Examples with And org.w3._2007.rif.And used on opensource projects

Example 6 with And

use of org.w3._2007.rif.And in project hale by halestudio.

the class ModelRifToRifTranslator method createLogicalFilter.

private void createLogicalFilter(List<Formula> list, ModelRifMappingCondition mappingCondition) {
    // $NON-NLS-1$
    log.fine("Creating logical filter");
    Formula logicFilterFormula = factory.createFormula();
    if (mappingCondition.getLogicalType().equals(NOT)) {
        INeg negation = factory.createINeg();
        logicFilterFormula.setINeg(negation);
        // Formula subNegationFormula = factory.createFormula();
        List<Formula> notList = new ArrayList<Formula>();
        // notList.add(subNegationFormula);
        createChildFilters(mappingCondition, notList);
        negation.setFormula(notList.get(0));
        // $NON-NLS-1$
        log.fine("Filter is a NOT filter");
    } else {
        if (mappingCondition.getLogicalType().equals(AND)) {
            And and1 = factory.createAnd();
            logicFilterFormula.setAnd(and1);
            createChildFilters(mappingCondition, and1.getFormula());
            // $NON-NLS-1$
            log.fine("Filter is an AND filter");
        } else if (mappingCondition.getLogicalType().equals(OR)) {
            Or or = factory.createOr();
            logicFilterFormula.setOr(or);
            createChildFilters(mappingCondition, or.getFormula());
            // $NON-NLS-1$
            log.fine("Filter is an OR filter");
        }
    }
    list.add(logicFilterFormula);
}

Example 7 with And

use of org.w3._2007.rif.And in project hale by halestudio.

the class ModelRifToRifTranslator method processChildren.

private void processChildren(ModelSentence s, final Exists exists, Do do1) {
    Formula existsFormula = factory.createFormula();
    And and = factory.createAnd();
    existsFormula.setAnd(and);
    exists.setFormula(existsFormula);
    Actions actions = factory.createDoActions();
    do1.setActions(actions);
    for (RifVariable instanceVariable : s.getVariables(Type.INSTANCE)) {
        // source instance variables
        if (!instanceVariable.isActionVar()) {
            recurseChildren(exists, do1, instanceVariable, s, true);
        } else // target instance variables
        {
            recurseChildren(exists, do1, instanceVariable, s, false);
        }
    }
    Map<RifVariable, Frame> map = new LinkedHashMap<RifVariable, Frame>();
    for (PropertyMapping mapping : s.getPropertyMappings()) {
        RifVariable contextVariable = mapping.getTarget().getContextVariable();
        Frame match = map.get(contextVariable);
        if (match == null) {
            map.put(contextVariable, initialiseFrame(contextVariable));
        }
    }
    for (StaticAssignment staticAssignment : s.getStaticAssignments()) {
        RifVariable contextVariable = staticAssignment.getTarget().getContextVariable();
        Frame match = map.get(contextVariable);
        if (match == null) {
            map.put(contextVariable, initialiseFrame(contextVariable));
        }
    }
    for (PropertyMapping mapping : s.getPropertyMappings()) {
        Frame frame = map.get(mapping.getTarget().getContextVariable());
        createAssignmentSlot(mapping, frame);
    }
    for (StaticAssignment staticAssignment : s.getStaticAssignments()) {
        Frame frame = map.get(staticAssignment.getTarget().getContextVariable());
        createStaticAssignmentSlot(staticAssignment, frame);
    }
    for (ModelRifMappingCondition mappingCondition : s.getMappingConditions()) {
        createFilter(exists.getFormula().getAnd().getFormula(), mappingCondition);
    }
    for (Frame frame : map.values()) {
        Assert assert1 = factory.createAssert();
        Target target = factory.createAssertTarget();
        target.setFrame(frame);
        assert1.setTarget(target);
        actions.getACTION().add(assert1);
    }
}

Example 8 with And

use of org.w3._2007.rif.And in project airavata by apache.

