Example usage for org.apache.shiro SecurityUtils getSubject

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

  1. HOME
  2. Java
  3. org.apache.shiro
  4. org.apache.shiro.*
  5. SecurityUtils
  6. 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.study.web.component.subject.SearchResultListPanel.java

License:Open Source License

private AjaxLink buildLink(Item<SubjectVO> item, final AbstractDetailModalWindow modalWindow,
        final List<RelationshipVo> relatives, final FeedbackPanel feedbackPanel) {

    AjaxLink link = null;/*  w  ww .  j  a  v a  2 s .c om*/
    final SubjectVO subject = item.getModelObject();
    if ("Male".equalsIgnoreCase(subject.getLinkSubjectStudy().getPerson().getGenderType().getName())) {
        subject.setParentType("Father");
    } else {
        subject.setParentType("Mother");
    }

    Boolean inbreedAllowed = (Boolean) SecurityUtils.getSubject().getSession()
            .getAttribute(Constants.INBREED_ALLOWED);

    if (BooleanUtils.isTrue(inbreedAllowed)) {
        final String result = getCircularRelationships(subject, relatives);
        item.getModelObject().setMessage(result);
        if (isConsiderParentAge(subject) && result != null) {
            link = new AjaxConfirmLink(Constants.SUBJECT_UID,
                    new StringResourceModel("pedigree.parent.dob.circular.warning", this, item.getModel()),
                    item.getModel()) {
                @Override
                public void onClick(AjaxRequestTarget target) {
                    processParentSelection(subject, modalWindow, relatives, feedbackPanel, target);
                }
            };
        } else if (isConsiderParentAge(subject)) {
            link = new AjaxConfirmLink(Constants.SUBJECT_UID,
                    new StringResourceModel("pedigree.parent.dob.warning", this, item.getModel()),
                    item.getModel()) {
                @Override
                public void onClick(AjaxRequestTarget target) {
                    processParentSelection(subject, modalWindow, relatives, feedbackPanel, target);
                }
            };
        } else if (result != null) {
            link = new AjaxConfirmLink(Constants.SUBJECT_UID,
                    new StringResourceModel("pedigree.parent.circular.warning", this, item.getModel()),
                    item.getModel()) {
                @Override
                public void onClick(AjaxRequestTarget target) {
                    processParentSelection(subject, modalWindow, relatives, feedbackPanel, target);
                }
            };
        } else {
            link = new ArkBusyAjaxLink(Constants.SUBJECT_UID) {
                @Override
                public void onClick(AjaxRequestTarget target) {
                    processParentSelection(subject, modalWindow, relatives, feedbackPanel, target);
                }
            };
        }

    } else {
        if (isConsiderParentAge(subject)) {
            link = new AjaxConfirmLink(Constants.SUBJECT_UID,
                    new StringResourceModel("pedigree.parent.dob.warning", this, item.getModel()),
                    item.getModel()) {
                @Override
                public void onClick(AjaxRequestTarget target) {
                    processParentSelection(subject, modalWindow, relatives, feedbackPanel, target);
                }
            };
        } else {
            link = new ArkBusyAjaxLink(Constants.SUBJECT_UID) {
                @Override
                public void onClick(AjaxRequestTarget target) {
                    processParentSelection(subject, modalWindow, relatives, feedbackPanel, target);
                }
            };
        }
    }
    Label nameLinkLabel = new Label(Constants.SUBJECT_KEY_LBL, subject.getLinkSubjectStudy().getSubjectUID());
    link.add(nameLinkLabel);
    return link;
}

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

License:Open Source License

/**
 * Create new parent relationship in database for valid relationship.
 * /*  ww w .jav  a2 s  .  c  o  m*/
 * @param subject
 * @param modalWindow
 * @param relatives
 * @param feedbackPanel
 * @param target
 */
private void processParentSelection(final SubjectVO subject, final AbstractDetailModalWindow modalWindow,
        final List<RelationshipVo> relatives, final FeedbackPanel feedbackPanel, AjaxRequestTarget target) {

    String message;

    Boolean inbreedAllowed = (Boolean) SecurityUtils.getSubject().getSession()
            .getAttribute(Constants.INBREED_ALLOWED);

    if (BooleanUtils.isNotTrue(inbreedAllowed)
            && (message = getCircularRelationships(subject, relatives)) != null && message.length() > 0) {
        this.error(message);
        target.add(feedbackPanel);
        return;
    }

