public static String getDocumentSetJson(Document doc) {
try {
JSONObject input = doc.getInputJson();
JSONObject aidr = input.getJSONObject("aidr");
// Add features
if (!aidr.has("features")) {
ArrayList<DocumentFeature> features = doc.getFeatures(DocumentFeature.class);
JSONArray featureArray = new JSONArray();
for (DocumentFeature f : features) featureArray.put(f.toJSONObject());
aidr.put("features", featureArray);
}
// Add labels
if (!aidr.has("nominal_labels")) {
ArrayList<NominalLabelBC> labels = doc.getLabels(NominalLabelBC.class);
JSONArray labelArray = new JSONArray();
if (!labels.isEmpty()) {
// logger.info("labels field is non-empty");
for (NominalLabelBC l : labels) {
try {
JSONObject labelJson = getLabelJson(doc.crisisID.intValue(), l);
labelArray.put(labelJson);
// logger.info("Added label: " + l);
} catch (RuntimeException e) {
logger.error("Exception while converting document to JSON:" + l);
logger.error(elog.toStringException(e));
}
}
} else {
// logger.warn("Empty nominal_labels field! Inserting a dummy nominal label.");
labelArray.put(createEmptyLabelJson());
}
aidr.put("nominal_labels", labelArray);
// logger.info("Added nominal_labels with size = " + labelArray.length());
}
return unicodeEscaper.translate(input.toString());
} catch (JSONException e) {
logger.error("Error in creating JSON from document: " + doc);
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
}
private String tomaMxToJson(List<DaTomaMx> tomaMxList) {
String jsonResponse = "";
Map<Integer, Object> mapResponse = new HashMap<Integer, Object>();
Integer indice = 0;
for (DaTomaMx tomaMx : tomaMxList) {
Map<String, String> map = new HashMap<String, String>();
map.put("idTomaMx", tomaMx.getIdTomaMx());
// map.put("fechaHoraOrden",DateToString(orden.getFechaHSolicitud(),"dd/MM/yyyy hh:mm:ss a"));
map.put(
"fechaTomaMx", DateUtil.DateToString(tomaMx.getFechaHTomaMx(), "dd/MM/yyyy hh:mm:ss a"));
map.put("estadoMx", tomaMx.getEstadoMx().getValor());
map.put("codSilais", tomaMx.getIdNotificacion().getCodSilaisAtencion().getNombre());
map.put("codUnidadSalud", tomaMx.getIdNotificacion().getCodUnidadAtencion().getNombre());
map.put(
"separadaMx",
(tomaMx.getMxSeparada() != null ? (tomaMx.getMxSeparada() ? "Si" : "No") : ""));
map.put("tipoMuestra", tomaMx.getCodTipoMx().getNombre());
if (tomaMx.getIdNotificacion().getUrgente() != null) {
map.put("urgente", tomaMx.getIdNotificacion().getUrgente().getValor());
} else {
map.put("urgente", "--");
}
// map.put("tipoExamen",orden.getCodDx().getNombre());
// Si hay fecha de inicio de sintomas se muestra
Date fechaInicioSintomas =
tomaMx
.getIdNotificacion()
.getFechaInicioSintomas(); // envioMxService.getFechaInicioSintomas(tomaMx.getIdNotificacion().getIdNotificacion());
if (fechaInicioSintomas != null)
map.put("fechaInicioSintomas", DateUtil.DateToString(fechaInicioSintomas, "dd/MM/yyyy"));
else map.put("fechaInicioSintomas", " ");
// hospitalizado
String[] arrayHosp = {"13", "17", "11", "16", "10", "12"};
boolean hosp = false;
if (tomaMx.getCodUnidadAtencion() != null) {
int h =
Arrays.binarySearch(
arrayHosp, String.valueOf(tomaMx.getCodUnidadAtencion().getTipoUnidad()));
hosp = h > 0;
