Examples with ElementRefBean org.akaza.openclinica.bean.odmbeans.ElementRefBean used on opensource projects

Example 16 with ElementRefBean

use of org.akaza.openclinica.bean.odmbeans.ElementRefBean in project OpenClinica by OpenClinica.

the class OdmExtractDAO method setOCItemDataDNs.

protected void setOCItemDataDNs(OdmClinicalDataBean data, String idataIds, HashMap<Integer, String> idataOidPoses) {
    this.setOCItemDataDNsTypesExpected();
    HashMap<String, ArrayList<ChildNoteBean>> pDNs = new HashMap<String, ArrayList<ChildNoteBean>>();
    // HashMap<String, ArrayList<DiscrepancyNoteBean>> sDNs = new HashMap<String, ArrayList<DiscrepancyNoteBean>>();
    logger.debug("Begin to execute GetOCItemDataDNsSql");
    logger.debug("getOCItemDataDNsSql= " + this.getOCItemDataDNsSql(idataIds));
    ArrayList rows = select(this.getOCItemDataDNsSql(idataIds));
    Iterator iter = rows.iterator();
    while (iter.hasNext()) {
        HashMap row = (HashMap) iter.next();
        Integer idataId = (Integer) row.get("item_data_id");
        Integer pdnId = (Integer) row.get("parent_dn_id");
        Integer dnId = (Integer) row.get("dn_id");
        String description = (String) row.get("description");
        String detailedNote = (String) row.get("detailed_notes");
        Integer ownerId = (Integer) row.get("owner_id");
        Date dateCreated = (Date) row.get("date_created");
        String status = (String) row.get("status");
        String noteType = (String) row.get("name");
        if (pdnId != null && pdnId > 0) {
            String key = idataId + "-" + pdnId;
            ChildNoteBean cn = new ChildNoteBean();
            cn.setDateCreated(dateCreated);
            cn.setDescription(description);
            cn.setDetailedNote(detailedNote);
            cn.setStatus(status);
            cn.setOid("CDN_" + dnId);
            ElementRefBean userRef = new ElementRefBean();
            userRef.setElementDefOID("USR_" + ownerId);
            cn.setUserRef(userRef);
            ArrayList<ChildNoteBean> cns = pDNs.containsKey(key) ? pDNs.get(key) : new ArrayList<ChildNoteBean>();
            cns.add(cn);
            pDNs.put(key, cns);
        } else {
            DiscrepancyNoteBean dn = new DiscrepancyNoteBean();
            String k = idataId + "-" + dnId;
            if (pDNs != null && pDNs.containsKey(k)) {
                dn.setChildNotes(pDNs.get(k));
                dn.setNumberOfChildNotes(dn.getChildNotes().size());
            }
            dn.setDateUpdated(dateCreated);
            dn.setNoteType(noteType);
            dn.setStatus(status);
            dn.setOid("DN_" + dnId);
            ElementRefBean userRef = new ElementRefBean();
            userRef.setElementDefOID("USR_" + ownerId);
            if (idataOidPoses.containsKey(idataId)) {
                String[] poses = idataOidPoses.get(idataId).split("---");
                int p0 = Integer.parseInt(poses[0]);
                int p1 = Integer.parseInt(poses[1]);
                int p2 = Integer.parseInt(poses[2]);
                int p3 = Integer.parseInt(poses[3]);
                int p4 = Integer.parseInt(poses[4]);
                String entityID = data.getExportSubjectData().get(p0).getExportStudyEventData().get(p1).getExportFormData().get(p2).getItemGroupData().get(p3).getItemData().get(p4).getItemOID();
                data.getExportSubjectData().get(p0).getExportStudyEventData().get(p1).getExportFormData().get(p2).getItemGroupData().get(p3).getItemData().get(p4).getDiscrepancyNotes().setEntityID(entityID);
                data.getExportSubjectData().get(p0).getExportStudyEventData().get(p1).getExportFormData().get(p2).getItemGroupData().get(p3).getItemData().get(p4).getDiscrepancyNotes().getDiscrepancyNotes().add(dn);
            }
        }
    }
}

Example 17 with ElementRefBean

use of org.akaza.openclinica.bean.odmbeans.ElementRefBean in project OpenClinica by OpenClinica.

