private void validateStudy6(FormProcessor fp, Validator v) { v.addValidation( "medlineIdentifier", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "url", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "urlDescription", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); errors = v.validate(); study.setMedlineIdentifier(fp.getString("medlineIdentifier")); study.setResultsReference(fp.getBoolean("resultsReference")); study.setUrl(fp.getString("url")); study.setUrlDescription(fp.getString("urlDescription")); // request.setAttribute("interventions",session.getAttribute( // "interventions")); if (!errors.isEmpty()) { request.setAttribute("formMessages", errors); } }
private boolean updateStudy2(FormProcessor fp) { study.setOldStatus(study.getStatus()); study.setStatus(Status.get(fp.getInt("statusId"))); if (StringUtil.isBlank(fp.getString(INPUT_VER_DATE))) { study.setProtocolDateVerification(null); } else { study.setProtocolDateVerification(fp.getDate(INPUT_VER_DATE)); } study.setDatePlannedStart(fp.getDate(INPUT_START_DATE)); if (StringUtil.isBlank(fp.getString(INPUT_END_DATE))) { study.setDatePlannedEnd(null); } else { study.setDatePlannedEnd(fp.getDate(INPUT_END_DATE)); } study.setPhase(fp.getString("phase")); if (fp.getInt("genetic") == 1) { study.setGenetic(true); } else { study.setGenetic(false); } String interventional = resadmin.getString("interventional"); return interventional.equalsIgnoreCase(study.getProtocolType()); }
private void validateStudy2(FormProcessor fp, Validator v) { v.addValidation(INPUT_START_DATE, Validator.IS_A_DATE); if (!StringUtil.isBlank(fp.getString(INPUT_END_DATE))) { v.addValidation(INPUT_END_DATE, Validator.IS_A_DATE); } if (!StringUtil.isBlank(fp.getString(INPUT_VER_DATE))) { v.addValidation(INPUT_VER_DATE, Validator.IS_A_DATE); } errors = v.validate(); logger.info("has validation errors"); try { local_df.parse(fp.getString(INPUT_START_DATE)); fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE)); } try { local_df.parse(fp.getString(INPUT_VER_DATE)); fp.addPresetValue(INPUT_VER_DATE, local_df.format(fp.getDate(INPUT_VER_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_VER_DATE, fp.getString(INPUT_VER_DATE)); } try { local_df.parse(fp.getString(INPUT_END_DATE)); fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE)); } updateStudy2(fp); setPresetValues(fp.getPresetValues()); }
@Override public void processRequest() throws Exception { resetPanel(); panel.setStudyInfoShown(false); panel.setOrderedData(true); panel.setSubmitDataModule(false); panel.setExtractData(false); panel.setCreateDataset(false); setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering")); setToPanel( resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading")); setToPanel( resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version")); setToPanel( resword.getString("CRF_spreadsheet_template"), respage.getString("br_download_blank_CRF_spreadsheet_from")); setToPanel( resword.getString("example_CRF_br_spreadsheets"), respage.getString("br_download_example_CRF_instructions_from")); FormProcessor fp = new FormProcessor(request); // checks which module the requests are from, manage or admin String module = fp.getString(MODULE); request.setAttribute(MODULE, module); int crfId = fp.getInt(CRF_ID); if (crfId == 0) { addPageMessage(respage.getString("please_choose_a_CRF_to_view")); forwardPage(Page.CRF_LIST); } else { CRFDAO cdao = new CRFDAO(sm.getDataSource()); CRFVersionDAO vdao = new CRFVersionDAO(sm.getDataSource()); CRFBean crf = (CRFBean) cdao.findByPK(crfId); ArrayList<CRFVersionBean> versions = (ArrayList<CRFVersionBean>) vdao.findAllByCRF(crfId); crf.setVersions(versions); // Collection<RuleSetBean> items = // getRuleSetService().getRuleSetsByCrf(crf); Collection<TableColumnHolder> items = populate(crf, versions); TableFacade tableFacade = createTableFacade("rules", request); tableFacade.setItems(items); // set the items tableFacade.setExportTypes(response, CSV, JEXCEL); tableFacade.setStateAttr("restore"); Limit limit = tableFacade.getLimit(); if (limit.isExported()) { export(tableFacade); // return null; // In Spring returning null tells the controller // not to do anything. } String html = html(tableFacade); request.setAttribute("rules", html); // Set the Html in the // request for the JSP. request.setAttribute(CRF, crf); forwardPage(Page.VIEW_CRF); } }
private StudyBean createStudyBean(FormProcessor fp) { StudyBean newStudy = study; newStudy.setId(fp.getInt("studyId")); newStudy.setName(fp.getString("name")); newStudy.setOfficialTitle(fp.getString("officialTitle")); newStudy.setIdentifier(fp.getString("uniqueProId")); newStudy.setSecondaryIdentifier(fp.getString("secondProId")); newStudy.setPrincipalInvestigator(fp.getString("prinInvestigator")); newStudy.setSummary(fp.getString("description")); newStudy.setProtocolDescription(fp.getString("protocolDescription")); newStudy.setSponsor(fp.getString("sponsor")); newStudy.setCollaborators(fp.getString("collaborators")); return newStudy; }
private void validateStudy4(FormProcessor fp, Validator v) { v.addValidation( "conditions", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 500); v.addValidation( "keywords", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "eligibility", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 500); errors = v.validate(); if (fp.getInt("expectedTotalEnrollment") <= 0) { Validator.addError( errors, "expectedTotalEnrollment", respage.getString("expected_total_enrollment_must_be_a_positive_number")); } study.setConditions(fp.getString("conditions")); study.setKeywords(fp.getString("keywords")); study.setEligibility(fp.getString("eligibility")); study.setGender(fp.getString("gender")); study.setAgeMax(fp.getString("ageMax")); study.setAgeMin(fp.getString("ageMin")); study.setHealthyVolunteerAccepted(fp.getBoolean("healthyVolunteerAccepted")); study.setExpectedTotalEnrollment(fp.getInt("expectedTotalEnrollment")); request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap); }
private void validateStudy1(FormProcessor fp, Validator v) { v.addValidation("name", Validator.NO_BLANKS); v.addValidation("uniqueProId", Validator.NO_BLANKS); v.addValidation("description", Validator.NO_BLANKS); v.addValidation("prinInvestigator", Validator.NO_BLANKS); v.addValidation("sponsor", Validator.NO_BLANKS); v.addValidation( "secondProId", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "collaborators", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 1000); v.addValidation( "protocolDescription", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 1000); errors = v.validate(); if (fp.getString("name").trim().length() > 100) { Validator.addError(errors, "name", resexception.getString("maximum_lenght_name_100")); } if (fp.getString("uniqueProId").trim().length() > 30) { Validator.addError( errors, "uniqueProId", resexception.getString("maximum_lenght_unique_protocol_30")); } if (fp.getString("description").trim().length() > 255) { Validator.addError( errors, "description", resexception.getString("maximum_lenght_brief_summary_255")); } if (fp.getString("prinInvestigator").trim().length() > 255) { Validator.addError( errors, "prinInvestigator", resexception.getString("maximum_lenght_principal_investigator_255")); } if (fp.getString("sponsor").trim().length() > 255) { Validator.addError(errors, "sponsor", resexception.getString("maximum_lenght_sponsor_255")); } if (fp.getString("officialTitle").trim().length() > 255) { Validator.addError( errors, "officialTitle", resexception.getString("maximum_lenght_official_title_255")); } study = createStudyBean(fp); }
private void validateStudy3(boolean isInterventional, Validator v, FormProcessor fp) { v.addValidation("purpose", Validator.NO_BLANKS); for (int i = 0; i < 10; i++) { String type = fp.getString("interType" + i); String name = fp.getString("interName" + i); if (!StringUtil.isBlank(type) && StringUtil.isBlank(name)) { v.addValidation("interName", Validator.NO_BLANKS); request.setAttribute( "interventionError", respage.getString("name_cannot_be_blank_if_type")); break; } if (!StringUtil.isBlank(name) && StringUtil.isBlank(type)) { v.addValidation("interType", Validator.NO_BLANKS); request.setAttribute( "interventionError", respage.getString("name_cannot_be_blank_if_name")); break; } } updateStudy3(isInterventional, fp); }
