@SuppressWarnings("unused") public static JSONObject createJsonObservation(Obs obs) { JSONObject jsonObs = new JSONObject(); jsonObs.put("observation_id", obs.getObsId()); jsonObs.put("concept_name", obs.getConcept().getDisplayString()); Date obsDate = obs.getObsDatetime() == null ? new Date() : obs.getObsDatetime(); SimpleDateFormat formatDateJava = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss"); String dateStr = obsDate.getTime() + ""; jsonObs.put("date", dateStr); if (obs.getConcept().getDatatype().isNumeric()) { // ADD MORE DATATYPES ConceptNumeric conceptNumeric = Context.getConceptService().getConceptNumeric(obs.getConcept().getId()); jsonObs.put("units_of_measurement", conceptNumeric.getUnits()); jsonObs.put("absolute_high", conceptNumeric.getHiAbsolute()); jsonObs.put("absolute_low", conceptNumeric.getLowAbsolute()); jsonObs.put("critical_high", conceptNumeric.getHiCritical()); jsonObs.put("critical_low", conceptNumeric.getLowCritical()); jsonObs.put("normal_high", conceptNumeric.getHiNormal()); jsonObs.put("normal_low", conceptNumeric.getLowNormal()); } jsonObs.put("value_type", obs.getConcept().getDatatype().getName()); jsonObs.put("value", obs.getValueAsString(Context.getLocale())); jsonObs.put("location", obs.getLocation().getDisplayString()); jsonObs.put("creator", obs.getCreator().getDisplayString()); Set<EncounterProvider> encounterProviders = obs.getEncounter().getEncounterProviders(); if (encounterProviders != null && encounterProviders.iterator().hasNext()) { EncounterProvider provider = encounterProviders.iterator().next(); if (provider.getProvider() != null) { jsonObs.put("provider", provider.getProvider().getName()); } } SearchAPI searchAPI = SearchAPI.getInstance(); if (!searchAPI.getSearchPhrase().getPhrase().equals("") && !searchAPI.getSearchPhrase().getPhrase().equals("*")) { for (ChartListItem item : searchAPI.getResults()) { if (item != null && item instanceof ObsItem && ((ObsItem) item).getObsId() != null) { if (((ObsItem) item).getObsId() == obs.getObsId()) { jsonObs.put("chosen", "true"); } } } } return jsonObs; }
@Test public void shouldEvaluateOBRORUR01TemplateForOBSGroup() throws Exception { // given Encounter encounter = new Encounter(); Date date = new Date(); encounter.setEncounterDatetime(date); encounter.setUuid("ENCOUNTER UUID"); EncounterType encounterType = new EncounterType(); encounterType.setName("ENCOUNTER TYPE NAME"); encounter.setEncounterType(encounterType); Location location = new Location(1); location.setUuid("LOCATION UUID"); location.setName("LOCATION NAME"); encounter.setLocation(location); Person provider = new Person(1); provider.setUuid("PROVIDER UUID"); provider.addName( new PersonName("PROVIDER GIVENNAME", "PROVIDER MIDDLENAME", "PROVIDER FAMILYNAME")); encounter.setProvider(provider); ConceptSource source = new ConceptSource(); source.setName("AMPATH"); ConceptMap map = new ConceptMap(); map.setSourceCode("200"); map.setSource(source); ConceptDatatype datatype = new ConceptDatatype(); datatype.setUuid(ConceptDatatype.NUMERIC_UUID); datatype.setHl7Abbreviation(ConceptDatatype.NUMERIC); ConceptNumeric concept = new ConceptNumeric(); concept.setDatatype(datatype); concept.addConceptMapping(map); concept.addName(new ConceptName("NumericConcept", Locale.ENGLISH)); concept.setUnits("mg"); Date dateCreated = new Date(213231421890234L); Obs obs = new Obs(2); obs.setConcept(concept); obs.setDateCreated(dateCreated); obs.setValueNumeric(10d); obs.setObsGroup(getObsGroup()); obs.getObsGroup().addGroupMember(obs); encounter.addObs(obs); obs = new Obs(3); obs.setConcept(concept); obs.setDateCreated(dateCreated); obs.setValueNumeric(23d); encounter.addObs(obs); Map<String, Object> bindings = new