Examples with StudyDAO org.akaza.openclinica.dao.managestudy.StudyDAO used on opensource projects

Example 11 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class ImportCRFDataService method validateStudyMetadata.

/*
     * meant to answer the following questions 3.a. is that study subject in that study? 3.b. is that study event def in
     * that study? 3.c. is that site in that study? 3.d. is that crf version in that study event def? 3.e. are those
     * item groups in that crf version? 3.f. are those items in that item group?
     */
public List<String> validateStudyMetadata(ODMContainer odmContainer, int currentStudyId) {
    List<String> errors = new ArrayList<String>();
    MessageFormat mf = new MessageFormat("");
    // throw new OpenClinicaException(mf.format(arguments), "");
    try {
        StudyDAO studyDAO = new StudyDAO(ds);
        String studyOid = odmContainer.getCrfDataPostImportContainer().getStudyOID();
        StudyBean studyBean = studyDAO.findByOid(studyOid);
        if (studyBean == null) {
            mf.applyPattern(respage.getString("your_study_oid_does_not_reference_an_existing"));
            Object[] arguments = { studyOid };
            errors.add(mf.format(arguments));
            // errors.add("Your Study OID " + studyOid + " does not
            // reference an existing Study or Site in the database. Please
            // check it and try again.");
            // throw an error here because getting the ID would be difficult
            // otherwise
            logger.debug("unknown study OID");
            throw new OpenClinicaException("Unknown Study OID", "");
        } else if (studyBean.getId() != currentStudyId) {
            mf.applyPattern(respage.getString("your_current_study_is_not_the_same_as"));
            Object[] arguments = { studyBean.getName() };
            // 
            // errors.add("Your current study is not the same as the Study "
            // + studyBean.getName()
            // + ", for which you are trying to enter data. Please log out
            // of your current study and into the study for which the data
            // is keyed.");
            errors.add(mf.format(arguments));
        }
        ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
        StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
        StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
        CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
        ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
        ItemDAO itemDAO = new ItemDAO(ds);
        if (subjectDataBeans != null) {
            // report all available errors, tbh
            for (SubjectDataBean subjectDataBean : subjectDataBeans) {
                String oid = subjectDataBean.getSubjectOID();
                StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(oid, studyBean.getId());
                if (studySubjectBean == null) {
                    mf.applyPattern(respage.getString("your_subject_oid_does_not_reference"));
                    Object[] arguments = { oid };
                    errors.add(mf.format(arguments));
                    // errors.add("Your Subject OID " + oid + " does not
                    // reference an existing Subject in the Study.");
                    logger.debug("logged an error with subject oid " + oid);
                }
                ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
                if (studyEventDataBeans != null) {
                    for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
                        String sedOid = studyEventDataBean.getStudyEventOID();
                        StudyEventDefinitionBean studyEventDefintionBean = studyEventDefinitionDAO.findByOidAndStudy(sedOid, studyBean.getId(), studyBean.getParentStudyId());
                        if (studyEventDefintionBean == null) {
                            mf.applyPattern(respage.getString("your_study_event_oid_for_subject_oid"));
                            Object[] arguments = { sedOid, oid };
                            errors.add(mf.format(arguments));
                            // errors.add("Your Study Event OID " + sedOid +
                            // " for Subject OID " + oid
                            // + " does not reference an existing Study
                            // Event in the Study.");
                            logger.debug("logged an error with se oid " + sedOid + " and subject oid " + oid);
                        }
                        ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
                        if (formDataBeans != null) {
                            for (FormDataBean formDataBean : formDataBeans) {
                                String formOid = formDataBean.getFormOID();
                                ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formOid);
                                // right now just check nulls
                                if (crfVersionBeans != null) {
                                    for (CRFVersionBean crfVersionBean : crfVersionBeans) {
                                        if (crfVersionBean == null) {
                                            mf.applyPattern(respage.getString("your_crf_version_oid_for_study_event_oid"));
                                            Object[] arguments = { formOid, sedOid };
                                            errors.add(mf.format(arguments));
                                            // errors.add("Your CRF Version
                                            // OID " + formOid + " for Study
                                            // Event OID " + sedOid
                                            // + " does not reference a
                                            // proper CRF Version in that
                                            // Study Event.");
                                            logger.debug("logged an error with form " + formOid + " and se oid " + sedOid);
                                        }
                                    }
                                } else {
                                    mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
                                    Object[] arguments = { formOid };
                                    errors.add(mf.format(arguments));
                                // errors.add("Your CRF Version OID " +
                                // formOid
                                // + " did not generate any results in
                                // the database. Please check it and try
                                // again.");
                                }
                                ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
                                if (itemGroupDataBeans != null) {
                                    for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
                                        String itemGroupOID = itemGroupDataBean.getItemGroupOID();
                                        List<ItemGroupBean> itemGroupBeans = itemGroupDAO.findAllByOid(itemGroupOID);
                                        if (itemGroupBeans != null) {
                                            logger.debug("number of item group beans: " + itemGroupBeans.size());
                                            logger.debug("item group oid: " + itemGroupOID);
                                            for (ItemGroupBean itemGroupBean : itemGroupBeans) {
                                                if (itemGroupBean == null) {
                                                    mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
                                                    Object[] arguments = { itemGroupOID, formOid };
                                                    errors.add(mf.format(arguments));
                                                // errors.add("Your Item
                                                // Group OID " +
                                                // itemGroupOID + " for
                                                // Form OID " + formOid
                                                // + " does not
                                                // reference a proper
                                                // Item Group in that
                                                // CRF Version.");
                                                }
                                            }
                                        } else {
                                            mf.applyPattern(respage.getString("the_item_group_oid_did_not"));
                                            Object[] arguments = { itemGroupOID };
                                            errors.add(mf.format(arguments));
                                        // errors.add("The Item Group
                                        // OID " + itemGroupOID
                                        // + " did not generate any
                                        // results in the database,
                                        // please check it and try
                                        // again.");
                                        }
                                        ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
                                        if (itemDataBeans != null) {
                                            for (ImportItemDataBean itemDataBean : itemDataBeans) {
                                                String itemOID = itemDataBean.getItemOID();
                                                List<ItemBean> itemBeans = itemDAO.findByOid(itemOID);
                                                if (itemBeans != null) {
                                                    logger.debug("found itembeans: ");
                                                    for (ItemBean itemBean : itemBeans) {
                                                        if (itemBean == null) {
                                                            mf.applyPattern(respage.getString("your_item_oid_for_item_group_oid"));
                                                            Object[] arguments = { itemOID, itemGroupOID };
                                                            errors.add(mf.format(arguments));
                                                        // errors.add(
                                                        // "Your
                                                        // Item OID " +
                                                        // itemOID + "
                                                        // for Item
                                                        // Group OID " +
                                                        // itemGroupOID
                                                        // + " does not
                                                        // reference a
                                                        // proper Item
                                                        // in the Item
                                                        // Group.");
                                                        } else {
                                                            logger.debug("found " + itemBean.getOid() + ", passing");
                                                        }
                                                    }
                                                }
                                            }
                                        } else {
                                            mf.applyPattern(respage.getString("the_item_group_oid_did_not_contain_item_data"));
                                            Object[] arguments = { itemGroupOID };
                                            errors.add(mf.format(arguments));
                                        // errors.add("The Item Group
                                        // OID " + itemGroupOID
                                        // + " did not contain any Item
                                        // Data in the XML file, please
                                        // check it and try again.");
                                        }
                                    }
                                } else {
                                    mf.applyPattern(respage.getString("your_study_event_contains_no_form_data"));
                                    Object[] arguments = { sedOid };
                                    errors.add(mf.format(arguments));
                                // errors.add("Your Study Event " +
                                // sedOid
                                // + " contains no Form Data, or the
                                // Form OIDs are incorrect. Please check
                                // it and try again.");
                                }
                            }
                        }
                    }
                }
            }
        }
    } catch (OpenClinicaException oce) {
    } catch (NullPointerException npe) {
        logger.debug("found a nullpointer here");
    }
    // if errors == null you pass, if not you fail
    return errors;
}

