Examples with Mapping org.exolab.castor.mapping.Mapping used on opensource projects

Example 1 with Mapping

use of org.exolab.castor.mapping.Mapping in project OpenClinica by OpenClinica.

the class ImportCRFDataServlet method processRequest.

@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);
        // 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);
                    }
                }
                // 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"));
                }
                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);
        }
    // }
    }
}

Example 2 with Mapping

use of org.exolab.castor.mapping.Mapping in project OpenClinica by OpenClinica.

the class ImportRuleServlet method handleLoadCastor.

private RulesPostImportContainer handleLoadCastor(File xmlFile) {
    RulesPostImportContainer ruleImport = null;
    try {
        // create an XMLContext instance
        XMLContext xmlContext = new XMLContext();
        // create and set a Mapping instance
        Mapping mapping = xmlContext.createMapping();
        // mapping.loadMapping(SpringServletAccess.getPropertiesDir(context) + "mapping.xml");
        mapping.loadMapping(getCoreResources().getURL("mapping.xml"));
        xmlContext.addMapping(mapping);
        // create a new Unmarshaller
        Unmarshaller unmarshaller = xmlContext.createUnmarshaller();
        unmarshaller.setWhitespacePreserve(false);
        unmarshaller.setClass(RulesPostImportContainer.class);
        // Create a Reader to the file to unmarshal from
        FileReader reader = new FileReader(xmlFile);
        ruleImport = (RulesPostImportContainer) unmarshaller.unmarshal(reader);
        ruleImport.initializeRuleDef();
        logRuleImport(ruleImport);
        return ruleImport;
    } catch (FileNotFoundException ex) {
        throw new OpenClinicaSystemException(ex.getMessage(), ex.getCause());
    } catch (IOException ex) {
        throw new OpenClinicaSystemException(ex.getMessage(), ex.getCause());
    } catch (MarshalException e) {
        throw new OpenClinicaSystemException(e.getMessage(), e.getCause());
    } catch (ValidationException e) {
        throw new OpenClinicaSystemException(e.getMessage(), e.getCause());
    } catch (MappingException e) {
        throw new OpenClinicaSystemException(e.getMessage(), e.getCause());
    }
}

Example 3 with Mapping

use of org.exolab.castor.mapping.Mapping in project OpenClinica by OpenClinica.

the class OpenRosaServices method getFormList.

/**
     * @api {get} /rest2/openrosa/:studyOID/formList Get Form List
     * @apiName getFormList
     * @apiPermission admin
     * @apiVersion 3.8.0
     * @apiParam {String} studyOID Study Oid.
     * @apiGroup Form
     * @apiDescription Retrieves a listing of the available OpenClinica forms.
     * @apiParamExample {json} Request-Example:
     *                  {
     *                  "studyOid": "S_SAMPLTE",
     *                  }
     * @apiSuccessExample {xml} Success-Response:
     *                    HTTP/1.1 200 OK
     *                    {
     *                    <xforms xmlns="http://openrosa.org/xforms/xformsList">
     *                    <xform>
     *                    <formID>F_FIRSTFORM_1</formID>
     *                    <name>First Form</name>
     *                    <majorMinorVersion>1</majorMinorVersion>
     *                    <version>1</version>
     *                    <hash>8678370cd92814d4e3216d58d821403f</hash>
     *                    <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
     *                    formId=F_FIRSTFORM_1</downloadUrl>
     *                    </xform>
     *                    <xform>
     *                    <formID>F_SECONDFORM_1</formID>
     *                    <name>Second Form</name>
     *                    <majorMinorVersion>1</majorMinorVersion>
     *                    <version>1</version>
     *                    <hash>7ee60d1c6516b730bbe9bdbd7cad942f</hash>
     *                    <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
     *                    formId=F_SECONDFORM_1</downloadUrl>
     *                    </xform>
     *                    </xforms>
     */
@GET
@Path("/{studyOID}/formList")
@Produces(MediaType.TEXT_XML)
public String getFormList(@Context HttpServletRequest request, @Context HttpServletResponse response, @PathParam("studyOID") String studyOID, @QueryParam("formID") String uniqueId, @RequestHeader("Authorization") String authorization, @Context ServletContext context) throws Exception {
    if (!mayProceedPreview(studyOID))
        return null;
    XFormList formList = null;
    try {
        if (StringUtils.isEmpty(uniqueId)) {
            List<CrfBean> crfs = crfDao.findAll();
            List<FormLayout> formLayouts = formLayoutDao.findAll();
            formList = new XFormList();
            for (CrfBean crf : crfs) {
                for (FormLayout formLayout : formLayouts) {
                    if (formLayout.getCrf().getCrfId() == crf.getCrfId()) {
                        XForm form = new XForm(crf, formLayout);
                        // TODO: Need to generate hash based on contents of
                        // XForm. Will be done in a later story.
                        // TODO: For now all XForms get a date based hash to
                        // trick Enketo into always downloading
                        // TODO: them.
                        String urlBase = getCoreResources().getDataInfo().getProperty("sysURL").split("/MainMenu")[0];
                        form.setDownloadURL(urlBase + "/rest2/openrosa/" + studyOID + "/formXml?formId=" + formLayout.getOcOid());
                        List<FormLayoutMedia> mediaList = formLayoutMediaDao.findByFormLayoutIdForNoteTypeMedia(formLayout.getFormLayoutId());
                        if (mediaList != null && mediaList.size() > 0) {
                            form.setManifestURL(urlBase + "/rest2/openrosa/" + studyOID + "/manifest?formId=" + formLayout.getOcOid());
                        }
                        formList.add(form);
                    }
                }
            }
        } else {
            formList = getForm(request, response, studyOID, uniqueId, authorization, context);
        }
        // Create the XML formList using a Castor mapping file.
        XMLContext xmlContext = new XMLContext();
        Mapping mapping = xmlContext.createMapping();
        mapping.loadMapping(getCoreResources().getURL("openRosaFormListMapping.xml"));
        xmlContext.addMapping(mapping);
        Marshaller marshaller = xmlContext.createMarshaller();
        StringWriter writer = new StringWriter();
        marshaller.setWriter(writer);
        marshaller.marshal(formList);
        // Set response headers
        Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("GMT"));
        Date currentDate = new Date();
        cal.setTime(currentDate);
        SimpleDateFormat format = new SimpleDateFormat("E, dd MMM yyyy HH:mm:ss zz");
        format.setCalendar(cal);
        response.setHeader("Content-Type", "text/xml; charset=UTF-8");
        response.setHeader("Date", format.format(currentDate));
        response.setHeader("X-OpenRosa-Version", "1.0");
        return writer.toString();
    } catch (Exception e) {
        LOGGER.error(e.getMessage());
        LOGGER.error(ExceptionUtils.getStackTrace(e));
        return "<Error>" + e.getMessage() + "</Error>";
    }
}