the class BESJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    TaskStatus taskStatus = new TaskStatus(TaskState.CREATED);
    StorageClient sc = null;
    ProcessContext processContext = taskContext.getParentProcessContext();
    // FIXME - use original output dir
    setInputOutputLocations(processContext);
    try {
        // con't reuse if UserDN has been changed.
        secProperties = getSecurityConfig(processContext);
    // try secProperties = secProperties.clone() if we can't use already initialized ClientConfigurations.
    } catch (GFacException e) {
        String msg = "Unicorn security context initialization error";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        return taskStatus;
    }
    try {
        JobSubmissionProtocol protocol = processContext.getJobSubmissionProtocol();
        JobSubmissionInterface jobSubmissionInterface = GFacUtils.getPreferredJobSubmissionInterface(processContext);
        String factoryUrl = null;
        if (protocol.equals(JobSubmissionProtocol.UNICORE)) {
            UnicoreJobSubmission unicoreJobSubmission = GFacUtils.getUnicoreJobSubmission(jobSubmissionInterface.getJobSubmissionInterfaceId());
            factoryUrl = unicoreJobSubmission.getUnicoreEndPointURL();
        }
        EndpointReferenceType eprt = EndpointReferenceType.Factory.newInstance();
        eprt.addNewAddress().setStringValue(factoryUrl);
        String userDN = processContext.getProcessModel().getUserDn();
        CreateActivityDocument cad = CreateActivityDocument.Factory.newInstance();
        // create storage
        StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, null);
        sc = storageCreator.createStorage();
        JobDefinitionType jobDefinition = JSDLGenerator.buildJSDLInstance(processContext, sc.getUrl()).getJobDefinition();
        cad.addNewCreateActivity().addNewActivityDocument().setJobDefinition(jobDefinition);
        log.info("Submitted JSDL: " + jobDefinition.getJobDescription());
        // copy files to local
        copyInputFilesToLocal(taskContext);
        // upload files if any
        DataTransferrer dt = new DataTransferrer(processContext, sc);
        dt.uploadLocalFiles();
        JobModel jobDetails = new JobModel();
        jobDetails.setTaskId(taskContext.getTaskId());
        jobDetails.setProcessId(taskContext.getProcessId());
        FactoryClient factory = new FactoryClient(eprt, secProperties);
        log.info("Activity Submitting to {} ... \n", factoryUrl);
        CreateActivityResponseDocument response = factory.createActivity(cad);
        log.info("Activity Submitted to {} ... \n", factoryUrl);
        EndpointReferenceType activityEpr = response.getCreateActivityResponse().getActivityIdentifier();
        log.info("Activity : " + activityEpr.getAddress().getStringValue() + " Submitted.");
        // factory.waitWhileActivityIsDone(activityEpr, 1000);
        jobId = WSUtilities.extractResourceID(activityEpr);
        if (jobId == null) {
            jobId = new Long(Calendar.getInstance().getTimeInMillis()).toString();
        }
        log.info("JobID: " + jobId);
        jobDetails.setJobId(jobId);
        jobDetails.setJobDescription(activityEpr.toString());
        jobDetails.setJobStatuses(Arrays.asList(new JobStatus(JobState.SUBMITTED)));
        processContext.setJobModel(jobDetails);
        GFacUtils.saveJobModel(processContext, jobDetails);
        GFacUtils.saveJobStatus(processContext, jobDetails);
        log.info(formatStatusMessage(activityEpr.getAddress().getStringValue(), factory.getActivityStatus(activityEpr).toString()));
        waitUntilDone(eprt, activityEpr, processContext, secProperties);
        ActivityStatusType activityStatus = null;
        activityStatus = getStatus(factory, activityEpr);
        log.info(formatStatusMessage(activityEpr.getAddress().getStringValue(), activityStatus.getState().toString()));
        ActivityClient activityClient;
        activityClient = new ActivityClient(activityEpr, secProperties);
        // now use the activity working directory property
        dt.setStorageClient(activityClient.getUspaceClient());
        List<OutputDataObjectType> copyOutput = null;
        if ((activityStatus.getState() == ActivityStateEnumeration.FAILED)) {
            String error = activityStatus.getFault().getFaultcode().getLocalPart() + "\n" + activityStatus.getFault().getFaultstring() + "\n EXITCODE: " + activityStatus.getExitCode();
            log.error(error);
            JobState applicationJobStatus = JobState.FAILED;
            jobDetails.setJobStatuses(Arrays.asList(new JobStatus(applicationJobStatus)));
            sendNotification(processContext, jobDetails);
            try {
                Thread.sleep(5000);
            } catch (InterruptedException e) {
            }
            // What if job is failed before execution and there are not stdouts generated yet?
            log.debug("Downloading any standard output and error files, if they were produced.");
            copyOutput = dt.downloadRemoteFiles();
        } else if (activityStatus.getState() == ActivityStateEnumeration.CANCELLED) {
            JobState applicationJobStatus = JobState.CANCELED;
            jobDetails.setJobStatuses(Arrays.asList(new JobStatus(applicationJobStatus)));
            GFacUtils.saveJobStatus(processContext, jobDetails);
            throw new GFacException(processContext.getExperimentId() + "Job Canceled");
        } else if (activityStatus.getState() == ActivityStateEnumeration.FINISHED) {
            try {
                Thread.sleep(5000);
            } catch (InterruptedException ignored) {
            }
            JobState applicationJobStatus = JobState.COMPLETE;
            jobDetails.setJobStatuses(Arrays.asList(new JobStatus(applicationJobStatus)));
            GFacUtils.saveJobStatus(processContext, jobDetails);
            log.info("Job Id: {}, exit code: {}, exit status: {}", jobDetails.getJobId(), activityStatus.getExitCode(), ActivityStateEnumeration.FINISHED.toString());
            // if (activityStatus.getExitCode() == 0) {
            // } else {
            // dt.downloadStdOuts();
            // }
            copyOutput = dt.downloadRemoteFiles();
        }
        if (copyOutput != null) {
            copyOutputFilesToStorage(taskContext, copyOutput);
            for (OutputDataObjectType outputDataObjectType : copyOutput) {
                GFacUtils.saveExperimentOutput(processContext, outputDataObjectType.getName(), outputDataObjectType.getValue());
            }
        }
        // dt.publishFinalOutputs();
        taskStatus.setState(TaskState.COMPLETED);
    } catch (AppCatalogException e) {
        log.error("Error while retrieving UNICORE job submission..", e);
        taskStatus.setState(TaskState.FAILED);
    } catch (Exception e) {
        log.error("BES task failed... ", e);
        taskStatus.setState(TaskState.FAILED);
    }
    return taskStatus;
}