@Override protected void processRequest() throws Exception { FormProcessor fp = new FormProcessor(request); String triggerName = fp.getString("tname"); String gName = fp.getString("gname"); String finalGroupName = ""; if ("".equals(gName) || "0".equals(gName)) { finalGroupName = groupName; } else { // should equal 1 finalGroupName = groupImportName; } String deleteMe = fp.getString("del"); scheduler = getScheduler(); Trigger trigger = scheduler.getTrigger(triggerName, finalGroupName); try { // System.out.println("found delete key: "+deleteMe); // System.out.println("found is sys admin: "+ub.isSysAdmin()); // System.out.println("found is tech admin: "+ub.isTechAdmin()); if (("y".equals(deleteMe)) && (ub.isSysAdmin())) { scheduler.deleteJob(triggerName, finalGroupName); // set return message here System.out.println("deleted job: " + triggerName); addPageMessage( "The following job " + triggerName + " and its corresponding Trigger have been deleted from the system."); } else { if (scheduler.getTriggerState(triggerName, finalGroupName) == Trigger.STATE_PAUSED) { scheduler.resumeTrigger(triggerName, finalGroupName); // trigger.setPriority(Trigger.DEFAULT_PRIORITY); System.out.println("-- resuming trigger! " + triggerName + " " + finalGroupName); addPageMessage( "This trigger " + triggerName + " has been resumed and will continue to run until paused or deleted."); // set message here } else { scheduler.pauseTrigger(triggerName, finalGroupName); // trigger.setPriority(Trigger.STATE_PAUSED); System.out.println("-- pausing trigger! " + triggerName + " " + finalGroupName); addPageMessage( "This trigger " + triggerName + " has been paused, and will not run again until it is restored."); // set message here } } } catch (NullPointerException e) { // TODO Auto-generated catch block e.printStackTrace(); } // all validation done on JSP side // forward back to view job servlet here // set a message if ("".equals(gName) || "0".equals(gName)) { forwardPage(Page.VIEW_JOB_SERVLET); } else { forwardPage(Page.VIEW_IMPORT_JOB_SERVLET); } }
@Override public void processRequest() throws Exception { CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource()); FormProcessor fp = new FormProcessor(request); int versionId = fp.getInt("id", true); String module = fp.getString("module"); request.setAttribute("module", module); String action = fp.getString("action"); if (versionId == 0) { addPageMessage(respage.getString("please_choose_a_CRF_version_to_remove")); forwardPage(Page.CRF_LIST_SERVLET); } else { if (StringUtil.isBlank(action)) { addPageMessage(respage.getString("no_action_specified")); forwardPage(Page.CRF_LIST_SERVLET); return; } CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId); SectionDAO secdao = new SectionDAO(sm.getDataSource()); EventCRFDAO evdao = new EventCRFDAO(sm.getDataSource()); // find all event crfs by version id ArrayList eventCRFs = evdao.findUndeletedWithStudySubjectsByCRFVersion(versionId); if ("confirm".equalsIgnoreCase(action)) { request.setAttribute("versionToRemove", version); request.setAttribute("eventCRFs", eventCRFs); forwardPage(Page.REMOVE_CRF_VERSION); } else { logger.info("submit to remove the crf version"); // version version.setStatus(Status.DELETED); version.setUpdater(ub); version.setUpdatedDate(new Date()); cvdao.update(version); // added below tbh 092007, seems that we don't remove the event // crfs in the second pass for (int ii = 0; ii < eventCRFs.size(); ii++) { EventCRFBean ecbean = (EventCRFBean) eventCRFs.get(ii); ecbean.setStatus(Status.AUTO_DELETED); ecbean.setUpdater(ub); ecbean.setUpdatedDate(new Date()); evdao.update(ecbean); } // added above tbh 092007, to fix task // all sections ArrayList sections = secdao.findAllByCRFVersionId(version.getId()); for (int j = 0; j < sections.size(); j++) { SectionBean section = (SectionBean) sections.get(j); if (!section.getStatus().equals(Status.DELETED)) { section.setStatus(Status.AUTO_DELETED); section.setUpdater(ub); section.setUpdatedDate(new Date()); secdao.update(section); } } // all item data related to event crfs ItemDataDAO idao = new ItemDataDAO(sm.getDataSource()); for (int i = 0; i < eventCRFs.size(); i++) { EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(i); if (!eventCRF.getStatus().equals(Status.DELETED)) { eventCRF.setStatus(Status.AUTO_DELETED); eventCRF.setUpdater(ub); eventCRF.setUpdatedDate(new Date()); evdao.update(eventCRF); ArrayList items = idao.findAllByEventCRFId(eventCRF.getId()); for (int j = 0; j < items.size(); j++) { ItemDataBean item = (ItemDataBean) items.get(j); if (!item.getStatus().equals(Status.DELETED)) { item.setStatus(Status.AUTO_DELETED); item.setUpdater(ub); item.setUpdatedDate(new Date()); idao.update(item); } } } } addPageMessage( respage.getString("the_CRF") + version.getName() + " " + respage.getString("has_been_removed_succesfully")); forwardPage(Page.CRF_LIST_SERVLET); } } }
@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(); String propertiesPath = CoreResources.PROPERTIES_DIR; myMap.loadMapping(propertiesPath + File.separator + "cd_odm_mapping.xml"); Unmarshaller um1 = new Unmarshaller(myMap); // um1.addNamespaceToPackageMapping("http://www.cdisc.org/ns/odm/v1.3" // , // "ODMContainer"); boolean fail = false; ODMContainer odmContainer = new 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); System.out.println( "Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID()); System.out.println( "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")); } } System.out.println("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) List<EventCRFBean> eventCRFBeans = getImportCRFDataService().fetchEventCRFBeans(odmContainer, ub); 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>(); System.out.println("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); System.out.println( "generated display item bean wrappers " + tempDisplayItemBeanWrappers.size()); System.out.println("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"); addPageMessage(respage.getString("an_error_was_thrown_while_validation_errors")); System.out.println("threw the null pointer at line 323, import"); // npe1.printStackTrace(); } catch (OpenClinicaException oce1) { fail = true; logger.debug( "threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage()); addPageMessage(oce1.getOpenClinicaMessage()); System.out.println("threw the openclinica message at line 327, import"); } } 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) { System.out.println("failed here - forwarding..."); forwardPage(Page.IMPORT_CRF_DATA); } else { addPageMessage(respage.getString("passing_crf_edit_checks")); session.setAttribute("importedData", displayItemBeanWrappers); session.setAttribute("validationErrors", totalValidationErrors); session.setAttribute("hardValidationErrors", hardValidationErrors); // 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 System.out.println("found total validation errors: " + totalValidationErrors.size()); logger.debug("+++ content of total validation errors: " + totalValidationErrors.toString()); SummaryStatsBean ssBean = getImportCRFDataService() .generateSummaryStatsBean(odmContainer, displayItemBeanWrappers); session.setAttribute("summaryStats", ssBean); // will have to set hard edit checks here as well session.setAttribute( "subjectData", odmContainer.getCrfDataPostImportContainer().getSubjectData()); System.out.println("did not fail - forwarding..."); forwardPage(Page.VERIFY_IMPORT_SERVLET); } } }
private void updateStudy3(boolean isInterventional, FormProcessor fp) { study.setPurpose(fp.getString("purpose")); ArrayList interventionArray = new ArrayList(); if (isInterventional) { study.setAllocation(fp.getString("allocation")); study.setMasking(fp.getString("masking")); study.setControl(fp.getString("control")); study.setAssignment(fp.getString("assignment")); study.setEndpoint(fp.getString("endpoint")); StringBuffer interventions = new StringBuffer(); for (int i = 0; i < 10; i++) { String type = fp.getString("interType" + i); String name = fp.getString("interName" + i); if (!StringUtil.isBlank(type) && !StringUtil.isBlank(name)) { InterventionBean ib = new InterventionBean(fp.getString("interType" + i), fp.getString("interName" + i)); interventionArray.add(ib); interventions.append(ib.toString()).append(","); } } study.setInterventions(interventions.toString()); } else { // type = observational study.setDuration(fp.getString("duration")); study.setSelection(fp.getString("selection")); study.setTiming(fp.getString("timing")); } request.setAttribute("interventions", interventionArray); }
@Override public void processRequest() throws Exception { resetPanel(); FormProcessor fp = new FormProcessor(request); Validator v = new Validator(request); int studyId = fp.getInt("id"); studyId = studyId == 0 ? fp.getInt("studyId") : studyId; String action = fp.getString("action"); StudyDAO sdao = new StudyDAO(sm.getDataSource()); boolean isInterventional = false; study = (StudyBean) sdao.findByPK(studyId); if (study.getId() != currentStudy.getId()) { addPageMessage( respage.getString("not_current_study") + respage.getString("change_study_contact_sysadmin")); forwardPage(Page.MENU_SERVLET); return; } study.setId(studyId); StudyConfigService scs = new StudyConfigService(sm.getDataSource()); study = scs.setParametersForStudy(study); request.setAttribute("studyToView", study); request.setAttribute("studyId", studyId + ""); request.setAttribute("studyPhaseMap", CreateStudyServlet.studyPhaseMap); ArrayList statuses = Status.toStudyUpdateMembersList(); statuses.add(Status.PENDING); request.setAttribute("statuses", statuses); String interventional = resadmin.getString("interventional"); isInterventional = interventional.equalsIgnoreCase(study.getProtocolType()); request.setAttribute("isInterventional", isInterventional ? "1" : "0"); String protocolType = study.getProtocolTypeKey(); // A. Hamid. 