}
if (hosp) {
map.put("hospitalizado", messageSource.getMessage("lbl.yes", null, null));
} else {
map.put("hospitalizado", messageSource.getMessage("lbl.no", null, null));
}
// Si hay persona
if (tomaMx.getIdNotificacion().getPersona() != null) {
/// se obtiene el nombre de la persona asociada a la ficha
String nombreCompleto = "";
nombreCompleto = tomaMx.getIdNotificacion().getPersona().getPrimerNombre();
if (tomaMx.getIdNotificacion().getPersona().getSegundoNombre() != null)
nombreCompleto =
nombreCompleto + " " + tomaMx.getIdNotificacion().getPersona().getSegundoNombre();
nombreCompleto =
nombreCompleto + " " + tomaMx.getIdNotificacion().getPersona().getPrimerApellido();
if (tomaMx.getIdNotificacion().getPersona().getSegundoApellido() != null)
nombreCompleto =
nombreCompleto + " " + tomaMx.getIdNotificacion().getPersona().getSegundoApellido();
map.put("persona", nombreCompleto);
// Se calcula la edad
int edad = calcularEdadAnios(tomaMx.getIdNotificacion().getPersona().getFechaNacimiento());
map.put("edad", String.valueOf(edad));
// se obtiene el sexo
map.put("sexo", tomaMx.getIdNotificacion().getPersona().getSexo().getValor());
if (edad > 12 && tomaMx.getIdNotificacion().getPersona().isSexoFemenino()) {
map.put(
"embarazada",
envioMxService.estaEmbarazada(tomaMx.getIdNotificacion().getIdNotificacion()));
} else map.put("embarazada", "--");
} else {
map.put("persona", " ");
map.put("edad", " ");
map.put("sexo", " ");
map.put("embarazada", "--");
}
// se arma estructura de diagnósticos o estudios
List<DaSolicitudDx> solicitudDxList =
envioMxService.getSolicitudesDxByIdTomaMx(tomaMx.getIdTomaMx());
Map<Integer, Object> mapSolicitudesList = new HashMap<Integer, Object>();
Map<String, String> mapSolicitud = new HashMap<String, String>();
if (solicitudDxList.size() > 0) {
int subIndice = 0;
for (DaSolicitudDx solicitudDx : solicitudDxList) {
mapSolicitud.put("nombre", solicitudDx.getCodDx().getNombre());
mapSolicitud.put("tipo", "Rutina");
mapSolicitud.put(
"fechaSolicitud",
DateUtil.DateToString(solicitudDx.getFechaHSolicitud(), "dd/MM/yyyy hh:mm:ss a"));
subIndice++;
mapSolicitudesList.put(subIndice, mapSolicitud);
mapSolicitud = new HashMap<String, String>();
}
map.put("solicitudes", new Gson().toJson(mapSolicitudesList));
} else {
List<DaSolicitudEstudio> solicitudEstudios =
envioMxService.getSolicitudesEstudioByIdTomaMx(tomaMx.getIdTomaMx());
int subIndice = 0;
for (DaSolicitudEstudio solicitudEstudio : solicitudEstudios) {
mapSolicitud.put("nombre", solicitudEstudio.getTipoEstudio().getNombre());
mapSolicitud.put("tipo", "Estudio");
mapSolicitud.put(
"fechaSolicitud",
DateUtil.DateToString(
solicitudEstudio.getFechaHSolicitud(), "dd/MM/yyyy hh:mm:ss a"));
subIndice++;
mapSolicitudesList.put(subIndice, mapSolicitud);
mapSolicitud = new HashMap<String, String>();
}
map.put("solicitudes", new Gson().toJson(mapSolicitudesList));
}
mapResponse.put(indice, map);
indice++;
}
jsonResponse = new Gson().toJson(mapResponse);
UnicodeEscaper escaper = UnicodeEscaper.above(127);
return escaper.translate(jsonResponse);
}
/**
* Helper class for converting between native Document objects and their JSON representation.
