Example usage for org.apache.shiro SecurityUtils getSubject

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.biospecimenupload.form.SearchForm.java

License:Open Source License

@SuppressWarnings("unchecked")
@Override//from   w  w  w  .  j  ava  2 s  .  c  o  m
protected void onSearch(AjaxRequestTarget target) {
    target.add(feedbackPanel);

    // Set study in context
    Long studyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    // Get a list of all Fields for the Study in context
    Study study = iArkCommonService.getStudy(studyId);

    Upload searchUpload = getModelObject().getUpload();
    searchUpload.setStudy(study);

    java.util.Collection<Upload> uploadCollection = iArkCommonService.searchUploads(searchUpload);

    if (uploadCollection != null && uploadCollection.size() == 0) {
        this.info("Uploads with the specified criteria do not exist in the system.");
        target.add(feedbackPanel);
    }

    getModelObject().setUploadCollection(uploadCollection);

    listView.removeAll();
    arkCrudContainerVO.getSearchResultPanelContainer().setVisible(true);// Make the WebMarkupContainer that houses the search results visible
    target.add(arkCrudContainerVO.getSearchResultPanelContainer());
}

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From source file:au.org.theark.lims.web.component.biotransaction.BioTransactionListPanel.java

License:Open Source License

@Override
protected void onBeforeRender() {
    Long sessionBiospecimenId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.lims.web.Constants.BIOSPECIMEN);

    if (sessionBiospecimenId != null) {
        Biospecimen biospecimen = null;/*  w  w  w .ja v a 2s.  c  o m*/
        boolean contextLoaded = false;
        try {
            biospecimen = iLimsService.getBiospecimen(sessionBiospecimenId);
            if (biospecimen != null) {
                contextLoaded = true;
            }
        } catch (EntityNotFoundException e) {
            log.error(e.getMessage());
        }

        if (contextLoaded) {
            cpModel.getObject().setBiospecimen(biospecimen);
            cpModel.getObject().getBioTransaction().setBiospecimen(biospecimen);
        }
    }

    super.onBeforeRender();
}

---

From source file:au.org.theark.lims.web.component.biotransaction.form.BioTransactionListForm.java

License:Open Source License

public void initialiseForm() {
    feedbackPanel = new FeedbackPanel("feedback");
    feedbackPanel.setOutputMarkupPlaceholderTag(true);
    add(feedbackPanel);//from w ww .j  a  va 2 s .  c  o m

    //transactionDateLbl = new Label("bioTransaction.transactionDate", simpleDateFormat.format(new Date()));
    transactionDate = new DateTextField("bioTransaction.transactionDate",
            new PatternDateConverter(au.org.theark.core.Constants.DD_MM_YYYY, false));
    ArkDatePicker dobDatePicker = new ArkDatePicker();
    dobDatePicker.bind(transactionDate);
    transactionDate.add(dobDatePicker);

    quantity = new TextField<Number>("bioTransaction.quantity");

    unitsLbl = new Label("bioTransaction.biospecimen.unit.name",
            cpModel.getObject().getBiospecimen().getUnit().getName());
    reasonLbl = new TextField<String>("bioTransaction.reason");
    recorderLbl = new Label("bioTransaction.recorder",
            SecurityUtils.getSubject().getPrincipals().getPrimaryPrincipal().toString());

    initStatus();
    initAccessRequest();
    initSaveButton();
    addFormComponents();
}

---

From source file:au.org.theark.lims.web.component.biotransaction.form.BioTransactionListForm.java

License:Open Source License

private void initSaveButton() {
    saveButton = new ArkBusyAjaxButton("saveButton") {
        private static final long serialVersionUID = 1L;

        @Override//w w w .  j a  v  a  2  s.co m
        public boolean isVisible() {
            return true;
        }

        @Override
        protected void onSubmit(AjaxRequestTarget target, Form<?> form) {
            // Set defaults
            //cpModel.getObject().getBioTransaction().setTransactionDate(new Date());
            cpModel.getObject().getBioTransaction()
                    .setRecorder(SecurityUtils.getSubject().getPrincipals().getPrimaryPrincipal().toString());