5001 if (study.getParentStudyId() > 0) { StudyBean parentStudy = (StudyBean) sdao.findByPK(study.getParentStudyId()); request.setAttribute("parentStudy", parentStudy); } ArrayList interventionArray = new ArrayList(); if (isInterventional) { interventionArray = parseInterventions((study)); setMaps(isInterventional, interventionArray); } else { setMaps(isInterventional, interventionArray); } if (!action.equals("submit")) { // First Load First Form if (study.getDatePlannedStart() != null) { fp.addPresetValue(INPUT_START_DATE, local_df.format(study.getDatePlannedStart())); } if (study.getDatePlannedEnd() != null) { fp.addPresetValue(INPUT_END_DATE, local_df.format(study.getDatePlannedEnd())); } if (study.getProtocolDateVerification() != null) { fp.addPresetValue(INPUT_VER_DATE, local_df.format(study.getProtocolDateVerification())); } setPresetValues(fp.getPresetValues()); // first load 2nd form } if (study == null) { addPageMessage(respage.getString("please_choose_a_study_to_edit")); forwardPage(Page.STUDY_LIST_SERVLET); return; } if (action.equals("submit")) { validateStudy1(fp, v); validateStudy2(fp, v); validateStudy3(isInterventional, v, fp); validateStudy4(fp, v); validateStudy5(fp, v); validateStudy6(fp, v); confirmWholeStudy(fp, v); request.setAttribute("studyToView", study); if (!errors.isEmpty()) { System.out.println("found errors : " + errors.toString()); request.setAttribute("formMessages", errors); forwardPage(Page.UPDATE_STUDY_NEW); } else { study.setProtocolType(protocolType); submitStudy(study); addPageMessage(respage.getString("the_study_has_been_updated_succesfully")); ArrayList pageMessages = (ArrayList) request.getAttribute(PAGE_MESSAGE); session.setAttribute("pageMessages", pageMessages); response.sendRedirect(request.getContextPath() + "/pages/studymodule"); // forwardPage(Page.MANAGE_STUDY_MODULE); } } else { forwardPage(Page.UPDATE_STUDY_NEW); } }
@Override public void processRequest() throws Exception { FormProcessor fp = new FormProcessor(request); // Determine whether to limit the displayed DN's to a certain DN type int resolutionStatus = 0; try { resolutionStatus = Integer.parseInt(request.getParameter("resolutionStatus")); } catch (NumberFormatException nfe) { // Show all DN's resolutionStatus = -1; } // request.setAttribute(RESOLUTION_STATUS,resolutionStatus); // Determine whether we already have a collection of resolutionStatus // Ids, and if not // create a new attribute. If there is no resolution status, then the // Set object should be cleared, // because we do not have to save a set of filter IDs. boolean hasAResolutionStatus = resolutionStatus >= 1 && resolutionStatus <= 5; Set<Integer> resolutionStatusIds = (HashSet) session.getAttribute(RESOLUTION_STATUS); // remove the session if there is no resolution status if (!hasAResolutionStatus && resolutionStatusIds != null) { session.removeAttribute(RESOLUTION_STATUS); resolutionStatusIds = null; } if (hasAResolutionStatus) { if (resolutionStatusIds == null) { resolutionStatusIds = new HashSet<Integer>(); } resolutionStatusIds.add(resolutionStatus); session.setAttribute(RESOLUTION_STATUS, resolutionStatusIds); } int discNoteType = 0; try { discNoteType = Integer.parseInt(request.getParameter("type")); } catch (NumberFormatException nfe) { // Show all DN's discNoteType = -1; } request.setAttribute(DISCREPANCY_NOTE_TYPE, discNoteType); /* * DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil(); // * Generate a summary of how we are filtering; Map<String, List<String>> * filterSummary = discNoteUtil.generateFilterSummary(discNoteType, * resolutionStatusIds); * * if (!filterSummary.isEmpty()) { request.setAttribute(FILTER_SUMMARY, * filterSummary); } */ // checks which module the requests are from String module = fp.getString(MODULE); request.setAttribute(MODULE, module); int definitionId = fp.getInt("defId"); int tabId = fp.getInt("tab"); if (definitionId <= 0) { addPageMessage(respage.getString("please_choose_an_ED_ta_to_vies_details")); forwardPage(Page.LIST_SUBJECT_DISC_NOTE_SERVLET); return; } request.setAttribute("eventDefinitionId", definitionId); ListDiscNotesForCRFTableFactory factory = new ListDiscNotesForCRFTableFactory(); factory.setStudyEventDefinitionDao(getStudyEventDefinitionDao()); factory.setSubjectDAO(getSubjectDAO()); factory.setStudySubjectDAO(getStudySubjectDAO()); factory.setStudyEventDAO(getStudyEventDAO()); factory.setStudyBean(currentStudy); factory.setStudyGroupClassDAO(getStudyGroupClassDAO()); factory.setSubjectGroupMapDAO(getSubjectGroupMapDAO()); factory.setStudyDAO(getStudyDAO()); factory.setStudyGroupDAO(getStudyGroupDAO()); factory.setCurrentRole(currentRole); factory.setCurrentUser(ub); factory.setEventCRFDAO(getEventCRFDAO()); factory.setEventDefintionCRFDAO(getEventDefinitionCRFDAO()); factory.setCrfDAO(getCrfDAO()); factory.setDiscrepancyNoteDAO(getDiscrepancyNoteDAO()); // factory.setStudyHasDiscNotes(allThreadedDiscNotes != null && // !allThreadedDiscNotes.isEmpty()); factory.setDiscNoteType(discNoteType); factory.setModule(module); factory.setResolutionStatus(resolutionStatus); factory.setResolutionStatusIds(resolutionStatusIds); factory.setSelectedStudyEventDefinition( (StudyEventDefinitionBean) getStudyEventDefinitionDao().findByPK(definitionId)); String listDiscNotesForCRFHtml = factory.createTable(request, response).render(); request.setAttribute("listDiscNotesForCRFHtml", listDiscNotesForCRFHtml); request.setAttribute("defId", definitionId); forwardPage(Page.LIST_DNOTES_FOR_CRF); }
protected void processRequest() throws Exception { FormProcessor fp = new FormProcessor(request); StudyDAO sdao = new StudyDAO(sm.getDataSource()); addEntityList( "studies", sdao.findAll(), "A user cannot be created, because there is no study to set as an active study for the user.", Page.ADMIN_SYSTEM); addEntityList( "roles", getRoles(), "A user cannot be created, because there are no roles to set as a role within the active study for the user.", Page.ADMIN_SYSTEM); ArrayList types = UserType.toArrayList(); types.remove(UserType.INVALID); if (!ub.isTechAdmin()) { types.remove(UserType.TECHADMIN); } addEntityList( "types", types, "A user cannot be created, because there are no user types within the active study for the user.", Page.ADMIN_SYSTEM); if (!fp.isSubmitted()) { forwardPage(Page.CREATE_ACCOUNT); } else { UserAccountDAO udao = new UserAccountDAO(sm.getDataSource()); Validator v = new Validator(request); // username must not be blank, // must be in the format specified by Validator.USERNAME, // and must be unique v.addValidation(INPUT_USERNAME, Validator.NO_BLANKS); v.addValidation( INPUT_USERNAME, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 64); v.addValidation(INPUT_USERNAME, Validator.IS_A_USERNAME); v.addValidation(INPUT_USERNAME, Validator.USERNAME_UNIQUE, udao); v.addValidation(INPUT_FIRST_NAME, Validator.NO_BLANKS); v.addValidation(INPUT_LAST_NAME, Validator.NO_BLANKS); v.addValidation( INPUT_FIRST_NAME, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 50); v.addValidation( INPUT_LAST_NAME, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 50); v.addValidation(INPUT_EMAIL, Validator.NO_BLANKS); v.addValidation( INPUT_EMAIL, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 120); v.addValidation(INPUT_EMAIL, Validator.IS_A_EMAIL); v.addValidation(INPUT_INSTITUTION, Validator.NO_BLANKS); v.addValidation( INPUT_INSTITUTION, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation(INPUT_STUDY, Validator.ENTITY_EXISTS, sdao); v.addValidation(INPUT_ROLE, Validator.IS_VALID_TERM, TermType.ROLE); HashMap errors = v.validate(); if (errors.isEmpty()) { UserAccountBean createdUserAccountBean = new UserAccountBean(); createdUserAccountBean.setName(fp.getString(INPUT_USERNAME)); createdUserAccountBean.setFirstName(fp.getString(INPUT_FIRST_NAME)); createdUserAccountBean.setLastName(fp.getString(INPUT_LAST_NAME)); createdUserAccountBean.setEmail(fp.getString(INPUT_EMAIL)); createdUserAccountBean.setInstitutionalAffiliation(fp.getString(INPUT_INSTITUTION)); SecurityManager secm = SecurityManager.getInstance(); String password = secm.genPassword(); String passwordHash = secm.encrytPassword(password); createdUserAccountBean.setPasswd(passwordHash); createdUserAccountBean.setPasswdTimestamp(null); createdUserAccountBean.setLastVisitDate(null); createdUserAccountBean.setStatus(Status.AVAILABLE); createdUserAccountBean.setPasswdChallengeQuestion(""); createdUserAccountBean.setPasswdChallengeAnswer(""); createdUserAccountBean.setPhone(""); createdUserAccountBean.setOwner(ub); int studyId = fp.getInt(INPUT_STUDY); Role r = Role.get(fp.getInt(INPUT_ROLE)); createdUserAccountBean = addActiveStudyRole(createdUserAccountBean, studyId, r); UserType type = UserType.get(fp.getInt("type")); logger.warning("*** found type: " + fp.getInt("type")); logger.warning("*** setting type: " + type.getDescription()); createdUserAccountBean.addUserType(type); createdUserAccountBean = (UserAccountBean) udao.create(createdUserAccountBean); String displayPwd = fp.getString(INPUT_DISPLAY_PWD); if (createdUserAccountBean.isActive()) { addPageMessage( "The user account \"" + createdUserAccountBean.getName() + "\" was created successfully. "); if ("no".equalsIgnoreCase(displayPwd)) { try { sendNewAccountEmail(createdUserAccountBean, password); } catch (Exception e) { addPageMessage( "There was an error sending the account-creating email. Please contact the user directly regarding account creation. You may reset the user's password by editing the user's account."); } } else { addPageMessage( "User Password: "******". Please write down the password and provide it directly to the user."); } } else { addPageMessage( "The user account \"" + createdUserAccountBean.getName() + "\" could not be created due to a database error."); } if (createdUserAccountBean.isActive()) { request.setAttribute( ViewUserAccountServlet.ARG_USER_ID, new Integer(createdUserAccountBean.getId()).toString()); forwardPage(Page.VIEW_USER_ACCOUNT_SERVLET); } else { forwardPage(Page.LIST_USER_ACCOUNTS_SERVLET); } } else { String textFields[] = { INPUT_USERNAME, INPUT_FIRST_NAME, INPUT_LAST_NAME, INPUT_EMAIL, INPUT_INSTITUTION, INPUT_DISPLAY_PWD }; fp.setCurrentStringValuesAsPreset(textFields); String ddlbFields[] = {INPUT_STUDY, INPUT_ROLE, INPUT_TYPE}; fp.setCurrentIntValuesAsPreset(ddlbFields); HashMap presetValues = fp.getPresetValues(); setPresetValues(presetValues); setInputMessages(errors); addPageMessage("There were some errors in your submission. See below for details."); forwardPage(Page.CREATE_ACCOUNT); } } }