*
* @author jrogstadius
*/
public class DocumentJSONConverter {
private static Logger logger = Logger.getLogger(DocumentJSONConverter.class);
private static ErrorLog elog = new ErrorLog();
private static final String name = "DocumentJsonConverter";
private static long lastModelInfoUpdate = 0;
private static HashMap<Integer, HashMap<Integer, ModelFamilyEC>> activeModelFamiliesByID =
new HashMap<>();
private static HashMap<Integer, HashMap<String, ModelFamilyEC>> activeModelFamiliesByCode =
new HashMap<>();
private static HashMap<String, Integer> activeCrisisIDs = new HashMap<>();
private static UnicodeEscaper unicodeEscaper = UnicodeEscaper.above(127);
public static Document parseDocument(String jsonInput) throws JSONException, IOException {
// logger.info("Going to parse received doc on REDIS: " + jsonInput);
JSONObject jsonObj = new JSONObject(jsonInput);
if (!jsonObj.has("aidr")) {
logger.error("Missing aidr field in input object");
throw new JSONException("Missing aidr field in input object");
}
JSONObject aidr = jsonObj.getJSONObject("aidr");
if (!aidr.has("doctype")) {
logger.error("Missing doctype in input object");
throw new JSONException("Missing doctype in input object");
}
String doctype = aidr.getString("doctype");
Document doc = null;
switch (doctype) {
case DocumentType.TWIITER_DOC:
doc = parseTweet(jsonObj);
break;
case DocumentType.SMS_DOC:
doc = parseSMS(jsonObj);
break;
default:
logger.error("Exception when parsing input document: Unhandled doctype");
throw new RuntimeException("Exception when parsing input document: Unhandled doctype");
}
if (!aidr.has("crisis_code")) {
logger.error("Exception when parsing input document: Missing crisis_code");
throw new RuntimeException("Exception when parsing input document: Missing crisis_code");
}
doc.crisisID = new Long(getCrisisID(aidr.getString("crisis_code")));
doc.crisisCode = aidr.getString("crisis_code");
doc.inputJson = jsonObj;
// logger.info("Done creating new doc: " + aidr + ", has nominal_labels = " +
// aidr.has("nominal_labels"));
return doc;
}
public static SMS parseSMS(JSONObject input) {
// TODO: the following code is only a placeholder!
// logger.info("parsing as SMS doc");
try {
SMS sms = new SMS();
sms.setText(input.getString("text"));
sms.setDoctype(DocumentType.SMS_DOC);
JSONObject aidrJSON = input.getJSONObject("aidr");
AIDR aidrObj = new AIDR();
aidrObj.setCrisis_code(aidrJSON.getString("crisis_code"));
aidrObj.setCrisis_name(aidrJSON.getString("crisis_name"));
aidrObj.setDoctype(aidrJSON.getString("doctype"));
sms.setAidr(aidrObj);
return sms;
} catch (JSONException e) {
logger.error("Json exception in parsing tweet: " + input);
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
}
public static Tweet parseTweet(JSONObject input) {
// Example of a tweet in JSON format:
// https://dev.twitter.com/docs/api/1/get/search
// logger.info("parsing as twitter doc");
try {
Tweet t = new Tweet();
JSONObject user;
user = input.getJSONObject("user");
t.userID = user.getLong("id");
t.text = input.getString("text");
t.isRetweet = !input.isNull("retweeted_status");
t.setDoctype(DocumentType.TWIITER_DOC);
if (input.has("coordinates") && !input.isNull("coordinates")) {
JSONObject geo = (JSONObject) input.getJSONObject("coordinates");
if (geo.getString("type") == "Point") {
JSONArray coords = geo.getJSONArray("coordinates");
GeoLabel.LonLatPair geotag = new GeoLabel.LonLatPair();
geotag.setLongitude(coords.getDouble(0));
geotag.setLatitude(coords.getDouble(1));
}
}
return t;
} catch (JSONException e) {
logger.error("Json exception in parsing tweet: " + input);
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
}
public static String getDocumentSetJson(Document doc) {
try {
JSONObject input = doc.getInputJson();
JSONObject aidr = input.getJSONObject("aidr");
// Add features
if (!aidr.has("features")) {
ArrayList<DocumentFeature> features = doc.getFeatures(DocumentFeature.class);
JSONArray featureArray = new JSONArray();
for (DocumentFeature f : features) featureArray.put(f.toJSONObject());
aidr.put("features", featureArray);
}
// Add labels
if (!aidr.has("nominal_labels")) {
ArrayList<NominalLabelBC> labels = doc.getLabels(NominalLabelBC.class);
JSONArray labelArray = new JSONArray();
if (!labels.isEmpty()) {
// logger.info("labels field is non-empty");
for (NominalLabelBC l : labels) {
try {
JSONObject labelJson = getLabelJson(doc.crisisID.intValue(), l);
labelArray.put(labelJson);
// logger.info("Added label: " + l);
} catch (RuntimeException e) {
logger.error("Exception while converting document to JSON:" + l);
logger.error(elog.toStringException(e));
}
}
} else {
// logger.warn("Empty nominal_labels field! Inserting a dummy nominal label.");
labelArray.put(createEmptyLabelJson());
}
aidr.put("nominal_labels", labelArray);
// logger.info("Added nominal_labels with size = " + labelArray.length());
}
return unicodeEscaper.translate(input.toString());
} catch (JSONException e) {
logger.error("Error in creating JSON from document: " + doc);
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
}
public static <T extends DocumentFeature> String getFeaturesJson(
Class<T> featureFilter, Document docSet) {
if (featureFilter == WordSet.class) {
ArrayList<T> items = docSet.getFeatures(featureFilter);
ArrayList<String> allWords = new ArrayList<String>();
for (T item : items) {
WordSet words = (WordSet) item;
allWords.addAll(words.getWords());
}
String s = "{\"words\":[\"" + Helpers.join(allWords, "\",\"") + "\"]}";
return s;
} else {
logger.warn("Not implemented: " + featureFilter);
throw new RuntimeException("Not implemented");
}
}
public static NominalLabelBC parseNominalLabel(JSONObject input) {
try {
int crisisID = getCrisisID(input.getString("crisis_code"));
ModelFamilyEC modelFamily = getModelFamily(crisisID, input.getString("attribute_code"));
NominalAttributeEC attr = modelFamily.getNominalAttribute();
NominalLabelBC l =
new NominalLabelBC(
input.getLong("source_id"),
attr.getNominalAttributeID(),
attr.getNominalLabel(input.getString("label_code")).getNominalLabelID(),
input.getDouble(
"confidence")); // TODO: Remove this, training samples should be "true"
if (input.has("from_human")) l.setHumanLabel(input.getBoolean("from_human"));
return l;
} catch (JSONException e) {
logger.error("Error in parsing nominal label for: " + input);
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
}
public static JSONObject createEmptyLabelJson() {
// logger.info("Going to insert an empty nominal_labels");
JSONObject obj = new JSONObject();
try {
obj.put("source_id", 0);
obj.put("attribute_code", JSONObject.NULL);
obj.put("attribute_name", JSONObject.NULL);
obj.put("attribute_description", JSONObject.NULL);
obj.put("label_code", JSONObject.NULL);
obj.put("label_name", JSONObject.NULL);
obj.put("label_description", JSONObject.NULL);
obj.put("confidence", JSONObject.NULL);
obj.put("from_human", false);
} catch (JSONException e) {
logger.error("Error in creating empty json object");
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
return obj;
}
public static JSONObject getLabelJson(int crisisID, DocumentLabel label) {
try {
if (label instanceof NominalLabelBC) {
// logger.info("Going to insert existing label to nominal_labels");