            Double qtyAvail = iLimsService.getQuantityAvailable(cpModel.getObject().getBiospecimen());
            Double txnQuantity = cpModel.getObject().getBioTransaction().getQuantity();

            if (txnQuantity == null) {
                error("Field 'Quantity' is required");
                target.add(feedbackPanel);
            } else if (cpModel.getObject().getBioTransaction().getStatus() == null) {
                error("Field 'Status' is required");
                target.add(feedbackPanel);
            } else {
                // Make quantity minus if positive and Aliquoted, Processed or   Delivered
                String status = cpModel.getObject().getBioTransaction().getStatus().getName();
                if (status != null
                        && (status.equalsIgnoreCase("Aliquoted") || status.equalsIgnoreCase("Processed")
                                || status.equalsIgnoreCase("Delivered"))
                        && txnQuantity != null && txnQuantity > 0) {
                    txnQuantity = (-1 * txnQuantity);
                    cpModel.getObject().getBioTransaction().setQuantity(txnQuantity);
                }

                // Check that quantity specified not greater than available
                if (txnQuantity < 0 && (Math.abs(txnQuantity) > (qtyAvail == null ? 0 : qtyAvail))) {
                    error("When aliquoting, processing or delivering, transaction quantity may not exceed total quantity available.");
                    target.add(feedbackPanel);
                } else {
                    cpModel.getObject().getBioTransaction()
                            .setUnit(cpModel.getObject().getBiospecimen().getUnit()); //TODO: Unit
                    iLimsService.createBioTransaction(cpModel.getObject());
                    info("Transaction saved successfully");

                    // update biospecimen (qty avail)
                    qtyAvail = iLimsService.getQuantityAvailable(cpModel.getObject().getBiospecimen());
                    cpModel.getObject().getBiospecimen().setQuantity(qtyAvail);
                    try {
                        iLimsService.updateBiospecimen(cpModel.getObject());
                    } catch (ArkSystemException e) {
                        this.error(e.getMessage());
                    }

                    // refresh transaction form
                    BioTransaction bioTransaction = new BioTransaction();
                    bioTransaction.setBiospecimen(cpModel.getObject().getBiospecimen());
                    bioTransaction.setUnit(cpModel.getObject().getBiospecimen().getUnit()); //TODO: Unit
                    cpModel.getObject().setBioTransaction(bioTransaction);

                    target.add(form.getParent().getParent());
                    target.add(feedbackPanel);
                }
            }
        }

        //         @Override
        //         public boolean isEnabled() {
        //            Biospecimen b = cpModel.getObject().getBiospecimen();
        //            if(b==null){
        //               return false;
        //            }
        //            Double qa = iLimsService.getQuantityAvailable(b);
        //            return (qa != null && qa > 0);
        //         }

        @Override
        protected void onError(AjaxRequestTarget target, Form<?> form) {
            target.add(feedbackPanel);
        }
    };
}

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From source file:au.org.theark.lims.web.component.bioupload.BioUploadContainerPanel.java

License:Open Source License

protected WebMarkupContainer initialiseSearchResults() {
    searchResultPanel = new SearchResultListPanel("searchResults", feedBackPanel, containerForm,
            arkCrudContainerVO);//from  ww w  .java 2  s. c  o  m

    iModel = new LoadableDetachableModel<Object>() {
        private static final long serialVersionUID = 1L;

        @Override
        protected Object load() {
            // Return all Uploads for the Study in context
            java.util.Collection<Upload> studyUploads = new ArrayList<Upload>();
            Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
                    .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);

            //if (isActionPermitted() && sessionStudyId != null) {  TODO we need so make sure permission logic only occurs at the highest possible level
            if (sessionStudyId != null) {
                Upload studyUpload = new Upload();
                studyUpload.setStudy(iArkCommonService.getStudy(sessionStudyId));
                //explicitly search all bio uploads not based on ark function 
                //studyUpload.setArkFunction(arkFunction);
                studyUploads = iArkCommonService.searchUploadsForBio(studyUpload);

            }
            listView.removeAll();
            return studyUploads;
        }
    };

    listView = searchResultPanel.buildPageableListView(iModel);
    listView.setReuseItems(true);
    PagingNavigator pageNavigator = new PagingNavigator("navigator", listView);
    searchResultPanel.add(pageNavigator);
    searchResultPanel.add(listView);
    arkCrudContainerVO.getSearchResultPanelContainer().add(searchResultPanel);
    searchResultPanel.setVisible(true);

    return arkCrudContainerVO.getSearchResultPanelContainer();
}

---

From source file:au.org.theark.lims.web.component.bioupload.BioUploadStep1.java

License:Open Source License

private void saveFileInMemory(AjaxRequestTarget target) {
    Long studyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    Study study = iArkCommonService.getStudy(studyId);
    FileUpload fileUpload = fileUploadField.getFileUpload();
    containerForm.getModelObject().setFileUpload(fileUpload);
    Payload payload = iArkCommonService.createPayload(fileUpload.getBytes());