HashMap<String, Object>(); bindings.put("encounter", encounter); bindings.put("implementationId", "MVP"); // when HL7Template hl7Template = hl7QueryService.getHL7TemplateByName("Generic Obs Group"); String evaluatedTemplate = hl7QueryService.evaluateTemplate(hl7Template, bindings); // then evaluatedTemplate = StringUtils.deleteWhitespace(evaluatedTemplate); Assert.assertEquals( "<ORU_R01.ORDER_OBSERVATION><OBR><OBR.1>0</OBR.1><OBR.4><CE.1>100</CE.1>" + "<CE.2>MEDICALRECORDOBSERVATIONS</CE.2><CE.3>LOCAL</CE.3></OBR.4><OBR.18>0</OBR.18>" + "<OBR.29><EIP.2><EI.3>ENCOUNTERUUID</EI.3></EIP.2></OBR.29></OBR><ORU_R01.OBSERVATION>" + "<OBX><OBX.1>1</OBX.1><OBX.2>NM</OBX.2><OBX.3><CE.1>200</CE.1><CE.2>NumericConcept</CE.2>" + "<CE.3>AMPATH</CE.3></OBX.3><OBX.5>23.0</OBX.5><OBX.6><CE.1>mg</CE.1><CE.3>UCUM</CE.3></OBX.6>" + "<OBX.14><TS.1>" + new HL7TemplateFunctions().formatDate(dateCreated, null) + "</TS.1>" + "</OBX.14></OBX></ORU_R01.OBSERVATION></ORU_R01.ORDER_OBSERVATION>" + "<ORU_R01.ORDER_OBSERVATION><OBR><OBR.1>2</OBR.1><OBR.4><CE.1>100</CE.1><CE.2>MedSet</CE.2>" + "<CE.3>LOCAL</CE.3></OBR.4><OBR.18>0</OBR.18><OBR.29><EIP.2><EI.3>ENCOUNTERUUID</EI.3></EIP.2></OBR.29" + "></OBR><ORU_R01.OBSERVATION><OBX><OBX.1>2</OBX.1><OBX.2>NM</OBX.2><OBX.3><CE.1>200</CE.1>" + "<CE.2>NumericConcept</CE.2><CE.3>AMPATH</CE.3></OBX.3><OBX.5>10.0</OBX.5><OBX.6><CE.1>mg</CE.1>" + "<CE.3>UCUM</CE.3></OBX.6><OBX.14><TS.1>" + new HL7TemplateFunctions().formatDate(dateCreated, null) + "</TS.1></OBX.14></OBX></ORU_R01.OBSERVATION></ORU_R01.ORDER_OBSERVATION>", evaluatedTemplate); }
/** * This method produces a model containing the following mappings: * * <pre> * (always) * (java.util.Date) now * (String) size * (Locale) locale * (String) portletUUID // unique for each instance of any portlet * (other parameters) * (if there's currently an authenticated user) * (User) authenticatedUser * (if the request has a patientId attribute) * (Integer) patientId * (Patient) patient * (List<Obs>) patientObs * (List<Encounter>) patientEncounters * (List<DrugOrder>) patientDrugOrders * (List<DrugOrder>) currentDrugOrders * (List<DrugOrder>) completedDrugOrders * (Obs) patientWeight // most recent weight obs * (Obs) patientHeight // most recent height obs * (Double) patientBmi // BMI derived from most recent weight and most recent height * (String) patientBmiAsString // BMI rounded to one decimal place, or "?" if unknown * (Integer) personId * (if the patient has any obs for the concept in the global property 'concept.reasonExitedCare') * (Obs) patientReasonForExit * (if the request has a personId or patientId attribute) * (Person) person * (List<Relationship>) personRelationships * (Map<RelationshipType, List<Relationship>>) personRelationshipsByType * (if the request has an encounterId attribute) * (Integer) encounterId * (Encounter) encounter * (Set<Obs>) encounterObs * (if the request has a userId attribute) * (Integer) userId * (User) user * (if the request has a patientIds attribute, which should be a (String) comma-separated list of patientIds) * (PatientSet) patientSet * (String) patientIds * (if the request has a conceptIds attribute, which should be a (String) commas-separated list of conceptIds) * (Map<Integer, Concept>) conceptMap * (Map<String, Concept>) conceptMapByStringIds * </pre> * * @should calculate bmi into patientBmiAsString * @should not fail with empty height and weight properties */ @SuppressWarnings("unchecked") public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { AdministrationService as = Context.getAdministrationService(); ConceptService cs = Context.getConceptService(); // find the portlet that was identified in the openmrs:portlet taglib Object uri = request.getAttribute("javax.servlet.include.servlet_path"); String portletPath = ""; Map<String, Object> model = null; { HttpSession session = request.getSession(); String uniqueRequestId = (String) request.getAttribute(WebConstants.INIT_REQ_UNIQUE_ID); String lastRequestId = (String) session.getAttribute(WebConstants.OPENMRS_PORTLET_LAST_REQ_ID); if (uniqueRequestId.equals(lastRequestId)) { model = (Map<String, Object>) session.getAttribute(WebConstants.OPENMRS_PORTLET_CACHED_MODEL); // remove cached parameters List<String> parameterKeys = (List<String>) model.get("parameterKeys"); for (String key : parameterKeys) { model.remove(key); } } if (model == null) { log.debug("creating new portlet model"); model = new HashMap<String, Object>(); session.setAttribute(WebConstants.OPENMRS_PORTLET_LAST_REQ_ID, uniqueRequestId); session.setAttribute(WebConstants.OPENMRS_PORTLET_CACHED_MODEL, model); } } if (uri != null) { long timeAtStart = System.currentTimeMillis(); portletPath = uri.toString(); // Allowable extensions are '' (no extension) and '.portlet' if (portletPath.endsWith("portlet")) portletPath = portletPath.replace(".portlet", ""); else if (portletPath.endsWith("jsp")) throw new ServletException( "Illegal extension used for portlet: '.jsp'. Allowable extensions are '' (no extension) and '.portlet'"); log.debug("Loading portlet: " + portletPath); String id = (String) request.getAttribute("org.openmrs.portlet.id"); String size = (String) request.getAttribute("org.openmrs.portlet.size"); Map<String, Object> params = (Map<String, Object>) request.getAttribute("org.openmrs.portlet.parameters"); Map<String, Object> moreParams = (Map<String, Object>) request.getAttribute("org.openmrs.portlet.parameterMap"); model.put("now", new Date()); model.put("id", id); model.put("size", size); model.put("locale", Context.getLocale()); model.put("portletUUID", UUID.randomUUID().toString().replace("-", "")); List<String> parameterKeys = new ArrayList<String>(params.keySet()); model.putAll(params); if (moreParams != null) { model.putAll(moreParams); parameterKeys.addAll(moreParams.keySet()); } model.put("parameterKeys", parameterKeys); // so we can clean these up in the next request // if there's an authenticated user, put them, and their patient set, in the model if (Context.getAuthenticatedUser() != null) { model.put("authenticatedUser", Context.getAuthenticatedUser()); } Integer personId = null; // if a patient id is available, put patient data documented above in the model Object o = request.getAttribute("org.openmrs.portlet.patientId"); if (o != null) { String patientVariation = ""; Integer patientId = (Integer) o; if (!model.containsKey("patient")) { // we can't continue if the user can't view patients if (Context.hasPrivilege(PrivilegeConstants.VIEW_PATIENTS)) { Patient p = Context.getPatientService().getPatient(patientId); model.put("patient", p); // add encounters if this user can view them if (Context.hasPrivilege(PrivilegeConstants.VIEW_ENCOUNTERS)) model.put( "patientEncounters", Context.getEncounterService().getEncountersByPatient(p)); if (Context.hasPrivilege(PrivilegeConstants.VIEW_OBS)) { List<Obs> patientObs = Context.getObsService().getObservationsByPerson(p); model.put("patientObs", patientObs); Obs latestWeight = null; Obs latestHeight = null; String bmiAsString = "?"; try { String weightString = as.getGlobalProperty("concept.weight"); ConceptNumeric weightConcept = null; if (StringUtils.hasLength(weightString)) weightConcept = cs.getConceptNumeric( cs.getConcept(Integer.valueOf(weightString)).getConceptId()); String heightString = as.getGlobalProperty("concept.height"); ConceptNumeric heightConcept = null; if (StringUtils.hasLength(heightString)) heightConcept = cs.getConceptNumeric( cs.getConcept(Integer.valueOf(heightString)).getConceptId()); for (Obs obs : patientObs) { if (obs.getConcept().equals(weightConcept)) { if (latestWeight == null || obs.getObsDatetime().compareTo(latestWeight.getObsDatetime()) > 0) latestWeight = obs; } else if (obs.getConcept().equals(heightConcept)) { if (latestHeight == null || obs.getObsDatetime().compareTo(latestHeight.getObsDatetime()) > 0) latestHeight = obs; } } if (latestWeight != null) model.put("patientWeight", latestWeight); if (latestHeight != null) model.put("patientHeight", latestHeight); if (latestWeight != null && latestHeight != null) { double weightInKg; double heightInM; if (weightConcept.getUnits().equals("kg")) weightInKg = latestWeight.getValueNumeric(); else if (weightConcept.getUnits().equals("lb")) weightInKg = latestWeight.getValueNumeric() * 0.45359237; else throw new IllegalArgumentException( "Can't handle units of weight concept: " + weightConcept.getUnits()); if (heightConcept.getUnits().equals("cm")) heightInM = latestHeight.getValueNumeric() / 100; else if (heightConcept.getUnits().equals("m")) heightInM = latestHeight.getValueNumeric(); else if (heightConcept.getUnits().equals("in")) heightInM = latestHeight.getValueNumeric() * 0.0254; else throw new IllegalArgumentException( "Can't handle units of height concept: " + heightConcept.getUnits()); double bmi = weightInKg / (heightInM * heightInM); model.put("patientBmi", bmi); String temp = "" + bmi; bmiAsString = temp.substring(0, temp.indexOf('.') + 2); } } catch (Exception ex) { if (latestWeight != null && latestHeight != null) log.error( "Failed to calculate BMI even though a weight and height were found", ex); } model.put("patientBmiAsString", bmiAsString); } else { model.put("patientObs", new HashSet<Obs>()); } // information about whether or not the patient has exited care Obs reasonForExitObs = null; String reasonForExitConceptString = as.getGlobalProperty("concept.reasonExitedCare"); if (StringUtils.hasLength(reasonForExitConceptString)) { Concept reasonForExitConcept = cs.getConcept(reasonForExitConceptString); if (reasonForExitConcept != null) { List<Obs> patientExitObs = Context.getObsService() .getObservationsByPersonAndConcept(p, reasonForExitConcept); if (patientExitObs != null) { log.debug("Exit obs is size " + patientExitObs.size()); if (patientExitObs.size() == 1) { reasonForExitObs = patientExitObs.iterator().next(); Concept exitReason = reasonForExitObs.getValueCoded(); Date exitDate = reasonForExitObs.getObsDatetime(); if (exitReason != null && exitDate != null) { patientVariation = "Exited"; } } else { if (patientExitObs.size() == 0) { log.debug("Patient has no reason for exit"); } else { log.error("Too many reasons for exit - not putting data into model"); } } } } } model.put("patientReasonForExit", reasonForExitObs); if (Context.hasPrivilege(PrivilegeConstants.VIEW_ORDERS)) { List<DrugOrder> drugOrderList = Context.getOrderService().getDrugOrdersByPatient(p); model.put("patientDrugOrders", drugOrderList); List<DrugOrder> currentDrugOrders = new ArrayList<DrugOrder>(); List<DrugOrder> discontinuedDrugOrders = new ArrayList<DrugOrder>(); Date rightNow = new Date(); for (Iterator<DrugOrder> iter = drugOrderList.iterator(); iter.hasNext(); ) { DrugOrder next = iter.next(); if (next.isCurrent() || next.isFuture()) currentDrugOrders.add(next); if (next.isDiscontinued(rightNow)) discontinuedDrugOrders.add(next); } model.put("currentDrugOrders", currentDrugOrders); model.put("completedDrugOrders", discontinuedDrugOrders); List<RegimenSuggestion> standardRegimens = Context.getOrderService().getStandardRegimens(); if (standardRegimens != null) model.put("standardRegimens", standardRegimens); } if (Context.hasPrivilege(PrivilegeConstants.VIEW_PROGRAMS) && Context.hasPrivilege(PrivilegeConstants.VIEW_PATIENT_PROGRAMS)) { model.put( "patientPrograms", Context.getProgramWorkflowService() .getPatientPrograms(p, null, null, null, null, null, false)); model.put( "patientCurrentPrograms", Context.getProgramWorkflowService() .getPatientPrograms(p, null, null, new Date(), new Date(), null, false)); } model.put("patientId", patientId); if (p != null) { personId = p.getPatientId(); model.put("personId", personId); } model.put("patientVariation", patientVariation); } } } // if a person id is available, put person and relationships in the model if (personId == null) { o = request.getAttribute("org.openmrs.portlet.personId"); if (o != null) { personId = (Integer) o; model.put("personId", personId); } } if (personId != null) { if (!model.containsKey("person")) { Person p = (Person) model.get("patient"); if (p == null) p = Context.getPersonService().getPerson(personId); model.put("person", p); if (Context.hasPrivilege(PrivilegeConstants.VIEW_RELATIONSHIPS)) { List<Relationship> relationships = new ArrayList<Relationship>(); relationships.addAll(Context.getPersonService().getRelationshipsByPerson(p)); Map<RelationshipType, List<Relationship>> relationshipsByType = new HashMap<RelationshipType, List<Relationship>>(); for (Relationship rel : relationships) { List<Relationship> list = relationshipsByType.get(rel.getRelationshipType()); if (list == null) { list = new ArrayList<Relationship>(); relationshipsByType.put(rel.getRelationshipType(), list); } list.add(rel); } model.put("personRelationships", relationships); model.put("personRelationshipsByType", relationshipsByType); } } } // if an encounter id is available, put "encounter" and "encounterObs" in the model o = request.getAttribute("org.openmrs.portlet.encounterId"); if (o != null && !model.containsKey("encounterId")) { if (!model.containsKey("encounter")) { if (Context.hasPrivilege(PrivilegeConstants.VIEW_ENCOUNTERS)) { Encounter e = Context.getEncounterService().getEncounter((Integer) o); model.put("encounter", e); if (Context.hasPrivilege(PrivilegeConstants.VIEW_OBS)) model.put("encounterObs", e.getObs()); } model.put("encounterId", (Integer) o); } } // if a user id is available, put "user" in the model o = request.getAttribute("org.openmrs.portlet.userId"); if (o != null) { if (!model.containsKey("user")) { if (Context.hasPrivilege(PrivilegeConstants.VIEW_USERS)) { User u = Context.getUserService().getUser((Integer) o); model.put("user", u); } model.put("userId", (Integer) o); } } // if a list of patient ids is available, make a patientset out of it o = request.getAttribute("org.openmrs.portlet.patientIds"); if (o != null && !"".equals(o) && !model.containsKey("patientIds")) { if (!model.containsKey("patientSet")) { Cohort ps = new Cohort((String) o); model.put("patientSet", ps); model.put("patientIds", (String) o); } } o = model.get("conceptIds"); if (o != null && !"".equals(o)) { if (!model.containsKey("conceptMap")) { log.debug("Found conceptIds parameter: " + o); Map<Integer, Concept> concepts = new HashMap<Integer, Concept>(); Map<String, Concept> conceptsByStringIds = new HashMap<String, Concept>(); String conceptIds = (String) o; String[] ids = conceptIds.split(","); for (String cId : ids) { try { Integer i = Integer.valueOf(cId); Concept c = cs.getConcept(i); concepts.put(i, c); conceptsByStringIds.put(i.toString(), c); } catch (Exception ex) { } } model.put("conceptMap", concepts); model.put("conceptMapByStringIds", conceptsByStringIds); } } populateModel(request, model); log.debug(portletPath + " took " + (System.currentTimeMillis() - timeAtStart) + " ms"); } return new ModelAndView(portletPath, "model", model); }