NominalLabelBC l = (NominalLabelBC) label;
ModelFamilyEC family = getModelFamily(crisisID, l.getAttributeID());
JSONObject obj = new JSONObject();
obj.put("source_id", l.getSourceID());
obj.put("attribute_code", family.getNominalAttribute().getCode());
obj.put("attribute_name", family.getNominalAttribute().getName());
obj.put("attribute_description", family.getNominalAttribute().getDescription());
NominalLabelEC lEC = family.getNominalAttribute().getNominalLabel(l.getNominalLabelID());
obj.put("label_code", lEC.getNominalLabelCode());
obj.put("label_name", lEC.getName());
obj.put("label_description", lEC.getDescription());
obj.put("confidence", l.getConfidence());
obj.put("from_human", l.isHumanLabel());
return obj;
}
} catch (JSONException e) {
logger.error("Error in creating json object from: " + label);
logger.error(elog.toStringException(e));
throw new RuntimeException(e);
}
logger.error("Unsupported label type: " + label.getClass().getSimpleName());
throw new RuntimeException("Unsupported label type: " + label.getClass().getSimpleName());
}
private static int getCrisisID(String crisisCode) {
if ((System.currentTimeMillis() - lastModelInfoUpdate) > 300000
|| (!activeCrisisIDs.containsKey(crisisCode)
&& (System.currentTimeMillis() - lastModelInfoUpdate) > 10000)) {
updateModelInfo();
}
if (!activeCrisisIDs.containsKey(crisisCode))
throw new RuntimeException("Crisis code has not been defined: " + crisisCode);
return activeCrisisIDs.get(crisisCode);
}
private static ModelFamilyEC getModelFamily(int crisisID, int attributeID) {
if ((System.currentTimeMillis() - lastModelInfoUpdate) > 300000
|| ((!activeModelFamiliesByID.containsKey(crisisID)
|| !activeModelFamiliesByID.get(crisisID).containsKey(attributeID))
&& (System.currentTimeMillis() - lastModelInfoUpdate) > 10000)) {
updateModelInfo();
}
if (!activeModelFamiliesByID.containsKey(crisisID)
|| !activeModelFamiliesByID.get(crisisID).containsKey(attributeID))
throw new RuntimeException(
"ModelInfo is missing for crisis " + crisisID + " and attribute " + attributeID);
return activeModelFamiliesByID.get(crisisID).get(attributeID);
}
private static ModelFamilyEC getModelFamily(int crisisID, String attributeCode) {
if ((System.currentTimeMillis() - lastModelInfoUpdate) > 300000
|| ((!activeModelFamiliesByCode.containsKey(crisisID)
|| !activeModelFamiliesByCode.get(crisisID).containsKey(attributeCode))
&& (System.currentTimeMillis() - lastModelInfoUpdate) > 10000)) {
updateModelInfo();
}
if (!activeModelFamiliesByCode.containsKey(crisisID)
|| !activeModelFamiliesByCode.get(crisisID).containsKey(attributeCode))
throw new RuntimeException(
"ModelInfo is missing for crisis " + crisisID + " and attribute " + attributeCode);
return activeModelFamiliesByCode.get(crisisID).get(attributeCode);
}
private static void updateModelInfo() {
activeModelFamiliesByID.clear();
activeModelFamiliesByCode.clear();
activeCrisisIDs.clear();
activeCrisisIDs = DataStore.getCrisisIDs();
ArrayList<ModelFamilyEC> families = DataStore.getActiveModels();
for (ModelFamilyEC family : families) {
int crisisID = family.getCrisisID();
int attributeID = family.getNominalAttribute().getNominalAttributeID();
String attributeCode = family.getNominalAttribute().getCode();
if (!activeModelFamiliesByID.containsKey(crisisID)) {
activeModelFamiliesByID.put(crisisID, new HashMap<Integer, ModelFamilyEC>());
activeModelFamiliesByCode.put(crisisID, new HashMap<String, ModelFamilyEC>());
}
activeModelFamiliesByID.get(crisisID).put(attributeID, family);
activeModelFamiliesByCode.get(crisisID).put(attributeCode, family);
}
lastModelInfoUpdate = System.currentTimeMillis();
}
}