    LinkSubjectPedigree pedigreeRelationship = new LinkSubjectPedigree();

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

    Study study = iArkCommonService.getStudy(sessionStudyId);

    String subjectUID = (String) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.SUBJECTUID);

    String parentUID = subject.getLinkSubjectStudy().getSubjectUID();

    SubjectVO criteriaSubjectVo = new SubjectVO();
    criteriaSubjectVo.getLinkSubjectStudy().setStudy(study);
    criteriaSubjectVo.getLinkSubjectStudy().setSubjectUID(subjectUID);
    Collection<SubjectVO> subjects = iArkCommonService.getSubject(criteriaSubjectVo);
    SubjectVO subjectVo = subjects.iterator().next();
    pedigreeRelationship.setSubject(subjectVo.getLinkSubjectStudy());

    criteriaSubjectVo.getLinkSubjectStudy().setSubjectUID(parentUID);
    subjects = iArkCommonService.getSubject(criteriaSubjectVo);
    subjectVo = subjects.iterator().next();
    pedigreeRelationship.setRelative(subjectVo.getLinkSubjectStudy());

    String gender = subject.getLinkSubjectStudy().getPerson().getGenderType().getName();

    List<Relationship> relationships = iArkCommonService.getFamilyRelationships();
    for (Relationship relationship : relationships) {
        if ("Male".equalsIgnoreCase(gender) && "Father".equalsIgnoreCase(relationship.getName())) {
            pedigreeRelationship.setRelationship(relationship);
            break;
        }

        if ("Female".equalsIgnoreCase(gender) && "Mother".equalsIgnoreCase(relationship.getName())) {
            pedigreeRelationship.setRelationship(relationship);
            break;
        }
    }

    iStudyService.create(pedigreeRelationship);
    modalWindow.close(target);
}

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

License:Open Source License

/**
 * @deprecated//from ww  w . j a v a  2  s.c o m
 * 
 * After select a parent validate the pedigree for circular relationships
 * and create new parent relationship in database.
 * 
 * @param subject
 * @param modalWindow
 * @param relatives
 * @param feedbackPanel
 * @param target
 * 
 */
private void processParentSelectionOld(final SubjectVO subject, final AbstractDetailModalWindow modalWindow,
        final List<RelationshipVo> relatives, final FeedbackPanel feedbackPanel, AjaxRequestTarget target,
        boolean inbreedAllowed) {
    LinkSubjectPedigree pedigreeRelationship = new LinkSubjectPedigree();

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

    Study study = iArkCommonService.getStudy(sessionStudyId);

    String subjectUID = (String) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.SUBJECTUID);

    String parentUID = subject.getLinkSubjectStudy().getSubjectUID();

    // Circular validation
    StringBuilder pedigree = new StringBuilder();
    ArrayList<String> dummyParents = new ArrayList<String>();
    boolean firstLine = true;

    List<RelationshipVo> existingRelatives = new ArrayList<RelationshipVo>();
    existingRelatives.addAll(relatives);

    RelationshipVo proband = new RelationshipVo();
    proband.setIndividualId(subjectUID);
    System.out.println("Existing relatives list size: " + existingRelatives.size());
    for (RelationshipVo relative : existingRelatives) {
        System.out.println("Existing relatives UID: " + relative.getIndividualId() + " Father: "
                + relative.getFatherId() + " Mother:" + relative.getMotherId());
        if ("Father".equalsIgnoreCase(relative.getRelationship())) {
            proband.setFatherId(relative.getIndividualId());
        }

        if ("Mother".equalsIgnoreCase(relative.getRelationship())) {
            proband.setMotherId(relative.getIndividualId());
        }
    }

    if (subject.getLinkSubjectStudy().getPerson().getGenderType().getName().startsWith("M")) {
        proband.setFatherId(parentUID);
    } else if (subject.getLinkSubjectStudy().getPerson().getGenderType().getName().startsWith("F")) {
        proband.setMotherId(parentUID);
    }
    existingRelatives.add(proband);

    List<RelationshipVo> newRelatives = iStudyService.generateSubjectPedigreeRelativeList(parentUID,
            sessionStudyId);

