Java tutorial
/** * This Source Code Form is subject to the terms of the Mozilla Public License, * v. 2.0. If a copy of the MPL was not distributed with this file, You can * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under * the terms of the Healthcare Disclaimer located at http://openmrs.org/license. * * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS * graphic logo is a trademark of OpenMRS Inc. */ package org.openmrs.api.db.hibernate; import java.io.StringWriter; import java.lang.reflect.Field; import java.text.DateFormat; import java.text.ParseException; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Calendar; import java.util.Collection; import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.ListIterator; import java.util.Locale; import java.util.Map; import java.util.Set; import java.util.Vector; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.transform.Result; import javax.xml.transform.Source; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerFactory; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.hibernate.CacheMode; import org.hibernate.Criteria; import org.hibernate.FetchMode; import org.hibernate.Query; import org.hibernate.SessionFactory; import org.hibernate.criterion.ProjectionList; import org.hibernate.criterion.Projections; import org.hibernate.criterion.Restrictions; import org.hibernate.type.StringType; import org.openmrs.Cohort; import org.openmrs.Concept; import org.openmrs.Drug; import org.openmrs.DrugOrder; import org.openmrs.Encounter; import org.openmrs.EncounterType; import org.openmrs.Form; import org.openmrs.Location; import org.openmrs.Obs; import org.openmrs.Order; import org.openmrs.Patient; import org.openmrs.PatientIdentifier; import org.openmrs.PatientIdentifierType; import org.openmrs.PatientProgram; import org.openmrs.PatientState; import org.openmrs.Person; import org.openmrs.PersonAttributeType; import org.openmrs.PersonName; import org.openmrs.Program; import org.openmrs.ProgramWorkflow; import org.openmrs.ProgramWorkflowState; import org.openmrs.Provider; import org.openmrs.Relationship; import org.openmrs.RelationshipType; import org.openmrs.api.EncounterService; import org.openmrs.api.ObsService; import org.openmrs.api.PatientService; import org.openmrs.api.PatientSetService; import org.openmrs.api.PatientSetService.Modifier; import org.openmrs.api.PatientSetService.PatientLocationMethod; import org.openmrs.api.PatientSetService.TimeModifier; import org.openmrs.api.context.Context; import org.openmrs.api.db.DAOException; import org.openmrs.api.db.PatientSetDAO; import org.w3c.dom.Document; import org.w3c.dom.Element; /** * Hibernate specific implementation of the PatientSetDAO. <br> * <br> * This class should not be instantiated. Rather, it is injected into the PatientSetService by * Spring. * * @see org.openmrs.api.context.Context * @see org.openmrs.api.PatientSetService * @see org.openmrs.api.db.PatientSetDAO */ public class HibernatePatientSetDAO implements PatientSetDAO { protected final Log log = LogFactory.getLog(getClass()); /** * Hibernate sessionFactory.getCurrentSession() factory */ private SessionFactory sessionFactory; /** * Set sessionFactory.getCurrentSession() factory * * @param sessionFactory SessionFactory to set */ public void setSessionFactory(SessionFactory sessionFactory) { this.sessionFactory = sessionFactory; } /** * @deprecated * @see org.openmrs.api.db.PatientSetDAO#exportXml(org.openmrs.Cohort) */ public String exportXml(Cohort ps) throws DAOException { StringBuffer ret = new StringBuffer("<patientset>"); for (Integer patientId : ps.getMemberIds()) { ret.append(exportXml(patientId)); } ret.append("</patientset>"); return ret.toString(); } DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); private Element obsElementHelper(Document doc, Locale locale, Obs obs) { Element obsNode = doc.createElement("obs"); Concept c = obs.getConcept(); obsNode.setAttribute("obs_id", obs.getObsId().toString()); obsNode.setAttribute("concept_id", c.getConceptId().toString()); obsNode.setAttribute("concept_name", c.getName(locale).getName()); if (obs.getObsDatetime() != null) { obsNode.setAttribute("datetime", df.format(obs.getObsDatetime())); } if (obs.getAccessionNumber() != null) { obsNode.setAttribute("accession_number", obs.getAccessionNumber()); } if (obs.getComment() != null) { obsNode.setAttribute("comment", obs.getComment()); } if (obs.getObsGroup() != null) { obsNode.setAttribute("obs_group_id", obs.getObsGroup().getObsId().toString()); } if (obs.getValueGroupId() != null) { obsNode.setAttribute("value_group_id", obs.getValueGroupId().toString()); } String value = null; String dataType = null; if (obs.getValueCoded() != null) { Concept valueConcept = obs.getValueCoded(); obsNode.setAttribute("value_coded_id", valueConcept.getConceptId().toString()); obsNode.setAttribute("value_coded", valueConcept.getName(locale).getName()); dataType = "coded"; value = valueConcept.getName(locale).getName(); } if (obs.getValueAsBoolean() != null) { obsNode.setAttribute("value_boolean", obs.getValueAsBoolean().toString()); dataType = "boolean"; value = obs.getValueAsBoolean().toString(); } if (obs.getValueDatetime() != null) { obsNode.setAttribute("value_datetime", df.format(obs.getValueDatetime())); dataType = "datetime"; value = obs.getValueDatetime().toString(); } if (obs.getValueNumeric() != null) { obsNode.setAttribute("value_numeric", obs.getValueNumeric().toString()); dataType = "numeric"; value = obs.getValueNumeric().toString(); } if (obs.getValueText() != null) { obsNode.setAttribute("value_text", obs.getValueText()); dataType = "text"; value = obs.getValueText(); } if (obs.getValueModifier() != null) { obsNode.setAttribute("value_modifier", obs.getValueModifier()); if (value != null) { value = obs.getValueModifier() + " " + value; } } obsNode.setAttribute("data_type", dataType); obsNode.appendChild(doc.createTextNode(value)); return obsNode; } /** * Note that the formatting may depend on locale * * @deprecated */ @Deprecated public String exportXml(Integer patientId) throws DAOException { Locale locale = Context.getLocale(); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); Document doc = null; PatientService patientService = Context.getPatientService(); EncounterService encounterService = Context.getEncounterService(); Patient p = patientService.getPatient(patientId); List<Encounter> encounters = encounterService.getEncountersByPatientId(patientId); try { DocumentBuilder builder = factory.newDocumentBuilder(); doc = builder.newDocument(); Element root = (Element) doc.createElement("patient_data"); doc.appendChild(root); Element patientNode = doc.createElement("patient"); patientNode.setAttribute("patient_id", p.getPatientId().toString()); boolean firstName = true; Element namesNode = doc.createElement("names"); for (PersonName name : p.getNames()) { if (firstName) { if (name.getGivenName() != null) { patientNode.setAttribute("given_name", name.getGivenName()); } if (name.getMiddleName() != null) { patientNode.setAttribute("middle_name", name.getMiddleName()); } if (name.getFamilyName() != null) { patientNode.setAttribute("family_name", name.getFamilyName()); } if (name.getFamilyName2() != null) { patientNode.setAttribute("family_name2", name.getFamilyName2()); } firstName = false; } Element nameNode = doc.createElement("name"); if (name.getGivenName() != null) { nameNode.setAttribute("given_name", name.getGivenName()); } if (name.getMiddleName() != null) { nameNode.setAttribute("middle_name", name.getMiddleName()); } if (name.getFamilyName() != null) { nameNode.setAttribute("family_name", name.getFamilyName()); } if (name.getFamilyName2() != null) { nameNode.setAttribute("family_name2", name.getFamilyName2()); } namesNode.appendChild(nameNode); } patientNode.appendChild(namesNode); patientNode.setAttribute("gender", p.getGender()); /* if (p.getRace() != null) { patientNode.setAttribute("race", p.getRace()); } */ if (p.getBirthdate() != null) { patientNode.setAttribute("birthdate", df.format(p.getBirthdate())); } if (p.getBirthdateEstimated() != null) { patientNode.setAttribute("birthdate_estimated", p.getBirthdateEstimated().toString()); } /* if (p.getBirthplace() != null) { patientNode.setAttribute("birthplace", p.getBirthplace()); } */ /* if (p.getCitizenship() != null) { patientNode.setAttribute("citizenship", p.getCitizenship()); } */ /* if (p.getMothersName() != null) { patientNode.setAttribute("mothers_name", p.getMothersName()); } if (p.getCivilStatus() != null) { patientNode.setAttribute("civil_status", p.getCivilStatus().getName(locale, false).getName()); } */ if (p.getDeathDate() != null) { patientNode.setAttribute("death_date", df.format(p.getDeathDate())); } if (p.getDeathdateEstimated() != null) { patientNode.setAttribute("deathdate_estimated", p.getDeathdateEstimated().toString()); } if (p.getCauseOfDeath() != null) { patientNode.setAttribute("cause_of_death", p.getCauseOfDeath().getName(locale, false).getName()); } /* if (p.getHealthDistrict() != null) { patientNode.setAttribute("health_district", p.getHealthDistrict()); } if (p.getHealthCenter() != null) { patientNode.setAttribute("health_center", p.getHealthCenter().getName()); patientNode.setAttribute("health_center_id", p.getHealthCenter().getLocationId().toString()); } */ for (Encounter e : encounters) { Element encounterNode = doc.createElement("encounter"); if (e.getEncounterDatetime() != null) { encounterNode.setAttribute("datetime", df.format(e.getEncounterDatetime())); } Element metadataNode = doc.createElement("metadata"); { Location l = e.getLocation(); if (l != null) { Element temp = doc.createElement("location"); temp.setAttribute("location_id", l.getLocationId().toString()); temp.appendChild(doc.createTextNode(l.getName())); metadataNode.appendChild(temp); } EncounterType t = e.getEncounterType(); if (t != null) { Element temp = doc.createElement("encounter_type"); temp.setAttribute("encounter_type_id", t.getEncounterTypeId().toString()); temp.appendChild(doc.createTextNode(t.getName())); metadataNode.appendChild(temp); } Form f = e.getForm(); if (f != null) { Element temp = doc.createElement("form"); temp.setAttribute("form_id", f.getFormId().toString()); temp.appendChild(doc.createTextNode(f.getName())); metadataNode.appendChild(temp); } Person u = e.getProvider(); if (u != null) { Element temp = doc.createElement("provider"); temp.setAttribute("provider_id", u.getPersonId().toString()); temp.appendChild(doc.createTextNode(u.getPersonName().getFullName())); metadataNode.appendChild(temp); } } encounterNode.appendChild(metadataNode); Collection<Obs> observations = e.getObs(); if (observations != null && observations.size() > 0) { Element observationsNode = doc.createElement("observations"); for (Obs obs : observations) { Element obsNode = obsElementHelper(doc, locale, obs); observationsNode.appendChild(obsNode); } encounterNode.appendChild(observationsNode); } Set<Order> orders = e.getOrders(); if (orders != null && orders.size() != 0) { Element ordersNode = doc.createElement("orders"); for (Order order : orders) { Element orderNode = doc.createElement("order"); orderNode.setAttribute("order_id", order.getOrderId().toString()); Concept concept = order.getConcept(); orderNode.setAttribute("concept_id", concept.getConceptId().toString()); orderNode.appendChild(doc.createTextNode(concept.getName(locale).getName())); if (order.getInstructions() != null) { orderNode.setAttribute("instructions", order.getInstructions()); } if (order.getDateActivated() != null) { orderNode.setAttribute("date_activated", df.format(order.getDateActivated())); } if (order.getAutoExpireDate() != null) { orderNode.setAttribute("auto_expire_date", df.format(order.getAutoExpireDate())); } if (order.getOrderer() != null) { orderNode.setAttribute("orderer", formatProvider(order.getOrderer())); } if (order.getDateStopped() != null) { orderNode.setAttribute("date_stopped", df.format(order.getDateStopped())); } if (order.getOrderReason() != null) { orderNode.setAttribute("order_reason", order.getOrderReason().getName(locale, false).getName()); } ordersNode.appendChild(orderNode); } } patientNode.appendChild(encounterNode); } ObsService obsService = Context.getObsService(); List<Obs> allObservations = obsService.getObservationsByPerson(p); if (allObservations != null && allObservations.size() > 0) { log.debug("allObservations has " + allObservations.size() + " obs"); Set<Obs> undoneObservations = new HashSet<Obs>(); for (Obs obs : allObservations) { if (obs.getEncounter() == null) { undoneObservations.add(obs); } } log.debug("undoneObservations has " + undoneObservations.size() + " obs"); if (undoneObservations.size() > 0) { Element observationsNode = doc.createElement("observations"); for (Obs obs : undoneObservations) { Element obsNode = obsElementHelper(doc, locale, obs); observationsNode.appendChild(obsNode); log.debug("added node " + obsNode + " to observationsNode"); } patientNode.appendChild(observationsNode); } } root.appendChild(patientNode); } catch (Exception ex) { throw new DAOException(ex); } String ret = null; try { Source source = new DOMSource(doc); StringWriter sw = new StringWriter(); Result result = new StreamResult(sw); Transformer xformer = TransformerFactory.newInstance().newTransformer(); xformer.transform(source, result); ret = sw.toString(); } catch (Exception ex) { throw new DAOException(ex); } return ret; } @SuppressWarnings("unchecked") public Cohort getAllPatients() { Query query = sessionFactory.getCurrentSession() .createQuery("select patientId from Patient p where p.voided = '0'"); Set<Integer> ids = new HashSet<Integer>(); ids.addAll(query.list()); return new Cohort("All patients", "", ids); } /** * given program, workflow, and state, within a given date range * * @param program The program the patient must have been in * @param stateList List of states the patient must have been in (implies a workflow) (can be * null) * @param fromDate If not null, then only patients in the given program/workflow/state on or * after this date * @param toDate If not null, then only patients in the given program/workflow/state on or * before this date * @return Cohort of Patients matching criteria */ public Cohort getPatientsByProgramAndState(Program program, List<ProgramWorkflowState> stateList, Date fromDate, Date toDate) { Integer programId = program == null ? null : program.getProgramId(); List<Integer> stateIds = null; if (stateList != null && stateList.size() > 0) { stateIds = new ArrayList<Integer>(); for (ProgramWorkflowState state : stateList) { stateIds.add(state.getProgramWorkflowStateId()); } } List<String> clauses = new ArrayList<String>(); clauses.add("pp.voided = false"); if (programId != null) { clauses.add("pp.program_id = :programId"); } if (stateIds != null) { clauses.add("ps.state in (:stateIds)"); clauses.add("ps.voided = false"); } if (fromDate != null) { clauses.add("(pp.date_completed is null or pp.date_completed >= :fromDate)"); if (stateIds != null) { clauses.add("(ps.end_date is null or ps.end_date >= :fromDate)"); } } if (toDate != null) { clauses.add("(pp.date_enrolled is null or pp.date_enrolled <= :toDate)"); if (stateIds != null) { clauses.add("(ps.start_date is null or ps.start_date <= :toDate)"); } } StringBuilder sql = new StringBuilder(); sql.append("select pp.patient_id "); sql.append("from patient_program pp "); sql.append("inner join patient p on pp.patient_id = p.patient_id and p.voided = false "); if (stateIds != null) { sql.append("inner join patient_state ps on pp.patient_program_id = ps.patient_program_id "); } for (ListIterator<String> i = clauses.listIterator(); i.hasNext();) { sql.append(i.nextIndex() == 0 ? " where " : " and "); sql.append(i.next()); } sql.append(" group by pp.patient_id"); log.debug("query: " + sql); Query query = sessionFactory.getCurrentSession().createSQLQuery(sql.toString()); if (programId != null) { query.setInteger("programId", programId); } if (stateIds != null) { query.setParameterList("stateIds", stateIds); } if (fromDate != null) { query.setDate("fromDate", fromDate); } if (toDate != null) { query.setDate("toDate", toDate); } return new Cohort(query.list()); } /** * a given program. If fromDate != null, then only those patients who were in the program at any * time after that date if toDate != null, then only those patients who were in the program at * any time before that date */ public Cohort getPatientsInProgram(Integer programId, Date fromDate, Date toDate) { String sql = "select pp.patient_id from patient_program pp "; sql += " inner join patient p on pp.patient_id = p.patient_id and p.voided = false "; sql += " where pp.voided = false and pp.program_id = :programId "; if (fromDate != null) { sql += " and (date_completed is null or date_completed >= :fromDate) "; } if (toDate != null) { sql += " and (date_enrolled is null or date_enrolled <= :toDate) "; } log.debug("sql: " + sql); Query query = sessionFactory.getCurrentSession().createSQLQuery(sql); query.setCacheMode(CacheMode.IGNORE); query.setInteger("programId", programId); if (fromDate != null) { query.setDate("fromDate", fromDate); } if (toDate != null) { query.setDate("toDate", toDate); } return new Cohort(query.list()); } public Cohort getPatientsHavingObs(Integer conceptId, PatientSetService.TimeModifier timeModifier, PatientSetService.Modifier modifier, Object value, Date fromDate, Date toDate) { if (conceptId == null && value == null) { throw new IllegalArgumentException("Can't have conceptId == null and value == null"); } if (conceptId == null && (timeModifier != TimeModifier.ANY && timeModifier != TimeModifier.NO)) { throw new IllegalArgumentException("If conceptId == null, timeModifier must be ANY or NO"); } if (conceptId == null && modifier != Modifier.EQUAL) { throw new IllegalArgumentException("If conceptId == null, modifier must be EQUAL"); } Concept concept = null; if (conceptId != null) { concept = Context.getConceptService().getConcept(conceptId); } Number numericValue = null; String stringValue = null; Concept codedValue = null; Date dateValue = null; String valueSql = null; if (value != null) { if (concept == null) { if (value instanceof Concept) { codedValue = (Concept) value; } else { codedValue = Context.getConceptService().getConceptByName(value.toString()); } valueSql = "o.value_coded"; } else if (concept.getDatatype().isNumeric()) { if (value instanceof Number) { numericValue = (Number) value; } else { numericValue = new Double(value.toString()); } valueSql = "o.value_numeric"; } else if (concept.getDatatype().isText()) { stringValue = value.toString(); valueSql = "o.value_text"; if (modifier == null) { modifier = Modifier.EQUAL; } } else if (concept.getDatatype().isCoded()) { if (value instanceof Concept) { codedValue = (Concept) value; } else { codedValue = Context.getConceptService().getConceptByName(value.toString()); } valueSql = "o.value_coded"; } else if (concept.getDatatype().isDate()) { if (value instanceof Date) { dateValue = (Date) value; } else { try { dateValue = Context.getDateFormat().parse(value.toString()); } catch (ParseException ex) { throw new IllegalArgumentException("Cannot interpret " + dateValue + " as a date in the format " + Context.getDateFormat()); } } valueSql = "o.value_datetime"; } else if (concept.getDatatype().isBoolean()) { if (value instanceof Concept) { codedValue = (Concept) value; } else { boolean asBoolean = false; if (value instanceof Boolean) { asBoolean = ((Boolean) value).booleanValue(); } else { asBoolean = Boolean.valueOf(value.toString()); } codedValue = asBoolean ? Context.getConceptService().getTrueConcept() : Context.getConceptService().getFalseConcept(); } valueSql = "o.value_coded"; } } StringBuilder sb = new StringBuilder(); boolean useValue = value != null; boolean doSqlAggregation = timeModifier == TimeModifier.MIN || timeModifier == TimeModifier.MAX || timeModifier == TimeModifier.AVG; boolean doInvert = false; String dateSql = ""; String dateSqlForSubquery = ""; if (fromDate != null) { dateSql += " and o.obs_datetime >= :fromDate "; dateSqlForSubquery += " and obs_datetime >= :fromDate "; } if (toDate != null) { dateSql += " and o.obs_datetime <= :toDate "; dateSqlForSubquery += " and obs_datetime <= :toDate "; } if (timeModifier == TimeModifier.ANY || timeModifier == TimeModifier.NO) { if (timeModifier == TimeModifier.NO) { doInvert = true; } sb.append("select o.person_id from obs o " + "inner join patient p on o.person_id = p.patient_id and p.voided = false " + "where o.voided = false "); if (conceptId != null) { sb.append("and concept_id = :concept_id "); } sb.append(dateSql); } else if (timeModifier == TimeModifier.FIRST || timeModifier == TimeModifier.LAST) { boolean isFirst = timeModifier == PatientSetService.TimeModifier.FIRST; sb.append("select o.person_id " + "from obs o inner join (" + " select person_id, " + (isFirst ? "min" : "max") + "(obs_datetime) as obs_datetime" + " from obs" + " where voided = false and concept_id = :concept_id " + dateSqlForSubquery + " group by person_id" + ") subq on o.person_id = subq.person_id and o.obs_datetime = subq.obs_datetime " + " inner join patient p on o.person_id = p.patient_id and p.voided = false " + "where o.voided = false and o.concept_id = :concept_id "); } else if (doSqlAggregation) { String sqlAggregator = timeModifier.toString(); valueSql = sqlAggregator + "(" + valueSql + ")"; sb.append("select o.person_id " + "from obs o " + "inner join patient p on o.person_id = p.patient_id and p.voided = false " + "where o.voided = false and concept_id = :concept_id " + dateSql + "group by o.person_id "); } else { throw new IllegalArgumentException("TimeModifier '" + timeModifier + "' not recognized"); } if (useValue) { sb.append(doSqlAggregation ? " having " : " and "); sb.append(valueSql + " "); sb.append(modifier.getSqlRepresentation() + " :value"); } if (!doSqlAggregation) { sb.append(" group by o.person_id "); } log.debug("query: " + sb); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); query.setCacheMode(CacheMode.IGNORE); if (conceptId != null) { query.setInteger("concept_id", conceptId); } if (useValue) { if (numericValue != null) { query.setDouble("value", numericValue.doubleValue()); } else if (codedValue != null) { query.setInteger("value", codedValue.getConceptId()); } else if (stringValue != null) { query.setString("value", stringValue); } else if (dateValue != null) { query.setDate("value", dateValue); } else { throw new IllegalArgumentException( "useValue is true, but numeric, coded, string, boolean, and date values are all null"); } } if (fromDate != null) { query.setDate("fromDate", fromDate); } if (toDate != null) { query.setDate("toDate", toDate); } Cohort ret; if (doInvert) { ret = getAllPatients(); ret.getMemberIds().removeAll(query.list()); } else { ret = new Cohort(query.list()); } return ret; } /** * <pre> * Returns the set of patients that have encounters, with several optional parameters: * of type encounterType * at a given location * from filling out a specific form * on or after fromDate * on or before toDate * patients with at least minCount of the given encounters * patients with up to maxCount of the given encounters * </pre> */ public Cohort getPatientsHavingEncounters(List<EncounterType> encounterTypeList, Location location, Form form, Date fromDate, Date toDate, Integer minCount, Integer maxCount) { List<Integer> encTypeIds = null; if (encounterTypeList != null && encounterTypeList.size() > 0) { encTypeIds = new ArrayList<Integer>(); for (EncounterType t : encounterTypeList) { encTypeIds.add(t.getEncounterTypeId()); } } Integer locationId = location == null ? null : location.getLocationId(); Integer formId = form == null ? null : form.getFormId(); List<String> whereClauses = new ArrayList<String>(); whereClauses.add("e.voided = false"); if (encTypeIds != null) { whereClauses.add("e.encounter_type in (:encTypeIds)"); } if (locationId != null) { whereClauses.add("e.location_id = :locationId"); } if (formId != null) { whereClauses.add("e.form_id = :formId"); } if (fromDate != null) { whereClauses.add("e.encounter_datetime >= :fromDate"); } if (toDate != null) { whereClauses.add("e.encounter_datetime <= :toDate"); } List<String> havingClauses = new ArrayList<String>(); if (minCount != null) { havingClauses.add("count(*) >= :minCount"); } if (maxCount != null) { havingClauses.add("count(*) >= :maxCount"); } StringBuilder sb = new StringBuilder(); sb.append(" select e.patient_id from encounter e "); sb.append(" inner join patient p on e.patient_id = p.patient_id and p.voided = false "); for (ListIterator<String> i = whereClauses.listIterator(); i.hasNext();) { sb.append(i.nextIndex() == 0 ? " where " : " and "); sb.append(i.next()); } sb.append(" group by e.patient_id "); for (ListIterator<String> i = havingClauses.listIterator(); i.hasNext();) { sb.append(i.nextIndex() == 0 ? " having " : " and "); sb.append(i.next()); } log.debug("query: " + sb); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); if (encTypeIds != null) { query.setParameterList("encTypeIds", encTypeIds); } if (locationId != null) { query.setInteger("locationId", locationId); } if (formId != null) { query.setInteger("formId", formId); } if (fromDate != null) { query.setDate("fromDate", fromDate); } if (toDate != null) { query.setDate("toDate", toDate); } if (minCount != null) { query.setInteger("minCount", minCount); } if (maxCount != null) { query.setInteger("maxCount", maxCount); } return new Cohort(query.list()); } /** * within <code>startTime</code> and <code>endTime</code> * * @param conceptId * @param startTime * @param endTime * @return PatientSet */ public Cohort getPatientsHavingDateObs(Integer conceptId, Date startTime, Date endTime) { StringBuffer sb = new StringBuffer(); sb.append("select o.person_id from obs o " + "where concept_id = :concept_id "); sb.append(" and o.value_datetime between :startValue and :endValue"); sb.append(" and o.voided = '0'"); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); query.setCacheMode(CacheMode.IGNORE); query.setInteger("concept_id", conceptId); query.setDate("startValue", startTime); query.setDate("endValue", endTime); return new Cohort(query.list()); } public Cohort getPatientsHavingNumericObs(Integer conceptId, PatientSetService.TimeModifier timeModifier, PatientSetService.Modifier modifier, Number value, Date fromDate, Date toDate) { Concept concept = Context.getConceptService().getConcept(conceptId); if (!concept.isNumeric()) { // throw new IllegalArgumentException(concept + " is not numeric"); } StringBuffer sb = new StringBuffer(); boolean useValue = modifier != null && value != null; boolean doSqlAggregation = timeModifier == TimeModifier.MIN || timeModifier == TimeModifier.MAX || timeModifier == TimeModifier.AVG; String valueSql = "o.value_numeric"; boolean doInvert = false; String dateSql = ""; if (fromDate != null) { dateSql += " and o.obs_datetime >= :fromDate "; } if (toDate != null) { dateSql += " and o.obs_datetime <= :toDate "; } if (timeModifier == TimeModifier.ANY || timeModifier == TimeModifier.NO) { if (timeModifier == TimeModifier.NO) { doInvert = true; } sb.append("select o.person_id from obs o " + "where voided = false and concept_id = :concept_id "); sb.append(dateSql); } else if (timeModifier == TimeModifier.FIRST || timeModifier == TimeModifier.LAST) { boolean isFirst = timeModifier == PatientSetService.TimeModifier.FIRST; sb.append("select o.person_id " + "from obs o inner join (" + " select person_id, " + (isFirst ? "min" : "max") + "(obs_datetime) as obs_datetime" + " from obs" + " where voided = false and concept_id = :concept_id " + dateSql + " group by person_id" + ") subq on o.person_id = subq.person_id and o.obs_datetime = subq.obs_datetime " + "where o.voided = false and o.concept_id = :concept_id "); } else if (doSqlAggregation) { String sqlAggregator = timeModifier.toString(); valueSql = sqlAggregator + "(o.value_numeric)"; sb.append("select o.person_id " + "from obs o where o.voided = false and concept_id = :concept_id " + dateSql + "group by o.person_id "); } else { throw new IllegalArgumentException("TimeModifier '" + timeModifier + "' not recognized"); } if (useValue) { sb.append(doSqlAggregation ? "having " : " and "); sb.append(valueSql + " "); sb.append(modifier.getSqlRepresentation() + " :value"); } if (!doSqlAggregation) { sb.append(" group by o.person_id "); } log.debug("query: " + sb); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); query.setCacheMode(CacheMode.IGNORE); query.setInteger("concept_id", conceptId); if (useValue) { query.setDouble("value", value.doubleValue()); } if (fromDate != null) { query.setDate("fromDate", fromDate); } if (toDate != null) { query.setDate("toDate", fromDate); } Cohort ret; if (doInvert) { ret = getAllPatients(); ret.getMemberIds().removeAll(query.list()); } else { ret = new Cohort(query.list()); } return ret; } public Cohort getPatientsByCharacteristics(String gender, Date minBirthdate, Date maxBirthdate, Integer minAge, Integer maxAge, Boolean aliveOnly, Boolean deadOnly) throws DAOException { return getPatientsByCharacteristics(gender, minBirthdate, maxBirthdate, minAge, maxAge, aliveOnly, deadOnly, null); } public Cohort getPatientsByCharacteristics(String gender, Date minBirthdate, Date maxBirthdate, Integer minAge, Integer maxAge, Boolean aliveOnly, Boolean deadOnly, Date effectiveDate) throws DAOException { if (effectiveDate == null) { effectiveDate = new Date(); } StringBuffer queryString = new StringBuffer("select patientId from Patient patient"); List<String> clauses = new ArrayList<String>(); clauses.add("patient.voided = false"); if (gender != null) { gender = gender.toUpperCase(); clauses.add("patient.gender = :gender"); } if (minBirthdate != null) { clauses.add("patient.birthdate >= :minBirthdate"); } if (maxBirthdate != null) { clauses.add("patient.birthdate <= :maxBirthdate"); } if (aliveOnly != null && aliveOnly) { clauses.add("patient.dead = false"); } if (deadOnly != null && deadOnly) { clauses.add("patient.dead = true"); } Date maxBirthFromAge = null; if (minAge != null) { Calendar cal = Calendar.getInstance(); cal.setTime(effectiveDate); cal.add(Calendar.YEAR, -minAge); maxBirthFromAge = cal.getTime(); clauses.add("patient.birthdate <= :maxBirthFromAge"); } Date minBirthFromAge = null; if (maxAge != null) { Calendar cal = Calendar.getInstance(); cal.setTime(effectiveDate); cal.add(Calendar.YEAR, -(maxAge + 1)); minBirthFromAge = cal.getTime(); clauses.add("patient.birthdate > :minBirthFromAge"); } clauses.add("(patient.birthdate is null or patient.birthdate <= :effectiveDate)"); boolean first = true; for (String clause : clauses) { if (first) { queryString.append(" where ").append(clause); first = false; } else { queryString.append(" and ").append(clause); } } Query query = sessionFactory.getCurrentSession().createQuery(queryString.toString()); query.setCacheMode(CacheMode.IGNORE); if (gender != null) { query.setString("gender", gender); } if (minBirthdate != null) { query.setDate("minBirthdate", minBirthdate); } if (maxBirthdate != null) { query.setDate("maxBirthdate", maxBirthdate); } if (minAge != null) { query.setDate("maxBirthFromAge", maxBirthFromAge); } if (maxAge != null) { query.setDate("minBirthFromAge", minBirthFromAge); } query.setDate("effectiveDate", effectiveDate); return new Cohort(query.list()); } private static final long MS_PER_YEAR = 365L * 24 * 60 * 60 * 1000L; @SuppressWarnings("unchecked") public Map<Integer, String> getShortPatientDescriptions(Collection<Integer> patientIds) throws DAOException { Map<Integer, String> ret = new HashMap<Integer, String>(); Query query = sessionFactory.getCurrentSession().createQuery( "select patient.personId, patient.gender, patient.birthdate from Patient patient where voided = false"); query.setCacheMode(CacheMode.IGNORE); List<Object[]> temp = query.list(); long now = System.currentTimeMillis(); for (Object[] results : temp) { if (!patientIds.contains(results[0])) { continue; } StringBuffer sb = new StringBuffer(); if ("M".equals(results[1])) { sb.append("Male"); } else { sb.append("Female"); } Date bd = (Date) results[2]; if (bd != null) { int age = (int) ((now - bd.getTime()) / MS_PER_YEAR); sb.append(", ").append(age).append(" years old"); } ret.put((Integer) results[0], sb.toString()); } return ret; } @SuppressWarnings("unchecked") public Map<Integer, Map<String, Object>> getCharacteristics(Cohort patients) throws DAOException { Map<Integer, Map<String, Object>> ret = new HashMap<Integer, Map<String, Object>>(); Collection<Integer> ids = patients.getMemberIds(); Query query = sessionFactory.getCurrentSession().createQuery( "select patient.personId, patient.gender, patient.birthdate from Patient patient where patient.voided = false"); query.setCacheMode(CacheMode.IGNORE); List<Object[]> temp = query.list(); long now = System.currentTimeMillis(); for (Object[] results : temp) { Integer patientId = (Integer) results[0]; if (!ids.contains(patientId)) { continue; } Map<String, Object> holder = new HashMap<String, Object>(); holder.put("gender", results[1]); Date bd = (Date) results[2]; if (bd != null) { int age = (int) ((now - bd.getTime()) / MS_PER_YEAR); holder.put("age_years", age); holder.put("birthdate", bd); } ret.put(patientId, holder); } return ret; } @SuppressWarnings("unchecked") /** * fromDate and toDate are both inclusive */ public Map<Integer, List<Obs>> getObservations(Cohort patients, Concept concept, Date fromDate, Date toDate) throws DAOException { Map<Integer, List<Obs>> ret = new HashMap<Integer, List<Obs>>(); /* Query query = sessionFactory.getCurrentSession().createQuery("select obs, obs.patientId " + "from Obs obs where obs.conceptId = :conceptId " + " and obs.patientId in :ids " + "order by obs.obsDatetime asc"); query.setInteger("conceptId", conceptId); query.set List<Object[]> temp = query.list(); for (Object[] holder : temp) { Obs obs = (Obs) holder[0]; Integer ptId = (Integer) holder[1]; List<Obs> forPatient = ret.get(ptId); if (forPatient == null) { forPatient = new ArrayList<Obs>(); ret.put(ptId, forPatient); } forPatient.add(obs); } */ Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Obs.class); criteria.setCacheMode(CacheMode.IGNORE); criteria.add(Restrictions.eq("concept", concept)); // only add this where clause if patients were passed in if (patients != null) { criteria.add(Restrictions.in("person.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); criteria.addOrder(org.hibernate.criterion.Order.desc("obsDatetime")); log.debug("criteria: " + criteria); List<Obs> temp = criteria.list(); for (Obs obs : temp) { Integer ptId = obs.getPersonId(); List<Obs> forPatient = ret.get(ptId); if (forPatient == null) { forPatient = new ArrayList<Obs>(); ret.put(ptId, forPatient); } forPatient.add(obs); } return ret; } @SuppressWarnings("unchecked") public Map<Integer, List<List<Object>>> getObservationsValues(Cohort patients, Concept c, List<String> attributes, Integer limit, boolean showMostRecentFirst) { Map<Integer, List<List<Object>>> ret = new HashMap<Integer, List<List<Object>>>(); List<String> aliases = new Vector<String>(); Boolean conditional = false; Criteria criteria = sessionFactory.getCurrentSession().createCriteria("org.openmrs.Obs", "obs"); criteria.setCacheMode(CacheMode.IGNORE); List<String> columns = new Vector<String>(); for (String attribute : attributes) { List<String> classNames = new Vector<String>(); if (attribute == null) { columns = findObsValueColumnName(c); if (columns.size() > 1) { conditional = true; } continue; //log.debug("c: " + c.getConceptId() + " attribute: " + attribute); } else if ("valueDate".equals(attribute)) { // pass -- same column name } else if ("valueTime".equals(attribute)) { // pass -- same column name } else if ("valueDatetime".equals(attribute)) { // pass -- same column name } else if ("obsDatetime".equals(attribute)) { // pass -- same column name } else if ("location".equals(attribute)) { // pass -- same column name classNames.add("obs.location"); attribute = "location.name"; } else if ("comment".equals(attribute)) { // pass -- same column name } else if ("encouterType".equals(attribute)) { classNames.add("obs.encounter"); classNames.add("encounter.encounterType"); attribute = "encounterType.name"; } else if ("provider".equals(attribute)) { classNames.add("obs.encounter"); attribute = "encounter.provider"; } else { throw new DAOException("Attribute: " + attribute + " is not recognized. Please add reference in " + this.getClass()); } for (String className : classNames) { // if aliasing is necessary if (!aliases.contains(className)) { // if we haven't aliased this already criteria.createAlias(className, className.split("\\.")