private String getInputStartMinute() { return fp.getString(INPUT_STARTDATE_PREFIX + "Minute"); }
private void confirmWholeStudy(FormProcessor fp, Validator v) { errors = v.validate(); if (study.getStatus().isLocked()) { study.getStudyParameterConfig().setDiscrepancyManagement("false"); } else { study .getStudyParameterConfig() .setDiscrepancyManagement(fp.getString("discrepancyManagement")); } study.getStudyParameterConfig().setCollectDob(fp.getString("collectDob")); study.getStudyParameterConfig().setGenderRequired(fp.getString("genderRequired")); study .getStudyParameterConfig() .setInterviewerNameRequired(fp.getString("interviewerNameRequired")); study .getStudyParameterConfig() .setInterviewerNameDefault(fp.getString("interviewerNameDefault")); study.getStudyParameterConfig().setInterviewDateEditable(fp.getString("interviewDateEditable")); study.getStudyParameterConfig().setInterviewDateRequired(fp.getString("interviewDateRequired")); study .getStudyParameterConfig() .setInterviewerNameEditable(fp.getString("interviewerNameEditable")); study.getStudyParameterConfig().setInterviewDateDefault(fp.getString("interviewDateDefault")); study.getStudyParameterConfig().setSubjectIdGeneration(fp.getString("subjectIdGeneration")); study .getStudyParameterConfig() .setSubjectPersonIdRequired(fp.getString("subjectPersonIdRequired")); study.getStudyParameterConfig().setSubjectIdPrefixSuffix(fp.getString("subjectIdPrefixSuffix")); study.getStudyParameterConfig().setPersonIdShownOnCRF(fp.getString("personIdShownOnCRF")); study .getStudyParameterConfig() .setSecondaryLabelViewable(fp.getString("secondaryLabelViewable")); study .getStudyParameterConfig() .setAdminForcedReasonForChange(fp.getString("adminForcedReasonForChange")); if (!errors.isEmpty()) { request.setAttribute("formMessages", errors); } }
/** * Constructs study bean from request * * @param request * @return */ private StudyBean createStudyBean() { FormProcessor fp = new FormProcessor(request); StudyBean study = (StudyBean) session.getAttribute("newStudy"); study.setName(fp.getString("name")); study.setIdentifier(fp.getString("uniqueProId")); study.setSecondaryIdentifier(fp.getString("secondProId")); study.setSummary(fp.getString("description")); study.setPrincipalInvestigator(fp.getString("prinInvestigator")); study.setExpectedTotalEnrollment(fp.getInt("expectedTotalEnrollment")); java.util.Date startDate = null; java.util.Date endDate = null; try { local_df.setLenient(false); startDate = local_df.parse(fp.getString("startDate")); } catch (ParseException fe) { startDate = study.getDatePlannedStart(); logger.info(fe.getMessage()); } study.setDatePlannedStart(startDate); try { local_df.setLenient(false); endDate = local_df.parse(fp.getString("endDate")); } catch (ParseException fe) { endDate = study.getDatePlannedEnd(); } study.setDatePlannedEnd(endDate); study.setFacilityCity(fp.getString("facCity")); study.setFacilityContactDegree(fp.getString("facConDrgree")); study.setFacilityName(fp.getString("facName")); study.setFacilityContactEmail(fp.getString("facConEmail")); study.setFacilityContactPhone(fp.getString("facConPhone")); study.setFacilityContactName(fp.getString("facConName")); study.setFacilityContactDegree(fp.getString("facConDegree")); study.setFacilityCountry(fp.getString("facCountry")); // study.setFacilityRecruitmentStatus(fp.getString("facRecStatus")); study.setFacilityState(fp.getString("facState")); study.setFacilityZip(fp.getString("facZip")); study.setStatus(Status.get(fp.getInt("statusId"))); ArrayList parameters = study.getStudyParameters(); for (int i = 0; i < parameters.size(); i++) { StudyParamsConfig scg = (StudyParamsConfig) parameters.get(i); String value = fp.getString(scg.getParameter().getHandle()); logger.info("get value:" + value); scg.getValue().setParameter(scg.getParameter().getHandle()); scg.getValue().setValue(value); } // YW 10-12-2007 << study .getStudyParameterConfig() .setInterviewerNameRequired(fp.getString("interviewerNameRequired")); study .getStudyParameterConfig() .setInterviewerNameDefault(fp.getString("interviewerNameDefault")); study.getStudyParameterConfig().setInterviewDateRequired(fp.getString("interviewDateRequired")); study.getStudyParameterConfig().setInterviewDateDefault(fp.getString("interviewDateDefault")); // YW >> return study; }
@Override public void processRequest() throws Exception { FormProcessor fp = new FormProcessor(request); String action = request.getParameter("action"); session.setAttribute("sdvOptions", this.setSDVOptions()); if (StringUtil.isBlank(action)) { if (currentStudy.getParentStudyId() > 0) { addPageMessage(respage.getString("you_cannot_create_site_itself_site")); forwardPage(Page.SITE_LIST_SERVLET); } else { StudyBean newStudy = new StudyBean(); newStudy.setParentStudyId(currentStudy.getId()); // get default facility info from property file newStudy.setFacilityName(SQLInitServlet.getField(CreateStudyServlet.FAC_NAME)); newStudy.setFacilityCity(SQLInitServlet.getField(CreateStudyServlet.FAC_CITY)); newStudy.setFacilityState(SQLInitServlet.getField(CreateStudyServlet.FAC_STATE)); newStudy.setFacilityCountry(SQLInitServlet.getField(CreateStudyServlet.FAC_COUNTRY)); newStudy.setFacilityContactDegree( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_DEGREE)); newStudy.setFacilityContactEmail( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_EMAIL)); newStudy.setFacilityContactName( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_NAME)); newStudy.setFacilityContactPhone( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_PHONE)); newStudy.setFacilityZip(SQLInitServlet.getField(CreateStudyServlet.FAC_ZIP)); List<StudyParamsConfig> parentConfigs = currentStudy.getStudyParameters(); // logger.info("parentConfigs size:" + parentConfigs.size()); ArrayList configs = new ArrayList(); for (StudyParamsConfig scg : parentConfigs) { // StudyParamsConfig scg = (StudyParamsConfig) // parentConfigs.get(i); if (scg != null) { // find the one that sub study can change if (scg.getValue().getId() > 0 && scg.getParameter().isOverridable()) { logger.info("parameter:" + scg.getParameter().getHandle()); logger.info("value:" + scg.getValue().getValue()); // YW 10-12-2007, set overridable study parameters // for a site if (scg.getParameter().getHandle().equalsIgnoreCase("interviewerNameRequired")) { scg.getValue().setValue(fp.getString("interviewerNameRequired")); } else if (scg.getParameter() .getHandle() .equalsIgnoreCase("interviewerNameDefault")) { scg.getValue().setValue(fp.getString("interviewerNameDefault")); } else if (scg.getParameter().getHandle().equalsIgnoreCase("interviewDateRequired")) { scg.getValue().setValue(fp.getString("interviewDateRequired")); } else if (scg.getParameter().getHandle().equalsIgnoreCase("interviewDateDefault")) { scg.getValue().setValue(fp.getString("interviewDateDefault")); } // YW >> configs.add(scg); } } } newStudy.setStudyParameters(configs); // YW 10-12-2007 << newStudy .getStudyParameterConfig() .setInterviewerNameRequired(fp.getString("interviewerNameRequired")); newStudy .getStudyParameterConfig() .setInterviewerNameDefault(fp.getString("interviewerNameDefault")); newStudy .getStudyParameterConfig() .setInterviewDateRequired(fp.getString("interviewDateRequired")); newStudy .getStudyParameterConfig() .setInterviewDateDefault(fp.getString("interviewDateDefault")); // YW >> // BWP 3169 1-12-2008 << newStudy .getStudyParameterConfig() .setInterviewerNameEditable( currentStudy.getStudyParameterConfig().getInterviewerNameEditable()); newStudy .getStudyParameterConfig() .setInterviewDateEditable( currentStudy.getStudyParameterConfig().getInterviewDateEditable()); // >> try { local_df.parse(fp.getString(INPUT_START_DATE)); fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE)); } try { local_df.parse(fp.getString(INPUT_END_DATE)); fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE)); } // tbh 3946 07/2009 try { local_df.parse(fp.getString(INPUT_VER_DATE)); fp.addPresetValue(INPUT_VER_DATE, local_df.format(fp.getDate(INPUT_VER_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_VER_DATE, fp.getString(INPUT_VER_DATE)); } // >> tbh setPresetValues(fp.getPresetValues()); session.setAttribute("newStudy", newStudy); session.setAttribute("definitions", this.initDefinitions(newStudy)); request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap); request.setAttribute("statuses", Status.toActiveArrayList()); forwardPage(Page.CREATE_SUB_STUDY); } } else { if ("confirm".equalsIgnoreCase(action)) { confirmStudy(); } else if ("back".equalsIgnoreCase(action)) { StudyBean newStudy = (StudyBean) session.getAttribute("newStudy"); try { fp.addPresetValue(INPUT_START_DATE, local_df.format(newStudy.getDatePlannedEnd())); } catch (Exception pe) { fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE)); } try { fp.addPresetValue(INPUT_END_DATE, local_df.format(newStudy.getDatePlannedStart())); } catch (Exception pe) { fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE)); } try { fp.addPresetValue( INPUT_VER_DATE, local_df.format(newStudy.getProtocolDateVerification())); } catch (Exception pe) { fp.addPresetValue(INPUT_VER_DATE, fp.getString(INPUT_VER_DATE)); } setPresetValues(fp.getPresetValues()); request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap); request.setAttribute("statuses", Status.toActiveArrayList()); forwardPage(Page.CREATE_SUB_STUDY); } else if ("submit".equalsIgnoreCase(action)) { submitStudy(); } } }
