(key);
     be.setId_src(BiologicalEntity.ENTREZ);
     be.setType(BiologicalEntity.GENE);
     return be;
   }
   sql =
       "SELECT geneid FROM geneAlias, gene WHERE gene.taxid=9606 AND geneAlias.alias='"
           + key
           + "' AND geneAlias.id_list=geneid";
   s = DBUtil.querySingle(sql);
   if (s != null) {
     BiologicalEntity be = new BiologicalEntity();
     be.setId(s);
     be.setName(key);
     be.setId_src(BiologicalEntity.ENTREZ);
     be.setType(BiologicalEntity.GENE);
     return be;
   }
   System.err.println("Cannot find an entry for " + key);
   return null;
 }