Example 9 with And

use of org.w3._2007.rif.And in project webcert by sklintyg.

the class FragaSvarServiceImpl method getFragaSvar.

@Override
@Transactional(value = "jpaTransactionManager", readOnly = true)
public List<FragaSvarView> getFragaSvar(String intygId) {
    List<FragaSvar> fragaSvarList = fragaSvarRepository.findByIntygsReferensIntygsId(intygId);
    WebCertUser user = webCertUserService.getUser();
    validateSekretessmarkering(intygId, fragaSvarList, user);
    List<String> hsaEnhetIds = user.getIdsOfSelectedVardenhet();
    // Filter questions to that current user only sees questions issued to
    // units with active employment role
    fragaSvarList.removeIf(fragaSvar -> fragaSvar.getVardperson() != null && !hsaEnhetIds.contains(fragaSvar.getVardperson().getEnhetsId()));
    // Finally sort by senasteHandelseDatum
    // We do the sorting in code, since we need to sort on a derived
    // property and not a direct entity persisted
    // property in which case we could have used an order by in the query.
    fragaSvarList.sort(SENASTE_HANDELSE_DATUM_COMPARATOR);
    List<ArendeDraft> drafts = arendeDraftService.listAnswerDrafts(intygId);
    List<AnsweredWithIntyg> bmi = AnsweredWithIntygUtil.findAllKomplementForGivenIntyg(intygId, utkastRepository);
    List<FragaSvarView> fragaSvarWithBesvaratMedIntygInfo = fragaSvarList.stream().map(fs -> FragaSvarView.create(fs, fs.getFrageSkickadDatum() == null ? null : AnsweredWithIntygUtil.returnOldestKompltOlderThan(fs.getFrageSkickadDatum(), bmi), drafts.stream().filter(d -> Long.toString(fs.getInternReferens()).equals(d.getQuestionId())).findAny().map(ArendeDraft::getText).orElse(null))).collect(Collectors.toList());
    return fragaSvarWithBesvaratMedIntygInfo;
}

Example 10 with And

use of org.w3._2007.rif.And in project nhin-d by DirectProject.

the class DocumentRepositoryAbstract method provideAndRegisterDocumentSet.

