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

Example 21 with If

use of org.w3._2007.rif.If 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 22 with If

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

the class AbstractSMSHandler method invoke.

@Override
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
    try {
        initSecurityProperties(jobExecutionContext);
        JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
        JobSubmissionProtocol protocol = preferredJobSubmissionInterface.getJobSubmissionProtocol();
        String interfaceId = preferredJobSubmissionInterface.getJobSubmissionInterfaceId();
        String factoryUrl = null;
        if (protocol.equals(JobSubmissionProtocol.UNICORE)) {
            UnicoreJobSubmission unicoreJobSubmission = GFacUtils.getUnicoreJobSubmission(interfaceId);
            factoryUrl = unicoreJobSubmission.getUnicoreEndPointURL();
        }
        storageClient = null;
        if (!isSMSInstanceExisting(jobExecutionContext)) {
            EndpointReferenceType eprt = EndpointReferenceType.Factory.newInstance();
            eprt.addNewAddress().setStringValue(factoryUrl);
            StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, null);
            try {
                storageClient = storageCreator.createStorage();
            } catch (Exception e2) {
                log.error("Cannot create storage..");
                throw new GFacHandlerException("Cannot create storage..", e2);
            }
            jobExecutionContext.setProperty(PROP_SMS_EPR, storageClient.getEPR());
        } else {
            EndpointReferenceType eprt = (EndpointReferenceType) jobExecutionContext.getProperty(PROP_SMS_EPR);
            try {
                storageClient = new StorageClient(eprt, secProperties);
            } catch (Exception e) {
                throw new GFacHandlerException("Cannot create storage..", e);
            }
        }
        dataTransferrer = new DataTransferrer(jobExecutionContext, storageClient);
    } catch (AppCatalogException e) {
        throw new GFacHandlerException("Error occurred while retrieving unicore job submission interface..", e);
    }
}

Example 23 with If

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

the class StorageCreator method findServerName.

protected String findServerName(String besUrl, EndpointReferenceType smsEpr) throws Exception {
    int besIndex = besUrl.indexOf("StorageFactory?res");
    String ss = besUrl.substring(0, besIndex);
    ss = ss + "Registry";
    EndpointReferenceType eprt = WSUtilities.makeServiceEPR(ss, "default_registry", Registry.REGISTRY_PORT);
    RegistryClient registry = new RegistryClient(eprt, secProps);
    // first, check if server name is already in the EPR...
    String dn = WSUtilities.extractServerIDFromEPR(smsEpr);
    if (dn != null) {
        return dn;
    }
    // otherwise find a matching service in the registry
    String url = smsEpr.getAddress().getStringValue();
    if (url.contains("/services/"))
        url = url.substring(0, url.indexOf("/services"));
    if (log.isDebugEnabled())
        log.debug("Checking for services at " + url);
    for (EntryType entry : registry.listEntries()) {
        if (entry.getMemberServiceEPR().getAddress().getStringValue().startsWith(url)) {
            dn = WSUtilities.extractServerIDFromEPR(entry.getMemberServiceEPR());
            if (dn != null) {
                return dn;
            }
        }
    }
    return null;
}

Example 24 with If

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

the class FragaSvarServiceImpl method saveNewQuestion.