private String getInputStartHalf() { return fp.getString(INPUT_STARTDATE_PREFIX + "Half"); }
private String getInputEndHour() { return fp.getString(INPUT_ENDDATE_PREFIX + "Hour"); }
private String getInputEndMinute() { return fp.getString(INPUT_ENDDATE_PREFIX + "Minute"); }
@Override protected void processRequest() throws Exception { checkStudyLocked(Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_locked")); panel.setStudyInfoShown(false); fp = new FormProcessor(request); FormDiscrepancyNotes discNotes = null; int studySubjectId = fp.getInt(INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT); // input from manage subject matrix, user has specified definition id int studyEventDefinitionId = fp.getInt(INPUT_STUDY_EVENT_DEFINITION); // TODO: make this sensitive to permissions StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource()); StudySubjectBean ssb; if (studySubjectId <= 0) { ssb = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT); } else { // YW 11-08-2007, << a new study event could not be added if its // study subject has been removed ssb = (StudySubjectBean) sdao.findByPK(studySubjectId); Status s = ssb.getStatus(); if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) { addPageMessage( resword.getString("study_event") + resterm.getString("could_not_be") + resterm.getString("added") + "." + respage.getString("study_subject_has_been_deleted")); request.setAttribute("id", new Integer(studySubjectId).toString()); forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET); } // YW >> request.setAttribute(INPUT_REQUEST_STUDY_SUBJECT, "no"); } // running this crashes the server, or so we think...instead, let's grab a count // or remove it altogether tbh 10/2009 // ArrayList subjects = sdao.findAllActiveByStudyOrderByLabel(currentStudy); // TODO: make this sensitive to permissions StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource()); StudyBean studyWithEventDefinitions = currentStudy; if (currentStudy.getParentStudyId() > 0) { studyWithEventDefinitions = new StudyBean(); studyWithEventDefinitions.setId(currentStudy.getParentStudyId()); } // find all active definitions with CRFs ArrayList eventDefinitions = seddao.findAllActiveByStudy(studyWithEventDefinitions); // EventDefinitionCRFDAO edcdao = new // EventDefinitionCRFDAO(sm.getDataSource()); // ArrayList definitionsWithCRF = new ArrayList(); // for (int i=0; i<eventDefinitions.size(); i++) { // StudyEventDefinitionBean sed = // (StudyEventDefinitionBean)eventDefinitions.get(i); // logger.info("StudyEventDefinition name[" + sed.getName() + "]"); // ArrayList edcs = edcdao.findAllByEventDefinitionId(sed.getId()); // if (!edcs.isEmpty()) { // definitionsWithCRF.add(sed); // } // } // Collections.sort(definitionsWithCRF); Collections.sort(eventDefinitions); /* * ArrayList eventDefinitionsScheduled = new ArrayList(); for (int i = * 0; i < eventDefinitions.size(); i++) { StudyEventDefinitionBean sed = * (StudyEventDefinitionBean) eventDefinitions.get(i); if * (sed.getType().equalsIgnoreCase("scheduled")) { * eventDefinitionsScheduled.add(sed); } } */ // all definitions will appear in scheduled event creation box-11/26/05 ArrayList eventDefinitionsScheduled = eventDefinitions; if (!fp.isSubmitted()) { // StudyEventDAO sed = new StudyEventDAO(sm.getDataSource()); // sed.updateSampleOrdinals_v092(); HashMap presetValues = new HashMap(); // YW 08-16-2007 << set default as blank for time presetValues.put(INPUT_STARTDATE_PREFIX + "Hour", new Integer(-1)); presetValues.put(INPUT_STARTDATE_PREFIX + "Minute", new Integer(-1)); presetValues.put(INPUT_STARTDATE_PREFIX + "Half", new String("")); presetValues.put(INPUT_ENDDATE_PREFIX + "Hour", new Integer(-1)); presetValues.put(INPUT_ENDDATE_PREFIX + "Minute", new Integer(-1)); presetValues.put(INPUT_ENDDATE_PREFIX + "Half", new String("")); for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1)); presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1)); presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half", new String("")); presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1)); presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1)); presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half", new String("")); } // SimpleDateFormat sdf = new SimpleDateFormat("MM/dd/yyyy"); // example of taking the above line and transferring to i18n on the // below line, tbh String dateValue = local_df.format(new Date(System.currentTimeMillis())); presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue); for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date", dateValue); // location presetValues.put(INPUT_SCHEDULED_LOCATION[i], currentStudy.getFacilityCity()); presetValues.put(this.DISPLAY_SCHEDULED[i], "none"); } presetValues.put(INPUT_LOCATION, currentStudy.getFacilityCity()); // defualt if (ssb != null && ssb.isActive()) { presetValues.put(INPUT_STUDY_SUBJECT, ssb); String requestStudySubject = (String) request.getAttribute(INPUT_REQUEST_STUDY_SUBJECT); if (requestStudySubject != null) { presetValues.put(INPUT_REQUEST_STUDY_SUBJECT, requestStudySubject); dateValue = local_df.format(new Date()); presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue); } } if (studyEventDefinitionId > 0) { StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId); presetValues.put(INPUT_STUDY_EVENT_DEFINITION, sed); } // tbh logger.info("set preset values: " + presetValues.toString()); System.out.println("set preset values: " + presetValues.toString()); logger.info("found def.w.CRF list, size " + eventDefinitions.size()); // tbh setPresetValues(presetValues); ArrayList subjects = new ArrayList(); setupBeans(subjects, eventDefinitions); discNotes = new FormDiscrepancyNotes(); session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes); request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled); setInputMessages(new HashMap()); forwardPage(Page.CREATE_NEW_STUDY_EVENT); } else { // tbh // String dateCheck = (String)request.getAttribute("startDate"); // String endCheck = (String)request.getAttribute("endDate"); // logger.info(dateCheck+"; "+endCheck); String dateCheck2 = request.getParameter("startDate"); String endCheck2 = request.getParameter("endDate"); logger.info(dateCheck2 + "; " + endCheck2); // YW, 3-12-2008, 2220 fix << String strEnd = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX); String strEndScheduled[] = new String[ADDITIONAL_SCHEDULED_NUM]; for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { strEndScheduled[i] = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX_SCHEDULED[i]); } Date start = getInputStartDate(); Date end = null; Date[] startScheduled = new Date[ADDITIONAL_SCHEDULED_NUM]; for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { startScheduled[i] = getInputStartDateScheduled(i); } Date[] endScheduled = new Date[ADDITIONAL_SCHEDULED_NUM]; // YW >> // for (java.util.Enumeration enu = request.getAttributeNames(); // enu.hasMoreElements() ;) { // logger.info(">>> found "+enu.nextElement().toString()); // } // tbh discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); if (discNotes == null) { discNotes = new FormDiscrepancyNotes(); session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes); } DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes); v.addValidation(INPUT_STARTDATE_PREFIX, Validator.IS_DATE_TIME); v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX); if (!strEnd.equals("")) { v.addValidation(INPUT_ENDDATE_PREFIX, Validator.IS_DATE_TIME); v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX); } v.addValidation( INPUT_STUDY_EVENT_DEFINITION, Validator.ENTITY_EXISTS_IN_STUDY, seddao, studyWithEventDefinitions); // v.addValidation(INPUT_STUDY_SUBJECT, Validator.ENTITY_EXISTS_IN_STUDY, sdao, currentStudy); // removed tbh 11/2009 v.addValidation(INPUT_LOCATION, Validator.NO_BLANKS); v.addValidation(INPUT_STUDY_SUBJECT_LABEL, Validator.NO_BLANKS); v.addValidation( INPUT_LOCATION, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 2000); v.alwaysExecuteLastValidation(INPUT_LOCATION); boolean hasScheduledEvent = false; for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { if (!StringUtil.isBlank(fp.getString(this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]))) { // logger.info("has scheduled definition******"); v.addValidation( this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], Validator.ENTITY_EXISTS_IN_STUDY, seddao, studyWithEventDefinitions); v.addValidation(INPUT_SCHEDULED_LOCATION[i], Validator.NO_BLANKS); v.addValidation( INPUT_SCHEDULED_LOCATION[i], Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 2000); v.alwaysExecuteLastValidation(INPUT_SCHEDULED_LOCATION[i]); v.addValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME); v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i]); if (!strEndScheduled[i].equals("")) { v.addValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME); v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i]); } hasScheduledEvent = true; fp.addPresetValue(DISPLAY_SCHEDULED[i], "all"); } else { fp.addPresetValue(DISPLAY_SCHEDULED[i], "none"); } } HashMap errors = v.validate(); // logger.info("v is not null *****"); String location = resword.getString("location"); // don't allow user to use the default value 'Location' since // location // is a required field if (!StringUtil.isBlank(fp.getString(INPUT_LOCATION)) && fp.getString(INPUT_LOCATION).equalsIgnoreCase(location)) { Validator.addError(errors, INPUT_LOCATION, restext.getString("not_a_valid_location")); } StudyEventDefinitionBean definition = (StudyEventDefinitionBean) seddao.findByPK(fp.getInt(INPUT_STUDY_EVENT_DEFINITION)); // StudySubjectBean studySubject = (StudySubjectBean) // sdao.findByPK(fp.getInt(INPUT_STUDY_SUBJECT)); // sdao.findByLabelAndStudy(label, study) StudySubjectBean studySubject = (StudySubjectBean) sdao.findByLabelAndStudy(fp.getString(INPUT_STUDY_SUBJECT_LABEL), currentStudy); // >> 4358 tbh, 11/2009 // what if we are sent here from AddNewSubjectServlet.java??? we need to get that study // subject bean if (request.getAttribute(INPUT_STUDY_SUBJECT) != null) { studySubject = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT); } // << tbh if (studySubject.getLabel() == "") { // add an error here, tbh System.out.println("tripped the error here 20091109"); Validator.addError( errors, INPUT_STUDY_SUBJECT, respage.getString("must_enter_subject_ID_for_identifying")); } if (!subjectMayReceiveStudyEvent(sm.getDataSource(), definition, studySubject)) { Validator.addError( errors, INPUT_STUDY_EVENT_DEFINITION, restext.getString("not_added_since_event_not_repeating")); } ArrayList<StudyEventDefinitionBean> definitionScheduleds = new ArrayList<StudyEventDefinitionBean>(); int[] scheduledDefinitionIds = new int[ADDITIONAL_SCHEDULED_NUM]; if (hasScheduledEvent) { for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { int pk = fp.getInt(INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]); if (pk > 0) { StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(pk); System.out.println( "scheduled def:" + pk + " " + INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i] + " " + sedb.getName()); definitionScheduleds.add(sedb); scheduledDefinitionIds[i] = pk; if (!subjectMayReceiveStudyEvent(sm.getDataSource(), sedb, studySubject)) { Validator.addError( errors, INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], restext.getString("not_added_since_event_not_repeating")); } } else { definitionScheduleds.add(new StudyEventDefinitionBean()); } } } // YW, 3-12-2008, 2220 fix >> if (!"".equals(strEnd) && !errors.containsKey(INPUT_STARTDATE_PREFIX) && !errors.containsKey(INPUT_ENDDATE_PREFIX)) { end = getInputEndDate(); if (!fp.getString(INPUT_STARTDATE_PREFIX + "Date") .equals(fp.getString(INPUT_ENDDATE_PREFIX + "Date"))) { if (end.before(start)) { Validator.addError( errors, INPUT_ENDDATE_PREFIX, resexception.getString("input_provided_not_occure_after_previous_start_date_time")); } } else { // if in same date, only check when both had time entered if (fp.timeEntered(INPUT_STARTDATE_PREFIX) && fp.timeEntered(INPUT_ENDDATE_PREFIX)) { if (end.before(start) || end.equals(start)) { Validator.addError( errors, INPUT_ENDDATE_PREFIX, resexception.getString( "input_provided_not_occure_after_previous_start_date_time")); } } } } String prevStartPrefix = INPUT_STARTDATE_PREFIX; Set<Integer> pickedSeds = new TreeSet<Integer>(); pickedSeds.add(studyEventDefinitionId); HashMap<Integer, Integer> scheduledSeds = new HashMap<Integer, Integer>(); scheduledSeds.put(studyEventDefinitionId, -1); for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { if (scheduledDefinitionIds[i] > 0 && !errors.containsKey(INPUT_STARTDATE_PREFIX_SCHEDULED[i]) && !errors.containsKey(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) { if (scheduledSeds.containsKey(scheduledDefinitionIds[i])) { int prevStart = scheduledSeds.get(scheduledDefinitionIds[i]); prevStartPrefix = prevStart == -1 ? INPUT_STARTDATE_PREFIX : INPUT_STARTDATE_PREFIX_SCHEDULED[prevStart]; Date prevStartDate = prevStart == -1 ? this.getInputStartDate() : this.getInputStartDateScheduled( Integer.parseInt( prevStartPrefix.charAt(prevStartPrefix.length() - 1) + "")); if (fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date") .equals(fp.getString(prevStartPrefix + "Date"))) { // if in same day, only check when both have time // inputs. boolean schStartTime = fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i]); boolean startTime = fp.timeEntered(prevStartPrefix); if (schStartTime && startTime) { if (startScheduled[i].before(prevStartDate)) { Validator.addError( errors, INPUT_STARTDATE_PREFIX_SCHEDULED[i], resexception.getString( "input_provided_not_occure_after_previous_start_date_time")); } } } else { if (startScheduled[i].before(prevStartDate)) { Validator.addError( errors, INPUT_STARTDATE_PREFIX_SCHEDULED[i], resexception.getString( "input_provided_not_occure_after_previous_start_date_time")); } } } scheduledSeds.put(scheduledDefinitionIds[i], i); if (!strEndScheduled[i].equals("")) { endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]); String prevEndPrefix = i > 0 ? INPUT_ENDDATE_PREFIX_SCHEDULED[i - 1] : INPUT_ENDDATE_PREFIX; if (!fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date") .equals(fp.getString(prevEndPrefix + "Date"))) { if (endScheduled[i].before(startScheduled[i])) { Validator.addError( errors, INPUT_ENDDATE_PREFIX_SCHEDULED[i], resexception.getString( "input_provided_not_occure_after_previous_start_date_time")); } } else { // if in same date, only check when both had time // entered if (fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i]) && fp.timeEntered(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) { if (endScheduled[i].before(startScheduled[i]) || endScheduled[i].equals(startScheduled[i])) { Validator.addError( errors, INPUT_ENDDATE_PREFIX_SCHEDULED[i], resexception.getString( "input_provided_not_occure_after_previous_start_date_time")); } } } } } } // YW >> System.out.println("we have errors; number of this; " + errors.size()); if (!errors.isEmpty()) { logger.info("we have errors; number of this; " + errors.size()); System.out.println( "found request study subject: " + fp.getString(INPUT_REQUEST_STUDY_SUBJECT)); addPageMessage(respage.getString("errors_in_submission_see_below")); setInputMessages(errors); fp.addPresetValue(INPUT_STUDY_EVENT_DEFINITION, definition); fp.addPresetValue(INPUT_STUDY_SUBJECT, studySubject); fp.addPresetValue(INPUT_STUDY_SUBJECT_LABEL, fp.getString(INPUT_STUDY_SUBJECT_LABEL)); fp.addPresetValue(INPUT_REQUEST_STUDY_SUBJECT, fp.getString(INPUT_REQUEST_STUDY_SUBJECT)); fp.addPresetValue(INPUT_LOCATION, fp.getString(INPUT_LOCATION)); for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { fp.addPresetValue(INPUT_SCHEDULED_LOCATION[i], fp.getString(INPUT_SCHEDULED_LOCATION[i])); } String prefixes[] = new String[2 + 2 * ADDITIONAL_SCHEDULED_NUM]; prefixes[0] = INPUT_STARTDATE_PREFIX; prefixes[1] = INPUT_ENDDATE_PREFIX; int b = ADDITIONAL_SCHEDULED_NUM + 2; for (int i = 2; i < b; ++i) { prefixes[i] = INPUT_STARTDATE_PREFIX_SCHEDULED[i - 2]; } for (int i = b; i < ADDITIONAL_SCHEDULED_NUM + b; ++i) { prefixes[i] = INPUT_ENDDATE_PREFIX_SCHEDULED[i - b]; } fp.setCurrentDateTimeValuesAsPreset(prefixes); if (hasScheduledEvent) { for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { fp.addPresetValue( INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], definitionScheduleds.get(i)); } } setPresetValues(fp.getPresetValues()); ArrayList subjects = new ArrayList(); setupBeans(subjects, eventDefinitions); request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled); forwardPage(Page.CREATE_NEW_STUDY_EVENT); } else { System.out.println("error is empty"); StudyEventDAO sed = new StudyEventDAO(sm.getDataSource()); StudyEventBean studyEvent = new StudyEventBean(); studyEvent.setStudyEventDefinitionId(definition.getId()); studyEvent.setStudySubjectId(studySubject.getId()); // YW 08-17-2007 << if ("-1".equals(getInputStartHour()) && "-1".equals(getInputStartMinute()) && "".equals(getInputStartHalf())) { studyEvent.setStartTimeFlag(false); } else { studyEvent.setStartTimeFlag(true); } // YW >> studyEvent.setDateStarted(start); // comment to find bug 1389, tbh logger.info("found start date: " + local_df.format(start)); Date startScheduled2[] = new