@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;
}
/** @see org.openmrs.api.db.ObsDAO#saveObs(org.openmrs.Obs) */
public Obs saveObs(Obs obs) throws DAOException {
if (obs.hasGroupMembers() && obs.getObsId() != null) {
// hibernate has a problem updating child collections
// if the parent object was already saved so we do it
// explicitly here
for (Obs member : obs.getGroupMembers()) if (member.getObsId() == null) saveObs(member);
}
sessionFactory.getCurrentSession().saveOrUpdate(obs);
return obs;
}
/**
* Compares two Obs for similarity. The comparison is done on obsId of both this and the given
* <code>obs</code> object. If either has a null obsId, then they are not equal
*
* @param obj
* @return boolean True if the obsIds match, false otherwise or if either obsId is null.
*/
public boolean equals(Object obj) {
if (obj instanceof Obs) {
Obs o = (Obs) obj;
if (this.getObsId() != null && o.getObsId() != null)
return (this.getObsId().equals(o.getObsId()));
/*
* return (this.getConcept().equals(o.getConcept()) &&
* this.getPatient().equals(o.getPatient()) &&
* this.getEncounter().equals(o.getEncounter()) &&
* this.getLocation().equals(o.getLocation()));
*/
}
// if the obsIds don't match, its possible that they are the same
// exact object. Check that now on the way out.
return this == obj;
}
@Test
public void testParsingDispositionWithTransferLocation() throws Exception {
Concept admit =
new ConceptBuilder(
null,
conceptService.getConceptDatatypeByName("N/A"),
conceptService.getConceptClassByName("Misc"))
.addName("Transfer")
.get();
when(emrConceptService.getConcept("test:transfer")).thenReturn(admit);
Obs dispositionObs =
dispositionDescriptor.buildObsGroup(
new Disposition(
"emrapi.transfer",
"Transfer",
"test:transfer",
Collections.<String>emptyList(),
Collections.<DispositionObs>emptyList()),
emrConceptService);
Obs transferLocationObs = new Obs();
transferLocationObs.setObsId(100);
transferLocationObs.setConcept(dispositionDescriptor.getInternalTransferLocationConcept());
transferLocationObs.setValueText("3");
dispositionObs.addGroupMember(transferLocationObs);
Location transferLocation = new Location();
transferLocation.setName("Outpatient clinic");
when(locationService.getLocation(3)).thenReturn(transferLocation);
encounter.addObs(doNotGoToServiceToFormatMembers(dispositionObs));
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
SimpleObject expectedTransferLocationObject =
SimpleObject.create("obsId", transferLocationObs.getObsId());
expectedTransferLocationObject.put("question", "Transfer location");
expectedTransferLocationObject.put("answer", "Outpatient clinic");
List<SimpleObject> expectedAdditionalObsList = new ArrayList<SimpleObject>();
expectedAdditionalObsList.add(expectedTransferLocationObject);
assertThat(parsed.getDiagnoses().size(), is(0));
assertThat(parsed.getDispositions().size(), is(1));
assertThat(parsed.getObs().size(), is(0));
assertThat(path(parsed.getDispositions(), 0, "disposition"), is((Object) "Transfer"));
assertThat(
path(parsed.getDispositions(), 0, "additionalObs"), is((Object) expectedAdditionalObsList));
}
@Test
public void testParsingDispositionWithDateOfDeath() throws Exception {
Concept admit =
new ConceptBuilder(
null,
conceptService.getConceptDatatypeByName("N/A"),
conceptService.getConceptClassByName("Misc"))
.addName("Death")
.get();
when(emrConceptService.getConcept("test:death")).thenReturn(admit);
Obs dispositionObs =
dispositionDescriptor.buildObsGroup(
new Disposition(
"emrapi.death",
"Death",
"test:death",
Collections.<String>emptyList(),
Collections.<DispositionObs>emptyList()),
emrConceptService);
Date dateOfDeath = new DateTime(2012, 2, 20, 10, 10, 10).toDate();
Obs dateOfDeathObs = new Obs();
dateOfDeathObs.setObsId(100);
dateOfDeathObs.setConcept(dispositionDescriptor.getDateOfDeathConcept());
dateOfDeathObs.setValueDate(dateOfDeath);
dispositionObs.addGroupMember(dateOfDeathObs);
encounter.addObs(doNotGoToServiceToFormatMembers(dispositionObs));
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
SimpleObject expectedAdmissionLocationObject =
SimpleObject.create("obsId", dateOfDeathObs.getObsId());
expectedAdmissionLocationObject.put("question", "Date of death");
expectedAdmissionLocationObject.put("answer", "20 Feb 2012 10:10 AM");
List<SimpleObject> expectedAdditionalObsList = new ArrayList<SimpleObject>();
expectedAdditionalObsList.add(expectedAdmissionLocationObject);
assertThat(parsed.getDiagnoses().size(), is(0));
assertThat(parsed.getDispositions().size(), is(1));
assertThat(parsed.getObs().size(), is(0));
assertThat(path(parsed.getDispositions(), 0, "disposition"), is((Object) "Death"));
assertThat(
path(parsed.getDispositions(), 0, "additionalObs"), is((Object) expectedAdditionalObsList));
}
/**
* This is an equivalent to a copy constructor. Creates a new copy of the given <code>obsToCopy
* </code> with a null obs id
*
* @param obsToCopy The Obs that is going to be copied
* @return a new Obs object with all the same attributes as the given obs
*/
public static Obs newInstance(Obs obsToCopy) {
Obs newObs =
new Obs(
obsToCopy.getPerson(),
obsToCopy.getConcept(),
obsToCopy.getObsDatetime(),
obsToCopy.getLocation());
newObs.setObsGroup(obsToCopy.getObsGroup());
newObs.setAccessionNumber(obsToCopy.getAccessionNumber());
newObs.setValueCoded(obsToCopy.getValueCoded());
newObs.setValueDrug(obsToCopy.getValueDrug());
newObs.setValueGroupId(obsToCopy.getValueGroupId());
newObs.setValueDatetime(obsToCopy.getValueDatetime());
newObs.setValueNumeric(obsToCopy.getValueNumeric());
newObs.setValueModifier(obsToCopy.getValueModifier());
newObs.setValueText(obsToCopy.getValueText());
newObs.setComment(obsToCopy.getComment());
newObs.setOrder(obsToCopy.getOrder());
newObs.setEncounter(obsToCopy.getEncounter());
newObs.setDateStarted(obsToCopy.getDateStarted());
newObs.setDateStopped(obsToCopy.getDateStopped());
newObs.setCreator(obsToCopy.getCreator());
newObs.setDateCreated(obsToCopy.getDateCreated());
newObs.setVoided(obsToCopy.getVoided());
newObs.setVoidedBy(obsToCopy.getVoidedBy());
newObs.setDateVoided(obsToCopy.getDateVoided());
newObs.setVoidReason(obsToCopy.getVoidReason());
newObs.setValueComplex(obsToCopy.getValueComplex());
newObs.setComplexData(obsToCopy.getComplexData());
if (obsToCopy.getGroupMembers() != null)
for (Obs member : obsToCopy.getGroupMembers()) {
// if the obs hasn't been saved yet, no need to duplicate it
if (member.getObsId() == null) newObs.addGroupMember(member);
else newObs.addGroupMember(Obs.newInstance(member));
}
return newObs;
}
/**
*
* Returns the encounter with the obs that aren't used when populating form are removed.
* This *doesn't* save the encounter.
* TODO: handle Orders?
*
* @param e
* @param htmlform
* @return
* @throws Exception
*/
public static Encounter trimEncounterToMatchForm(Encounter e, HtmlForm htmlform) throws Exception {
//this should move existing obs from session to tag handlers.