the class OdmExtractDAO method applyStudyEventDef.

private void applyStudyEventDef(MetaDataVersionBean metadata, String formOID) {
    StudyEventDefBean studyEventDef = new StudyEventDefBean();
    studyEventDef.setOid(MetadataUnit.FAKE_STUDY_EVENT_OID);
    studyEventDef.setName(MetadataUnit.FAKE_SE_NAME);
    studyEventDef.setRepeating(MetadataUnit.FAKE_SE_REPEATING);
    ElementRefBean formRefBean = new ElementRefBean();
    formRefBean.setElementDefOID(formOID);
    studyEventDef.getFormRefs().add(formRefBean);
    metadata.getStudyEventDefs().add(studyEventDef);
}

Example 18 with ElementRefBean

use of org.akaza.openclinica.bean.odmbeans.ElementRefBean in project OpenClinica by OpenClinica.

the class OdmExtractDAO method getStudyEventAndFormMetaOC1_3.

public void getStudyEventAndFormMetaOC1_3(int parentStudyId, int studyId, MetaDataVersionBean metadata, String odmVersion, boolean isIncludedSite) {
    ArrayList<StudyEventDefBean> seds = (ArrayList<StudyEventDefBean>) metadata.getStudyEventDefs();
    ArrayList<FormDefBean> forms = (ArrayList<FormDefBean>) metadata.getFormDefs();
    for (StudyEventDefBean sed : seds) {
        List<ElementRefBean> formRefs = sed.getFormRefs();
        for (ElementRefBean formRef : formRefs) {
            ConfigurationParameters conf = new ConfigurationParameters();
            EventDefinitionCRFBean edc = getEventDefCRF(sed, formRef, studyId);
            CRFBean cBean = (CRFBean) crfdao.findByPK(edc.getCrfId());
            String crfPath = sed.getOid() + "." + cBean.getOid();
            conf = populateConfigurationParameters(edc, conf, crfPath);
            formRef.setConfigurationParameters(conf);
            int defaultVersionId = edc.getDefaultVersionId();
            formRef.setFormLayoutRefs(getFormLayoutRefs(formRef, defaultVersionId));
        }
    }
    HashMap<String, EventDefinitionDetailsBean> sedDetails = new HashMap<String, EventDefinitionDetailsBean>();
    HashMap<String, FormDetailsBean> formDetails = new HashMap<String, FormDetailsBean>();
    this.setStudyEventAndFormMetaOC1_3TypesExpected();
    logger.debug("Begin to execute GetStudyEventAndFormMetaOC1_3Sql");
    logger.debug("getStudyEventAndFormMetaOC1_3SQl= " + this.getStudyEventAndFormMetaOC1_3Sql(parentStudyId, studyId, isIncludedSite));
    ArrayList rows = this.select(this.getStudyEventAndFormMetaOC1_3Sql(parentStudyId, studyId, isIncludedSite));
    Iterator iter = rows.iterator();
    String sedOIDs = "";
    while (iter.hasNext()) {
        HashMap row = (HashMap) iter.next();
        Integer cvId = (Integer) row.get("crf_version_id");
        String sedOID = (String) row.get("definition_oid");
        String cvOID = (String) row.get("cv_oid");
        String sedDesc = (String) row.get("description");
        String category = (String) row.get("category");
        String cvDesc = (String) row.get("version_description");
        String notes = (String) row.get("revision_notes");
        String cOID = (String) row.get("crf_oid");
        String crfDescription = (String) row.get("crf_description");
        String nullValue = (String) row.get("null_values");
        Integer dvId = (Integer) row.get("default_version_id");
        Boolean pwdRequired = (Boolean) row.get("electronic_signature");
        Boolean doubleEntry = (Boolean) row.get("double_entry");
        Boolean hideCrf = (Boolean) row.get("hide_crf");
        Boolean participantForm = (Boolean) row.get("participant_form");
        Boolean allowAnonymousSubmission = (Boolean) row.get("allow_anonymous_submission");
        String submissionUrl = (String) row.get("submission_url");
        Integer sdvId = (Integer) row.get("source_data_verification_code");
        Boolean offline = (Boolean) row.get("active");
        if (sedDetails.containsKey(sedOID)) {
