Java tutorial
/* * OpenClinica is distributed under the * GNU Lesser General Public License (GNU LGPL). * For details see: http://www.openclinica.org/license * copyright 2003-2005 Akaza Research */ package org.akaza.openclinica.control.submit; import org.akaza.openclinica.bean.core.DataEntryStage; import org.akaza.openclinica.bean.core.Role; import org.akaza.openclinica.bean.core.Status; import org.akaza.openclinica.bean.rule.FileUploadHelper; import org.akaza.openclinica.bean.rule.XmlSchemaValidationHelper; import org.akaza.openclinica.bean.submit.CRFVersionBean; import org.akaza.openclinica.bean.submit.DisplayItemBeanWrapper; import org.akaza.openclinica.bean.submit.EventCRFBean; import org.akaza.openclinica.bean.submit.crfdata.ODMContainer; import org.akaza.openclinica.bean.submit.crfdata.SummaryStatsBean; import org.akaza.openclinica.control.SpringServletAccess; import org.akaza.openclinica.control.core.SecureController; import org.akaza.openclinica.control.form.FormProcessor; import org.akaza.openclinica.control.form.Validator; import org.akaza.openclinica.core.form.StringUtil; import org.akaza.openclinica.dao.core.CoreResources; import org.akaza.openclinica.exception.OpenClinicaException; import org.akaza.openclinica.i18n.core.LocaleResolver; import org.akaza.openclinica.view.Page; import org.akaza.openclinica.web.InsufficientPermissionException; import org.akaza.openclinica.web.SQLInitServlet; import org.akaza.openclinica.web.crfdata.ImportCRFDataService; import org.apache.commons.lang.exception.ExceptionUtils; import org.exolab.castor.mapping.Mapping; import org.exolab.castor.xml.Unmarshaller; import java.io.File; import java.io.FileInputStream; import java.io.InputStreamReader; import java.text.MessageFormat; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Locale; /** * Create a new CRF verison by uploading excel file. Makes use of several other classes to validate and provide accurate * validation. More specifically, uses XmlSchemaValidationHelper, ImportCRFDataService, ODMContainer, and others to * import all the XML in the ODM 1.3 standard. * * @author Krikor Krumlian, Tom Hickerson updated Apr-May 2008 */ public class ImportCRFDataServlet extends SecureController { Locale locale; private ImportCRFDataService dataService; XmlSchemaValidationHelper schemaValidator = new XmlSchemaValidationHelper(); FileUploadHelper uploadHelper = new FileUploadHelper(); // < ResourceBundleresword,resexception,respage; /** * */ @Override public void mayProceed() throws InsufficientPermissionException { checkStudyLocked(Page.MENU_SERVLET, respage.getString("current_study_locked")); checkStudyFrozen(Page.MENU_SERVLET, respage.getString("current_study_frozen")); locale = LocaleResolver.getLocale(request); if (ub.isSysAdmin()) { return; } Role r = currentRole.getRole(); if (r.equals(Role.STUDYDIRECTOR) || r.equals(Role.COORDINATOR) || r.equals(Role.INVESTIGATOR) || r.equals(Role.RESEARCHASSISTANT) || r.equals(Role.RESEARCHASSISTANT2)) { return; } addPageMessage(respage.getString("no_have_correct_privilege_current_study") + respage.getString("change_study_contact_sysadmin")); throw new InsufficientPermissionException(Page.MENU_SERVLET, resexception.getString("may_not_submit_data"), "1"); } @Override public void processRequest() throws Exception { resetPanel(); panel.setStudyInfoShown(false); panel.setOrderedData(true); FormProcessor fp = new FormProcessor(request); // checks which module the requests are from String module = fp.getString(MODULE); // keep the module in the session session.setAttribute(MODULE, module); String action = request.getParameter("action"); CRFVersionBean version = (CRFVersionBean) session.getAttribute("version"); File xsdFile = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-3-0.xsd"); File xsdFile2 = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-2-1.xsd"); if (StringUtil.isBlank(action)) { logger.info("action is blank"); request.setAttribute("version", version); forwardPage(Page.IMPORT_CRF_DATA); } if ("confirm".equalsIgnoreCase(action)) { String dir = SQLInitServlet.getField("filePath"); if (!new File(dir).exists()) { logger.info("The filePath in datainfo.properties is invalid " + dir); addPageMessage(respage.getString("filepath_you_defined_not_seem_valid")); forwardPage(Page.IMPORT_CRF_DATA); } // All the uploaded files