/**
     * Handle an incoming ProvideAndRegisterDocumentSetRequestType object and
     * transform to XDM or relay to another XDR endponit.
     * 
     * @param prdst
     *            The incoming ProvideAndRegisterDocumentSetRequestType object
     * @return a RegistryResponseType object
     * @throws Exception
     */
protected RegistryResponseType provideAndRegisterDocumentSet(ProvideAndRegisterDocumentSetRequestType prdst) throws Exception {
    RegistryResponseType resp = null;
    try {
        getHeaderData();
        @SuppressWarnings("unused") InitialContext ctx = new InitialContext();
        DirectDocuments documents = xdsDirectDocumentsTransformer.transform(prdst);
        List<String> forwards = new ArrayList<String>();
        // Get endpoints (first check direct:to header, then go to intendedRecipients)
        if (StringUtils.isNotBlank(directTo))
            forwards = Arrays.asList((new URI(directTo).getSchemeSpecificPart()));
        else {
            forwards = ParserHL7.parseRecipients(documents);
        }
        messageId = UUID.randomUUID().toString();
        // TODO patID and subsetId
        String patId = "PATID TBD";
        String subsetId = "SUBSETID";
        getAuditMessageGenerator().provideAndRegisterAudit(messageId, remoteHost, endpoint, to, thisHost, patId, subsetId, pid);
        // Send to SMTP endpoints
        if (getResolver().hasSmtpEndpoints(forwards)) {
            // Get a reply address (first check direct:from header, then go to authorPerson)
            if (StringUtils.isNotBlank(directFrom))
                replyEmail = (new URI(directFrom)).getSchemeSpecificPart();
            else {
                replyEmail = documents.getSubmissionSet().getAuthorPerson();
                replyEmail = StringUtils.splitPreserveAllTokens(replyEmail, "^")[0];
                replyEmail = StringUtils.contains(replyEmail, "@") ? replyEmail : "nhindirect@nhindirect.org";
            }
            LOGGER.info("SENDING EMAIL TO " + getResolver().getSmtpEndpoints(forwards) + " with message id " + messageId);
            // Construct message wrapper
            DirectMessage message = new DirectMessage(replyEmail, getResolver().getSmtpEndpoints(forwards));
            message.setSubject("XD* Originated Message");
            message.setBody("Please find the attached XDM file.");
            message.setDirectDocuments(documents);
            // Send mail
            MailClient mailClient = getMailClient();
            mailClient.mail(message, messageId, suffix);
        }
        // Send to XD endpoints
        for (String reqEndpoint : getResolver().getXdEndpoints(forwards)) {
            String endpointUrl = getResolver().resolve(reqEndpoint);
            String to = StringUtils.remove(endpointUrl, "?wsdl");
            Long threadId = new Long(Thread.currentThread().getId());
            LOGGER.info("THREAD ID " + threadId);
            ThreadData threadData = new ThreadData(threadId);
            threadData.setTo(to);
            List<Document> docs = prdst.getDocument();
            // Make a copy of the original documents
            List<Document> originalDocs = new ArrayList<Document>();
            for (Document d : docs) originalDocs.add(d);
            // Clear document list
            docs.clear();
            // Re-add documents
            for (Document d : originalDocs) {
                Document doc = new Document();
                doc.setId(d.getId());
                DataHandler dh = d.getValue();
                ByteArrayOutputStream buffOS = new ByteArrayOutputStream();
                dh.writeTo(buffOS);
                byte[] buff = buffOS.toByteArray();
                DataSource source = new ByteArrayDataSource(buff, documents.getDocument(d.getId()).getMetadata().getMimeType());
                DataHandler dhnew = new DataHandler(source);
                doc.setValue(dhnew);
                docs.add(doc);
            }
            LOGGER.info(" SENDING TO ENDPOINT " + to);
            DocumentRepositoryProxy proxy = new DocumentRepositoryProxy(endpointUrl, new DirectSOAPHandlerResolver());
            RegistryResponseType rrt = proxy.provideAndRegisterDocumentSetB(prdst);
            String test = rrt.getStatus();
            if (test.indexOf("Failure") >= 0) {
                String error = "";
                try {
                    error = rrt.getRegistryErrorList().getRegistryError().get(0).getCodeContext();
                } catch (Exception x) {
                }
                throw new Exception("Failure Returned from XDR forward:" + error);
            }
            getAuditMessageGenerator().provideAndRegisterAuditSource(messageId, remoteHost, endpoint, to, thisHost, patId, subsetId, pid);
        }
        resp = getRepositoryProvideResponse(messageId);
        relatesTo = messageId;
        action = "urn:ihe:iti:2007:ProvideAndRegisterDocumentSet-bResponse";
        to = endpoint;
        setHeaderData();
    } catch (Exception e) {
        e.printStackTrace();
        throw (e);
    }
    return resp;
}