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.subjectlims.lims.biospecimen.form.BiospecimenModalDetailForm.java

License:Open Source License

@Override
protected void onSave(AjaxRequestTarget target) {
    boolean saveOk = true;
    org.apache.shiro.subject.Subject currentUser = SecurityUtils.getSubject();
    try {//from w  ww . j a  v  a  2  s. c o m
        if (cpModel.getObject().getBiospecimen().getId() == null) {
            // Save/Process/Aliquot
            if (cpModel.getObject().getBiospecimenProcessing().isEmpty()) { //empty
                // Normal Save functionality
                // Initial transaction detail
                currentUser = SecurityUtils.getSubject();
                cpModel.getObject().getBioTransaction().setRecorder(currentUser.getPrincipal().toString());
                cpModel.getObject().getBioTransaction().setUnit(cpModel.getObject().getBiospecimen().getUnit()); //TODO: soon in web form

                iLimsService.createBiospecimen(cpModel.getObject());

                // Update location
                if (cpModel.getObject().getBiospecimenLocationVO().getIsAllocated()) {
                    if (cpModel.getObject().getInvCell() != null
                            && cpModel.getObject().getInvCell().getBiospecimen() != null) {
                        iInventoryService.updateInvCell(cpModel.getObject().getInvCell());
                    }
                }
                this.info("Biospecimen " + cpModel.getObject().getBiospecimen().getBiospecimenUid()
                        + " was created successfully");
                setQuantityLabel();
            } else if (cpModel.getObject().getBiospecimenProcessing()
                    .equalsIgnoreCase(au.org.theark.lims.web.Constants.BIOSPECIMEN_PROCESSING_PROCESSING)) {
                // Process the biospecimen
                try {
                    LimsVO limsVo = cpModel.getObject();
                    Biospecimen biospecimen = limsVo.getBiospecimen();
                    Biospecimen parentBiospecimen = iLimsService
                            .getBiospecimen(biospecimen.getParent().getId());
                    double qtyUsedFromParent = limsVo.getParentBiospecimen().getQuantity();

                    if (qtyUsedFromParent > parentBiospecimen.getQuantity()) {
                        StringBuffer errorMessage = new StringBuffer();

                        errorMessage.append("Cannot process more than ");
                        errorMessage.append(parentBiospecimen.getQuantity());
                        errorMessage.append(parentBiospecimen.getUnit().getName());
                        errorMessage.append(" of the parent biospecimen");

                        this.error(errorMessage);
                        saveOk = false;
                    } else {
                        // Process the biospecimen and it's parent
                        iLimsService.createBiospecimen(limsVo);

                        // Add parent transaction
                        LimsVO parentLimsVo = new LimsVO();
                        parentLimsVo.setBiospecimen(parentBiospecimen);
                        parentLimsVo.getBioTransaction().setId(null);
                        parentLimsVo.getBioTransaction().setUnit(biospecimen.getUnit()); //TODO: soon in web form
                        parentLimsVo.getBioTransaction().setBiospecimen(parentBiospecimen);
                        parentLimsVo.getBioTransaction().setTransactionDate(Calendar.getInstance().getTime());
                        parentLimsVo.getBioTransaction()
                                .setReason("Processed for: " + biospecimen.getBiospecimenUid());
                        parentLimsVo.getBioTransaction().setRecorder(currentUser.getPrincipal().toString());

                        // NOTE: Removing from parent is negative-value transaction
                        parentLimsVo.getBioTransaction().setQuantity(qtyUsedFromParent * -1);
                        BioTransactionStatus bioTransactionStatus = iLimsService
                                .getBioTransactionStatusByName("Processed");
                        parentLimsVo.getBioTransaction().setStatus(bioTransactionStatus);
                        iLimsService.createBioTransaction(parentLimsVo);

                        this.info("Biospecimen " + cpModel.getObject().getBiospecimen().getBiospecimenUid()
                                + " was created successfully");
                        setQuantityLabel();
                    }
                } catch (EntityNotFoundException e) {
                    log.error(e.getMessage());
                }
            } else if (cpModel.getObject().getBiospecimenProcessing()
                    .equalsIgnoreCase(au.org.theark.lims.web.Constants.BIOSPECIMEN_PROCESSING_ALIQUOTING)) {
                // Aliquot the biospecimen
                try {
                    LimsVO limsVo = cpModel.getObject();
                    Biospecimen biospecimen = limsVo.getBiospecimen();
                    BioTransaction bioTransaction = limsVo.getBioTransaction();
                    Biospecimen parentBiospecimen = iLimsService
                            .getBiospecimen(biospecimen.getParent().getId());

                    if (bioTransaction.getQuantity() > parentBiospecimen.getQuantity()) {
                        StringBuffer errorMessage = new StringBuffer();

                        errorMessage.append("Cannot aliquot more than ");
                        errorMessage.append(parentBiospecimen.getQuantity());
                        errorMessage.append(parentBiospecimen.getUnit().getName());
                        errorMessage.append(" of the parent biospecimen");

                        this.error(errorMessage);
                        saveOk = false;
                    } else {
                        // Aliquot the biospecimen and it's parent
                        iLimsService.createBiospecimen(limsVo);

                        // Add parent transaction
                        LimsVO parentLimsVo = new LimsVO();
                        //parentLimsVo.setBiospecimen(parentBiospecimen);
                        parentLimsVo.getBioTransaction().setId(null);
                        parentLimsVo.getBioTransaction().setBiospecimen(parentBiospecimen);
                        parentLimsVo.getBioTransaction().setUnit(biospecimen.getUnit()); //TODO: soon in web form
                        parentLimsVo.getBioTransaction().setTransactionDate(Calendar.getInstance().getTime());
                        parentLimsVo.getBioTransaction()
                                .setReason("Sub-Aliquot for: " + biospecimen.getBiospecimenUid());
                        parentLimsVo.getBioTransaction().setRecorder(currentUser.getPrincipal().toString());

                        // NOTE: Removing from parent is negative-value transaction
                        parentLimsVo.getBioTransaction().setQuantity(bioTransaction.getQuantity() * -1);
                        BioTransactionStatus bioTransactionStatus = iLimsService
                                .getBioTransactionStatusByName("Aliquoted");
                        parentLimsVo.getBioTransaction().setStatus(bioTransactionStatus);
                        iLimsService.createBioTransaction(parentLimsVo);

                        this.info("Biospecimen " + cpModel.getObject().getBiospecimen().getBiospecimenUid()
                                + " was created successfully");
                        setQuantityLabel();
                    }
                } catch (EntityNotFoundException e) {
                    log.error(e.getMessage());
                }
            }
        } else {
            // Update location
            if (cpModel.getObject().getBiospecimenLocationVO().getIsAllocated()) {
                if (cpModel.getObject().getInvCell() != null
                        && cpModel.getObject().getInvCell().getBiospecimen() != null) {
                    iInventoryService.updateInvCell(cpModel.getObject().getInvCell());
                }
            }

            // Update qty avail
            cpModel.getObject().getBiospecimen()
                    .setQuantity(iLimsService.getQuantityAvailable(cpModel.getObject().getBiospecimen()));

            // Update biospecimen
            iLimsService.updateBiospecimen(cpModel.getObject());

            this.info("Biospecimen " + cpModel.getObject().getBiospecimen().getBiospecimenUid()
                    + " was updated successfully");

            // Hide/show barcode image
            barcodeImage.setVisible(cpModel.getObject().getBiospecimen().getBarcoded());
            target.add(barcodeImage);
            setQuantityLabel();
        }

        if (saveOk) {
            // Allow the Biospecimen custom data to be saved any time save is performed
            if (biospecimenCFDataEntryPanel instanceof BiospecimenCustomDataDataViewPanel) {
                ((BiospecimenCustomDataDataViewPanel) biospecimenCFDataEntryPanel).saveCustomData();
            }

            // refresh the custom field data entry panel (if necessary)
            if (initialiseBiospecimenCFDataEntry()) {
                arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(biospecimenCFDataEntryPanel);
            }

            // refresh the bio transactions (if necessary)
            if (initialiseBioTransactionListPanel()) {
                arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(bioTransactionListPanel);
            }

            // refresh the location panel
            if (initialiseBiospecimenLocationPanel()) {
                arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(biospecimenLocationPanel);
            }

            // Disable initial transaction details, and hide inital quantity text box
            bioTransactionDetailWmc.setEnabled(true);
            bioTransactionQuantityTxtFld.setVisible(false);
            quantityTxtFld.setVisible(true);
            // quantityTxtFld.setModelObject(bioTransactionQuantityTxtFld.getModelObject());
            target.add(bioTransactionDetailWmc);

            barcodeImage.setVisible(cpModel.getObject().getBiospecimen().getBarcoded());
            target.add(barcodeImage);

            // Enable/re-enable buttons panel
            initialiseBiospecimenButtonsPanel();

            target.add(biospecimenbuttonsPanel);

            cpModel.getObject().setBiospecimenProcessing("");
            parentQuantityTxtFld.setVisible(false);
            target.add(parentQuantityTxtFld);
            onSavePostProcess(target);
        }
    } catch (ArkSystemException e) {
        this.error(e.getMessage());
    }
    processErrors(target);
}

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

License:Open Source License

/**
 * Takes all details of a biospecimen, copies to a new Biospecimen, then allows editing of details before save
 * /*ww w .java  2s.  com*/
 * @param target
 */
protected void onCloneBiospecimen(AjaxRequestTarget target) {
    final Biospecimen clonedBiospecimen = cpModel.getObject().getBiospecimen();
    final String clonedBiospecimenUid = clonedBiospecimen.getBiospecimenUid();
    final Biospecimen biospecimen = new Biospecimen();

    try {
        // Copy parent biospecimen details to new biospecimen
        PropertyUtils.copyProperties(biospecimen, clonedBiospecimen);

        // Amend specific fields/detail
        biospecimen.setId(null);

        if (biospecimen.getStudy().getAutoGenerateBiospecimenUid()) {
            biospecimen.setBiospecimenUid(Constants.AUTO_GENERATED);
        } else {
            biospecimen.setBiospecimenUid(null);
        }

        // Cloning not a child biospecimen
        // biospecimen.setParent(clonedBiospecimen);
        // biospecimen.setParentUid(clonedBiospecimen.getBiospecimenUid());

        biospecimen.setSampleType(clonedBiospecimen.getSampleType());
        biospecimen.setBioCollection(clonedBiospecimen.getBioCollection());
        biospecimen.setQuantity(null);
        biospecimen.setUnit(clonedBiospecimen.getUnit());
        biospecimen.setComments("Clone of " + clonedBiospecimenUid);
        biospecimen.setBarcoded(false);
        biospecimen.setQuantity(clonedBiospecimen.getQuantity());
        biospecimen.setUnit(clonedBiospecimen.getUnit());
        biospecimen.setTreatmentType(clonedBiospecimen.getTreatmentType());
        biospecimen.setChildren(new ArrayList<Biospecimen>(0));

        Study studyFromClone = clonedBiospecimen.getStudy();
        // There should be a study and only then do the rest of the code here
        if (studyFromClone != null) {
            Study study = iArkCommonService.getStudy(studyFromClone.getId());
            biospecimen.setStudy(study);
            // Reset the biospecimen detail
            cpModel.getObject().setBiospecimen(biospecimen);

            // Set the bioTransaction detail
            org.apache.shiro.subject.Subject currentUser = SecurityUtils.getSubject();
            cpModel.getObject().getBioTransaction().setRecorder(currentUser.getPrincipal().toString());
            cpModel.getObject().getBioTransaction().setQuantity(null);
            cpModel.getObject().getBioTransaction().setUnit(biospecimen.getUnit());

            enableQuantityTreatment(target);
            CompoundPropertyModel<BiospecimenCustomDataVO> bioCFDataCpModel = new CompoundPropertyModel<BiospecimenCustomDataVO>(
                    new BiospecimenCustomDataVO());
            bioCFDataCpModel.getObject().setBiospecimen(biospecimen);
            bioCFDataCpModel.getObject().setArkFunction(iArkCommonService
                    .getArkFunctionByName(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_BIOSPECIMEN));
            biospecimenCFDataEntryPanel = new BiospecimenCustomDataDataViewPanel("biospecimenCFDataEntryPanel",
                    bioCFDataCpModel).initialisePanel(null);
            arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(biospecimenCFDataEntryPanel);