Example 4 with Mapping

use of org.exolab.castor.mapping.Mapping in project camel by apache.

the class AbstractCastorDataFormat method createXMLContext.

protected XMLContext createXMLContext(ClassResolver resolver, ClassLoader contextClassLoader) throws Exception {
    XMLContext xmlContext = new XMLContext();
    if (ObjectHelper.isNotEmpty(getMappingFile())) {
        Mapping xmlMap;
        if (contextClassLoader != null) {
            xmlMap = new Mapping(contextClassLoader);
        } else {
            xmlMap = new Mapping();
        }
        xmlMap.loadMapping(resolver.loadResourceAsURL(getMappingFile()));
        xmlContext.addMapping(xmlMap);
    }
    if (getPackages() != null) {
        xmlContext.addPackages(getPackages());
    }
    if (getClassNames() != null) {
        for (String name : getClassNames()) {
            Class<?> clazz = resolver.resolveClass(name);
            xmlContext.addClass(clazz);
        }
    }
    return xmlContext;
}

Example 5 with Mapping

use of org.exolab.castor.mapping.Mapping in project spring-framework by spring-projects.

the class CastorMarshaller method createXMLContext.

/**
	 * Create the Castor {@code XMLContext}. Subclasses can override this to create a custom context.
	 * <p>The default implementation loads mapping files if defined, or the target class or packages if defined.
	 * @return the created resolver
	 * @throws MappingException when the mapping file cannot be loaded
	 * @throws IOException in case of I/O errors
	 * @see XMLContext#addMapping(org.exolab.castor.mapping.Mapping)
	 * @see XMLContext#addClass(Class)
	 */
protected XMLContext createXMLContext(Resource[] mappingLocations, Class<?>[] targetClasses, String[] targetPackages) throws MappingException, ResolverException, IOException {
    XMLContext context = new XMLContext();
    if (!ObjectUtils.isEmpty(mappingLocations)) {
        Mapping mapping = new Mapping();
        for (Resource mappingLocation : mappingLocations) {
            mapping.loadMapping(SaxResourceUtils.createInputSource(mappingLocation));
        }
        context.addMapping(mapping);
    }
    if (!ObjectUtils.isEmpty(targetClasses)) {
        context.addClasses(targetClasses);
    }
    if (!ObjectUtils.isEmpty(targetPackages)) {
        context.addPackages(targetPackages);
    }
    if (this.castorProperties != null) {
        for (Map.Entry<String, String> property : this.castorProperties.entrySet()) {
            context.setProperty(property.getKey(), property.getValue());
        }
    }
    return context;
}