public RCallServicesREngine(REngine rs, String envir) {
this.rs = rs;
try {
env = rs.parseAndEval(envir);
} catch (org.rosuda.REngine.REngineException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
} catch (REXPMismatchException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
try {
rs.parseAndEval(
"options(error = function() { assign(\"" + ERROR_VAR + "\", geterrmessage()})",
env,
true);
} catch (org.rosuda.REngine.REngineException e) {
throw new REngineException(e);
} catch (REXPMismatchException e) {
throw new REngineException(e);
}
}
@Override
protected void doPost(HttpServletRequest req, HttpServletResponse resp)
throws ServletException, IOException {
Connection conn = SQLConnectionFactory.getConnection();
ServletUtil util = new ServletUtil();
UserSession us = new UserSession();
long uid = -1;
try {
uid = us.getUserId(req, resp, conn);
} catch (Exception e) {
util.setResponse(resp, "[\"Error: Error loading session data.\"]");
try {
conn.close();
} catch (SQLException e1) {
e1.printStackTrace();
}
return;
}
String network = req.getParameter("network");
long fid = -1;
try {
fid = Long.parseLong(network);
Util u = new Util();
if (!u.dataexists(conn, "usersessions.Networks", uid, fid)) {
util.setResponse(resp, "[\"Error: Error loading network.\"]");
try {
conn.close();
} catch (SQLException e1) {
e1.printStackTrace();
}
return;
}
} catch (Exception e) {
util.setResponse(resp, "[\"Error: Error loading network.\"]");
try {
conn.close();
} catch (SQLException e1) {
e1.printStackTrace();
}
return;
}
Gson gson = new Gson();
String[] genelists = req.getParameterValues("genes[]");
String[] diseaselists = req.getParameterValues("diseases[]");
String[] regionlists = req.getParameterValues("regions[]");
String[] snplists = req.getParameterValues("snps[]");
// int ts = Integer.parseInt(traitsrc);
int ts = 2; // Just GWAS for now.
// boolean promoter = req.getParameter("promoter").equals("true");
SIIndexUtil siu = new SIIndexUtil();
Integer[] sids =
siu.getIndices(conn, uid, fid, ts, genelists, diseaselists, regionlists, snplists);
String fminsize = req.getParameter("minsize");
String fmaxsize = req.getParameter("maxsize");
int minsize = 1;
int maxsize = Integer.MAX_VALUE;
try {
minsize = Integer.parseInt(fminsize);
maxsize = Integer.parseInt(fmaxsize);
} catch (NumberFormatException e) {
}
AIEJson heatmap = null;
AnnotationInteractionEnrichment sph = new AnnotationInteractionEnrichment();
try {
heatmap = sph.generateHeatmap(conn, fid, sids, minsize, maxsize);
} catch (SQLException e1) {
e1.printStackTrace();
} catch (REngineException e) {
e.printStackTrace();
} catch (REXPMismatchException e) {
e.printStackTrace();
}
try {
conn.close();
} catch (SQLException e) {
e.printStackTrace();
}
resp.setContentType("application/json");
PrintWriter out = resp.getWriter();
out.print(gson.toJson(heatmap, AIEJson.class));
out.flush();
}