            // refresh the bioTransaction panel
            initialiseBioTransactionListPanel();
            arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(bioTransactionListPanel);

            // refresh the location panel
            cpModel.getObject().setBiospecimenLocationVO(new BiospecimenLocationVO());
            initialiseBiospecimenLocationPanel();
            arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(biospecimenLocationPanel);
            target.add(biospecimenLocationPanel);

            // Notify in progress
            this.info("Cloning biospecimen " + clonedBiospecimenUid + ", please save to confirm");
            target.add(feedbackPanel);

            // hide button panel
            biospecimenbuttonsPanel.setVisible(false);
            target.add(biospecimenbuttonsPanel);
        } else {
            log.error("Cannot find a study for the cloned biospecimen.");
        }
    } catch (IllegalAccessException e) {
        log.error(e.getMessage());
    } catch (InvocationTargetException e) {
        log.error(e.getMessage());
    } catch (NoSuchMethodException e) {
        log.error(e.getMessage());
    }

}

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

License:Open Source License

/**
 * Handle processing or aliquoting of a parent biospecimen. Process essentially changing the type of a parent biospecimen. Aliquot essentially
 * taking an amount from a parent biospecimen.
 * //w w w .  j  av  a 2s  . c  o  m
 * @param target
 *           AjxaxRequestTarget
 * @param processOrAliquot
 *           indication to whether a process or an aliquot
 * @param comment
 *           comment to add to biospecimen comments
 */
protected void processOrAliquot(AjaxRequestTarget target, String processOrAliquot, String comment) {
    final Biospecimen parentBiospecimen = cpModel.getObject().getBiospecimen();
    final String parentBiospecimenUid = parentBiospecimen.getBiospecimenUid();
    final Biospecimen biospecimen = new Biospecimen();

    cpModel.getObject().setParentBiospecimen(parentBiospecimen);

    try {
        // Copy parent biospecimen details to new biospecimen
        PropertyUtils.copyProperties(biospecimen, parentBiospecimen);

        // Amend specific fields/detail
        biospecimen.setId(null);

        if (biospecimen.getStudy().getAutoGenerateBiospecimenUid()) {
            biospecimen.setBiospecimenUid(Constants.AUTO_GENERATED);
        } else {
            biospecimen.setBiospecimenUid(null);
        }
        /***
         * TRAV TO INVESTIGATE ASAP
        // Cloning not a child biospecimen
        // biospecimen.setParent(clonedBiospecimen);
        // biospecimen.setParentUid(clonedBiospecimen.getBiospecimenUid());
        **/

        biospecimen.setParent(parentBiospecimen);
        biospecimen.setParentUid(parentBiospecimen.getBiospecimenUid());
        biospecimen.setSampleType(parentBiospecimen.getSampleType());
        biospecimen.setBioCollection(parentBiospecimen.getBioCollection());
        biospecimen.setQuantity(null);
        biospecimen.setUnit(parentBiospecimen.getUnit());
        biospecimen.setComments(comment + parentBiospecimenUid);
        biospecimen.setBarcoded(false);
        biospecimen.setTreatmentType(parentBiospecimen.getTreatmentType());
        biospecimen.setChildren(new ArrayList<Biospecimen>(0));