    RelationshipVo parent = new RelationshipVo();
    parent.setIndividualId(parentUID);
    for (RelationshipVo relative : newRelatives) {
        if ("Father".equalsIgnoreCase(relative.getRelationship())) {
            parent.setFatherId(relative.getIndividualId());
        }

        if ("Mother".equalsIgnoreCase(relative.getRelationship())) {
            parent.setMotherId(relative.getIndividualId());
        }
    }

    newRelatives.add(parent);

    for (RelationshipVo relative : newRelatives) {
        if (!existingRelatives.contains(relative)) {
            existingRelatives.add(relative);
        } else {
            for (RelationshipVo existingRelative : existingRelatives) {
                if (relative.getIndividualId().equals(existingRelative.getIndividualId())) {
                    if (existingRelative.getFatherId() == null) {
                        existingRelative.setFatherId(relative.getFatherId());
                    }
                    if (existingRelative.getMotherId() == null) {
                        existingRelative.setMotherId(relative.getMotherId());
                    }
                }
            }
        }
    }

    for (RelationshipVo relative : existingRelatives) {
        String dummyParent = "D-";
        String father = relative.getFatherId();
        String mother = relative.getMotherId();
        String individual = relative.getIndividualId();

        if (father != null) {
            dummyParent = dummyParent + father;
        }

        if (mother != null) {
            dummyParent = dummyParent + mother;
        }

        if (!"D-".equals(dummyParent) && !dummyParents.contains(dummyParent)) {
            dummyParents.add(dummyParent);
            if (father != null) {
                if (firstLine) {
                    pedigree.append(father + " " + dummyParent);
                    firstLine = false;
                } else {
                    pedigree.append("\n" + father + " " + dummyParent);
                }
            }
            if (mother != null) {
                if (firstLine) {
                    pedigree.append(mother + " " + dummyParent);
                    firstLine = false;
                } else {
                    pedigree.append("\n" + mother + " " + dummyParent);
                }
            }
            pedigree.append("\n" + dummyParent + " " + individual);
        } else if (!"D-".equals(dummyParent)) {
            if (firstLine) {
                pedigree.append(dummyParent + " " + individual);
                firstLine = false;
            } else {
                pedigree.append("\n" + dummyParent + " " + individual);
            }
        }
    }

    // TODO comment this block to disable circular validations for inbred
    // relatives

    if (!inbreedAllowed) {
        Set<String> circularUIDs = PedigreeUploadValidator.getCircularUIDs(pedigree);
        if (circularUIDs.size() > 0) {
            this.error("Performing this action will create a circular relationship in the pedigree.");
            StringBuffer sb = new StringBuffer(
                    "The proposed action will cause a pedigree cycle involving subjects with UID:");
            boolean first = true;
            for (String uid : circularUIDs) {
                if (first) {
                    sb.append(uid);
                    first = false;
                } else {
                    sb.append(", " + uid);
                }
            }
            sb.append(".");
            this.error(sb.toString());
            target.add(feedbackPanel);
            return;
        }
    }

    // Assign new parent relationships

    SubjectVO criteriaSubjectVo = new SubjectVO();
    criteriaSubjectVo.getLinkSubjectStudy().setStudy(study);
    criteriaSubjectVo.getLinkSubjectStudy().setSubjectUID(subjectUID);
    Collection<SubjectVO> subjects = iArkCommonService.getSubject(criteriaSubjectVo);
    SubjectVO subjectVo = subjects.iterator().next();
    pedigreeRelationship.setSubject(subjectVo.getLinkSubjectStudy());

    criteriaSubjectVo.getLinkSubjectStudy().setSubjectUID(parentUID);
    subjects = iArkCommonService.getSubject(criteriaSubjectVo);
    subjectVo = subjects.iterator().next();
    pedigreeRelationship.setRelative(subjectVo.getLinkSubjectStudy());

    String gender = subject.getLinkSubjectStudy().getPerson().getGenderType().getName();

    List<Relationship> relationships = iArkCommonService.getFamilyRelationships();
    for (Relationship relationship : relationships) {
        if ("Male".equalsIgnoreCase(gender) && "Father".equalsIgnoreCase(relationship.getName())) {
            pedigreeRelationship.setRelationship(relationship);
            break;
        }

        if ("Female".equalsIgnoreCase(gender) && "Mother".equalsIgnoreCase(relationship.getName())) {
            pedigreeRelationship.setRelationship(relationship);
            break;
        }
    }

    iStudyService.create(pedigreeRelationship);
    modalWindow.close(target);
}

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

License:Open Source License

/**
 * Check for circular relationships among the given relative list.
 * /*from  w w w. j  av a2  s.  c o m*/
 * @param subject
 * @param relatives
 * @return
 */
private String getCircularRelationships(final SubjectVO subject, final List<RelationshipVo> relatives) {
    Long sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);

    String subjectUID = (String) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.SUBJECTUID);

    String parentUID = subject.getLinkSubjectStudy().getSubjectUID();

    List<RelationshipVo> existingRelatives = new ArrayList<RelationshipVo>();
    existingRelatives.addAll(relatives);

    RelationshipVo proband = new RelationshipVo();
    proband.setIndividualId(subjectUID);
    for (RelationshipVo relative : existingRelatives) {
        if ("Father".equalsIgnoreCase(relative.getRelationship())) {
            proband.setFatherId(relative.getIndividualId());
        }

        if ("Mother".equalsIgnoreCase(relative.getRelationship())) {
            proband.setMotherId(relative.getIndividualId());
        }
    }

    if (subject.getLinkSubjectStudy().getPerson().getGenderType().getName().startsWith("M")) {
        proband.setFatherId(parentUID);
    } else if (subject.getLinkSubjectStudy().getPerson().getGenderType().getName().startsWith("F")) {
        proband.setMotherId(parentUID);
    }
    existingRelatives.add(proband);

    List<RelationshipVo> newRelatives = iStudyService.generateSubjectPedigreeRelativeList(parentUID,
            sessionStudyId);

    RelationshipVo parent = new RelationshipVo();
    parent.setIndividualId(parentUID);
    for (RelationshipVo relative : newRelatives) {
        if ("Father".equalsIgnoreCase(relative.getRelationship())) {
            parent.setFatherId(relative.getIndividualId());
        }

        if ("Mother".equalsIgnoreCase(relative.getRelationship())) {
            parent.setMotherId(relative.getIndividualId());
        }
    }

    newRelatives.add(parent);

    for (RelationshipVo relative : newRelatives) {
        if (!existingRelatives.contains(relative)) {
            existingRelatives.add(relative);
        } else {
            for (RelationshipVo existingRelative : existingRelatives) {
                if (relative.getIndividualId().equals(existingRelative.getIndividualId())) {
                    if (existingRelative.getFatherId() == null) {
                        existingRelative.setFatherId(relative.getFatherId());
                    }
                    if (existingRelative.getMotherId() == null) {
                        existingRelative.setMotherId(relative.getMotherId());
                    }
                }
            }
        }
    }

    StringBuilder pedigree = PedigreeUploadValidator.generatePedigreeGraph(existingRelatives);

    Set<String> circularUIDs = PedigreeUploadValidator.getCircularUIDs(pedigree);
    if (circularUIDs.size() > 0) {
        StringBuffer sb = new StringBuffer(
                "Setting this relationship lead to consanguineous pedigree structure among following subject UIDs:");
        boolean first = true;
        for (String uid : circularUIDs) {
            if (first) {
                sb.append(uid);
                first = false;
            } else {
                sb.append(", " + uid);
            }
        }
        sb.append(".");
        return sb.toString();
    }

    return null;

}

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

License:Open Source License

/**
 * @param id/* w  ww.  j  a va  2s . c  o m*/
 * @param studyLogoMarkup
 * @param studyNameMarkup
 */
public SubjectContainerPanel(String id, WebMarkupContainer arkContextMarkup, WebMarkupContainer studyNameMarkup,
        WebMarkupContainer studyLogoMarkup) {
    super(id);
    this.arkContextMarkup = arkContextMarkup;
    this.studyNameMarkup = studyNameMarkup;
    this.studyLogoMarkup = studyLogoMarkup;

    /* Initialise the CPM */
    cpModel = new CompoundPropertyModel<SubjectVO>(new SubjectVO());

    // Restrict to subjects in current study in session
    sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    if (sessionStudyId != null) {
        study = iArkCommonService.getStudy(sessionStudyId);
        List<Study> studyListForUser = iArkCommonService.getParentAndChildStudies(sessionStudyId);
        cpModel.getObject().setStudyList(studyListForUser);
    }

    containerForm = new ContainerForm("containerForm", cpModel);
    containerForm.add(initialiseFeedBackPanel());
    containerForm.add(initialiseDetailPanel());
    containerForm.add(initialiseSearchResults());
    containerForm.add(initialiseSearchPanel());

    prerenderContextCheck();

    add(containerForm);
}

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

License:Open Source License

/**
 * Re-use in pedigree panel/*  w  ww . j  av  a  2s  .  co m*/
 * 
 * @param id
 * @param studyLogoMarkup
 * @param studyNameMarkup
 * @param modalWindow
 */
public SubjectContainerPanel(String id, WebMarkupContainer arkContextMarkup, WebMarkupContainer studyNameMarkup,
        WebMarkupContainer studyLogoMarkup, AbstractDetailModalWindow modalWindow, String gender,
        List<RelationshipVo> relatives) {
    super(id);
    this.arkContextMarkup = arkContextMarkup;
    this.studyNameMarkup = studyNameMarkup;
    this.studyLogoMarkup = studyLogoMarkup;

    /* Initialise the CPM */

    SubjectVO subjectVO = new SubjectVO();
    subjectVO.setEnableNewButton(false);
    cpModel = new CompoundPropertyModel<SubjectVO>(subjectVO);

    // Restrict to subjects in current study in session
    sessionStudyId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.STUDY_CONTEXT_ID);
    if (sessionStudyId != null) {
        study = iArkCommonService.getStudy(sessionStudyId);
        List<Study> studyListForUser = iArkCommonService.getParentAndChildStudies(sessionStudyId);
        cpModel.getObject().setStudyList(studyListForUser);
    }

    containerForm = new ContainerForm("containerForm", cpModel);
    containerForm.add(initialiseFeedBackPanel());
    containerForm.add(initialiseSearchResults(modalWindow, gender, relatives));
    containerForm.add(initialiseSearchPanel());

    arkCrudContainerVO.getSearchPanelContainer().get("searchComponentPanel").get("searchForm").get("genderType")
            .setEnabled(false);
    arkCrudContainerVO.getSearchPanelContainer().get("searchComponentPanel").get("searchForm").get("study")
            .setEnabled(false);

    add(containerForm);
}

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

License:Open Source License

@SuppressWarnings("unchecked")
protected void prerenderContextCheck() {
    // Get the Person in Context and determine the Person Type
    Long sessionPersonId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.PERSON_CONTEXT_ID);

    if ((sessionStudyId != null) && (sessionPersonId != null)) {
        String sessionPersonType = (String) SecurityUtils.getSubject().getSession()
                .getAttribute(au.org.theark.core.Constants.PERSON_TYPE);
        if (sessionPersonType.equals(au.org.theark.core.Constants.PERSON_CONTEXT_TYPE_SUBJECT)) {
            Person person;//w w w.  j a va2 s .  c om
            boolean contextLoaded = false;
            try {
                person = studyService.getPerson(sessionPersonId);
                SubjectVO subjectVO = new SubjectVO();
                subjectVO.getLinkSubjectStudy().setPerson(person); // must
                // have
                // Person
                subjectVO.getLinkSubjectStudy().setStudy(study); // must
                // have
                // Study
                List<SubjectVO> subjectList = (List<SubjectVO>) iArkCommonService.getSubject(subjectVO);
                subjectList.get(0).setStudyList(cpModel.getObject().getStudyList());
                containerForm.setModelObject(subjectList.get(0));
                contextLoaded = true;
            } catch (EntityNotFoundException e) {
                log.error(e.getMessage());
            } catch (ArkSystemException e) {
                log.error(e.getMessage());
            }

            if (contextLoaded) {
                // Available/assigned child studies
                List<Study> availableChildStudies = new ArrayList<Study>(0);
                List<Study> selectedChildStudies = new ArrayList<Study>(0);

                if (containerForm.getModelObject().getLinkSubjectStudy().getStudy().getParentStudy() != null) {
                    availableChildStudies = iStudyService.getChildStudyListOfParent(
                            containerForm.getModelObject().getLinkSubjectStudy().getStudy());
                    selectedChildStudies = iArkCommonService.getAssignedChildStudyListForPerson(
                            containerForm.getModelObject().getLinkSubjectStudy().getStudy(),
                            containerForm.getModelObject().getLinkSubjectStudy().getPerson());
                }

                containerForm.getModelObject().setAvailableChildStudies(availableChildStudies);
                containerForm.getModelObject().setSelectedChildStudies(selectedChildStudies);