    containerForm.getModelObject().getUpload().setPayload(payload);
    String filename = containerForm.getModelObject().getFileUpload().getClientFileName();
    String fileFormatName = filename.substring(filename.lastIndexOf('.') + 1).toUpperCase();
    au.org.theark.core.model.study.entity.FileFormat fileFormat = new au.org.theark.core.model.study.entity.FileFormat();
    fileFormat = iArkCommonService.getFileFormatByName(fileFormatName);
    byte[] byteArray = fileUpload.getMD5();
    String checksum = getHex(byteArray);

    containerForm.getModelObject().getUpload().setStudy(study);
    containerForm.getModelObject().getUpload().setFileFormat(fileFormat);
    containerForm.getModelObject().getUpload().setChecksum(checksum);
    containerForm.getModelObject().getUpload().setFilename(filename);
    containerForm.getModelObject().getUpload().setStartTime(new Date(System.currentTimeMillis()));
    if (containerForm.getModelObject().getUpload().getUploadType() != null) {
        if (containerForm.getModelObject().getUpload().getUploadType().getName()
                .equalsIgnoreCase("Biospecimen Custom Data")) {
            containerForm.getModelObject().getUpload().setArkFunction(
                    iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_BIOSPECIMEN));
        } else if (containerForm.getModelObject().getUpload().getUploadType().getName()
                .equalsIgnoreCase("Biocollection Custom Data")) {
            //containerForm.getModelObject().getUpload().setArkFunction(iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_LIMS_COLLECTION));
            containerForm.getModelObject().getUpload().setArkFunction(
                    iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_LIMS_CUSTOM_FIELD));
        } else {/*from  w ww.j  av  a 2 s  .  c o m*/
            log.error("\n\n\n\n\n\n\n\n\n\n\n uploadType unrecognized");
        }
        //containerForm.getModelObject().getUpload().setArkFunction(iArkCommonService.getArkFunctionByName(Constants.FUNCTION_KEY_VALUE_SUBJECT_UPLOAD));
        log.info("\n\n\n\n\n\n\n\n\n\n\n\n upload type = "
                + containerForm.getModelObject().getUpload().getUploadType().getName());
    } else {
        log.error("\n\n\n\n\n\n\n\n\n\n\n uploadType is null");
    }
    wizardForm.setFileName(filename);

    containerForm.getModelObject().getUpload()
            .setUploadStatus(iArkCommonService.getUploadStatusFor(Constants.UPLOAD_STATUS_AWAITING_VALIDATION));
    try {
        iArkCommonService.createUpload(containerForm.getModelObject().getUpload());
    } catch (Exception e) {
        error("There was a problem during the upload process.");
        getWizardForm().onError(target, null);
    }
}

---

From source file:au.org.theark.lims.web.component.bioupload.BioUploadStep4.java

License:Open Source License

@Override
public void onStepOutNext(AbstractWizardForm<?> form, AjaxRequestTarget target) {
    form.getNextButton().setEnabled(false);
    target.add(form.getNextButton());/*from www.  j  a v  a2s.c om*/
    // Filename seems to be lost from model when moving between steps in wizard?  is this a symptom of something greater?
    containerForm.getModelObject().getUpload().setFilename(wizardForm.getFileName());

    String fileFormat = containerForm.getModelObject().getUpload().getFileFormat().getName();
    char delimiterChar = containerForm.getModelObject().getUpload().getDelimiterType().getDelimiterCharacter();
    try {
        List<String> uidsToUpload = containerForm.getModelObject().getUidsToUpload();
        //log.info("________________________________________________________" + "about to try passing list of uids is of size " + uidsToUpload.size() );
        InputStream inputStream = containerForm.getModelObject().getFileUpload().getInputStream();
        long size = containerForm.getModelObject().getFileUpload().getSize();
        Long uploadId = containerForm.getModelObject().getUpload().getId();
        String report = generateInitialUploadReport();

        Subject currentUser = SecurityUtils.getSubject();
        Long studyId = (Long) currentUser.getSession()
                .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);

        if (containerForm.getModelObject().getUpload().getUploadType().getName()
                .equalsIgnoreCase("Subject Demographic Data")) {
            StudyDataUploadExecutor task = new StudyDataUploadExecutor(iArkCommonService, iLimsService,
                    inputStream, uploadId, //null user
                    studyId, fileFormat, delimiterChar, size, report, uidsToUpload);
            task.run();
        } else if (containerForm.getModelObject().getUpload().getUploadType().getName()
                .equalsIgnoreCase("Study-specific (custom) Data")) {
            BioSpecimenCustomDataUploadExecutor task = new BioSpecimenCustomDataUploadExecutor(
                    iArkCommonService, iLimsService, inputStream, uploadId, //null user
                    studyId, fileFormat, delimiterChar, size, report, uidsToUpload);
            task.run();
        }