will be saved in filePath/crf/original/ String theDir = dir + "crf" + File.separator + "original" + File.separator; if (!new File(theDir).isDirectory()) { new File(theDir).mkdirs(); logger.info("Made the directory " + theDir); } // MultipartRequest multi = new MultipartRequest(request, theDir, 50 * 1024 * 1024); File f = null; try { f = uploadFile(theDir, version); } catch (Exception e) { logger.warn("*** Found exception during file upload***"); e.printStackTrace(); } if (f == null) { forwardPage(Page.IMPORT_CRF_DATA); } // TODO // validation steps // 1. valid xml - validated by file uploader below // LocalConfiguration config = LocalConfiguration.getInstance(); // config.getProperties().setProperty( // "org.exolab.castor.parser.namespaces", // "true"); // config // .getProperties() // .setProperty("org.exolab.castor.sax.features", // "http://xml.org/sax/features/validation, // http://apache.org/xml/features/validation/schema, // http://apache.org/xml/features/validation/schema-full-checking"); // // above sets to validate against namespace Mapping myMap = new Mapping(); // @pgawade 18-April-2011 Fix for issue 8394 String ODM_MAPPING_DIRPath = CoreResources.ODM_MAPPING_DIR; myMap.loadMapping(ODM_MAPPING_DIRPath + File.separator + "cd_odm_mapping.xml"); Unmarshaller um1 = new Unmarshaller(myMap); // um1.addNamespaceToPackageMapping("http://www.openclinica.org/ns/odm_ext_v130/v3.1", "OpenClinica"); // um1.addNamespaceToPackageMapping("http://www.cdisc.org/ns/odm/v1.3" // , // "ODMContainer"); boolean fail = false; ODMContainer odmContainer = new ODMContainer(); session.removeAttribute("odmContainer"); try { // schemaValidator.validateAgainstSchema(f, xsdFile); // utf-8 compliance, tbh 06/2009 InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8"); odmContainer = (ODMContainer) um1.unmarshal(isr); logger.debug("Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID()); logger.debug("found length of subject list: " + odmContainer.getCrfDataPostImportContainer().getSubjectData().size()); // 2. validates against ODM 1.3 // check it all below, throw an exception and route to a // different // page if not working // TODO this block of code needs the xerces serializer in order // to // work // StringWriter myWriter = new StringWriter(); // Marshaller m1 = new Marshaller(myWriter); // // m1.setProperty("org.exolab.castor.parser.namespaces", // "true"); // m1 // .setProperty("org.exolab.castor.sax.features", // "http://xml.org/sax/features/validation, // http://apache.org/xml/features/validation/schema, // http://apache.org/xml/features/validation/schema-full-checking // "); // // m1.setMapping(myMap); // m1.setNamespaceMapping("", // "http://www.cdisc.org/ns/odm/v1.3"); // m1.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 // ODM1-3.xsd"); // m1.marshal(odmContainer); // if you havent thrown it, you wont throw it here addPageMessage(respage.getString("passed_xml_validation")); } catch (Exception me1) { me1.printStackTrace(); // expanding it to all exceptions, but hoping to catch Marshal // Exception or SAX Exceptions logger.info("found exception with xml transform"); // logger.info("trying 1.2.1"); try { schemaValidator.validateAgainstSchema(f, xsdFile2); // for backwards compatibility, we also try to validate vs // 1.2.1 ODM 06/2008 InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8"); odmContainer = (ODMContainer) um1.unmarshal(isr); } catch (Exception me2) { // not sure if we want to report me2 MessageFormat mf = new MessageFormat(""); mf.applyPattern(respage.getString("your_xml_is_not_well_formed")); Object[] arguments = { me1.getMessage() }; addPageMessage(mf.format(arguments)); // // addPageMessage("Your XML is not well-formed, and does not // comply with the ODM 1.3 Schema. Please check it, and try // again. It returned the message: " // + me1.getMessage()); // me1.printStackTrace(); forwardPage(Page.IMPORT_CRF_DATA); // you can't really wait to forward because then you throw // NPEs // in the next few parts of the code } } // TODO need to output further here // 2.a. is the study the same one that the user is in right now? // 3. validates against study metadata // 3.a. is that study subject in that study? // 3.b. is that study event def in that study? // 3.c. is that site in that study? // 3.d. is that crf version in that study event