Example usage for org.apache.shiro SecurityUtils getSubject

List of usage examples for org.apache.shiro SecurityUtils getSubject

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Introduction

In this page you can find the example usage for org.apache.shiro SecurityUtils getSubject.

Prototype

public static Subject getSubject()

Source Link

Document

Returns the currently accessible Subject available to the calling code depending on runtime environment.

Usage

From source file:au.org.theark.lims.web.component.barcodelabel.BarcodeLabelContainerPanel.java

License:Open Source License

public BarcodeLabelContainerPanel(String id, WebMarkupContainer arkContextMarkup) {
    super(id);/*from   w ww .j a  v a  2 s. c o  m*/
    this.arkContextMarkup = arkContextMarkup;
    BarcodeLabel barcodeLabel = new BarcodeLabel();
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    if (sessionStudyId != null) {
        Study study = iArkCommonService.getStudy(sessionStudyId);
        barcodeLabel.setStudy(study);
    }
    cpModel = new CompoundPropertyModel<BarcodeLabel>(barcodeLabel);
    arkCrudContainerVO = new ArkCrudContainerVO();

    initialisePanel();
}

From source file:au.org.theark.lims.web.component.barcodelabel.BarcodeLabelContainerPanel.java

License:Open Source License

/**
 * Returns a list of Studies the user is permitted to access
 * /*from   ww  w.  j a v  a2  s .  c om*/
 * @return
 */
private List<Study> getStudyListForUser() {
    List<Study> studyListForUser = new ArrayList<Study>(0);
    try {
        Subject currentUser = SecurityUtils.getSubject();
        ArkUser arkUser = iArkCommonService.getArkUser(currentUser.getPrincipal().toString());
        ArkUserVO arkUserVo = new ArkUserVO();
        arkUserVo.setArkUserEntity(arkUser);

        Long sessionArkModuleId = (Long) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.ARK_MODULE_KEY);
        ArkModule arkModule = null;
        arkModule = iArkCommonService.getArkModuleById(sessionArkModuleId);
        studyListForUser = iArkCommonService.getStudyListForUserAndModule(arkUserVo, arkModule);
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
    return studyListForUser;
}

From source file:au.org.theark.lims.web.component.barcodelabel.form.DetailForm.java

License:Open Source License

/**
 * Returns study in context//  w w w.j  ava 2s  .  co m
 * 
 * @return
 */
private List<Study> getStudyListForUser() {
    List<Study> studyListForUser = new ArrayList<Study>(0);
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    Study study = null;
    if (sessionStudyId != null) {
        study = iArkCommonService.getStudy(sessionStudyId);
        studyListForUser.add(study);
    }
    return studyListForUser;
}

From source file:au.org.theark.lims.web.component.barcodelabel.form.SearchForm.java

License:Open Source License

/**
 * Returns a list of Studies the user is permitted to access
 * /*  w w  w. j a  va 2s .c o  m*/
 * @return
 */
private List<Study> getStudyListForUser() {
    List<Study> studyListForUser = new ArrayList<Study>(0);
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    Study study = null;
    if (sessionStudyId != null) {
        study = iArkCommonService.getStudy(sessionStudyId);
        studyListForUser.add(study);
    }

    try {
        Subject currentUser = SecurityUtils.getSubject();
        ArkUser arkUser = iArkCommonService.getArkUser(currentUser.getPrincipal().toString());
        ArkUserVO arkUserVo = new ArkUserVO();
        arkUserVo.setArkUserEntity(arkUser);
        studyListForUser = iArkCommonService.getArkAuthorisationDao().getStudiesWithRoleForUser(arkUserVo,
                iArkCommonService.getArkAuthorisationDao().getArkRoleByName("LIMS Administrator"));
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
    return studyListForUser;
}

From source file:au.org.theark.lims.web.component.biocollectioncustomdata.BioCollectionCustomDataContainerPanel.java