[1]); aliases.add(className); } } columns.add(attribute); } String aliasName = "obs"; // set up the query ProjectionList projections = Projections.projectionList(); projections.add(Projections.property("obs.personId")); for (String col : columns) { if (col.contains(".")) { projections.add(Projections.property(col)); } else { projections.add(Projections.property(aliasName + "." + col)); } } criteria.setProjection(projections); // only restrict on patient ids if some were passed in if (patients != null) { criteria.add(Restrictions.in("obs.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("obs.concept", c)); criteria.add(Restrictions.eq("obs.voided", false)); if (showMostRecentFirst) { criteria.addOrder(org.hibernate.criterion.Order.desc("obs.obsDatetime")); } else { criteria.addOrder(org.hibernate.criterion.Order.asc("obs.obsDatetime")); } long start = System.currentTimeMillis(); List<Object[]> rows = criteria.list(); log.debug("Took: " + (System.currentTimeMillis() - start) + " ms to run the patient/obs query"); // set up the return map for (Object[] rowArray : rows) { //log.debug("row[0]: " + row[0] + " row[1]: " + row[1] + (row.length > 2 ? " row[2]: " + row[2] : "")); Integer ptId = (Integer) rowArray[0]; List<List<Object>> oldArr = ret.get(ptId); // if we have already fetched all of the results the user wants if (limit != null && limit > 0 && oldArr != null && oldArr.size() >= limit) { // the user provided a limit value and this patient already has more than // that number of values. // do nothing with this row } else { Boolean tmpConditional = conditional.booleanValue(); // get all columns int index = 1; List<Object> row = new Vector<Object>(); while (index < rowArray.length) { Object value = rowArray[index++]; if (tmpConditional) { if (index == 2 && value != null) { // skip null first value if we must row.add(value); } else { row.add(rowArray[index]); } tmpConditional = false; index++; // increment counter for next column. (Skips over value_concept) } else { row.add(value == null ? "" : value); } } // if we haven't seen a different row for this patient already: if (oldArr == null) { List<List<Object>> arr = new Vector<List<Object>>(); arr.add(row); ret.put(ptId, arr); } // if we have seen a row for this patient already else { oldArr.add(row); ret.put(ptId, oldArr); } } } return ret; } public static List<String> findObsValueColumnName(Concept c) { String abbrev = c.getDatatype().getHl7Abbreviation(); List<String> columns = new Vector<String>(); if ("BIT".equals(abbrev)) { columns.add("valueCoded"); } else if ("CWE".equals(abbrev)) { columns.add("valueDrug"); columns.add("valueCoded"); } else if ("NM".equals(abbrev) || "SN".equals(abbrev)) { columns.add("valueNumeric"); } else if ("DT".equals(abbrev) || "TM".equals(abbrev) || "TS".equals(abbrev)) { columns.add("valueDatetime"); } else if ("ST".equals(abbrev)) { columns.add("valueText"); } return columns; } @SuppressWarnings("unchecked") public Map<Integer, Encounter> getEncountersByType(Cohort patients, List<EncounterType> encTypes) { Map<Integer, Encounter> ret = new HashMap<Integer, Encounter>(); // default query Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Encounter.class); criteria.setCacheMode(CacheMode.IGNORE); // this "where clause" is only necessary if patients were passed in if (patients != null && patients.size() > 0) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); if (encTypes != null && encTypes.size() > 0) { criteria.add(Restrictions.in("encounterType", encTypes)); } criteria.addOrder(org.hibernate.criterion.Order.desc("patient.personId")); criteria.addOrder(org.hibernate.criterion.Order.desc("encounterDatetime")); List<Encounter> encounters = criteria.list(); // set up the return map for (Encounter enc : encounters) { Integer ptId = enc.getPatientId(); if (!ret.containsKey(ptId)) { ret.put(ptId, enc); } } return ret; } /** * Gets a list of encounters associated with the given form, filtered by the given patient set. * * @param patients the patients to filter by (null will return all encounters for all patients) * @param forms the forms to filter by */ @SuppressWarnings("unchecked") public List<Encounter> getEncountersByForm(Cohort patients, List<Form> forms) { // default query Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Encounter.class); criteria.setCacheMode(CacheMode.IGNORE); // this "where clause" is only necessary if patients were passed in if (patients != null && patients.size() > 0) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); if (forms != null && forms.size() > 0) { criteria.add(Restrictions.in("form", forms)); } criteria.addOrder(org.hibernate.criterion.Order.desc("patient.personId")); criteria.addOrder(org.hibernate.criterion.Order.desc("encounterDatetime")); return criteria.list(); } @SuppressWarnings("unchecked") public Map<Integer, Object> getEncounterAttrsByType(Cohort patients, List<EncounterType> encTypes, String attr, Boolean earliestFirst) { Map<Integer, Object> ret = new HashMap<Integer, Object>(); // default query Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Encounter.class); criteria.setCacheMode(CacheMode.IGNORE); // this "where clause" is only necessary if patients were specified if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); if (encTypes != null && encTypes.size() > 0) { criteria.add(Restrictions.in("encounterType", encTypes)); } criteria.setProjection(Projections.projectionList().add(Projections.property("patient.personId")) .add(Projections.property(attr))); criteria.addOrder(org.hibernate.criterion.Order.desc("patient.personId")); if (earliestFirst) { criteria.addOrder(org.hibernate.criterion.Order.asc("encounterDatetime")); } else { criteria.addOrder(org.hibernate.criterion.Order.desc("encounterDatetime")); } List<Object[]> attrs = criteria.list(); // set up the return map for (Object[] row : attrs) { Integer ptId = (Integer) row[0]; if (!ret.containsKey(ptId)) { ret.put(ptId, row[1]); } } return ret; } @SuppressWarnings("unchecked") public Map<Integer, Encounter> getEncounters(Cohort patients) { Map<Integer, Encounter> ret = new HashMap<Integer, Encounter>(); // default query Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Encounter.class); criteria.setCacheMode(CacheMode.IGNORE); // only include this where clause if patients were passed in if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); criteria.addOrder(org.hibernate.criterion.Order.desc("patient.personId")); criteria.addOrder(org.hibernate.criterion.Order.desc("encounterDatetime")); List<Encounter> encounters = criteria.list(); // set up the return map for (Encounter enc : encounters) { Integer ptId = enc.getPatientId(); if (!ret.containsKey(ptId)) { ret.put(ptId, enc); } } return ret; } @SuppressWarnings("unchecked") public Map<Integer, Encounter> getFirstEncountersByType(Cohort patients, List<EncounterType> types) { Map<Integer, Encounter> ret = new HashMap<Integer, Encounter>(); // default query Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Encounter.class); criteria.setCacheMode(CacheMode.IGNORE); // this "where clause" is only needed if patients were specified if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); if (types != null && types.size() > 0) { criteria.add(Restrictions.in("encounterType", types)); } criteria.addOrder(org.hibernate.criterion.Order.desc("patient.personId")); criteria.addOrder(org.hibernate.criterion.Order.asc("encounterDatetime")); List<Encounter> encounters = criteria.list(); // set up the return map for (Encounter enc : encounters) { Integer ptId = enc.getPatientId(); if (!ret.containsKey(ptId)) { ret.put(ptId, enc); } } return ret; } @SuppressWarnings("unchecked") public Map<Integer, Object> getPatientAttributes(Cohort patients, String className, String property, boolean returnAll) throws DAOException { Map<Integer, Object> ret = new HashMap<Integer, Object>(); className = "org.openmrs." + className; // default query Criteria criteria = null; // make 'patient.