FormEntrySession session = new FormEntrySession(e.getPatient(), e, FormEntryContext.Mode.VIEW, htmlform, null); // session gets a null HttpSession
session.getHtmlToDisplay();
if (log.isDebugEnabled()){
Map<Concept, List<Obs>> map = session.getContext().getExistingObs();
if (map != null){
for (Map.Entry<Concept, List<Obs>> existingObs : map.entrySet()){
List<Obs> oList = existingObs.getValue();
for (Obs oInner : oList)
log.debug("Obs in existingObs " + existingObs.getKey() + " " + oInner.getConcept());
}
}
Map<Obs, Set<Obs>> map2 = session.getContext().getExistingObsInGroups();
if (map2 != null){
for (Map.Entry<Obs, Set<Obs>> existingObsInGroups : map2.entrySet()){
Set<Obs> oList = existingObsInGroups.getValue();
for (Obs oInner : oList)
log.debug("Obs in existingObsInGroups " + existingObsInGroups.getKey().getConcept() + " " + oInner.getConcept());
}
}
}
Encounter ret = new Encounter();
ret.setCreator(e.getCreator());
ret.setEncounterDatetime(e.getEncounterDatetime());
EncounterCompatibility.setProvider(ret, EncounterCompatibility.getProvider(e));
ret.setLocation(e.getLocation());
ret.setDateCreated(e.getDateCreated());
ret.setPatient(e.getPatient());
//renders new encounter unsave-able:
ret.setEncounterId(e.getEncounterId());
for (Obs oTest : e.getAllObs()){
boolean found = false;
if (session.getContext().getExistingObs() != null && !oTest.isObsGrouping()){
List<Obs> obsList = session.getContext().getExistingObs().get(oTest.getConcept());
if (obsList != null && obsList.size() > 0){
for (Obs o : obsList){
if (o.getObsId().equals(oTest.getObsId())){
found = true;
continue;
}
}
}
}
if (!found && session.getContext().getExistingObsInGroups() != null){
for (Map.Entry<Obs, Set<Obs>> mapEntry : session.getContext().getExistingObsInGroups().entrySet()){
if (mapEntry.getKey().equals(oTest)){
found = true;
continue;
} else {
Set<Obs> oSet = mapEntry.getValue();
//note: oSet.contains fails for some reason
for (Obs o:oSet){
if (o.getObsId().equals(oTest.getObsId())){
found = true;
continue;
}
}
}
}
}
if (!found)
ret.addObs(oTest);
}
session = null;
return ret;
}
@Override
public Integer getObsId() {
return obs.getObsId();
}
/**
* Save obs corresponding to given http servlet request, http servlet response, radiologyOrder,
* obs, obs, obsErrors
*
* @param request the http servlet request with all parameters
* @param response the http servlet response
* @param radiologyOrder the corresponding radiology order
* @param obs the obs
* @param obsErrors the result of the parameter binding
* @return ModelAndView populated with obs matching the given criteria
* @should save obs with given parameters
* @should return populated model and view if binding errors occur
* @should return populated model and view if edit reason is empty and obs id not null
* @should return populated model and view if edit reason is null and obs id not null
* @should return redirecting model and view for not authenticated user
* @should edit obs with edit reason and complex concept
* @should edit obs with edit reason, complex concept and request which is an instance of
* multihttpserveletrequest
* @should edit obs with edit reason concept not complex and request which is an instance of
* multihttpserveletrequest
* @should populate model and view with obs occuring thrown APIException
*/
@RequestMapping(
value = "/module/radiology/radiologyObs.form",
method = RequestMethod.POST,
params = "saveObs")
ModelAndView saveObs(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "editReason", required = false) String editReason,
@RequestParam(value = "orderId", required = true) RadiologyOrder radiologyOrder,
@ModelAttribute("obs") Obs obs,
BindingResult obsErrors) {
HttpSession httpSession = request.getSession();
new ObsValidator().validate(obs, obsErrors);
if (obsErrors.hasErrors()) {
return populateModelAndView(radiologyOrder, obs);
}
if (Context.isAuthenticated()) {
try {
// if the user is just editing the obs
if (obs.getObsId() != null && (editReason == null || editReason.isEmpty())) {
obsErrors.reject("editReason", "Obs.edit.reason.empty");
return populateModelAndView(radiologyOrder, obs);
}
if (obs.getConcept().isComplex()) {
if (request instanceof MultipartHttpServletRequest) {
MultipartHttpServletRequest multipartRequest = (MultipartHttpServletRequest) request;
MultipartFile complexDataFile = multipartRequest.getFile("complexDataFile");
if (complexDataFile != null && !complexDataFile.isEmpty()) {