        Study studyFromParent = parentBiospecimen.getStudy();
        // There should be a study and only then do the rest of the code here
        if (studyFromParent != null) {
            Study study = iArkCommonService.getStudy(studyFromParent.getId());
            biospecimen.setStudy(study);
            // Reset the biospecimen detail
            cpModel.getObject().setBiospecimen(biospecimen);
            cpModel.getObject().setBiospecimenProcessing(processOrAliquot);
            // Set the bioTransaction detail
            org.apache.shiro.subject.Subject currentUser = SecurityUtils.getSubject();
            cpModel.getObject().getBioTransaction().setRecorder(currentUser.getPrincipal().toString());
            cpModel.getObject().getBioTransaction().setQuantity(null);
            cpModel.getObject().getBioTransaction().setUnit(biospecimen.getUnit()); //TODO: unit
            enableQuantityTreatment(target);
            CompoundPropertyModel<BiospecimenCustomDataVO> bioCFDataCpModel = new CompoundPropertyModel<BiospecimenCustomDataVO>(
                    new BiospecimenCustomDataVO());
            bioCFDataCpModel.getObject().setBiospecimen(biospecimen);
            bioCFDataCpModel.getObject().setArkFunction(iArkCommonService
                    .getArkFunctionByName(au.org.theark.core.Constants.FUNCTION_KEY_VALUE_BIOSPECIMEN));
            biospecimenCFDataEntryPanel = new BiospecimenCustomDataDataViewPanel("biospecimenCFDataEntryPanel",
                    bioCFDataCpModel).initialisePanel(null);
            arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(biospecimenCFDataEntryPanel);
            // refresh the bioTransaction panel
            initialiseBioTransactionListPanel();
            arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(bioTransactionListPanel);
            // refresh the location panel
            cpModel.getObject().setBiospecimenLocationVO(new BiospecimenLocationVO());
            initialiseBiospecimenLocationPanel();
            arkCrudContainerVo.getDetailPanelFormContainer().addOrReplace(biospecimenLocationPanel);
            target.add(biospecimenLocationPanel);
            // Notify in progress
            this.info(processOrAliquot + " biospecimen " + cpModel.getObject().getBiospecimen().getParentUid()
                    + ", please save to confirm");
            target.add(feedbackPanel);

            // hide button panel
            biospecimenbuttonsPanel.setVisible(false);
            target.add(biospecimenbuttonsPanel);
        } else {
            log.error("Cannot find a study for the parent biospecimen.");
        }
    } catch (IllegalAccessException e) {
        log.error(e.getMessage());
    } catch (InvocationTargetException e) {
        log.error(e.getMessage());
    } catch (NoSuchMethodException e) {
        log.error(e.getMessage());
    }
}

From source file:au.org.theark.lims.web.component.subjectlims.lims.form.ContainerForm.java

License:Open Source License

/**
 * Returns a list of Studies the user is permitted to access
 * //from   w w w. jav a 2  s  . c o m
 * @return
 */
public List<Study> getStudyListForUser() {
    List<Study> studyList = 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);
        studyList = iArkCommonService.getStudyListForUserAndModule(arkUserVo, arkModule);

        Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
        if (sessionStudyId != null) {
            studyList = iArkCommonService.getParentAndChildStudies(sessionStudyId);
            getModelObject().setStudyList(studyList);
        }
        getModelObject().setStudyList(studyList);
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
    return studyList;
}

From source file:au.org.theark.lims.web.component.subjectlims.subject.form.ContainerForm.java

License:Open Source License

/**
 * Returns a list of Studies the user is permitted to access
 * /* w  w w  .  j  av a2s .  c  o m*/
 * @return
 */
public List<Study> getStudyListForUser() {
    List<Study> studyList = 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);
        studyList = iArkCommonService.getStudyListForUserAndModule(arkUserVo, arkModule);
        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);
            studyList = iArkCommonService.getParentAndChildStudies(sessionStudyId);
            getModelObject().setStudyList(studyList);
        }
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
    return studyList;
}

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

License:Open Source License

protected void onCancel(AjaxRequestTarget target) {
    // Set study in context back to limsVo.study
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    if (sessionStudyId != null) {
        //Study study = iArkCommonService.getStudy(sessionStudyId);
        LimsVO limsVo = new LimsVO();
        //limsVo.setStudy(study);
        containerForm.setModelObject(limsVo);