**' reference 'patient' like alias instead of object if ("org.openmrs.Patient".equals(className)) { criteria = sessionFactory.getCurrentSession().createCriteria("org.openmrs.Patient", "patient"); } else if ("org.openmrs.Person".equals(className)) { criteria = sessionFactory.getCurrentSession().createCriteria("org.openmrs.Person", "person"); } else { criteria = sessionFactory.getCurrentSession().createCriteria(className); } criteria.setCacheMode(CacheMode.IGNORE); // set up the query ProjectionList projectionList = Projections.projectionList(); // if Person, PersonName, or PersonAddress if (className.contains("Person")) { projectionList.add(Projections.property("person.personId")); projectionList.add(Projections.property(property)); if (patients != null) { criteria.add(Restrictions.in("person.personId", patients.getMemberIds())); } // do not include voided person rows if ("org.openmrs.Person".equals(className)) { // the voided column on the person table is mapped to the person object // through the getPersonVoided() to distinguish it from patient/user.voided criteria.add(Restrictions.eq("personVoided", false)); } else { // this is here to support PersonName and PersonAddress criteria.add(Restrictions.eq("voided", false)); } } // if one of the Patient tables else { projectionList.add(Projections.property("patient.personId")); projectionList.add(Projections.property(property)); if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } // do not include voided patients criteria.add(Restrictions.eq("voided", false)); } criteria.setProjection(projectionList); // add 'preferred' sort order if necessary try { boolean hasPreferred = false; for (Field f : Class.forName(className).getDeclaredFields()) { if ("preferred".equals(f.getName())) { hasPreferred = true; } } if (hasPreferred) { criteria.addOrder(org.hibernate.criterion.Order.desc("preferred")); } } catch (ClassNotFoundException e) { log.warn("Class not found: " + className); } criteria.addOrder(org.hibernate.criterion.Order.desc("dateCreated")); List<Object[]> rows = criteria.list(); // set up the return map if (returnAll) { for (Object[] row : rows) { Integer ptId = (Integer) row[0]; Object columnValue = row[1]; if (!ret.containsKey(ptId)) { Object[] arr = { columnValue }; ret.put(ptId, arr); } else { Object[] oldArr = (Object[]) ret.get(ptId); Object[] newArr = new Object[oldArr.length + 1]; System.arraycopy(oldArr, 0, newArr, 0, oldArr.length); newArr[oldArr.length] = columnValue; ret.put(ptId, newArr); } } } else { for (Object[] row : rows) { Integer ptId = (Integer) row[0]; Object columnValue = row[1]; if (!ret.containsKey(ptId)) { ret.put(ptId, columnValue); } } } return ret; } /** * @see org.openmrs.api.db.PatientSetDAO#getPersonAttributes(org.openmrs.Cohort, * java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean) */ @SuppressWarnings("unchecked") public Map<Integer, Object> getPersonAttributes(Cohort patients, String attributeTypeName, String joinClass, String joinProperty, String outputColumn, boolean returnAll) { Map<Integer, Object> ret = new HashMap<Integer, Object>(); StringBuilder queryString = new StringBuilder(); // set up the query queryString.append("select attr.person.personId, "); if (joinClass != null && joinProperty != null && outputColumn != null) { queryString.append("joinedClass."); queryString.append(outputColumn); queryString.append(" from PersonAttribute attr, PersonAttributeType t, "); queryString.append(joinClass); queryString.append(" joinedClass where t = attr.attributeType "); queryString.append("and attr.value = joinedClass."); queryString.append(joinProperty + " "); } else { queryString.append( "attr.value from PersonAttribute attr, PersonAttributeType t where t = attr.attributeType "); } queryString.append("and t.name = :typeName "); queryString.append("order by attr.voided asc, attr.dateCreated desc"); Query query = sessionFactory.getCurrentSession().createQuery(queryString.toString()); query.setString("typeName", attributeTypeName); log.debug("query: " + queryString); List<Object[]> rows = query.list(); // set up the return map for (Object[] row : rows) { Integer ptId = (Integer) row[0]; if (patients == null || patients.contains(ptId)) { if (returnAll) { Object columnValue = row[1]; if (!ret.containsKey(ptId)) { Object[] arr = { columnValue }; ret.put(ptId, arr); } else { Object[] oldArr = (Object[]) ret.get(ptId); Object[] newArr = new Object[oldArr.length + 1]; System.arraycopy(oldArr, 0, newArr, 0, oldArr.length); newArr[oldArr.length] = columnValue; ret.put(ptId, newArr); } } else { Object columnValue = row[1]; if (!ret.containsKey(ptId)) { ret.put(ptId, columnValue); } } } } return ret; } public Cohort getPatientsHavingTextObs(Integer conceptId, String value, TimeModifier timeModifier) throws DAOException { Query query; StringBuffer sb = new StringBuffer(); sb.append("select o.person_id from obs o "); if (timeModifier != null) { if (timeModifier.equals(TimeModifier.LAST)) { log.debug("timeModifier is NOT NULL, and appears to be LAST, so we'll try to add a subquery"); sb.append("inner join (select person_id, max(obs_datetime) as obs_datetime from obs where "); sb.append( "concept_id = :concept_id group by person_id) sub on o.person_id = sub.person_id and o.obs_datetime = sub.obs_datetime "); } else { log.debug("timeModifier is NOT NULL, and appears to not be LAST, so we won't do anything"); } } else { log.debug("timeModifier is NULL, skipping to full query"); } sb.append("where o.concept_id = :concept_id "); boolean useVal = false; if (value != null) { sb.append("and o.value_text = :value "); useVal = true; } else { sb.append("and o.value_text is not null "); } sb.append("group by o.person_id "); query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); query.setCacheMode(CacheMode.IGNORE); query.setInteger("concept_id", conceptId); if (useVal) { query.setString("value", value); } return new Cohort(query.list()); } public Cohort getPatientsHavingLocation(Integer locationId, PatientSetService.PatientLocationMethod method) { StringBuffer sb = new StringBuffer(); boolean argumentAsString = false; if (method == PatientLocationMethod.ANY_ENCOUNTER) { sb.append(" select e.patient_id from "); sb.append(" encounter e "); sb.append(" inner join patient p on e.patient_id = p.patient_id and p.voided = false "); sb.append(" where e.location_id = :location_id "); sb.append(" group by e.patient_id "); } else if (method == PatientLocationMethod.EARLIEST_ENCOUNTER) { sb.append(" select e.patient_id "); sb.append(" from encounter e "); sb.append(" inner join patient p on e.patient_id = p.patient_id and p.voided = false "); sb.append(" inner join ("); sb.append(" select patient_id, min(encounter_datetime) as earliest "); sb.append(" from encounter "); sb.append(" group by patient_id) subq "); sb.append(" on e.patient_id = subq.patient_id and e.encounter_datetime = subq.earliest "); sb.append(" where e.location_id = :location_id "); sb.append(" group by e.patient_id "); } else if (method == PatientLocationMethod.LATEST_ENCOUNTER) { sb.append(" select e.patient_id "); sb.append(" from encounter e "); sb.append(" inner join patient p on e.patient_id = p.patient_id and p.voided = false "); sb.append(" inner join ("); sb.append(" select patient_id, max(encounter_datetime) as earliest "); sb.append(" from encounter "); sb.append(" group by patient_id) subq "); sb.append(" on e.patient_id = subq.patient_id and e.encounter_datetime = subq.earliest "); sb.append(" where e.location_id = :location_id "); sb.append(" group by e.patient_id "); } else { sb.append(" select patient_id from patient p, person_attribute attr, person_attribute_type type "); sb.append(" where type.name = 'Health Center' "); sb.append(" and type.person_attribute_type_id = attr.person_attribute_type_id "); sb.append(" and attr.value = :location_id "); sb.append(" and attr.person_id = p.patient_id "); sb.append(" and attr.voided = false "); sb.append(" and p.voided = false "); argumentAsString = true; } log.debug("query: " + sb); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); if (argumentAsString) { query.setString("location_id", locationId.toString()); } else { query.setInteger("location_id", locationId); } return new Cohort(query.list()); } public Cohort convertPatientIdentifier(List<String> identifiers) throws DAOException { StringBuffer sb = new StringBuffer(); sb.append("select distinct(patient_id) from patient_identifier p "); sb.append("where identifier in (:identifiers)"); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); query.setCacheMode(CacheMode.IGNORE); query.setParameterList("identifiers", identifiers, new StringType()); return new Cohort(query.list()); } @SuppressWarnings("unchecked") public List<Patient> getPatients(Collection<Integer> patientIds) throws DAOException { List<Patient> ret = new ArrayList<Patient>(); if (!patientIds.isEmpty()) { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Patient.class); criteria.setCacheMode(CacheMode.IGNORE); criteria.add(Restrictions.in("patientId", patientIds)); criteria.add(Restrictions.eq("voided", false)); log.debug("criteria: " + criteria); List<Patient> temp = criteria.list(); for (Patient p : temp) { ret.add(p); } } return ret; } /** * Returns a Map from patientId to a Collection of drugIds for drugs active for the patients on * that date If patientIds is null then do this for all patients Does not return anything for * voided patients * * @throws DAOException */ @SuppressWarnings("unchecked") public Map<Integer, Collection<Integer>> getActiveDrugIds(Collection<Integer> patientIds, Date fromDate, Date toDate) throws DAOException { Set<Integer> idsLookup = patientIds == null ? null : (patientIds instanceof HashSet ? (HashSet<Integer>) patientIds : new HashSet<Integer>(patientIds)); Map<Integer, Collection<Integer>> ret = new HashMap<Integer, Collection<Integer>>(); List<String> whereClauses = new ArrayList<String>(); whereClauses.add("o.voided = false"); if (toDate != null) { whereClauses.add("o.date_activated <= :toDate"); } if (fromDate != null) { whereClauses.add("(o.auto_expire_date is null or o.auto_expire_date > :fromDate)"); whereClauses.add("(o.date_stopped is null or o.date_stopped > :fromDate)"); } StringBuilder sql = new StringBuilder("select o.patient_id, d.drug_inventory_id " + "from orders o " + " inner join patient p on o.patient_id = p.patient_id and p.voided = false " + " inner join drug_order d on o.order_id = d.order_id "); for (ListIterator<String> i = whereClauses.listIterator(); i.hasNext();) { sql.append((i.nextIndex() == 0 ? " where " : " and ")).append(i.next()); } log.debug("sql= " + sql); Query query = sessionFactory.getCurrentSession().createSQLQuery(sql.toString()); query.setCacheMode(CacheMode.IGNORE); if (toDate != null) { query.setDate("toDate", toDate); } if (fromDate != null) { query.setDate("fromDate", fromDate); } List<Object[]> results = (List<Object[]>) query.list(); for (Object[] row : results) { Integer patientId = (Integer) row[0]; if (idsLookup == null || idsLookup.contains(patientId)) { Integer drugId = (Integer) row[1]; Collection<Integer> drugIds = ret.get(patientId); if (drugIds == null) { drugIds = new HashSet<Integer>(); ret.put(patientId, drugIds); } drugIds.add(drugId); } } return ret; } @SuppressWarnings("unchecked") public Map<Integer, PatientState> getCurrentStates(Cohort ps, ProgramWorkflow wf) throws DAOException { Map<Integer, PatientState> ret = new HashMap<Integer, PatientState>(); if (ps == null || ps.getMemberIds().size() > 0) { Date now = new Date(); Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientState.class); criteria.setFetchMode("patient", FetchMode.JOIN); criteria.setCacheMode(CacheMode.IGNORE); //criteria.add(Restrictions.in("patientProgram.patient.personId", ids)); // only include this where clause if patients were passed in if (ps != null) { criteria.createCriteria("patientProgram") .add(Restrictions.in("patient.personId", ps.getMemberIds())); } //criteria.add(Restrictions.eq("state.programWorkflow", wf)); criteria.createCriteria("state").add(Restrictions.eq("programWorkflow", wf)); criteria.add(Restrictions.eq("voided", false)); criteria.add(Restrictions.or(Restrictions.isNull("startDate"), Restrictions.le("startDate", now))); criteria.add(Restrictions.or(Restrictions.isNull("endDate"), Restrictions.ge("endDate", now))); log.debug("criteria: " + criteria); List<PatientState> temp = criteria.list(); for (PatientState state : temp) { Integer ptId = state.getPatientProgram().getPatient().getPatientId(); ret.put(ptId, state); } } return ret; } /** * This method assumes the patient is not simultaneously enrolled in the program more than once. * if (includeVoided == true) then include voided programs if (includePast == true) then include * program which are already complete In all cases this only returns the latest program * enrollment for each patient. */ @SuppressWarnings("unchecked") public Map<Integer, PatientProgram> getPatientPrograms(Cohort ps, Program program, boolean includeVoided, boolean includePast) throws DAOException { Map<Integer, PatientProgram> ret = new HashMap<Integer, PatientProgram>(); Date now = new Date(); Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientProgram.class); criteria.setFetchMode("patient", FetchMode.JOIN); criteria.setCacheMode(CacheMode.IGNORE); // this "where clause" is only necessary if patients were passed in if (ps != null) { criteria.add(Restrictions.in("patient.personId", ps.getMemberIds())); } criteria.add(Restrictions.eq("program", program)); if (!includeVoided) { criteria.add(Restrictions.eq("voided", false)); } criteria.add(Restrictions.or(Restrictions.isNull("dateEnrolled"), Restrictions.le("dateEnrolled", now))); if (!includePast) { criteria.add( Restrictions.or(Restrictions.isNull("dateCompleted"), Restrictions.ge("dateCompleted", now))); } log.debug("criteria: " + criteria); List<PatientProgram> temp = criteria.list(); for (PatientProgram prog : temp) { Integer ptId = prog.getPatient().getPatientId(); ret.put(ptId, prog); } return ret; } @SuppressWarnings("unchecked") public Map<Integer, List<DrugOrder>> getCurrentDrugOrders(Cohort patients, List<Concept> drugConcepts) throws DAOException { Map<Integer, List<DrugOrder>> ret = new HashMap<Integer, List<DrugOrder>>(); Date now = new Date(); Criteria criteria = sessionFactory.getCurrentSession().createCriteria(DrugOrder.class); criteria.setFetchMode("patient", FetchMode.JOIN); criteria.setCacheMode(CacheMode.IGNORE); // this "where clause" is only necessary if patients were passed in if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } //criteria.add(Restrictions.in("encounter.patient.personId", ids)); //criteria.createCriteria("encounter").add(Restrictions.in("patient.personId", ids)); if (drugConcepts != null) { criteria.add(Restrictions.in("concept", drugConcepts)); } criteria.add(Restrictions.eq("voided", false)); criteria.add(Restrictions.le("dateActivated", now)); criteria.add(Restrictions.and( Restrictions.or(Restrictions.isNull("autoExpireDate"), Restrictions.gt("autoExpireDate", now)), Restrictions.or(Restrictions.isNull("dateStopped"), Restrictions.gt("dateStopped", now)))); criteria.addOrder(org.hibernate.criterion.Order.asc("dateActivated")); log.debug("criteria: " + criteria); List<DrugOrder> temp = criteria.list(); for (DrugOrder regimen : temp) { Integer ptId = regimen.getPatient().getPatientId(); List<DrugOrder> list = ret.get(ptId); if (list == null) { list = new ArrayList<DrugOrder>(); ret.put(ptId, list); } list.add(regimen); } return ret; } @SuppressWarnings("unchecked") public Map<Integer, List<DrugOrder>> getDrugOrders(Cohort patients, List<Concept> drugConcepts) throws DAOException { Map<Integer, List<DrugOrder>> ret = new HashMap<Integer, List<DrugOrder>>(); if (patients != null && patients.size() == 0) { return ret; } Criteria criteria = sessionFactory.getCurrentSession().createCriteria(DrugOrder.class); criteria.setFetchMode("patient", FetchMode.JOIN); criteria.setCacheMode(CacheMode.IGNORE); // only include this where clause if patients were passed in if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } if (drugConcepts != null) { criteria.add(Restrictions.in("concept", drugConcepts)); } criteria.add(Restrictions.eq("voided", false)); criteria.addOrder(org.hibernate.criterion.Order.asc("dateActivated")); log.debug("criteria: " + criteria); List<DrugOrder> temp = criteria.list(); for (DrugOrder regimen : temp) { Integer ptId = regimen.getPatient().getPatientId(); List<DrugOrder> list = ret.get(ptId); if (list == null) { list = new ArrayList<DrugOrder>(); ret.put(ptId, list); } list.add(regimen); } return ret; } /* * This is a small hack to make the relationships work right in Neal's report code. It will be refactored * when I implement a relationship type filter for the cohort builder. -DJ */ @SuppressWarnings("unchecked") public Map<Integer, List<Person>> getRelatives(Cohort patients, RelationshipType relType, boolean forwards) { if (relType == null) { throw new IllegalArgumentException("Must give a relationship type"); } Map<Integer, List<Person>> ret = new HashMap<Integer, List<Person>>(); if (patients != null && patients.size() == 0) { return ret; } Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Relationship.class); criteria.add(Restrictions.eq("voided", false)); if (patients != null) { if (forwards) { criteria.add(Restrictions.in("personA.personId", patients.getMemberIds())); } else { criteria.add(Restrictions.in("personB.personId", patients.getMemberIds())); } } log.debug("criteria: " + criteria); List<Relationship> rels = (List<Relationship>) criteria.list(); for (Relationship rel : rels) { Person fromPerson = forwards ? rel.getPersonA() : rel.getPersonB(); Person toPerson = forwards ? rel.getPersonB() : rel.getPersonA(); List<Person> holder = (List<Person>) ret.get(fromPerson.getPersonId()); if (holder == null) { holder = new ArrayList<Person>(); ret.put(fromPerson.getPersonId(), holder); } holder.add(toPerson); } return ret; } @SuppressWarnings("unchecked") public Map<Integer, List<Relationship>> getRelationships(Cohort patients, RelationshipType relType) { Map<Integer, List<Relationship>> ret = new HashMap<Integer, List<Relationship>>(); Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Relationship.class); criteria.setCacheMode(CacheMode.IGNORE); if (relType != null) { criteria.add(Restrictions.eq("relationshipType", relType)); } // this "where clause" is only useful if patients were passed in if (patients != null) { criteria.createCriteria("personB").add(Restrictions.in("personId", patients.getMemberIds())); } criteria.add(Restrictions.eq("voided", false)); log.debug("criteria: " + criteria); List<Relationship> temp = criteria.list(); for (Relationship rel : temp) { Integer ptId = rel.getPersonB().getPersonId(); List<Relationship> rels = ret.get(ptId); if (rels == null) { rels = new ArrayList<Relationship>(); ret.put(ptId, rels); } rels.add(rel); } return ret; } public Cohort getPatientsHavingPersonAttribute(PersonAttributeType attribute, String value) { StringBuilder sb = new StringBuilder(); sb.append(" select pat.patient_id "); sb.append(" from person p "); sb.append(" inner join patient pat on pat.patient_id = p.person_id and pat.voided = false "); sb.append(" inner join person_attribute a on p.person_id = a.person_id and a.voided = false "); sb.append(" where p.voided = false "); if (attribute != null) { sb.append(" and a.person_attribute_type_id = :typeId "); } if (value != null) { sb.append(" and a.value = :value "); } sb.append(" group by pat.patient_id "); log.debug("query: " + sb); Query query = sessionFactory.getCurrentSession().createSQLQuery(sb.toString()); if (attribute != null) { query.setInteger("typeId", attribute.getPersonAttributeTypeId()); } if (value != null) { query.setString("value", value); } return new Cohort(query.list()); } public Cohort getPatientsHavingDrugOrder(List<Drug> drugList, List<Concept> drugConceptList, Date startDateFrom, Date startDateTo, Date stopDateFrom, Date stopDateTo, Boolean discontinued, List<Concept> orderReason) { if (drugList != null && drugList.size() == 0) { drugList = null; } if (drugConceptList != null && drugConceptList.size() == 0) { drugConceptList = null; } StringBuilder sb = new StringBuilder(); sb.append(" select distinct patient.id from DrugOrder where voided = false and patient.voided = false "); if (drugList != null) { sb.append(" and drug.id in (:drugIdList) "); } if (drugConceptList != null) { sb.append(" and concept.id in (:drugConceptIdList) "); } if (startDateFrom != null && startDateTo != null) { sb.append(" and dateActivated between :startDateFrom and :startDateTo "); } else { if (startDateFrom != null) { sb.append(" and dateActivated >= :startDateFrom "); } if (startDateTo != null) { sb.append(" and dateActivated <= :startDateTo "); } } if (orderReason != null && orderReason.size() > 0) { sb.append(" and orderReason.id in (:orderReasonIdList) "); } if (discontinued != null) { if (discontinued) { if (stopDateFrom != null && stopDateTo != null) { sb.append(" and dateStopped between :stopDateFrom and :stopDateTo "); } else { if (stopDateFrom != null) { sb.append(" and dateStopped >= :stopDateFrom "); } if (stopDateTo != null) { sb.append(" and dateStopped <= :stopDateTo "); } } } else { // discontinued == false if (stopDateFrom != null && stopDateTo != null) { sb.append(" and autoExpireDate between :stopDateFrom and :stopDateTo "); } else { if (stopDateFrom != null) { sb.append(" and autoExpireDate >= :stopDateFrom "); } if (stopDateTo != null) { sb.append(" and autoExpireDate <= :stopDateTo "); } } } } else { // discontinued == null, so we need either if (stopDateFrom != null && stopDateTo != null) { sb.append(" and coalesce(dateStopped, autoExpireDate) between :stopDateFrom and :stopDateTo "); } else { if (stopDateFrom != null) { sb.append(" and coalesce(dateStopped, autoExpireDate) >= :stopDateFrom "); } if (stopDateTo != null) { sb.append(" and coalesce(dateStopped, autoExpireDate) <= :stopDateTo "); } } } log.debug("sql = " + sb); Query query = sessionFactory.getCurrentSession().createQuery(sb.toString()); if (drugList != null) { List<Integer> ids = new ArrayList<Integer>(); for (Drug d : drugList) { ids.add(d.getDrugId()); } query.setParameterList("drugIdList", ids); } if (drugConceptList != null) { List<Integer> ids = new ArrayList<Integer>(); for (Concept c : drugConceptList) { ids.add(c.getConceptId()); } query.setParameterList("drugConceptIdList", ids); } if (startDateFrom != null) { query.setDate("startDateFrom", startDateFrom); } if (startDateTo != null) { query.setDate("startDateTo", startDateTo); } if (stopDateFrom != null) { query.setDate("stopDateFrom", stopDateFrom); } if (stopDateTo != null) { query.setDate("stopDateTo", stopDateTo); } if (discontinued != null) { query.setBoolean("discontinued", discontinued); } if (orderReason != null && orderReason.size() > 0) { List<Integer> ids = new ArrayList<Integer>(); for (Concept c : orderReason) { ids.add(c.getConceptId()); } query.setParameterList("orderReasonIdList", ids); } return new Cohort(query.list()); } /** * @param patients * @param types List<PatientIdentifierTypes> of types to get * @return Map of {@link PatientIdentifier}s */ @SuppressWarnings("unchecked") public Map<Integer, String> getPatientIdentifierByType(Cohort patients, List<PatientIdentifierType> types) { Map<Integer, String> patientIdentifiers = new HashMap<Integer, String>(); // default query Criteria criteria = sessionFactory.getCurrentSession().createCriteria(PatientIdentifier.class); // only get the "identifier" and "patientId" columns ProjectionList projections = Projections.projectionList(); projections.add(Projections.property("identifier")); projections.add(Projections.property("patient.personId")); criteria.setProjection(projections); criteria.setCacheMode(CacheMode.IGNORE); // Add patient restriction if necessary if (patients != null) { criteria.add(Restrictions.in("patient.personId", patients.getMemberIds())); } // all identifiers must be non-voided criteria.add(Restrictions.eq("voided", false)); // Add identifier type filter if (types != null && types.size() > 0) { criteria.add(Restrictions.in("identifierType", types)); } // Order by ID criteria.addOrder(org.hibernate.criterion.Order.desc("patient.personId")); List<Object[]> rows = criteria.list(); // set up the return map for (Object[] row : rows) { String identifier = (String) row[0]; Integer patientId = (Integer) row[1]; if (!patientIdentifiers.containsKey(patientId)) { patientIdentifiers.put(patientId, identifier); } } return patientIdentifiers; } /** * @see org.openmrs.api.db.PatientSetDAO#getPatientsByRelationship(org.openmrs.RelationshipType, * boolean, boolean, org.openmrs.Person) */ public Cohort getPatientsByRelationship(RelationshipType relType, boolean includeAtoB, boolean includeBtoA, Person target) { // since members of a relationship aren't necessarily Patients, but we're supposed to be returning // just patients, get all patients first to compare against: Cohort allPatients = getAllPatients(); if (relType != null) { if (includeAtoB && includeBtoA) { String hql = "select personA.id, personB.id from Relationship where relationshipType = :relType"; if (target != null) { hql += " and (personA.id = :targetId or personB.id = :targetId)"; } Query q = sessionFactory.getCurrentSession().createQuery(hql); q.setParameter("relType", relType); if (target != null) { q.setInteger("targetId", target.getPersonId()); } Cohort ret = new Cohort(); for (Object[] o : (List<Object[]>) q.list()) { ret.addMember((Integer) o[0]); ret.addMember((Integer) o[1]); } if (target != null) { ret.removeMember(target.getPersonId()); } return Cohort.intersect(allPatients, ret); } else if (includeAtoB) { String hql = "select personA.id from Relationship where relationshipType = :relType"; if (target != null) { hql += " and personB.id = :targetId"; } Query q = sessionFactory.getCurrentSession().createQuery(hql); q.setParameter("relType", relType); if (target != null) { q.setInteger("targetId", target.getPersonId()); } Cohort ret = new Cohort(); for (Integer id : (List<Integer>) q.list()) { ret.addMember(id); } return Cohort.intersect(allPatients, ret); } else if (includeBtoA) { String hql = "select personB.id from Relationship where relationshipType = :relType"; if (target != null) { hql += " and personA.id = :targetId"; } Query q = sessionFactory.getCurrentSession().createQuery(hql); q.setParameter("relType", relType); if (target != null) { q.setInteger("targetId", target.getPersonId()); } Cohort ret = new Cohort(); for (Integer id : (List<Integer>) q.list()) { ret.addMember(id); } return Cohort.intersect(allPatients, ret); } else { return new Cohort(); } } else { if (target != null) { Cohort ret = new Cohort(); Integer ptId = target.getPersonId(); Query query = sessionFactory.getCurrentSession().createSQLQuery( "select person_a, person_b from relationship where person_a = :ptId or person_b = :ptId"); query.setInteger("ptId", ptId); for (Object[] o : (List<Object[]>) query.list()) { ret.addMember((Integer) o[0]); ret.addMember((Integer) o[1]); } // don't include the target patient ret.removeMember(ptId); return Cohort.intersect(allPatients, ret); } else { // get everyone at either end of any relationship, and determine if they're a patient Cohort ret = new Cohort(); Query query = sessionFactory.getCurrentSession() .createSQLQuery("select person_a, person_b from relationship"); for (Object[] o : (List<Object[]>) query.list()) { ret.addMember((Integer) o[0]); ret.addMember((Integer) o[1]); } return Cohort.intersect(allPatients, ret); } } } @Override public Integer getCountOfPatients() { Query query = sessionFactory.getCurrentSession() .createQuery("select count(*) from Patient where voided = '0'"); return Integer.valueOf(query.uniqueResult().toString()); } @Override public Cohort getPatients(Integer start, Integer size) { Query query = sessionFactory.getCurrentSession() .createQuery("select distinct patientId from Patient p where p.voided = '0'"); if (start != null) { query.setFirstResult(start); } if (size != null) { query.setMaxResults(size); } Set<Integer> ids = new HashSet<Integer>(); ids.addAll(query.list()); return new Cohort("Batch of " + size + " patients starting at " + start, "", ids); } private String formatProvider(Provider p) { return p.getName(); } }