InputStream complexDataInputStream = complexDataFile.getInputStream();
ComplexData complexData =
new ComplexData(complexDataFile.getOriginalFilename(), complexDataInputStream);
obs.setComplexData(complexData);
// the handler on the obs.concept is called
// with
// the given complex data
obsService.saveObs(obs, editReason);
updateReadingPhysician(radiologyOrder.getStudy());
complexDataInputStream.close();
}
}
} else {
obsService.saveObs(obs, editReason);
updateReadingPhysician(radiologyOrder.getStudy());
}
httpSession.setAttribute(WebConstants.OPENMRS_MSG_ATTR, "Obs.saved");
} catch (APIException e) {
httpSession.setAttribute(WebConstants.OPENMRS_ERROR_ATTR, e.getMessage());
return populateModelAndView(radiologyOrder, obs);
} catch (IOException e) {
return populateModelAndView(radiologyOrder, obs);
}
}
return new ModelAndView(
"redirect:"
+ RADIOLOGY_OBS_FORM_URL
+ "orderId="
+ obs.getOrder().getId()
+ "&obsId="
+ obs.getId());
}
/**
* @see
* org.springframework.web.servlet.mvc.SimpleFormController#referenceData(javax.servlet.http.HttpServletRequest,
* java.lang.Object, org.springframework.validation.Errors)
*/
@Override
protected Map<String, Object> referenceData(HttpServletRequest request, Object obj, Errors error)
throws Exception {
Encounter encounter = (Encounter) obj;
// the generic returned key-value pair mapping
Map<String, Object> map = new HashMap<String, Object>();
// obsIds of obs that were edited
List<Integer> editedObs = new Vector<Integer>();
// the map returned to the form
// This is a mapping between the formfield and a list of the Obs/ObsGroup in that field
// This mapping is sorted according to the comparator in FormField.java
SortedMap<FormField, List<Obs>> obsMapToReturn = null;
String sortType =
Context.getAdministrationService()
.getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_ENCOUNTER_FORM_OBS_SORT_ORDER);
if ("weight".equals(sortType)) {
obsMapToReturn = new TreeMap<FormField, List<Obs>>(); // use FormField.compareTo
} else {
obsMapToReturn =
new TreeMap<FormField, List<Obs>>(
new NumberingFormFieldComparator()); // use custom comparator
}
// this maps the obs to form field objects for non top-level obs
// it is keyed on obs so that when looping over an exploded obsGroup
// the formfield can be fetched easily (in order to show the field numbers etc)
Map<Obs, FormField> otherFormFields = new HashMap<Obs, FormField>();
if (Context.isAuthenticated()) {
EncounterService es = Context.getEncounterService();
FormService fs = Context.getFormService();
// used to restrict the form field lookup
Form form = encounter.getForm();
List<EncounterType> encTypes = es.getAllEncounterTypes();
// Non-retired types first
Collections.sort(encTypes, new MetadataComparator(Context.getLocale()));
map.put("encounterTypes", encTypes);
map.put("encounterRoles", es.getAllEncounterRoles(false));
map.put("forms", Context.getFormService().getAllForms());
// loop over the encounter's observations to find the edited obs
for (Obs o : encounter.getObsAtTopLevel(true)) {
// only edited obs has previous version
if (o.hasPreviousVersion()) {
editedObs.add(o.getObsId());
}
// get the formfield for this obs
FormField ff = fs.getFormField(form, o.getConcept(), obsMapToReturn.keySet(), false);
if (ff == null) {
ff = new FormField();
}
// we only put the top-level obs in the obsMap. Those would
// be the obs that don't have an obs grouper
if (o.getObsGroup() == null) {
// populate the obs map with this formfield and obs
List<Obs> list = obsMapToReturn.get(ff);
if (list == null) {
list = new Vector<Obs>();
obsMapToReturn.put(ff, list);
}
list.add(o);
} else {
// this is not a top-level obs, just put the formField
// in a separate list and be done with it
otherFormFields.put(o, ff);
}
}
}
if (log.isDebugEnabled()) {
log.debug("setting obsMap in page context (size: " + obsMapToReturn.size() + ")");
}
map.put("obsMap", obsMapToReturn);
map.put("otherFormFields", otherFormFields);
map.put("locale", Context.getLocale());
map.put("editedObs", editedObs);
if (encounter.getPatient() != null) {
map.put(
"patientVisits", Context.getVisitService().getVisitsByPatient(encounter.getPatient()));
}
return map;
}
/**
* @return Returns the obsId of the parent obs group
* @deprecated The {@link #getObsGroup()} method should be used
* @see #getObsGroup()
*/
public Integer getObsGroupId() {
if (getObsGroup() == null) return null;
return obsGroup.getObsId();
}