    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
}

---

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

License:Open Source License

@Override
protected void onSearch(AjaxRequestTarget target) {
    target.add(feedbackPanel);/*from w  ww  .  j  a va 2s .  c  o m*/

    Long studyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    // Get a list of all Fields for the Study in context
    Study study = iArkCommonService.getStudy(studyId);
    Upload searchUpload = getModelObject().getUpload();
    searchUpload.setStudy(study);

    java.util.Collection<Upload> uploadCollection = iArkCommonService.searchUploads(searchUpload);

    if (uploadCollection != null && uploadCollection.size() == 0) {
        this.info("Uploads with the specified criteria does not exist in the system.");
        target.add(feedbackPanel);
    }

    getModelObject().setUploadCollection(uploadCollection);

    listView.removeAll();
    arkCrudContainerVO.getSearchResultPanelContainer().setVisible(true);// Make the WebMarkupContainer that houses the search results visible
    target.add(arkCrudContainerVO.getSearchResultPanelContainer());
}

---

From source file:au.org.theark.lims.web.component.button.zebra.biocollection.PrintBioCollectionLabelButton.java

License:Open Source License

/**
 * Construct an ajax button to send the specified barcodeString to a ZebraTLP2844 printer<br>
 * <b>NOTE:</b> Assumes there is an applet on the page with the name "jZebra"
 * // w w w.j  a v a2 s .c om
 * @param id the markup identifier
 * @param bioCollection the bioCollection in context
 * @param numberModel the number of labels to print
 */
public PrintBioCollectionLabelButton(String id, final BioCollection bioCollection, IModel<Number> numberModel) {
    super(id);
    setOutputMarkupPlaceholderTag(true);
    this.bioCollection = bioCollection;
    this.numberModel = numberModel;
    this.barcodesToPrint = (Number) numberModel.getObject();

    try {
        this.bioCollection = iLimsService.getBioCollection(bioCollection.getId());
        String sessionSubjectUID = (String) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.SUBJECTUID);
        LinkSubjectStudy linkSubjectStudy = null;
        Study study = bioCollection.getStudy();
        linkSubjectStudy = iArkCommonService.getSubjectByUID(sessionSubjectUID, study);
        this.bioCollection.setLinkSubjectStudy(linkSubjectStudy);
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }

    barcodeLabel = new BarcodeLabel();
    barcodeLabel.setStudy(bioCollection.getStudy());
    barcodeLabel.setName("zebra biocollection");
    barcodeLabel = iLimsAdminService.searchBarcodeLabel(barcodeLabel);
}

---

From source file:au.org.theark.lims.web.component.button.zebra.biocollection.PrintBiospecimensForBioCollectionButton.java

License:Open Source License

/**
 * Construct an ajax button to send the specified barcodeString for a particular BioCollection to a ZebraTLP2844 printer<br>
 * <b>NOTE:</b> Assumes there is an applet on the page with the name "jZebra"
 * //from   w  ww .  jav a  2  s. c  o  m
 * @param id
 * @param bioCollection
 */
public PrintBiospecimensForBioCollectionButton(String id, final BioCollection bioCollection, String printerName,
        IModel<Number> numberModel) {
    super(id);
    this.printerName = printerName;
    this.numberModel = numberModel;
    if (numberModel != null) {
        this.barcodesToPrint = (Number) numberModel.getObject();
    } else {
        this.barcodesToPrint = 1;
    }
    setOutputMarkupPlaceholderTag(true);
    this.bioCollection = bioCollection;
    try {
        this.bioCollection = iLimsService.getBioCollection(bioCollection.getId());
        String sessionSubjectUID = (String) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.SUBJECTUID);
        LinkSubjectStudy linkSubjectStudy = null;
        Study study = bioCollection.getStudy();
        linkSubjectStudy = iArkCommonService.getSubjectByUID(sessionSubjectUID, study);
        this.bioCollection.setLinkSubjectStudy(linkSubjectStudy);
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }

    barcodeLabel = new BarcodeLabel();
    barcodeLabel.setStudy(bioCollection.getStudy());
    barcodeLabel.setName(printerName);
    barcodeLabel = iLimsAdminService.searchBarcodeLabel(barcodeLabel);
}

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