Date[ADDITIONAL_SCHEDULED_NUM]; for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { startScheduled2[i] = getInputStartDateScheduled(i); } // tbh // YW, 3-12-2008, 2220 fix << if (!"".equals(strEnd)) { // YW >> if ("-1".equals(getInputEndHour()) && "-1".equals(getInputEndMinute()) && "".equals(getInputEndHalf())) { studyEvent.setEndTimeFlag(false); } else { studyEvent.setEndTimeFlag(true); } studyEvent.setDateEnded(end); } studyEvent.setOwner(ub); studyEvent.setStatus(Status.AVAILABLE); studyEvent.setLocation(fp.getString(INPUT_LOCATION)); studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED); // ArrayList subjectsExistingEvents = // sed.findAllByStudyAndStudySubjectId(currentStudy, // studySubject.getId()); studyEvent.setSampleOrdinal(sed.getMaxSampleOrdinal(definition, studySubject) + 1); studyEvent = (StudyEventBean) sed.create(studyEvent); if (!studyEvent.isActive()) { throw new OpenClinicaException(restext.getString("event_not_created_in_database"), "2"); } addPageMessage( restext.getString("X_event_wiht_definition") + definition.getName() + restext.getString("X_and_subject") + studySubject.getName() + respage.getString("X_was_created_succesfully")); // save discrepancy notes into DB FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource()); String[] eventFields = {INPUT_LOCATION, INPUT_STARTDATE_PREFIX, INPUT_ENDDATE_PREFIX}; for (String element : eventFields) { AddNewSubjectServlet.saveFieldNotes( element, fdn, dndao, studyEvent.getId(), "studyEvent", currentStudy); } // logger.info("here ok 3333333333333333"); if (hasScheduledEvent) { for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) { // should only do the following process if user inputs a // scheduled event, // which is scheduledDefinitionIds[i] > 0 if (scheduledDefinitionIds[i] > 0) { if (subjectMayReceiveStudyEvent( sm.getDataSource(), definitionScheduleds.get(i), studySubject)) { StudyEventBean studyEventScheduled = new StudyEventBean(); studyEventScheduled.setStudyEventDefinitionId(scheduledDefinitionIds[i]); studyEventScheduled.setStudySubjectId(studySubject.getId()); // YW 11-14-2007 if ("-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour")) && "-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute")) && "".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half"))) { studyEventScheduled.setStartTimeFlag(false); } else { studyEventScheduled.setStartTimeFlag(true); } // YW >> studyEventScheduled.setDateStarted(startScheduled[i]); // YW, 3-12-2008, 2220 fix<< if (!"".equals(strEndScheduled[i])) { endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]); if ("-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour")) && "-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute")) && "".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half"))) { studyEventScheduled.setEndTimeFlag(false); } else { studyEventScheduled.setEndTimeFlag(true); } } studyEventScheduled.setDateEnded(endScheduled[i]); // YW >> studyEventScheduled.setOwner(ub); studyEventScheduled.setStatus(Status.AVAILABLE); studyEventScheduled.setLocation(fp.getString(INPUT_SCHEDULED_LOCATION[i])); studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED); // subjectsExistingEvents = // sed.findAllByStudyAndStudySubjectId( // currentStudy, // studySubject.getId()); studyEventScheduled.setSampleOrdinal( sed.getMaxSampleOrdinal(definitionScheduleds.get(i), studySubject) + 1); // System.out.println("create scheduled events"); studyEventScheduled = (StudyEventBean) sed.create(studyEventScheduled); if (!studyEventScheduled.isActive()) { throw new OpenClinicaException( restext.getString("scheduled_event_not_created_in_database"), "2"); } AddNewSubjectServlet.saveFieldNotes( INPUT_SCHEDULED_LOCATION[i], fdn, dndao, studyEventScheduled.getId(), "studyEvent", currentStudy); // YW 3-12-2008, 2220 fix << AddNewSubjectServlet.saveFieldNotes( INPUT_STARTDATE_PREFIX_SCHEDULED[i], fdn, dndao, studyEventScheduled.getId(), "studyEvent", currentStudy); AddNewSubjectServlet.saveFieldNotes( INPUT_ENDDATE_PREFIX_SCHEDULED[i], fdn, dndao, studyEventScheduled.getId(), "studyEvent", currentStudy); // YW >> } else { addPageMessage( restext.getString("scheduled_event_definition") + definitionScheduleds.get(i).getName() + restext.getString("X_and_subject") + studySubject.getName() + restext.getString("not_created_since_event_not_repeating") + restext.getString("event_type_already_exists")); } } } } // if session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME); request.setAttribute( EnterDataForStudyEventServlet.INPUT_EVENT_ID, String.valueOf(studyEvent.getId())); response.encodeRedirectURL("EnterDataForStudyEvent?eventId=" + studyEvent.getId()); forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET); // we want to actually have url of entering data in browser, so // redirecting // response.sendRedirect(response.encodeRedirectURL( // "EnterDataForStudyEvent?eventId=" // + studyEvent.getId())); return; } } }
private String getInputEndHalf() { return fp.getString(INPUT_ENDDATE_PREFIX + "Half"); }
/** * Validates the first section of study and save it into study bean * * @param request * @param response * @throws Exception */ private void confirmStudy() throws Exception { Validator v = new Validator(request); FormProcessor fp = new FormProcessor(request); v.addValidation("name", Validator.NO_BLANKS); v.addValidation("uniqueProId", Validator.NO_BLANKS); v.addValidation("description", Validator.NO_BLANKS); v.addValidation("prinInvestigator", Validator.NO_BLANKS); if (!StringUtil.isBlank(fp.getString(INPUT_START_DATE))) { v.addValidation(INPUT_START_DATE, Validator.IS_A_DATE); } if (!StringUtil.isBlank(fp.getString(INPUT_END_DATE))) { v.addValidation(INPUT_END_DATE, Validator.IS_A_DATE); } if (!StringUtil.isBlank(fp.getString("facConEmail"))) { v.addValidation("facConEmail", Validator.IS_A_EMAIL); } // v.addValidation("statusId", Validator.IS_VALID_TERM); v.addValidation( "secondProId", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facName", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facCity", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facState", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 20); v.addValidation( "facZip", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 64); v.addValidation( "facCountry", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 64); v.addValidation( "facConName", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facConDegree", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facConPhone", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facConEmail", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); errors = v.validate(); if (fp.getString("name").trim().length() > 100) { Validator.addError(errors, "name", resexception.getString("maximum_lenght_name_100")); } if (fp.getString("uniqueProId").trim().length() > 30) { Validator.addError( errors, "uniqueProId", resexception.getString("maximum_lenght_unique_protocol_30")); } if (fp.getString("description").trim().length() > 255) { Validator.addError( errors, "description", resexception.getString("maximum_lenght_brief_summary_255")); } if (fp.getString("prinInvestigator").trim().length() > 255) { Validator.addError( errors, "prinInvestigator", resexception.getString("maximum_lenght_principal_investigator_255")); } if (fp.getInt("expectedTotalEnrollment") <= 0) { Validator.addError( errors, "expectedTotalEnrollment", respage.getString("expected_total_enrollment_must_be_a_positive_number")); } session.setAttribute("newStudy", createStudyBean()); if (errors.isEmpty()) { logger.info("no errors"); forwardPage(Page.CONFIRM_CREATE_SUB_STUDY); } else { try { local_df.parse(fp.getString(INPUT_START_DATE)); fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE)); } try { local_df.parse(fp.getString(INPUT_END_DATE)); fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE))); } catch (ParseException pe) { fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE)); } setPresetValues(fp.getPresetValues()); logger.info("has validation errors"); request.setAttribute("formMessages", errors); // request.setAttribute("facRecruitStatusMap", // CreateStudyServlet.facRecruitStatusMap); request.setAttribute("statuses", Status.toActiveArrayList()); forwardPage(Page.CREATE_SUB_STUDY); } }
private void validateStudy5(FormProcessor fp, Validator v) { if (!StringUtil.isBlank(fp.getString("facConEmail"))) { v.addValidation("facConEmail", Validator.IS_A_EMAIL); } v.addValidation( "facName", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facCity", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facState", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 20); v.addValidation( "facZip", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 64); v.addValidation( "facCountry", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 64); v.addValidation( "facConName", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facConDegree", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facConPhone", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); v.addValidation( "facConEmail", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255); errors = v.validate(); study.setFacilityCity(fp.getString("facCity")); study.setFacilityContactDegree(fp.getString("facConDrgree")); study.setFacilityName(fp.getString("facName")); study.setFacilityContactEmail(fp.getString("facConEmail")); study.setFacilityContactPhone(fp.getString("facConPhone")); study.setFacilityContactName(fp.getString("facConName")); study.setFacilityCountry(fp.getString("facCountry")); study.setFacilityContactDegree(fp.getString("facConDegree")); // newStudy.setFacilityRecruitmentStatus(fp.getString("facRecStatus")); study.setFacilityState(fp.getString("facState")); study.setFacilityZip(fp.getString("facZip")); if (errors.isEmpty()) { } else { request.setAttribute("formMessages", errors); request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap); } }