@Override
public FragaSvar saveNewQuestion(String intygId, String typ, Amne amne, String frageText) {
    // Argument check
    if (Strings.isNullOrEmpty(frageText)) {
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.INTERNAL_PROBLEM, "frageText cannot be empty!");
    }
    if (amne == null) {
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.INTERNAL_PROBLEM, "Amne cannot be null!");
    } else if (!VALID_VARD_AMNEN.contains(amne)) {
        // Businessrule RE-013
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.INTERNAL_PROBLEM, "Invalid Amne " + amne + " for new question from vard!");
    }
    // Fetch from Intygstjansten. Note that if Intygstjansten is unresponsive, the Intyg will be loaded from WebCert
    // if possible.
    IntygContentHolder intyg = intygService.fetchIntygData(intygId, typ, false);
    WebCertUser user = webCertUserService.getUser();
    // Get vardperson that posed the question
    // Is user authorized to save an answer to this question?
    verifyEnhetsAuth(intyg.getUtlatande().getGrundData().getSkapadAv().getVardenhet().getEnhetsid(), false);
    // Verksamhetsregel FS-001 (Is the certificate sent to FK)
    if (!isCertificateSentToFK(intyg.getStatuses())) {
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.INTERNAL_PROBLEM, "FS-001: Certificate must be sent to FK first before sending question!");
    }
    // Verify that certificate is not revoked
    if (intyg.isRevoked()) {
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.INTERNAL_PROBLEM, "FS-XXX: Cannot save Fraga when certificate is revoked!");
    }
    IntygsReferens intygsReferens = FragaSvarConverter.convertToIntygsReferens(intyg.getUtlatande());
    HoSPersonal hoSPersonal = IntygConverterUtil.buildHosPersonalFromWebCertUser(user, null);
    Vardperson vardPerson = FragaSvarConverter.convert(hoSPersonal);
    FragaSvar fraga = new FragaSvar();
    fraga.setFrageStallare(FrageStallare.WEBCERT.getKod());
    fraga.setAmne(amne);
    fraga.setFrageText(frageText);
    LocalDateTime now = LocalDateTime.now();
    fraga.setFrageSkickadDatum(now);
    fraga.setFrageSigneringsDatum(now);
    fraga.setIntygsReferens(intygsReferens);
    fraga.setVardperson(vardPerson);
    fraga.setStatus(Status.PENDING_EXTERNAL_ACTION);
    fraga.setVardAktorHsaId(user.getHsaId());
    fraga.setVardAktorNamn(user.getNamn());
    // Ok, lets save the question
    FragaSvar saved = fragaSvarRepository.save(fraga);
    // Send to external party (FK)
    SendMedicalCertificateQuestionType sendType = new SendMedicalCertificateQuestionType();
    QuestionToFkType question = FKQuestionConverter.convert(saved);
    // Remove ASAP.
    if ("true".equalsIgnoreCase(forceFullstandigtNamn)) {
        question.getLakarutlatande().getPatient().setFullstandigtNamn("---");
    }
    sendType.setQuestion(question);
    AttributedURIType logicalAddress = new AttributedURIType();
    logicalAddress.setValue(sendQuestionToFkLogicalAddress);
    SendMedicalCertificateQuestionResponseType response;
    try {
        response = sendQuestionToFKClient.sendMedicalCertificateQuestion(logicalAddress, sendType);
    } catch (SOAPFaultException e) {
        LOGGER.error("Failed to send question to FK, error was: " + e.getMessage());
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.EXTERNAL_SYSTEM_PROBLEM, e.getMessage());
    }
    if (!response.getResult().getResultCode().equals(ResultCodeEnum.OK)) {
        LOGGER.error("Failed to send question to FK, result was " + response.getResult().toString());
        throw new WebCertServiceException(WebCertServiceErrorCodeEnum.EXTERNAL_SYSTEM_PROBLEM, response.getResult().getErrorText());
    }
    monitoringService.logQuestionSent(saved.getExternReferens(), saved.getInternReferens(), (saved.getIntygsReferens() == null) ? null : saved.getIntygsReferens().getIntygsId(), saved.getVardAktorHsaId(), saved.getAmne());
    // Notify stakeholders
    sendNotification(saved, NotificationEvent.NEW_QUESTION_FROM_CARE);
    arendeDraftService.delete(intygId, null);
    return saved;
}

Example 25 with If

use of org.w3._2007.rif.If in project arctic-sea by 52North.

the class Soap12Decoder method getBodyContent.

private OwsServiceRequest getBodyContent(EnvelopeDocument doc) throws DecodingException {
    Body body = doc.getEnvelope().getBody();
    try {
        Node domNode = body.getDomNode();
        if (domNode.hasChildNodes()) {
            NodeList childNodes = domNode.getChildNodes();
            for (int i = 0; i < childNodes.getLength(); i++) {
                Node node = childNodes.item(i);
                if (node.getNodeType() == Node.ELEMENT_NODE) {
                    XmlObject content = XmlObject.Factory.parse(node);
                    // fix problem with invalid prefix in xsi:type value for
                    // om:result, e.g. OM_SWEArrayObservation or
                    // gml:ReferenceType
                    Map<?, ?> namespaces = XmlHelper.getNamespaces(doc.getEnvelope());
                    fixNamespaceForXsiType(content, namespaces);
                    XmlHelper.fixNamespaceForXsiType(content, SweConstants.QN_DATA_ARRAY_PROPERTY_TYPE_SWE_200);
                    return decodeXmlElement(content);
                }
            }
        }
        return decodeXmlElement(body);
    } catch (XmlException xmle) {
        throw new DecodingException("Error while parsing SOAP body element!", xmle);
    }
}