def? // 3.e. are those item groups in that crf version? // 3.f. are those items in that item group? List<String> errors = getImportCRFDataService().validateStudyMetadata(odmContainer, ub.getActiveStudyId()); if (errors != null) { // add to session // forward to another page logger.info(errors.toString()); for (String error : errors) { addPageMessage(error); } if (errors.size() > 0) { // fail = true; forwardPage(Page.IMPORT_CRF_DATA); } else { addPageMessage(respage.getString("passed_study_check")); addPageMessage(respage.getString("passed_oid_metadata_check")); } } logger.debug("passed error check"); // TODO ADD many validation steps before we get to the // session-setting below // 4. is the event in the correct status to accept data import? // -- scheduled, data entry started, completed // (and the event should already be created) // (and the event should be independent, ie not affected by other // events) Boolean eventCRFStatusesValid = getImportCRFDataService().eventCRFStatusesValid(odmContainer, ub); ImportCRFInfoContainer importCrfInfo = new ImportCRFInfoContainer(odmContainer, sm.getDataSource()); // The eventCRFBeans list omits EventCRFs that don't match UpsertOn rules. If EventCRF did not exist and // doesn't match upsert, it won't be created. List<EventCRFBean> eventCRFBeans = getImportCRFDataService().fetchEventCRFBeans(odmContainer, ub); List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>(); HashMap<String, String> totalValidationErrors = new HashMap<String, String>(); HashMap<String, String> hardValidationErrors = new HashMap<String, String>(); // The following map is used for setting the EventCRF status post import. HashMap<Integer, String> importedCRFStatuses = getImportCRFDataService() .fetchEventCRFStatuses(odmContainer); // @pgawade 17-May-2011 Fix for issue#9590 - collection of // eventCRFBeans is returned as null // when status of one the events in xml file is either stopped, // signed or locked. // Instead of repeating the code to fetch the events in xml file, // method in the ImportCRFDataService is modified for this fix. if (eventCRFBeans == null) { fail = true; addPageMessage(respage.getString("no_event_status_matching")); } else { ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>(); logger.info("found a list of eventCRFBeans: " + eventCRFBeans.toString()); // List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>(); // HashMap<String, String> totalValidationErrors = new // HashMap<String, String>(); // HashMap<String, String> hardValidationErrors = new // HashMap<String, String>(); logger.debug("found event crfs " + eventCRFBeans.size()); // -- does the event already exist? if not, fail if (!eventCRFBeans.isEmpty()) { for (EventCRFBean eventCRFBean : eventCRFBeans) { DataEntryStage dataEntryStage = eventCRFBean.getStage(); Status eventCRFStatus = eventCRFBean.getStatus(); logger.info("Event CRF Bean: id " + eventCRFBean.getId() + ", data entry stage " + dataEntryStage.getName() + ", status " + eventCRFStatus.getName()); if (eventCRFStatus.equals(Status.AVAILABLE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) { // actually want the negative // was status == available and the stage questions, but // when you are at 'data entry complete' your status is // set to 'unavailable'. // >> tbh 09/2008 // HOWEVER, when one event crf is removed and the rest // are good, what happens??? // need to create a list and inform that one is blocked // and the rest are not... // permittedEventCRFIds.add(new Integer(eventCRFBean.getId())); } else { // fail = true; // addPageMessage(respage.getString( // "the_event_crf_not_correct_status")); // forwardPage(Page.IMPORT_CRF_DATA); } } // so that we don't repeat this following message // did we exclude all the event CRFs? if not, pass, else fail if (eventCRFBeans.size() >= permittedEventCRFIds.size()) { addPageMessage(respage.getString("passed_event_crf_status_check")); } else { fail = true; addPageMessage(respage.getString("the_event_crf_not_correct_status")); } // do they all have to have the right status to move // forward? answer from bug tracker = no // 5. do the items contain the correct data types? // 6. are all the related OIDs present? // that is to say, do we chain all the way down? // this is covered by the OID Metadata Check // 7. do the edit checks pass? // only then can