@Override public void processRequest() throws Exception { FormProcessor fp = new FormProcessor(request); String action = request.getParameter("action"); if (StringUtil.isBlank(action)) { if (currentStudy.getParentStudyId() > 0) { addPageMessage(respage.getString("you_cannot_create_site_itself_site")); forwardPage(Page.SITE_LIST_SERVLET); } else { StudyBean newStudy = new StudyBean(); newStudy.setParentStudyId(currentStudy.getId()); // get default facility info from property file newStudy.setFacilityName(SQLInitServlet.getField(CreateStudyServlet.FAC_NAME)); newStudy.setFacilityCity(SQLInitServlet.getField(CreateStudyServlet.FAC_CITY)); newStudy.setFacilityState(SQLInitServlet.getField(CreateStudyServlet.FAC_STATE)); newStudy.setFacilityCountry(SQLInitServlet.getField(CreateStudyServlet.FAC_COUNTRY)); newStudy.setFacilityContactDegree( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_DEGREE)); newStudy.setFacilityContactEmail( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_EMAIL)); newStudy.setFacilityContactName( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_NAME)); newStudy.setFacilityContactPhone( SQLInitServlet.getField(CreateStudyServlet.FAC_CONTACT_PHONE)); newStudy.setFacilityZip(SQLInitServlet.getField(CreateStudyServlet.FAC_ZIP)); ArrayList parentConfigs = currentStudy.getStudyParameters(); // logger.info("parentConfigs size:" + parentConfigs.size()); ArrayList configs = new ArrayList(); for (int i = 0; i < parentConfigs.size(); i++) { StudyParamsConfig scg = (StudyParamsConfig) parentConfigs.get(i); if (scg != null) { // find the one that sub study can change if (scg.getValue().getId() > 0 && scg.getParameter().isOverridable()) { logger.info("parameter:" + scg.getParameter().getHandle()); logger.info("value:" + scg.getValue().getValue()); // YW 10-12-2007, set overridable study parameters // for a site if (scg.getParameter().getHandle().equalsIgnoreCase("interviewerNameRequired")) { scg.getValue().setValue(fp.getString("interviewerNameRequired")); } else if (scg.getParameter() .getHandle() .equalsIgnoreCase("interviewerNameDefault")) { scg.getValue().setValue(fp.getString("interviewerNameDefault")); } else if (scg.getParameter().getHandle().equalsIgnoreCase("interviewDateRequired")) { scg.getValue().setValue(fp.getString("interviewDateRequired")); } else if (scg.getParameter().getHandle().equalsIgnoreCase("interviewDateDefault")) { scg.getValue().setValue(fp.getString("interviewDateDefault")); } // YW >> configs.add(scg); } } } newStudy.setStudyParameters(configs); // YW 10-12-2007 << newStudy .getStudyParameterConfig() .setInterviewerNameRequired(fp.getString("interviewerNameRequired")); newStudy .getStudyParameterConfig() .setInterviewerNameDefault(fp.getString("interviewerNameDefault")); newStudy .getStudyParameterConfig() .setInterviewDateRequired(fp.getString("interviewDateRequired")); newStudy .getStudyParameterConfig() .setInterviewDateDefault(fp.getString("interviewDateDefault")); // YW >> session.setAttribute("newStudy", newStudy); request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap); request.setAttribute("statuses", Status.toActiveArrayList()); forwardPage(Page.CREATE_SUB_STUDY); } } else { if ("confirm".equalsIgnoreCase(action)) { confirmStudy(); } else if ("back".equalsIgnoreCase(action)) { request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap); request.setAttribute("statuses", Status.toActiveArrayList()); forwardPage(Page.CREATE_SUB_STUDY); } else if ("submit".equalsIgnoreCase(action)) { submitStudy(); } } }
private ArrayList<StudyEventDefinitionBean> createSiteEventDefinitions(StudyBean site) { FormProcessor fp = new FormProcessor(request); ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>(); StudyBean parentStudy = (StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId()); seds = (ArrayList<StudyEventDefinitionBean>) session.getAttribute("definitions"); if (seds == null || seds.size() <= 0) { StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource()); seds = sedDao.findAllByStudy(parentStudy); } CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource()); HashMap<String, Boolean> changes = new HashMap<String, Boolean>(); for (StudyEventDefinitionBean sed : seds) { EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource()); ArrayList<EventDefinitionCRFBean> edcs = sed.getCrfs(); int start = 0; for (EventDefinitionCRFBean edcBean : edcs) { int edcStatusId = edcBean.getStatus().getId(); if (edcStatusId == 5 || edcStatusId == 7) { } else { String order = start + "-" + edcBean.getId(); int defaultVersionId = fp.getInt("defaultVersionId" + order); String requiredCRF = fp.getString("requiredCRF" + order); String doubleEntry = fp.getString("doubleEntry" + order); String electronicSignature = fp.getString("electronicSignature" + order); String hideCRF = fp.getString("hideCRF" + order); int sdvId = fp.getInt("sdvOption" + order); ArrayList<String> selectedVersionIdList = fp.getStringArray("versionSelection" + order); int selectedVersionIdListSize = selectedVersionIdList.size(); String selectedVersionIds = ""; if (selectedVersionIdListSize > 0) { for (String id : selectedVersionIdList) { selectedVersionIds += id + ","; } selectedVersionIds = selectedVersionIds.substring(0, selectedVersionIds.length() - 1); } boolean changed = false; boolean isRequired = !StringUtil.isBlank(requiredCRF) && "yes".equalsIgnoreCase(requiredCRF.trim()) ? true : false; boolean isDouble = !StringUtil.isBlank(doubleEntry) && "yes".equalsIgnoreCase(doubleEntry.trim()) ? true : false; boolean hasPassword = !StringUtil.isBlank(electronicSignature) && "yes".equalsIgnoreCase(electronicSignature.trim()) ? true : false; boolean isHide = !StringUtil.isBlank(hideCRF) && "yes".equalsIgnoreCase(hideCRF.trim()) ? true : false; if (edcBean.getParentId() > 0) { int dbDefaultVersionId = edcBean.getDefaultVersionId(); if (defaultVersionId != dbDefaultVersionId) { changed = true; CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(defaultVersionId); edcBean.setDefaultVersionId(defaultVersionId); edcBean.setDefaultVersionName(defaultVersion.getName()); } if (isRequired != edcBean.isRequiredCRF()) { changed = true; edcBean.setRequiredCRF(isRequired); } if (isDouble != edcBean.isDoubleEntry()) { changed = true; edcBean.setDoubleEntry(isDouble); } if (hasPassword != edcBean.isElectronicSignature()) { changed = true; edcBean.setElectronicSignature(hasPassword); } if (isHide != edcBean.isHideCrf()) { changed = true; edcBean.setHideCrf(isHide); } if (!StringUtil.isBlank(selectedVersionIds) && !selectedVersionIds.equals(edcBean.getSelectedVersionIds())) { changed = true; String[] ids = selectedVersionIds.split(","); ArrayList<Integer> idList = new ArrayList<Integer>(); for (String id : ids) { idList.add(Integer.valueOf(id)); } edcBean.setSelectedVersionIdList(idList); edcBean.setSelectedVersionIds(selectedVersionIds); } if (sdvId > 0 && sdvId != edcBean.getSourceDataVerification().getCode()) { changed = true; edcBean.setSourceDataVerification(SourceDataVerification.getByCode(sdvId)); } } else { // only if definition-crf has been modified, will it be // saved for the site int defaultId = defaultVersionId > 0 ? defaultVersionId : edcBean.getDefaultVersionId(); if (defaultId == defaultVersionId) { if (isRequired == edcBean.isRequiredCRF()) { if (isDouble == edcBean.isDoubleEntry()) { if (hasPassword == edcBean.isElectronicSignature()) { if (isHide == edcBean.isHideCrf()) { if (selectedVersionIdListSize > 0) { if (selectedVersionIdListSize == edcBean.getVersions().size()) { if (sdvId > 0) { if (sdvId != edcBean.getSourceDataVerification().getCode()) { changed = true; edcBean.setSourceDataVerification( SourceDataVerification.getByCode(sdvId)); } } } else { changed = true; String[] ids = selectedVersionIds.split(","); ArrayList<Integer> idList = new ArrayList<Integer>(); for (String id : ids) { idList.add(Integer.valueOf(id)); } edcBean.setSelectedVersionIdList(idList); edcBean.setSelectedVersionIds(selectedVersionIds); } } } else { changed = true; edcBean.setHideCrf(isHide); } } else { changed = true; edcBean.setElectronicSignature(hasPassword); } } else { changed = true; edcBean.setDoubleEntry(isDouble); } } else { changed = true; edcBean.setRequiredCRF(isRequired); } } else { changed = true; CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(defaultVersionId); edcBean.setDefaultVersionId(defaultVersionId); edcBean.setDefaultVersionName(defaultVersion.getName()); } } changes.put(sed.getId() + "-" + edcBean.getId(), changed); ++start; } } } session.setAttribute("changed", changes); return seds; }