public String getStudyHost(String studyOid) throws Exception {
String ocUrl = CoreResources.getField("sysURL.base") + "rest2/openrosa/" + studyOid;
String pManageUrl = CoreResources.getField("portalURL");
String pManageUrlFull =
pManageUrl + "/app/rest/oc/authorizations?studyoid=" + studyOid + "&instanceurl=" + ocUrl;
CommonsClientHttpRequestFactory requestFactory = new CommonsClientHttpRequestFactory();
requestFactory.setReadTimeout(PARTICIPATE_READ_TIMEOUT);
RestTemplate rest = new RestTemplate(requestFactory);
try {
Authorization[] response = rest.getForObject(pManageUrlFull, Authorization[].class);
if (response.length > 0
&& response[0].getStudy() != null
&& response[0].getStudy().getHost() != null
&& !response[0].getStudy().getHost().equals("")) {
URL url = new URL(pManageUrl);
String port = "";
if (url.getPort() > 0) port = ":" + String.valueOf(url.getPort());
return url.getProtocol()
+ "://"
+ response[0].getStudy().getHost()
+ "."
+ url.getHost()
+ port
+ "/#/login";
}
} catch (Exception e) {
logger.error(e.getMessage());
logger.error(ExceptionUtils.getStackTrace(e));
}
return "";
}
public String registerStudy(String studyOid, String hostName) {
String ocUrl = CoreResources.getField("sysURL.base") + "rest2/openrosa/" + studyOid;
String pManageUrl =
CoreResources.getField("portalURL")
+ "/app/rest/oc/authorizations?studyoid="
+ studyOid
+ "&instanceurl="
+ ocUrl;
Authorization authRequest = new Authorization();
Study authStudy = new Study();
authStudy.setStudyOid(studyOid);
authStudy.setInstanceUrl(ocUrl);
authStudy.setHost(hostName);
authRequest.setStudy(authStudy);
CommonsClientHttpRequestFactory requestFactory = new CommonsClientHttpRequestFactory();
requestFactory.setReadTimeout(PARTICIPATE_READ_TIMEOUT);
RestTemplate rest = new RestTemplate(requestFactory);
try {
Authorization response = rest.postForObject(pManageUrl, authRequest, Authorization.class);
if (response != null && response.getAuthorizationStatus() != null)
return response.getAuthorizationStatus().getStatus();
} catch (Exception e) {
logger.error(e.getMessage());
logger.error(ExceptionUtils.getStackTrace(e));
}
return "";
}
public ExtractBean generateExtractBean(
DatasetBean dsetBean, StudyBean currentStudy, StudyBean parentStudy) {
ExtractBean eb = new ExtractBean(ds);
eb.setDataset(dsetBean);
eb.setShowUniqueId(CoreResources.getField("show_unique_id"));
eb.setStudy(currentStudy);
eb.setParentStudy(parentStudy);
eb.setDateCreated(new java.util.Date());
return eb;
}
private String loadRegistrationStatus(String studyOid) {
String ocUrl = CoreResources.getField("sysURL.base") + "rest2/openrosa/" + studyOid;
String pManageUrl =
CoreResources.getField("portalURL")
+ "/app/rest/oc/authorizations?studyoid="
+ studyOid
+ "&instanceurl="
+ ocUrl;
CommonsClientHttpRequestFactory requestFactory = new CommonsClientHttpRequestFactory();
requestFactory.setReadTimeout(PARTICIPATE_READ_TIMEOUT);
RestTemplate rest = new RestTemplate(requestFactory);
try {
Authorization[] response = rest.getForObject(pManageUrl, Authorization[].class);
if (response.length > 0 && response[0].getAuthorizationStatus() != null)
return response[0].getAuthorizationStatus().getStatus();
} catch (Exception e) {
logger.error(e.getMessage());
logger.debug(ExceptionUtils.getStackTrace(e));
}
return "";
}
public String getHostNameAvailability(String hostName) {
String pManageUrl =
CoreResources.getField("portalURL") + "/app/permit/studys/name?hostName=" + hostName;
CommonsClientHttpRequestFactory requestFactory = new CommonsClientHttpRequestFactory();
requestFactory.setReadTimeout(PARTICIPATE_READ_TIMEOUT);
RestTemplate rest = new RestTemplate(requestFactory);
String response = null;
try {
if (!validHostNameCheck(hostName)) return INVALID;
response = rest.getForObject(pManageUrl, String.class);
if (response.equals("UNAVAILABLE")) return UNAVAILABLE;
else if (response.equals("INVALID")) return INVALID;
else if (response.equals("AVAILABLE")) return AVAILABLE;
} catch (Exception e) {
logger.error(e.getMessage());
logger.error(ExceptionUtils.getStackTrace(e));