        // Refresh the contextUpdateTarget (remove)
        if (containerForm.getContextUpdateLimsWMC() != null) {
            Panel limsContainerPanel = new EmptyPanel("limsContainerPanel");
            limsContainerPanel.setOutputMarkupPlaceholderTag(true);
            containerForm.getContextUpdateLimsWMC().addOrReplace(limsContainerPanel);
            target.add(containerForm.getContextUpdateLimsWMC());
        }/*from w  ww . ja  v  a  2 s .  c o  m*/
    }
}

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

License:Open Source License

/**
 * Returns a list of Studies the user is permitted to access
 * //from  ww w  .jav  a 2  s  .  c o  m
 * @return
 */
public List<Study> getStudyListForUser() {
    List<Study> studyList = 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);
        studyList = iArkCommonService.getStudyListForUserAndModule(arkUserVo, arkModule);
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
    return studyList;
}

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

License:Open Source License

/**
 * Returns a list of Studies the user is permitted to access
 * /*from  ww w .j  a  v a 2 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);

        Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
        if (sessionStudyId != null) {
            studyListForUser = iArkCommonService.getParentAndChildStudies(sessionStudyId);
        }
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
    return studyListForUser;
}

From source file:au.org.theark.lims.web.component.subjectlims.subject.SearchResultListPanel.java

License:Open Source License

/**
 * Builds the link for selection of subject (gets from database to ensure persistence)s
 * //from   w ww.  ja  va2  s .  c  om
 * @param subject
 * @return
 */
private AjaxLink buildLink(final LinkSubjectStudy subject) {
    ArkBusyAjaxLink link = new ArkBusyAjaxLink("subjectUID") {
        @Override
        public void onClick(AjaxRequestTarget target) {
            LinkSubjectStudy subjectFromBackend = new LinkSubjectStudy();
            try {

                subjectFromBackend = iArkCommonService.getSubjectByUID(subject.getSubjectUID(),
                        subject.getStudy());
            } catch (EntityNotFoundException e) {
                log.error(e.getMessage());
            }

            // Set SubjectUID into context
            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.SUBJECTUID,
                    subjectFromBackend.getSubjectUID());
            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID,
                    subjectFromBackend.getStudy().getId());

            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID,
                    subject.getPerson().getId());
            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.PERSON_TYPE,
                    au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_SUBJECT);

            // Force clearing of Cache to re-load roles for the user for the study
            arkLdapRealm.clearCachedAuthorizationInfo(SecurityUtils.getSubject().getPrincipals());
            aafRealm.clearCachedAuthorizationInfo(SecurityUtils.getSubject().getPrincipals());

            LimsVO limsVo = new LimsVO();
            limsVo.setLinkSubjectStudy(subjectFromBackend);
            //limsVo.setStudy(subjectFromBackend.getStudy());
            containerForm.setModelObject(limsVo);

            // Set context items
            ContextHelper contextHelper = new ContextHelper();
            //contextHelper.setStudyContextLabel(target, subjectFromBackend.getStudy().getName(), arkContextMarkup);
            //contextHelper.setSubjectContextLabel(target, subjectFromBackend.getSubjectUID(), arkContextMarkup);

            // Always disable subjectUID
            DetailPanel details = (DetailPanel) arkCrudContainerVO.getDetailPanelContainer()
                    .get("detailsPanel");
            DetailForm detailsForm = (DetailForm) details.get("detailsForm");
            detailsForm.getSubjectUIDTxtFld().setEnabled(false);

            ArkCRUDHelper.preProcessDetailPanelOnSearchResults(target, arkCrudContainerVO);
            arkCrudContainerVO.getEditButtonContainer().setVisible(false);