        } else {
            EventDefinitionDetailsBean sedDetail = new EventDefinitionDetailsBean();
            sedDetail.setOid(sedOID);
            sedDetail.setCategory(category);
            sedDetail.setDescription(sedDesc);
            sedDetails.put(sedOID, sedDetail);
        }
        if (formDetails.containsKey(cOID)) {
            FormDetailsBean formDetail = formDetails.get(cOID);
            PresentInEventDefinitionBean p = new PresentInEventDefinitionBean();
            p.setStudyEventOid(sedOID);
            p.setDoubleDataEntry(doubleEntry == false ? "No" : "Yes");
            p.setHideCrf(hideCrf == false ? "No" : "Yes");
            p.setParticipantForm(participantForm == false ? "No" : "Yes");
            p.setIsDefaultVersion(cvId.equals(dvId) ? "Yes" : "No");
            p.setNullValues(nullValue);
            p.setPasswordRequired(pwdRequired == false ? "No" : "Yes");
            p.setAllowAnonymousSubmission(allowAnonymousSubmission == false ? "No" : "Yes");
            p.setOffline((offline == false) ? "No" : "Yes");
            p.setSubmissionUrl(submissionUrl);
            p.setSourceDataVerification(SourceDataVerification.getByCode(sdvId > 0 ? sdvId : 3).getDescription());
            formDetail.getPresentInEventDefinitions().add(p);
        } else {
            FormDetailsBean formDetail = new FormDetailsBean();
            formDetail.setOid(cOID);
            formDetail.setRevisionNotes(notes);
            formDetail.setParentFormOid(cOID);
            formDetail.setVersionDescription(cvDesc);
            formDetail.setDescription(crfDescription);
            // ArrayList sectionBeansRows = this.select(this.getSectionDetails(cvOID),cvId);
            formDetail = setSectionBean(formDetail, cvId);
            PresentInEventDefinitionBean p = new PresentInEventDefinitionBean();
            p.setStudyEventOid(sedOID);
            p.setDoubleDataEntry(doubleEntry == false ? "No" : "Yes");
            p.setHideCrf(hideCrf == false ? "No" : "Yes");
            p.setParticipantForm(participantForm == false ? "No" : "Yes");
            p.setIsDefaultVersion(cvId.equals(dvId) ? "Yes" : "No");
            p.setNullValues(nullValue);
            p.setPasswordRequired(pwdRequired == false ? "No" : "Yes");
            p.setAllowAnonymousSubmission(allowAnonymousSubmission == false ? "No" : "Yes");
            p.setOffline((offline == false) ? "No" : "Yes");
            p.setSubmissionUrl(submissionUrl);
            p.setSourceDataVerification(SourceDataVerification.getByCode(sdvId > 0 ? sdvId : 3).getDescription());
            formDetail.getPresentInEventDefinitions().add(p);
            formDetails.put(cOID, formDetail);
        }
    }
    for (StudyEventDefBean sedef : seds) {
        sedef.setEventDefinitionDetais(sedDetails.get(sedef.getOid()));
    }
    for (FormDefBean formdef : forms) {
        List<ElementRefBean> formLayoutRefs = getFormLayoutRefs(formdef);
        formdef.setFormLayoutRefs(formLayoutRefs);
        formdef.setFormDetails(formDetails.get(formdef.getOid()));
    }
}

Example 19 with ElementRefBean

use of org.akaza.openclinica.bean.odmbeans.ElementRefBean in project OpenClinica by OpenClinica.

the class OdmExtractDAO method getFormLayoutRefs.

List<ElementRefBean> getFormLayoutRefs(FormDefBean formDef) {
    CRFBean crfBean = crfdao.findByOid(formDef.getOid());
    List<FormLayoutBean> formLayouts = fldao.findAllByCRFId(crfBean.getId());
    List<ElementRefBean> elementRefs = new ArrayList<>();
    ElementRefBean element;
    for (FormLayoutBean formLayout : formLayouts) {
        element = new ElementRefBean();
        element.setName(formLayout.getName());
        element.setUrl(formLayout.getUrl());
        elementRefs.add(element);
    }
    return elementRefs;
}