/**
* this is the primary method that sends a query to the CIPRes REST service. It expects to receive
* an XML file, which it returns in Document if the root tag matc hes xmlRootTag
*/
public Document cipresQuery(HttpClient httpclient, String URL, String xmlRootTag) {
if (StringUtil.blank(URL)) return null;
try {
HttpGet httpget = new HttpGet(URL);
httpget.addHeader("cipres-appkey", CIPRESkey);
try {
HttpResponse response = httpclient.execute(httpget);
HttpEntity responseEntity = response.getEntity();
InputStream instream = responseEntity.getContent();
BufferedReader br = new BufferedReader(new InputStreamReader(instream));
String line = "";
StringBuffer sb = new StringBuffer();
while ((line = br.readLine()) != null) {
sb.append(line + StringUtil.lineEnding());
}
Document cipresResponseDoc = loadXMLFile(xmlRootTag, sb.toString());
if (cipresResponseDoc != null && verbose) {
ownerModule.logln(sb.toString());
}
if (cipresResponseDoc == null) {
Document errorDoc = loadXMLFile(sb.toString());
if (errorDoc != null) reportError(errorDoc, "Error in communicating with CIPRes", true);
}
EntityUtils.consume(response.getEntity());
return cipresResponseDoc;
} catch (IOException e) {
Debugg.printStackTrace(e);
} catch (Exception e) {
Debugg.printStackTrace(e);
}
} catch (Exception e) {
Debugg.printStackTrace(e);
}
return null;
}
/*.................................................................................................................*/
public void deleteJob(HttpClient httpclient, String URL) {
HttpDelete httpdelete = new HttpDelete(URL);
httpdelete.addHeader("cipres-appkey", CIPRESkey);
try {
HttpResponse response = httpclient.execute(httpdelete);
} catch (IOException e) {
Debugg.printStackTrace(e);
}
}
/*.................................................................................................................*/
public void cipresDownload(HttpClient httpclient, String URL, String filePath) {
HttpGet httpget = new HttpGet(URL);
httpget.addHeader("cipres-appkey", CIPRESkey);
try {
HttpResponse response = httpclient.execute(httpget);
HttpEntity responseEntity = response.getEntity();
BufferedInputStream bis = new BufferedInputStream(responseEntity.getContent());
BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(new File(filePath)));
int inByte;
while ((inByte = bis.read()) != -1) bos.write(inByte);
bis.close();
bos.close();
EntityUtils.consume(response.getEntity());
} catch (IOException e) {
Debugg.printStackTrace(e);
}
}
/** The core method that initiates a job on CIPRes. */
public boolean postJob(
HttpClient httpclient, MultipartEntityBuilder builder, MesquiteString jobURL) {
if (builder == null) return false;
String URL = baseURL + "/job/" + username;
HttpPost httppost = new HttpPost(URL);
httppost.addHeader("cipres-appkey", CIPRESkey);
// some of this from
// http://stackoverflow.com/questions/18964288/upload-a-file-through-an-http-form-via-multipartentitybuilder-with-a-progress
HttpEntity cipresEntity = builder.build();
httppost.setEntity(cipresEntity);
try {
HttpResponse response = httpclient.execute(httppost);
HttpEntity responseEntity = response.getEntity();
InputStream instream = responseEntity.getContent();
BufferedReader br = new BufferedReader(new InputStreamReader(instream));
StringBuffer sb = new StringBuffer();
String line = "";
while ((line = br.readLine()) != null) {
sb.append(line + StringUtil.lineEnding());
}
Document cipresResponseDoc = loadXMLFile("jobstatus", sb.toString()); // let's see how it went
boolean success = false;
if (cipresResponseDoc != null) {
processJobSubmissionResponse(cipresResponseDoc, jobURL);
if (verbose) ownerModule.logln(sb.toString());
if (jobURL != null) success = StringUtil.notEmpty(jobURL.getValue());
else success = true;
} else {
cipresResponseDoc = loadXMLFile(sb.toString());
reportError(cipresResponseDoc, "Error with CIPRes run", false);
}
EntityUtils.consume(response.getEntity());
return success;
} catch (IOException e) {
Debugg.printStackTrace(e);
}
return false;
}