}
return UNKNOWN;
}
public boolean validHostNameCheck(String hostName) {
String pManageBaseUrl = CoreResources.getField("portalURL");
if (hostName.contains(".")) return false;
try {
URL baseUrl = new URL(pManageBaseUrl);
String port = "";
if (baseUrl.getPort() > 0) port = ":" + String.valueOf(baseUrl.getPort());
// Check that hostname makes a valid URL
URL customerUrl =
new URL(baseUrl.getProtocol() + "://" + hostName + "." + baseUrl.getHost() + port);
// Check that hostname only contains alphanumeric characters and/or hyphens
if (hostName.matches("^[A-Za-z0-9-]+$")) return true;
} catch (MalformedURLException mue) {
logger.error("Error validating customer selected Participate subdomain.");
logger.error(mue.getMessage());
logger.error(ExceptionUtils.getStackTrace(mue));
}
return false;
}
public int createFile(
String zipName,
ArrayList names,
String dir,
ArrayList contents,
DatasetBean datasetBean,
long time,
ExportFormatBean efb,
boolean saveToDB) {
ArchivedDatasetFileBean fbFinal = new ArchivedDatasetFileBean();
// >> tbh #4915
zipName = zipName.replaceAll(" ", "_");
fbFinal.setId(0);
try {
File complete = new File(dir);
if (!complete.isDirectory()) {
complete.mkdirs();
}
int totalSize = 0;
ZipOutputStream z =
new ZipOutputStream(new FileOutputStream(new File(complete, zipName + ".zip")));
FileInputStream is = null;
for (int i = 0; i < names.size(); i++) {
String name = (String) names.get(i);
// >> tbh #4915
name = name.replaceAll(" ", "_");
String content = (String) contents.get(i);
File newFile = new File(complete, name);
// totalSize = totalSize + (int)newFile.length();
newFile.setLastModified(System.currentTimeMillis());
BufferedWriter w = new BufferedWriter(new FileWriter(newFile));
w.write(content);
w.close();
logger.info("finished writing the text file...");
// now, we write the file to the zip file
is = new FileInputStream(newFile);
logger.info("created zip output stream...");
z.putNextEntry(new java.util.zip.ZipEntry(name));
int bytesRead;
byte[] buff = new byte[512];
while ((bytesRead = is.read(buff)) != -1) {
z.write(buff, 0, bytesRead);
totalSize += 512;
}
z.closeEntry();
// A. Hamid. 4910
is.close();
if (CoreResources.getField("dataset_file_delete").equalsIgnoreCase("true")
|| CoreResources.getField("dataset_file_delete").equals("")) {
newFile.delete();
}
}
logger.info("writing buffer...");
// }
z.flush();
z.finish();
z.close();
if (is != null) {
try {
is.close();
} catch (java.io.IOException ie) {
ie.printStackTrace();
}
}
logger.info("finished zipping up file...");
// set up the zip to go into the database
if (saveToDB) {
ArchivedDatasetFileBean fb = new ArchivedDatasetFileBean();
fb.setName(zipName + ".zip");
fb.setFileReference(dir + zipName + ".zip");
// current location of the file on the system
fb.setFileSize(totalSize);
// set the above to compressed size?
fb.setRunTime((int) time);
// need to set this in milliseconds, get it passed from above
// methods?
fb.setDatasetId(datasetBean.getId());
fb.setExportFormatBean(efb);
fb.setExportFormatId(efb.getId());
fb.setOwner(userBean);
fb.setOwnerId(userBean.getId());
fb.setDateCreated(new Date(System.currentTimeMillis()));
boolean write = true;
ArchivedDatasetFileDAO asdfDAO = new ArchivedDatasetFileDAO(ds);
if (write) {
fbFinal = (ArchivedDatasetFileBean) asdfDAO.create(fb);
logger.info("Created ADSFile!: " + fbFinal.getId() + " for " + zipName + ".zip");
} else {
logger.info("duplicate found: " + fb.getName());
}
}
// created in database!
} catch (Exception e) {
logger.warn(e.getMessage());
System.out.println("-- exception at create file: " + e.getMessage());
e.printStackTrace();
}
return fbFinal.getId();
}
/**
* @api {post} /pages/api/v1/editform/:studyOid/submission Submit form data
* @apiName doSubmission
* @apiPermission admin
* @apiVersion 1.0.0
* @apiParam {String} studyOid Study Oid.
* @apiParam {String} ecid Key that will be used to look up subject context information while
* processing submission.
* @apiGroup Form
* @apiDescription Submits the data from a completed form.
*/
@POST
@Path("/{studyOID}/submission")
@Produces(MediaType.APPLICATION_XML)
public Response doSubmission(
@Context HttpServletRequest request,
@Context HttpServletResponse response,
@Context ServletContext servletContext,
@PathParam("studyOID") String studyOID,
@QueryParam(FORM_CONTEXT) String context) {
String output = null;
Response.ResponseBuilder builder = Response.noContent();
String studySubjectOid = null;
Integer studyEventDefnId = null;
Integer studyEventOrdinal = null;
String crfVersionOID = null;
CRFVersionDAO crfvdao = new CRFVersionDAO(dataSource);
try {
if (ServletFileUpload.isMultipartContent(request)) {
LOGGER.warn("WARNING: This prototype doesn't support multipart content.");
}
if (!mayProceedSubmission(studyOID))
builder.status(javax.ws.rs.core.Response.Status.NOT_ACCEPTABLE).build();
PFormCache cache = PFormCache.getInstance(servletContext);
HashMap<String, String> userContext = cache.getSubjectContext(context);
StudySubjectDAO ssdao = new StudySubjectDAO<String, ArrayList>(dataSource);
StudySubjectBean ssBean = getSSBean(userContext);
if (!mayProceedSubmission(studyOID, ssBean)) return null;
studyEventDefnId = Integer.valueOf(userContext.get("studyEventDefinitionID"));
studyEventOrdinal = Integer.valueOf(userContext.get("studyEventOrdinal"));
crfVersionOID = userContext.get("crfVersionOID");
StringWriter writer = new StringWriter();
String body = IOUtils.toString(request.getInputStream(), "UTF-8");
CRFVersionBean crfVersion = crfvdao.findByOid(crfVersionOID);
if (crfVersion.getXform() != null && !crfVersion.getXform().equals("")) {
body = body.substring(body.indexOf("<" + crfVersion.getXformName()));
int length = body.indexOf(" ");
body =
body.replace(
body.substring(body.lastIndexOf("<meta>"), body.lastIndexOf("</meta>") + 7), "");
body = body.substring(0, body.lastIndexOf("</" + crfVersion.getXformName()) + length + 2);
body = "<instance>" + body + "</instance>";
} else {
body = body.substring(body.indexOf("<F_"));
int length = body.indexOf(" ");
body =
body.replace(body.substring(body.indexOf("<meta>"), body.indexOf("</meta>") + 7), "");
body = body.substring(0, body.indexOf("</F_") + length + 2);
body = "<instance>" + body + "</instance>";
}
Errors errors =
getPformSubmissionService()
.saveProcess(
body,
ssBean.getOid(),
studyEventDefnId,
studyEventOrdinal,
crfvdao.findByOid(crfVersionOID));
// Set response headers
Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("GMT"));
Date currentDate = new Date();
cal.setTime(currentDate);
SimpleDateFormat format = new SimpleDateFormat("E, dd MMM yyyy HH:mm:ss zz");
format.setCalendar(cal);
builder.header("Date", format.format(currentDate));
builder.header("X-OpenRosa-Version", "1.0");
builder.type("text/xml; charset=utf-8");
if (!errors.hasErrors()) {
builder.entity(
"<OpenRosaResponse xmlns=\"http://openrosa.org/http/response\">"
+ "<message>success</message>"
+ "</OpenRosaResponse>");
LOGGER.debug("Successful OpenRosa submission");
} else {
LOGGER.error("Failed OpenRosa submission");
response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
response.flushBuffer();
}
} catch (Exception e) {
LOGGER.error(e.getMessage());
LOGGER.error(ExceptionUtils.getStackTrace(e));
return builder.status(javax.ws.rs.core.Response.Status.INTERNAL_SERVER_ERROR).build();
}
try {
// Notify Participate of successful form submission.
String pManageUrl = CoreResources.getField("portalURL") + "/app/rest/oc/submission";
Submission submission = new Submission();
Study pManageStudy = new Study();
pManageStudy.setInstanceUrl(
CoreResources.getField("sysURL.base") + "rest2/openrosa/" + studyOID);
pManageStudy.setStudyOid(studyOID);
submission.setStudy(pManageStudy);
submission.setStudy_event_def_id(studyEventDefnId);
submission.setStudy_event_def_ordinal(studyEventOrdinal);
submission.setCrf_version_id(crfvdao.findByOid(crfVersionOID).getId());
RestTemplate rest = new RestTemplate();
String result = rest.postForObject(pManageUrl, submission, String.class);
LOGGER.debug("Notified Participate of CRF submission with a result of: " + result);
} catch (Exception e) {
LOGGER.error("Unable to notify Participate of successful CRF submission.");
LOGGER.error(e.getMessage());
LOGGER.error(ExceptionUtils.getStackTrace(e));
}
return builder.status(javax.ws.rs.core.Response.Status.CREATED).build();
}