License:Open Source License

protected boolean prerenderContextCheck() {
    // Get the Study, SubjectUID and ArkModule from Context
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    Long sessionBioCollectionId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.lims.web.Constants.BIO_COLLECTION);
    Long sessionArkModuleId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.ARK_MODULE_KEY);

    boolean contextLoaded = false;
    if ((sessionStudyId != null) && (sessionBioCollectionId != null)) {
        BioCollection bioCollection = null;
        ArkModule arkModule = null;//w w w  .j a v  a2 s. c  o  m
        Study study = null;
        try {
            study = iArkCommonService.getStudy(sessionStudyId);
            cpModel.getObject().getBioCollection().setStudy(study);
            bioCollection = iLimsService.getBioCollection(sessionBioCollectionId);
            cpModel.getObject().setBioCollection(bioCollection);
            arkModule = iArkCommonService.getArkModuleById(sessionArkModuleId);
            // cpModel.getObject().setArkModule(arkModule);
            if (study != null && bioCollection != null && arkModule != null) {
                contextLoaded = true;
                //cpModel.getObject().setArkFunction(iArkCommonService.getArkFunctionByName(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_LIMS_COLLECTION));
                cpModel.getObject().setArkFunction(iArkCommonService.getArkFunctionByName(
                        au.org.theark.core.Constants.FUNCTION_KEY_VALUE_LIMS_CUSTOM_FIELD));
            }
        } catch (EntityNotFoundException e) {
            log.error(e.getMessage());
        }
    }
    return contextLoaded;
}

From source file:au.org.theark.lims.web.component.biospecimen.batchaliquot.form.BatchAliquotBiospecimenForm.java

License:Open Source License

private boolean onSave(AjaxRequestTarget target) {
    List<Biospecimen> biospecimenList = new ArrayList<Biospecimen>(0);
    if (validatedList()) {

        if (totalQuantityLessThanParentQuantity()) {
            // Loop through entire list
            for (Biospecimen biospecimen : getModelObject().getAliquots()) {
                biospecimen.setBioCollection(getModelObject().getParentBiospecimen().getBioCollection());
                biospecimen.setSampleType(getModelObject().getParentBiospecimen().getSampleType());
                biospecimen.setSampleDate(new Date());
                biospecimen.setStudy(getModelObject().getParentBiospecimen().getStudy());
                biospecimen.setLinkSubjectStudy(getModelObject().getParentBiospecimen().getLinkSubjectStudy());

                Set<BioTransaction> bioTransactions = new HashSet<BioTransaction>(0);

                // Inheriently create a transaction for the initial quantity
                BioTransaction bioTransaction = new BioTransaction();
                bioTransaction.setUnit(biospecimen.getUnit()); //TODO: soon in web form
                bioTransaction.setBiospecimen(biospecimen);
                bioTransaction.setTransactionDate(Calendar.getInstance().getTime());
                bioTransaction.setQuantity(biospecimen.getQuantity());
                bioTransaction/*w  ww .j  ava 2 s  .  c  o  m*/
                        .setReason(au.org.theark.lims.web.Constants.BIOTRANSACTION_STATUS_INITIAL_QUANTITY);
                bioTransaction.setRecorder(SecurityUtils.getSubject().getPrincipal().toString());

                BioTransactionStatus initialStatus = iLimsService.getBioTransactionStatusByName(
                        au.org.theark.lims.web.Constants.BIOTRANSACTION_STATUS_INITIAL_QUANTITY);
                bioTransaction.setStatus(initialStatus); //ensure that the initial transaction can be identified
                bioTransactions.add(bioTransaction);
                biospecimen.setBioTransactions(bioTransactions);

                if (biospecimen.getStudy().getAutoGenerateBiospecimenUid()) {
                    biospecimen.setBiospecimenUid(
                            iLimsService.getNextGeneratedBiospecimenUID(biospecimen.getStudy()));
                }

                biospecimenList.add(biospecimen);
            }
        }

        StringBuffer message = new StringBuffer();
        message.append("Created ");
        message.append(getModelObject().getNumberToCreate());
        message.append(" ");
        message.append("biospecimen aliquots");

        if (!biospecimenList.isEmpty()) {
            info("Batch aliquots created:");
            log.info("Attempting to create " + getModelObject().getAliquots().size() + " biospecimen aliquots");
            iLimsService.batchAliquotBiospecimens(biospecimenList);
        }

        return true;
    } else {
        return false;
    }
}

From source file:au.org.theark.lims.web.component.biospecimen.batchcreate.form.AutoGenBatchCreateBiospecimenForm.java