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

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

License:Open Source License

@SuppressWarnings("unchecked")
protected WebMarkupContainer initialiseSearchResults(AbstractDetailModalWindow modalWindow, final String gender,
        final List<RelationshipVo> relatives) {
    searchResultsPanel = new SearchResultListPanel("searchResults", arkContextMarkup, containerForm,
            arkCrudContainerVO, studyNameMarkup, studyLogoMarkup);
    searchResultsPanel.setOutputMarkupId(true);

    if (sessionStudyId != null) {
        LinkSubjectStudy linkSubjectStudy = new LinkSubjectStudy();
        linkSubjectStudy.setStudy(study);
        // containerForm.getModelObject().setLinkSubjectStudy(linkSubjectStudy);
    }/*from w  w  w  . java 2s .  c  o m*/

    // Data providor to paginate resultList
    subjectProvider = new ArkDataProvider<SubjectVO, IArkCommonService>(iArkCommonService) {

        private static final long serialVersionUID = 1L;

        private GenderType genderType;

        {
            Collection<GenderType> genderTypes = service.getGenderTypes();
            for (GenderType type : genderTypes) {
                if (gender.equalsIgnoreCase(type.getName())) {
                    this.genderType = type;
                    break;
                }
            }
        }

        public int size() {
            String subjectUID = (String) SecurityUtils.getSubject().getSession()
                    .getAttribute(au.org.theark.core.Constants.SUBJECTUID);
            model.getObject().getRelativeUIDs().add(subjectUID);
            // TODO comment this block to check inbred relatives
            Boolean inbreedAllowed = (Boolean) SecurityUtils.getSubject().getSession()
                    .getAttribute(Constants.INBREED_ALLOWED);
            if (BooleanUtils.isNotTrue(inbreedAllowed)) {
                for (RelationshipVo relationshipVo : relatives) {
                    model.getObject().getRelativeUIDs().add(relationshipVo.getIndividualId());
                }
            } else {
                List<RelationshipVo> childRelatives = iStudyService.getSubjectChildren(subjectUID,
                        sessionStudyId);
                for (RelationshipVo relationshipVo : childRelatives) {
                    model.getObject().getRelativeUIDs().add(relationshipVo.getIndividualId());
                }
            }
            model.getObject().getLinkSubjectStudy().getPerson().setGenderType(genderType);
            return (int) service.getStudySubjectCount(model.getObject());
        }

        public Iterator<SubjectVO> iterator(int first, int count) {
            List<SubjectVO> listSubjects = new ArrayList<SubjectVO>();
            if (isActionPermitted()) {
                model.getObject().getLinkSubjectStudy().getPerson().setGenderType(genderType);
                String subjectUID = (String) SecurityUtils.getSubject().getSession()
                        .getAttribute(au.org.theark.core.Constants.SUBJECTUID);
                model.getObject().getRelativeUIDs().add(subjectUID);
                // TODO comment this block to check inbred relatives
                Boolean inbreedAllowed = (Boolean) SecurityUtils.getSubject().getSession()
                        .getAttribute(Constants.INBREED_ALLOWED);
                if (BooleanUtils.isNotTrue(inbreedAllowed)) {
                    for (RelationshipVo relationshipVo : relatives) {
                        model.getObject().getRelativeUIDs().add(relationshipVo.getIndividualId());
                    }
                } else {
                    List<RelationshipVo> childRelatives = iStudyService.getSubjectChildren(subjectUID,
                            sessionStudyId);
                    for (RelationshipVo relationshipVo : childRelatives) {
                        model.getObject().getRelativeUIDs().add(relationshipVo.getIndividualId());
                    }
                }
                listSubjects = iArkCommonService.searchPageableSubjects(model.getObject(), first, count);
            }
            return listSubjects.iterator();
        }
    };
    subjectProvider.setModel(this.cpModel);

    dataView = searchResultsPanel.buildDataView(subjectProvider, modalWindow, relatives, feedBackPanel);
    dataView.setItemsPerPage(iArkCommonService.getRowsPerPage());

    AjaxPagingNavigator pageNavigator = new AjaxPagingNavigator("navigator", dataView) {

        private static final long serialVersionUID = 1L;

        @Override
        protected void onAjaxEvent(AjaxRequestTarget target) {
            target.add(searchResultsPanel);
        }
    };
    resultsWmc.add(pageNavigator);

