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();
  }
Exemplo n.º 8
0
  /**
   * @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();
  }