we pass on to VERIFY_IMPORT_SERVLET // do we overwrite? // XmlParser xp = new XmlParser(); // List<HashMap<String, String>> importedData = // xp.getData(f); // now we generate hard edit checks, and have to set that to the // screen. get that from the service, generate a summary bean to // set to either // page in the workflow, either verifyImport.jsp or import.jsp try { List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>(); tempDisplayItemBeanWrappers = getImportCRFDataService().lookupValidationErrors(request, odmContainer, ub, totalValidationErrors, hardValidationErrors, permittedEventCRFIds); logger.debug("generated display item bean wrappers " + tempDisplayItemBeanWrappers.size()); logger.debug("size of total validation errors: " + totalValidationErrors.size()); displayItemBeanWrappers.addAll(tempDisplayItemBeanWrappers); } catch (NullPointerException npe1) { // what if you have 2 event crfs but the third is a fake? fail = true; logger.debug("threw a NPE after calling lookup validation errors"); System.out.println(ExceptionUtils.getStackTrace(npe1)); addPageMessage(respage.getString("an_error_was_thrown_while_validation_errors")); // npe1.printStackTrace(); } catch (OpenClinicaException oce1) { fail = true; logger.debug("threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage()); addPageMessage(oce1.getOpenClinicaMessage()); } } else if (!eventCRFStatusesValid) { fail = true; addPageMessage(respage.getString("the_event_crf_not_correct_status")); } else { fail = true; addPageMessage(respage.getString("no_event_crfs_matching_the_xml_metadata")); } // for (HashMap<String, String> crfData : importedData) { // DisplayItemBeanWrapper displayItemBeanWrapper = // testing(request, // crfData); // displayItemBeanWrappers.add(displayItemBeanWrapper); // errors = displayItemBeanWrapper.getValidationErrors(); // // } } if (fail) { logger.debug("failed here - forwarding..."); forwardPage(Page.IMPORT_CRF_DATA); } else { addPageMessage(respage.getString("passing_crf_edit_checks")); session.setAttribute("odmContainer", odmContainer); session.setAttribute("importedData", displayItemBeanWrappers); session.setAttribute("validationErrors", totalValidationErrors); session.setAttribute("hardValidationErrors", hardValidationErrors); session.setAttribute("importedCRFStatuses", importedCRFStatuses); session.setAttribute("importCrfInfo", importCrfInfo); // above are updated 'statically' by the method that originally // generated the wrappers; soon the only thing we will use // wrappers for is the 'overwrite' flag logger.debug("+++ content of total validation errors: " + totalValidationErrors.toString()); SummaryStatsBean ssBean = getImportCRFDataService().generateSummaryStatsBean(odmContainer, displayItemBeanWrappers, importCrfInfo); session.setAttribute("summaryStats", ssBean); // will have to set hard edit checks here as well session.setAttribute("subjectData", odmContainer.getCrfDataPostImportContainer().getSubjectData()); forwardPage(Page.VERIFY_IMPORT_SERVLET); } // } } } /* * Given the MultipartRequest extract the first File validate that it is an xml file and then return it. */ private File getFirstFile() { File f = null; List<File> files = uploadHelper.returnFiles(request, context); for (File file : files) { // Enumeration files = multi.getFileNames(); // if (files.hasMoreElements()) { // String name = (String) files.nextElement(); // f = multi.getFile(name); f = file; if (f == null || f.getName() == null) { logger.info("file is empty."); Validator.addError(errors, "xml_file", "You have to provide an XML file!"); } else if (f.getName().indexOf(".xml") < 0 && f.getName().indexOf(".XML") < 0) { logger.info("file name:" + f.getName()); // TODO change the message below addPageMessage(respage.getString("file_you_uploaded_not_seem_xml_file")); f = null; } } return f; } /** * Uploads the xml file * * @param version * @throws Exception */ public File uploadFile(String theDir, CRFVersionBean version) throws Exception { return getFirstFile(); } public ImportCRFDataService getImportCRFDataService() { dataService = this.dataService != null ? dataService : new ImportCRFDataService(sm.getDataSource(), locale); return dataService; } @Override protected String getAdminServlet() { if (ub.isSysAdmin()) { return SecureController.ADMIN_SERVLET_CODE; } else { return ""; } } }