License:Open Source License

@Override
public void onBeforeRender() {
    // Get session data (used for subject search)
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    String sessionSubjectUID = (String) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.SUBJECTUID);

    if ((sessionStudyId != null) && (sessionSubjectUID != null)) {
        LinkSubjectStudy linkSubjectStudy = null;
        Study study = null;//from   ww  w. j a  va2s.com
        boolean contextLoaded = false;
        try {
            study = iArkCommonService.getStudy(sessionStudyId);
            linkSubjectStudy = iArkCommonService.getSubjectByUID(sessionSubjectUID, study);
            if (study != null && linkSubjectStudy != null) {
                contextLoaded = true;
            }
        } catch (EntityNotFoundException e) {
            log.error(e.getMessage());
        }

        if (contextLoaded) {
            // Successfully loaded from backend
            cpModel.getObject().setLinkSubjectStudy(linkSubjectStudy);
            cpModel.getObject().getBiospecimen().setLinkSubjectStudy(linkSubjectStudy);
            cpModel.getObject().getBiospecimen().setStudy(study);
        }
    }

    super.onBeforeRender();
    visitChildren(formVisitor);

    feedbackPanel.clearOriginalDestination();
}

From source file:au.org.theark.lims.web.component.biospecimen.batchcreate.form.ManualBatchCreateBiospecimenForm.java

License:Open Source License

@Override
public void onBeforeRender() {
    // Get session data (used for subject search)
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    String sessionSubjectUID = (String) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.SUBJECTUID);

    if ((sessionStudyId != null) && (sessionSubjectUID != null)) {
        LinkSubjectStudy linkSubjectStudy = null;
        Study study = null;/*from   ww w . j  a  v a2  s .c  om*/
        boolean contextLoaded = false;
        try {
            study = iArkCommonService.getStudy(sessionStudyId);
            linkSubjectStudy = iArkCommonService.getSubjectByUID(sessionSubjectUID, study);
            if (study != null && linkSubjectStudy != null) {
                contextLoaded = true;
            }
        } catch (EntityNotFoundException e) {
            log.error(e.getMessage());
        }

        if (contextLoaded) {
            // Successfully loaded from backend
            cpModel.getObject().setLinkSubjectStudy(linkSubjectStudy);
            cpModel.getObject().getBiospecimen().setLinkSubjectStudy(linkSubjectStudy);
            cpModel.getObject().getBiospecimen().setStudy(study);
        }
    }

    super.onBeforeRender();
    visitChildren(formVisitor);
}

From source file:au.org.theark.lims.web.component.biospecimen.BiospecimenContainerPanel.java

License:Open Source License

public BiospecimenContainerPanel(String id, WebMarkupContainer arkContextMarkup,
        WebMarkupContainer studyNameMarkup, WebMarkupContainer studyLogoMarkup, DefaultTreeModel treeModel) {
    super(id);/*  w  w w.  j a va2  s  .co  m*/
    this.arkContextMarkup = arkContextMarkup;
    this.studyNameMarkup = studyNameMarkup;
    this.studyLogoMarkup = studyLogoMarkup;

    limsVO.setTreeModel(treeModel);

    // Get session data (used for subject search)
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    Study study = iArkCommonService.getStudy(sessionStudyId);
    limsVO.setStudy(study);

    cpModel = new CompoundPropertyModel<LimsVO>(limsVO);
    arkCrudContainerVO = new ArkCrudContainerVO();

    initialisePanel();
}

From source file:au.org.theark.lims.web.component.biospecimen.form.BiospecimenListForm.java

License:Open Source License

private void setContextItems(AjaxRequestTarget target, LinkSubjectStudy linkSubjectStudy) {
    SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID,
            linkSubjectStudy.getStudy().getId());
    SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID,
            linkSubjectStudy.getPerson().getId());
    SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.PERSON_TYPE,
            au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_SUBJECT);
    SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.SUBJECTUID,
            linkSubjectStudy.getSubjectUID());

    ContextHelper contextHelper = new ContextHelper();
    contextHelper.setStudyContextLabel(target, linkSubjectStudy.getStudy().getName(), arkContextMarkup);
    contextHelper.setSubjectContextLabel(target, linkSubjectStudy.getSubjectUID(), arkContextMarkup);
    contextHelper.setSubjectNameContextLabel(target, linkSubjectStudy.getPerson().getFullName(),
            arkContextMarkup);/* w w w  .  j  a v  a 2  s.  c o  m*/

    // Set Study Logo
    StudyHelper studyHelper = new StudyHelper();
    studyHelper.setStudyLogo(linkSubjectStudy.getStudy(), target, studyNameMarkup, studyLogoMarkup,
            iArkCommonService);
}