            // Refresh the contextUpdateTarget (add)
            if (containerForm.getContextUpdateLimsWMC() != null) {
                Panel limsContainerPanel = new LimsContainerPanel("limsContainerPanel", arkContextMarkup,
                        containerForm.getModel());
                containerForm.getContextUpdateLimsWMC().setVisible(true);
                containerForm.getContextUpdateLimsWMC().addOrReplace(limsContainerPanel);
                //details.limsContainerPanel.replaceWith(limsContainerPanel);
                details.addOrReplace(containerForm.getContextUpdateLimsWMC());
                target.add(details);
            }

            // Set Study Logo
            studyHelper = new StudyHelper();
            StudyCrudContainerVO studyCrudContainerVO = new StudyCrudContainerVO();
            studyCrudContainerVO.setStudyNameMarkup(studyNameMarkup);
            studyCrudContainerVO.setStudyLogoMarkup(studyLogoMarkup);
            studyHelper.setStudyLogo(subjectFromBackend.getStudy(), target,
                    studyCrudContainerVO.getStudyNameMarkup(), studyCrudContainerVO.getStudyLogoMarkup(),
                    iArkCommonService);
        }
    };
    Label nameLinkLabel = new Label(Constants.SUBJECT_KEY_LBL, subject.getSubjectUID());
    link.add(nameLinkLabel);
    return link;
}

From source file:au.org.theark.lims.web.component.subjectlims.subject.SubjectContainerPanel.java

License:Open Source License

protected boolean prerenderContextCheck() {
    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);
    boolean contextLoaded = false;

    // Force clearing of Cache to re-load roles for the user for the study
    arkLdapRealm.clearCachedAuthorizationInfo(SecurityUtils.getSubject().getPrincipals());
    aafRealm.clearCachedAuthorizationInfo(SecurityUtils.getSubject().getPrincipals());

    Study study = null;/*from   w  ww  .ja v a2s  . c o m*/
    if (sessionStudyId != null) {
        study = iArkCommonService.getStudy(sessionStudyId);
    }

    if ((sessionStudyId != null) && (sessionSubjectUID != null)) {
        LinkSubjectStudy subjectFromBackend = new LinkSubjectStudy();

        try {
            subjectFromBackend = iArkCommonService.getSubjectByUID(sessionSubjectUID, study);

            // Set SubjectUID into context
            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.SUBJECTUID,
                    subjectFromBackend.getSubjectUID());
            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID,
                    subjectFromBackend.getStudy().getId());

            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID,
                    subjectFromBackend.getPerson().getId());
            SecurityUtils.getSubject().getSession().setAttribute(au.org.theark.core.Constants.PERSON_TYPE,
                    au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_SUBJECT);
        } catch (EntityNotFoundException e) {
            log.error(e.getMessage());
        }

        if (study != null && subjectFromBackend != null) {
            // Study and subject in context
            contextLoaded = true;
            LimsVO limsVo = new LimsVO();
            limsVo.setLinkSubjectStudy(subjectFromBackend);
            limsVo.setStudy(subjectFromBackend.getStudy());
            limsVo.setTreeModel(treeModel);
            containerForm.setModelObject(limsVo);
        }

        if (contextLoaded) {
            // Put into Detail View mode
            arkCrudContainerVO.getSearchPanelContainer().setVisible(false);
            arkCrudContainerVO.getSearchResultPanelContainer().setVisible(false);
            arkCrudContainerVO.getDetailPanelContainer().setVisible(true);
            arkCrudContainerVO.getDetailPanelFormContainer().setEnabled(false);
            //arkCrudContainerVO.getViewButtonContainer().setVisible(true);
            arkCrudContainerVO.getEditButtonContainer().setVisible(false);

            if (containerForm.getContextUpdateLimsWMC() != null) {
                Panel limsContainerPanel = new LimsContainerPanel("limsContainerPanel", arkContextMarkup,
                        containerForm.getModel());
                containerForm.getContextUpdateLimsWMC().setVisible(true);

                detailsPanel.addOrReplace(containerForm.getContextUpdateLimsWMC());
                containerForm.getContextUpdateLimsWMC().addOrReplace(limsContainerPanel);
                AjaxRequestTarget target = AjaxRequestTarget.get();
                target.add(detailsPanel);
            }
        }
    }

    return contextLoaded;
}