<%@ page language="java" contentType="text/html; charset=UTF-8" pageEncoding="UTF-8"%>
<%@ page trimDirectiveWhitespaces="true" %>
<%@ page import="java.io.IOException" %>
<%@ page import="java.io.InputStream" %>
<%@ page import="java.io.BufferedReader" %>
<%@ page import="java.io.File" %>
<%@ page import="java.nio.charset.Charset" %>
<%@ page import="java.io.InputStreamReader" %>
<%@ page import="org.apache.log4j.Logger" %>
<%@ page import="javax.servlet.http.Cookie" %>
<%!
public static void dumpCallInfo(HttpServletRequest request, Logger logger) {
logger.info("CallInfo...");
logger.info("request.getContentType: " + request.getContentType());
logger.info("Headers: ");
for (Object o: java.util.Collections.list(request.getHeaderNames())) {
logger.info(o + "=" + request.getHeader(o.toString()));
}
logger.info("Attributes: ");
for (Object o: java.util.Collections.list(request.getAttributeNames())) {
logger.info(o + "=" + request.getAttribute(o.toString()));
}
logger.info("Parameters: ");
for (Object o: java.util.Collections.list(request.getParameterNames())) {
for (String v: request.getParameterValues(o.toString())) {
logger.info(o + "=" + v);
}
}
}
%>
<%
Logger logger = Logger.getLogger("collation_editor/vmrcre_collation");
String requestURI = request.getRequestURI();
// strip the webapp name off the URI
requestURI = requestURI.substring(requestURI.indexOf("/", 2));
File collate_cli = new File(getServletContext().getRealPath(requestURI));
collate_cli = new File(collate_cli.getParent(), "collate_cli.py");
boolean reEncode = false;
//dumpCallInfo(request, logger);
String options = request.getParameter("options");
if (options != null) {
response.setContentType("application/json");
// collation
if (options.indexOf("\"data_input\"") > -1) {
}
// apparatus export
else {
response.setContentType("text/plain");
response.setHeader("Content-Disposition", "attachment; filename=\"negative-apparatus.xml\"");
response.setHeader("Set-Cookie", "fileDownload=true; path=/");
reEncode = true;
}
String args[] = new String[] {
"python3",
collate_cli.getAbsolutePath()
};
StringBuffer resultBuf = new StringBuffer();
StringBuffer errorBuf = new StringBuffer();
logger.info("About to call Cat's stuff.");
logger.debug("********************************************************* Input: " + options);
runCommand(args, resultBuf, errorBuf, options, logger);
logger.info("Finished calling Cat's stuff.");
if (reEncode) resultBuf = new StringBuffer(new String(resultBuf.toString().getBytes("iso8859-1"), "UTF-8"));
//logger.info("Result: " + resultBuf);
logger.debug("********************************************************* Result: " + resultBuf + "***** END RESULT *****");
if (errorBuf.length() > 0) logger.error("*********************************************** Collation Error: " + errorBuf);
%>
<%= resultBuf %>
<%
return;
}
%>
vmrcre_collation
collation from the collation_editor to collatex
Parameters
| options | data from collation_editor |
<%!
public static Thread startSlurpStreamThreaded(final InputStream is, final StringBuffer outBuf) {
Thread t = new Thread() {
InputStream myIS = is;
StringBuffer myOutBuf = outBuf;
public void run() {
try {
InputStreamReader isr = new InputStreamReader(myIS);
BufferedReader br = new BufferedReader(isr);
String line=null;
while ( (line = br.readLine()) != null)
myOutBuf.append(line + "\n");
}
catch (IOException ioe) {
ioe.printStackTrace();
}
}
};
t.start();
return t;
}
public static int runCommand(String command[], StringBuffer result, StringBuffer error, String toStdin, Logger logger) {
int retVal = -1;
try {
File cwd = new File(".");
String cmd = "";
for (String s: command) {
cmd += " [" + s + "]";
}
logger.debug("executing from cwd ("+cwd.getAbsolutePath()+"):" + cmd);
java.lang.Process p = Runtime.getRuntime().exec(command, new String[0], cwd);
p.getOutputStream().write(toStdin.getBytes(Charset.forName("UTF-8")));
Thread o = startSlurpStreamThreaded(p.getInputStream(), result);
Thread e = startSlurpStreamThreaded(p.getErrorStream(), error);
p.getOutputStream().close();
retVal = p.waitFor();
o.join();
e.join();
logger.debug("returned from executing executing....");
if (error.length() > 0) {
logger.warn("ERROR!!!!!!!!!!!!!!!!!!!!!!: " + error.toString());
}
}
catch (Exception e) {
logger.error("ERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!: " + e + "; retVal: " + retVal + "; stdout: " + result);
e.printStackTrace();
}
logger.debug("returned: " + retVal + "; stdout: " + result);
return retVal;
}
%>