Navigation

← Previous Changeset
Next Changeset →

Changeset 5182

Timestamp:

08/06/08 15:00:21 (5 months ago)

Author:

jegg

Message:

in patientmatching module, changed OrderedOpenMRSReader to HQL that seems to work for expected matching demographics. Blocking on more than 2 demographics is VERY slow, and while hopefully correct, it's not optimized at all

Files:

openmrs-modules/patientmatching/src/org/regenstrief/linkage/io/OrderedOpenMRSReader.java (modified) (13 diffs)

Legend:

: Unmodified
: Added
: Removed
: Modified
: Copied
: Moved

openmrs-modules/patientmatching/src/org/regenstrief/linkage/io/OrderedOpenMRSReader.java

r5157	r5182
1	1	package org.regenstrief.linkage.io;
2	2
	3	import java.lang.reflect.InvocationTargetException;
	4	import java.lang.reflect.Method;
3	5	import java.util.ArrayList;
4	6	import java.util.Iterator;
5	7	import java.util.List;
6	8
	9	import org.apache.commons.logging.Log;
	10	import org.apache.commons.logging.LogFactory;
7	11	import org.hibernate.Query;
8	12	import org.hibernate.SessionFactory;
9	13	import org.openmrs.Patient;
10	14	import org.openmrs.PatientIdentifierType;
	15	import org.openmrs.Person;
11	16	import org.openmrs.PersonAttributeType;
12	17	import org.openmrs.api.context.Context;
…	…
41	46
42	47	public final static String ATTRIBUTE_PREFIX = "(Attribute) ";
43		public final static String IDENT_PREFIX = "(Identifier)";
44
	48	public final static String IDENT_PREFIX = "(Identifier) ";
	49	public final static String GET_ID_METHOD = "getPersonId";
	50	//public final static String GET_PATIENT_ID_METHOD = "getPatientId";
	51	public final static String GET_PERSON_METHOD = "getPerson";
	52	public final static String GET_PATIENT_METHOD = "getPatient";
	53
	54
	55	private Log log = LogFactory.getLog(this.getClass());
45	56	private SessionFactory sessionFactory;
46	57
…	…
58	69	for(int i = 0; i < blocking_cols.length; i++){
59	70	List<Object> query_values = getDemographicValues(blocking_cols[i]);
60		Iterator<Object> it = query_values.iterator();
61		List<Object> values = new ArrayList<Object>();
62		while(it.hasNext()){
63		Object obj = it.next();
64		values.add(obj);
65		}
66		blocking_values.add(values);
67		values_iterators.add(values.iterator());
	71	if(query_values == null){
	72	log.warn("unable to get blocking values for " + blocking_cols[i]);
	73
	74	} else {
	75	Iterator<Object> it = query_values.iterator();
	76	List<Object> values = new ArrayList<Object>();
	77	while(it.hasNext()){
	78	Object obj = it.next();
	79	values.add(obj);
	80	}
	81	blocking_values.add(values);
	82	values_iterators.add(values.iterator());
	83	}
	84
68	85	}
69	86
…	…
124	141	Integer id = value_set.remove(0);
125	142	Patient p = Context.getPatientService().getPatient(id);
126
127	143	if(value_set.size() == 0){
128	144	// removed last ID at this point in blocking values, need to increment iterators and refill
…	…
132	148	}
133	149	}
	150
134	151	return PatientMatchingActivator.patientToRecord(p);
135	152	}
…	…
170	187	}
171	188
172		query_text = "SELECT DISTINCT o." + field + " FROM " + object_name + " o";
	189	query_text = "SELECT DISTINCT o." + field + " FROM " + object_name + " o where o." + field + " IS NOT NULL";
173	190	Query q = sessionFactory.getCurrentSession().createQuery(query_text);
174	191	ret = q.list();
…	…
182	199	// something like
183	200	// select distinct value from person_attribute where person_attribute_type_id = <id>
184		int id = pat.getPersonAttributeTypeId();
185		query_text = "SELECT DISTINCT p.value FROM PersonAttribute p WHERE p.attributeID = " + id;
	201	query_text = "SELECT DISTINCT p.value FROM PersonAttribute p WHERE p.attributeType = :type AND p.value IS NOT NULL";
186	202	Query q = sessionFactory.getCurrentSession().createQuery(query_text);
	203	q.setParameter("type", pat);
187	204	ret = q.list();
188	205	}
…	…
193	210	if(pit != null){
194	211	// HQL query to get all values
195		int id = pit.getPatientIdentifierTypeId();