Example 12 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class ImportCRFDataService method eventCRFStatusesValid.

/*
     * purpose: returns false if any of the forms/EventCRFs fail the UpsertOnBean rules.
     */
public boolean eventCRFStatusesValid(ODMContainer odmContainer, UserAccountBean ub) {
    ArrayList<EventCRFBean> eventCRFBeans = new ArrayList<EventCRFBean>();
    ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
    EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
    StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
    StudyDAO studyDAO = new StudyDAO(ds);
    StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
    UpsertOnBean upsert = odmContainer.getCrfDataPostImportContainer().getUpsertOn();
    // If Upsert bean is not present, create one with default settings
    if (upsert == null)
        upsert = new UpsertOnBean();
    String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
    StudyBean studyBean = studyDAO.findByOid(studyOID);
    ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
    for (SubjectDataBean subjectDataBean : subjectDataBeans) {
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            String sampleOrdinal = studyEventDataBean.getStudyEventRepeatKey() == null ? "1" : studyEventDataBean.getStudyEventRepeatKey();
            StudyEventDefinitionBean studyEventDefinitionBean = studyEventDefinitionDAO.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), studyBean.getParentStudyId());
            logger.info("find all by def and subject " + studyEventDefinitionBean.getName() + " study subject " + studySubjectBean.getName());
            StudyEventBean studyEventBean = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(), studyEventDefinitionBean.getId(), Integer.parseInt(sampleOrdinal));
            // locked
            if (studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.LOCKED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.STOPPED)) {
                return true;
            }
            for (FormDataBean formDataBean : formDataBeans) {
                CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
                ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
                for (CRFVersionBean crfVersionBean : crfVersionBeans) {
                    ArrayList<EventCRFBean> eventCrfBeans = eventCrfDAO.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersionBean);
                    // event crf, yet.
                    if (eventCrfBeans.isEmpty()) {
                        logger.debug("   found no event crfs from Study Event id " + studyEventBean.getId() + ", location " + studyEventBean.getLocation());
                        if ((studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SCHEDULED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.DATA_ENTRY_STARTED) || studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.COMPLETED))) {
                            if (!upsert.isNotStarted())
                                return false;
                        }
                    }
                    for (EventCRFBean ecb : eventCrfBeans) {
                        Integer ecbId = new Integer(ecb.getId());
                        if (!(ecb.getStage().equals(DataEntryStage.INITIAL_DATA_ENTRY) && upsert.isDataEntryStarted()) && !(ecb.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) && upsert.isDataEntryComplete()))
                            return false;
                    }
                }
            }
        }
    }
    return true;
}

Example 13 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class StudySubjectEndpoint method doesSubjectExist.

/**
 * @param subjectTransferBean
 * @return
 */
private boolean doesSubjectExist(SubjectTransferBean subjectTransferBean) {
    // TODO: Implement this
    StudySubjectDAO ssdao = new StudySubjectDAO(dataSource);
    StudyDAO studyDao = new StudyDAO(dataSource);
    StudyBean studyBean = studyDao.findByUniqueIdentifier(subjectTransferBean.getStudy().getIdentifier());
    StudySubjectBean ssbean = ssdao.findByLabelAndStudy(subjectTransferBean.getStudySubjectId(), studyBean);
    return ssbean.getId() > 0 ? true : false;
}

Example 14 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class SystemController method getStudyList.

public ArrayList<StudyBean> getStudyList() {
    StudyDAO sdao = new StudyDAO(dataSource);
    ArrayList<StudyBean> sBeans = (ArrayList<StudyBean>) sdao.findAllParents();
    return sBeans;
}

Example 15 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class StudyModuleController method deactivateParticipate.

@RequestMapping(value = "/{study}/deactivate", method = RequestMethod.GET)
public String deactivateParticipate(@PathVariable("study") String studyOid, HttpServletRequest request) throws Exception {
    studyDao = new StudyDAO(dataSource);
    StudyBean study = studyDao.findByOid(studyOid);
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(dataSource);
    StudyParameterValueBean spv = spvdao.findByHandleAndStudy(study.getId(), "participantPortal");
    spv.setStudyId(study.getId());
    spv.setParameter("participantPortal");
    spv.setValue("disabled");
    if (spv.getId() > 0)
        spvdao.update(spv);
    else
        spvdao.create(spv);
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    currentStudy.getStudyParameterConfig().setParticipantPortal("disabled");
    return "redirect:/pages/studymodule";
}