    List<IColumn<SubjectVO>> columns = new ArrayList<IColumn<SubjectVO>>();
    columns.add(new ExportableTextColumn<SubjectVO>(Model.of("SubjectUID"), "subjectUID"));
    columns.add(new ExportableTextColumn<SubjectVO>(Model.of("Full Name"), "subjectFullName"));
    columns.add(new ExportableTextColumn<SubjectVO>(Model.of("Preferred Name"),
            "linkSubjectStudy.person.preferredName"));
    columns.add(new ExportableDateColumn<SubjectVO>(Model.of("Date Of Birth"),
            "linkSubjectStudy.person.dateOfBirth", au.org.theark.core.Constants.DD_MM_YYYY));
    columns.add(new ExportableTextColumn<SubjectVO>(Model.of("Vital Status"),
            "linkSubjectStudy.person.vitalStatus.name"));
    columns.add(
            new ExportableTextColumn<SubjectVO>(Model.of("Gender"), "linkSubjectStudy.person.genderType.name"));
    columns.add(new ExportableTextColumn<SubjectVO>(Model.of("Subject Status"),
            "linkSubjectStudy.subjectStatus.name"));
    columns.add(new ExportableTextColumn<SubjectVO>(Model.of("Consent Status"),
            "linkSubjectStudy.consentStatus.name"));

    DataTable table = new DataTable("datatable", columns, dataView.getDataProvider(),
            iArkCommonService.getRowsPerPage());
    List<String> headers = new ArrayList<String>(0);
    headers.add("SubjectUID");
    headers.add("Full Name");
    headers.add("Preferred Name");
    headers.add("Date of Birth");
    headers.add("Vital Status");
    headers.add("Gender");
    headers.add("Subject Status");
    headers.add("Consent Status");

    String filename = study.getName() + "_subjects";
    RepeatingView toolbars = new RepeatingView("toolbars");
    ExportToolbar<String> exportToolBar = new ExportToolbar<String>(table, headers, filename);
    toolbars.add(new Component[] { exportToolBar });
    resultsWmc.add(toolbars);

    resultsWmc.add(dataView);
    searchResultsPanel.add(resultsWmc);
    arkCrudContainerVO.getSearchResultPanelContainer().add(searchResultsPanel);
    return arkCrudContainerVO.getSearchResultPanelContainer();
}

From source file:au.org.theark.study.web.component.subjectcustomdata.SubjectCustomDataContainerPanel.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);
    String sessionSubjectUID = (String) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.SUBJECTUID);
    Long sessionArkModuleId = (Long) SecurityUtils.getSubject().getSession()
            .getAttribute(au.org.theark.core.Constants.ARK_MODULE_KEY);

    boolean contextLoaded = false;
    if ((sessionStudyId != null) && (sessionSubjectUID != null)) {
        LinkSubjectStudy linkSubjectStudy = null;
        ArkModule arkModule = null;//from ww w . j av  a 2 s .  c om
        Study study = null;
        try {
            study = iArkCommonService.getStudy(sessionStudyId);
            cpModel.getObject().getLinkSubjectStudy().setStudy(study);
            linkSubjectStudy = iArkCommonService.getSubjectByUID(sessionSubjectUID, study);
            cpModel.getObject().setLinkSubjectStudy(linkSubjectStudy);
            arkModule = iArkCommonService.getArkModuleById(sessionArkModuleId);
            // cpModel.getObject().setArkModule(arkModule);
            if (study != null && linkSubjectStudy != null && arkModule != null) {
                contextLoaded = true;
                cpModel.getObject().setArkFunction(iArkCommonService.getArkFunctionByName(
                        au.org.theark.core.Constants.FUNCTION_KEY_VALUE_SUBJECT_CUSTOM_FIELD));
                customFieldCriteria.setStudy(study);
                customFieldCriteria.setArkFunction(cpModel.getObject().getArkFunction());
                //Get the subject persistance object from the custom field type.
                customFieldCriteria.setCustomFieldType(
                        iArkCommonService.getCustomFieldTypeByName(au.org.theark.core.Constants.SUBJECT));
            }
        } catch (EntityNotFoundException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    return contextLoaded;
}

From source file:au.org.theark.study.web.component.subjectUpload.form.SearchForm.java

License:Open Source License

@Override
protected void onSearch(AjaxRequestTarget target) {
    target.add(feedbackPanel);/* w w w . ja  v  a2s  .com*/

    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 search 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());
}