196		query_text = "SELECT DISTINCT p.value FROM PatientIdentifier p WHERE p.typeID = " + id;
	212	query_text = "SELECT DISTINCT p.identifier FROM PatientIdentifier p WHERE p.identifierType = :type AND p.identifier IS NOT NULL";
197	213	Query q = sessionFactory.getCurrentSession().createQuery(query_text);
	214	q.setParameter("type", pit);
198	215	ret = q.list();
199	216	}
…	…
208	225	// method strips the first
209	226	if(type_name.indexOf(ATTRIBUTE_PREFIX) != -1){
210		return type_name.~~replaceFirst(ATTRIBUTE_PREFIX,""~~);
	227	return type_name.substring(ATTRIBUTE_PREFIX.length());
211	228	} else if(type_name.indexOf(IDENT_PREFIX) != -1){
212		return type_name.~~replaceFirst(IDENT_PREFIX, ""~~);
	229	return type_name.substring(IDENT_PREFIX.length());
213	230	}
214	231	return type_name;
…	…
236	253	}
237	254
238		query_text = "SELECT o~~.personID~~ FROM " + object_name + " o WHERE " + field + " =:value";
	255	query_text = "SELECT o FROM " + object_name + " o WHERE " + field + " =:value";
239	256	Query q = sessionFactory.getCurrentSession().createQuery(query_text);
240		q.set~~Entity~~("value", value);
241		ret = ~~new ArrayList<Integer>(~~);
242		~~ret.addAll(q.list());~~
	257	q.setParameter("value", value);
	258	ret = getIDs(q.list());
	259
243	260	} else {
244	261	if(demographic.indexOf(ATTRIBUTE_PREFIX) != -1){
…	…
251	268	// select distinct value from person_attribute where person_attribute_type_id = <id>
252	269	int id = pat.getPersonAttributeTypeId();
253		query_text = "SELECT DISTINCT p~~.personID~~ FROM PersonAttribute p WHERE p.value = :value";
	270	query_text = "SELECT DISTINCT p FROM PersonAttribute p WHERE p.value = :value";
254	271	Query q = sessionFactory.getCurrentSession().createQuery(query_text);
255		q.setEntity("value", value);
256		ret = new ArrayList<Integer>();
257		ret.addAll(q.list());
	272	q.setParameter("value", value);
	273	ret = getIDs(q.list());
258	274	}
259	275	} else if(demographic.indexOf(IDENT_PREFIX) != -1){
…	…
264	280	// HQL query to get all values
265	281	int id = pit.getPatientIdentifierTypeId();
266		query_text = "SELECT DISTINCT p~~.personID FROM PatientIdentifier p WHERE p.value~~ = :value";
	282	query_text = "SELECT DISTINCT p FROM PatientIdentifier p WHERE p.identifier = :value";
267	283	Query q = sessionFactory.getCurrentSession().createQuery(query_text);
268		q.setEntity("value", value);
269		ret = new ArrayList<Integer>();
270		ret.addAll(q.list());
	284	q.setParameter("value", value);
	285	ret = getIDs(q.list());
271	286	}
272	287	}
…	…
277	292	}
278	293
	294	/*
	295	* Method checks for a method that returns the person ID, patient, or person
	296	* of the object returned from a query and inserts the IDs into a list
	297	*/
	298	private List<Integer> getIDs(List<Object> openmrs_objects){
	299	List<Integer> ret = new ArrayList<Integer>();
	300	Iterator<Object> it = openmrs_objects.iterator();
	301	try{
	302	while(it.hasNext()){
	303	Object o = it.next();
	304
	305	Class cls = o.getClass();
	306	Method[] methods = cls.getMethods();
	307	for(int i = 0; i < methods.length; i++){
	308	Method m = methods[i];
	309	if(m.getName().equals(GET_ID_METHOD)){
	310	Integer id = (Integer)m.invoke(o, (Object[])null);
	311	ret.add(id);
	312	i = methods.length;
	313	} else if(m.getName().equals(GET_PERSON_METHOD)){
	314	Person p = (Person)m.invoke(o, (Object[])null);
	315	ret.add(p.getPersonId());
	316	i = methods.length;
	317	} else if(m.getName().equals(GET_PATIENT_METHOD)){
	318	Patient p = (Patient)m.invoke(o, (Object[])null);
	319	ret.add(p.getPatientId());
	320	i = methods.length;
	321	}
	322	}
	323	}
	324	}
	325	catch(IllegalAccessException iae){
	326	log.warn("exception reading OpenMRS DB: " + iae.getMessage());
	327	}
	328	catch(InvocationTargetException ite){
	329	log.warn("exception reading OpenMRS DB: " + ite.getMessage());
	330	}
	331
	332	return ret;
	333	}
279	334	}

OpenMRS

Navigation

Changeset 5182

Legend:

openmrs-modules/patientmatching/src/org/regenstrief/linkage/io/OrderedOpenMRSReader.java

Download in other formats: