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.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Set; import java.util.Vector; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.collections.Transformer; import org.apache.commons.lang.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.hibernate.Criteria; import org.hibernate.FlushMode; import org.hibernate.Query; import org.hibernate.SQLQuery; import org.hibernate.SessionFactory; import org.hibernate.criterion.Criterion; import org.hibernate.criterion.MatchMode; import org.hibernate.criterion.Order; import org.hibernate.criterion.Projections; import org.hibernate.criterion.Restrictions; import org.hibernate.criterion.SimpleExpression; import org.hibernate.transform.DistinctRootEntityResultTransformer; import org.openmrs.Concept; import org.openmrs.ConceptAnswer; import org.openmrs.ConceptClass; import org.openmrs.ConceptComplex; import org.openmrs.ConceptDatatype; import org.openmrs.ConceptDescription; import org.openmrs.ConceptMap; import org.openmrs.ConceptMapType; import org.openmrs.ConceptName; import org.openmrs.ConceptNameTag; import org.openmrs.ConceptNumeric; import org.openmrs.ConceptProposal; import org.openmrs.ConceptReferenceTerm; import org.openmrs.ConceptReferenceTermMap; import org.openmrs.ConceptSearchResult; import org.openmrs.ConceptSet; import org.openmrs.ConceptSource; import org.openmrs.ConceptStopWord; import org.openmrs.Drug; import org.openmrs.DrugIngredient; import org.openmrs.OpenmrsObject; import org.openmrs.api.APIException; import org.openmrs.api.ConceptService; import org.openmrs.api.context.Context; import org.openmrs.api.db.ConceptDAO; import org.openmrs.api.db.DAOException; import org.openmrs.api.db.hibernate.search.LuceneQuery; import org.openmrs.collection.ListPart; import org.openmrs.util.ConceptMapTypeComparator; import org.openmrs.util.OpenmrsConstants; /** * The Hibernate class for Concepts, Drugs, and related classes. <br> * <br> * Use the {@link ConceptService} to access these methods * * @see ConceptService */ public class HibernateConceptDAO implements ConceptDAO { protected final Log log = LogFactory.getLog(getClass()); private SessionFactory sessionFactory; /** * Sets the session factory * * @param sessionFactory */ public void setSessionFactory(SessionFactory sessionFactory) { this.sessionFactory = sessionFactory; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptComplex(java.lang.Integer) */ public ConceptComplex getConceptComplex(Integer conceptId) { ConceptComplex cc; Object obj = sessionFactory.getCurrentSession().get(ConceptComplex.class, conceptId); // If Concept has already been read & cached, we may get back a Concept instead of // ConceptComplex. If this happens, we need to clear the object from the cache // and re-fetch it as a ConceptComplex if (obj != null && !obj.getClass().equals(ConceptComplex.class)) { sessionFactory.getCurrentSession().evict(obj); // remove from cache // session.get() did not work here, we need to perform a query to get a ConceptComplex Query query = sessionFactory.getCurrentSession() .createQuery("from ConceptComplex where conceptId = :conceptId") .setParameter("conceptId", conceptId); obj = query.uniqueResult(); } cc = (ConceptComplex) obj; return cc; } /** * @see org.openmrs.api.db.ConceptDAO#saveConcept(org.openmrs.Concept) */ public Concept saveConcept(Concept concept) throws DAOException { if ((concept.getConceptId() != null) && (concept.getConceptId() > 0)) { // this method checks the concept_numeric, concept_derived, etc tables // to see if a row exists there or not. This is needed because hibernate // doesn't like to insert into concept_numeric but update concept in the // same go. It assumes that its either in both tables or no tables insertRowIntoSubclassIfNecessary(concept); } sessionFactory.getCurrentSession().saveOrUpdate(concept); return concept; } /** * Convenience method that will check this concept for subtype values (ConceptNumeric, * ConceptDerived, etc) and insert a line into that subtable if needed. This prevents a * hibernate ConstraintViolationException * * @param concept the concept that will be inserted */ private void insertRowIntoSubclassIfNecessary(Concept concept) { // check the concept_numeric table if (concept instanceof ConceptNumeric) { String select = "SELECT 1 from concept_numeric WHERE concept_id = :conceptId"; Query query = sessionFactory.getCurrentSession().createSQLQuery(select); query.setInteger("conceptId", concept.getConceptId()); // Converting to concept numeric: A single concept row exists, but concept numeric has not been populated yet. if (query.uniqueResult() == null) { // we have to evict the current concept out of the session because // the user probably had to change the class of this object to get it // to now be a numeric // (must be done before the "insert into...") sessionFactory.getCurrentSession().clear(); //Just in case this was changed from concept_complex to numeric //We need to add a delete line for each concept sub class that is not concept_numeric deleteSubclassConcept("concept_complex", concept.getConceptId()); String insert = "INSERT INTO concept_numeric (concept_id, precise) VALUES (:conceptId, false)"; query = sessionFactory.getCurrentSession().createSQLQuery(insert); query.setInteger("conceptId", concept.getConceptId()); query.executeUpdate(); } else { // Converting from concept numeric: The concept and concept numeric rows both exist, so we need to delete concept_numeric. // concept is changed from numeric to something else // hence row should be deleted from the concept_numeric if (!concept.isNumeric()) { deleteSubclassConcept("concept_numeric", concept.getConceptId()); } else { // it is indeed numeric now... don't delete } } } // check the concept complex table else if (concept instanceof ConceptComplex) { String select = "SELECT 1 FROM concept_complex WHERE concept_id = :conceptId"; Query query = sessionFactory.getCurrentSession().createSQLQuery(select); query.setInteger("conceptId", concept.getConceptId()); // Converting to concept complex: A single concept row exists, but concept complex has not been populated yet. if (query.uniqueResult() == null) { // we have to evict the current concept out of the session because // the user probably had to change the class of this object to get it // to now be a ConceptComplex // (must be done before the "insert into...") sessionFactory.getCurrentSession().clear(); //Just in case this was changed from concept_numeric to complex //We need to add a delete line for each concept sub class that is not concept_complex deleteSubclassConcept("concept_numeric", concept.getConceptId()); // Add an empty row into the concept_complex table String insert = "INSERT INTO concept_complex (concept_id) VALUES (:conceptId)"; query = sessionFactory.getCurrentSession().createSQLQuery(insert); query.setInteger("conceptId", concept.getConceptId()); query.executeUpdate(); } else { // Converting from concept complex: The concept and concept complex rows both exist, so we need to delete the concept_complex row. // no stub insert is needed because either a concept row doesn't exist OR a concept_complex row does exist // concept is changed from complex to something else // hence row should be deleted from the concept_complex if (!concept.isComplex()) { deleteSubclassConcept("concept_complex", concept.getConceptId()); } else { // it is indeed numeric now... don't delete } } } } /** * Deletes a concept from a sub class table * * @param tableName the sub class table name * @param conceptId the concept id */ private void deleteSubclassConcept(String tableName, Integer conceptId) { String delete = "DELETE FROM " + tableName + " WHERE concept_id = :conceptId"; Query query = sessionFactory.getCurrentSession().createSQLQuery(delete); query.setInteger("conceptId", conceptId); query.executeUpdate(); } /** * @see org.openmrs.api.db.ConceptDAO#purgeConcept(org.openmrs.Concept) */ public void purgeConcept(Concept concept) throws DAOException { sessionFactory.getCurrentSession().delete(concept); } /** * @see org.openmrs.api.db.ConceptDAO#getConcept(java.lang.Integer) */ public Concept getConcept(Integer conceptId) throws DAOException { return (Concept) sessionFactory.getCurrentSession().get(Concept.class, conceptId); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptName(java.lang.Integer) */ public ConceptName getConceptName(Integer conceptNameId) throws DAOException { return (ConceptName) sessionFactory.getCurrentSession().get(ConceptName.class, conceptNameId); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptAnswer(java.lang.Integer) */ public ConceptAnswer getConceptAnswer(Integer conceptAnswerId) throws DAOException { return (ConceptAnswer) sessionFactory.getCurrentSession().get(ConceptAnswer.class, conceptAnswerId); } /** * @see org.openmrs.api.db.ConceptDAO#getAllConcepts(java.lang.String, boolean, boolean) */ @SuppressWarnings("unchecked") public List<Concept> getAllConcepts(String sortBy, boolean asc, boolean includeRetired) throws DAOException { boolean isNameField = false; try { Concept.class.getDeclaredField(sortBy); } catch (NoSuchFieldException e) { try { ConceptName.class.getDeclaredField(sortBy); isNameField = true; } catch (NoSuchFieldException e2) { sortBy = "conceptId"; } } String hql = ""; if (isNameField) { hql += "select concept"; } hql += " from Concept as concept"; boolean hasWhereClause = false; if (isNameField) { hasWhereClause = true; //This assumes every concept has a unique(avoid duplicates) fully specified name //which should be true for a clean concept dictionary hql += " left join concept.names as names where names.conceptNameType = 'FULLY_SPECIFIED'"; } if (!includeRetired) { if (hasWhereClause) { hql += " and"; } else { hql += " where"; } hql += " concept.retired = false"; } if (isNameField) { hql += " order by names." + sortBy; } else { hql += " order by concept." + sortBy; } hql += asc ? " asc" : " desc"; Query query = sessionFactory.getCurrentSession().createQuery(hql); return (List<Concept>) query.list(); } /** * @see org.openmrs.api.db.ConceptDAO#saveDrug(org.openmrs.Drug) */ public Drug saveDrug(Drug drug) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(drug); return drug; } /** * @see org.openmrs.api.db.ConceptDAO#getDrug(java.lang.Integer) */ public Drug getDrug(Integer drugId) throws DAOException { return (Drug) sessionFactory.getCurrentSession().get(Drug.class, drugId); } /** * @see org.openmrs.api.db.ConceptDAO#getDrugs(java.lang.String, org.openmrs.Concept, boolean) */ @SuppressWarnings("unchecked") public List<Drug> getDrugs(String drugName, Concept concept, boolean includeRetired) throws DAOException { Criteria searchCriteria = sessionFactory.getCurrentSession().createCriteria(Drug.class, "drug"); if (!includeRetired) { searchCriteria.add(Restrictions.eq("drug.retired", false)); } if (concept != null) { searchCriteria.add(Restrictions.eq("drug.concept", concept)); } if (drugName != null) { SimpleExpression eq = Restrictions.eq("drug.name", drugName); if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) { eq = eq.ignoreCase(); } searchCriteria.add(eq); } return (List<Drug>) searchCriteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getDrugsByIngredient(org.openmrs.Concept) */ @SuppressWarnings("unchecked") public List<Drug> getDrugsByIngredient(Concept ingredient) { Criteria searchDrugCriteria = sessionFactory.getCurrentSession().createCriteria(Drug.class, "drug"); Criterion rhs = Restrictions.eq("drug.concept", ingredient); searchDrugCriteria.createAlias("ingredients", "ingredients"); Criterion lhs = Restrictions.eq("ingredients.ingredient", ingredient); searchDrugCriteria.add(Restrictions.or(lhs, rhs)); return (List<Drug>) searchDrugCriteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getDrugs(java.lang.String) */ @Override public List<Drug> getDrugs(final String phrase) throws DAOException { LuceneQuery<Drug> drugQuery = newDrugQuery(phrase, true, false, Context.getLocale(), false, null, false); if (drugQuery == null) { return Collections.emptyList(); } return drugQuery.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptClass(java.lang.Integer) */ public ConceptClass getConceptClass(Integer i) throws DAOException { return (ConceptClass) sessionFactory.getCurrentSession().get(ConceptClass.class, i); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptClasses(java.lang.String) */ @SuppressWarnings("unchecked") public List<ConceptClass> getConceptClasses(String name) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptClass.class); if (name != null) { crit.add(Restrictions.eq("name", name)); } return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getAllConceptClasses(boolean) */ @SuppressWarnings("unchecked") public List<ConceptClass> getAllConceptClasses(boolean includeRetired) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptClass.class); // Minor bug - was assigning includeRetired instead of evaluating if (!includeRetired) { crit.add(Restrictions.eq("retired", false)); } return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptClass(org.openmrs.ConceptClass) */ public ConceptClass saveConceptClass(ConceptClass cc) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(cc); return cc; } /** * @see org.openmrs.api.db.ConceptDAO#purgeConceptClass(org.openmrs.ConceptClass) */ public void purgeConceptClass(ConceptClass cc) throws DAOException { sessionFactory.getCurrentSession().delete(cc); } /** * @see org.openmrs.api.db.ConceptDAO#deleteConceptNameTag(ConceptNameTag) */ public void deleteConceptNameTag(ConceptNameTag cnt) throws DAOException { sessionFactory.getCurrentSession().delete(cnt); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptDatatype(java.lang.Integer) */ public ConceptDatatype getConceptDatatype(Integer i) { return (ConceptDatatype) sessionFactory.getCurrentSession().get(ConceptDatatype.class, i); } /** * @see org.openmrs.api.db.ConceptDAO#getAllConceptDatatypes(boolean) */ @SuppressWarnings("unchecked") public List<ConceptDatatype> getAllConceptDatatypes(boolean includeRetired) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptDatatype.class); if (!includeRetired) { crit.add(Restrictions.eq("retired", false)); } return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptDatatypes(java.lang.String) */ @SuppressWarnings("unchecked") public List<ConceptDatatype> getConceptDatatypes(String name) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptDatatype.class); if (name != null) { crit.add(Restrictions.like("name", name, MatchMode.START)); } return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptDatatypeByName(String) */ public ConceptDatatype getConceptDatatypeByName(String name) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptDatatype.class); if (name != null) { criteria.add(Restrictions.eq("name", name)); } return (ConceptDatatype) criteria.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptDatatype(org.openmrs.ConceptDatatype) */ public ConceptDatatype saveConceptDatatype(ConceptDatatype cd) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(cd); return cd; } /** * @see org.openmrs.api.db.ConceptDAO#purgeConceptDatatype(org.openmrs.ConceptDatatype) */ public void purgeConceptDatatype(ConceptDatatype cd) throws DAOException { sessionFactory.getCurrentSession().delete(cd); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptNumeric(java.lang.Integer) */ public ConceptNumeric getConceptNumeric(Integer i) { ConceptNumeric cn; Object obj = sessionFactory.getCurrentSession().get(ConceptNumeric.class, i); // If Concept has already been read & cached, we may get back a Concept instead of // ConceptNumeric. If this happens, we need to clear the object from the cache // and re-fetch it as a ConceptNumeric if (obj != null && !obj.getClass().equals(ConceptNumeric.class)) { sessionFactory.getCurrentSession().evict(obj); // remove from cache // session.get() did not work here, we need to perform a query to get a ConceptNumeric Query query = sessionFactory.getCurrentSession() .createQuery("from ConceptNumeric where conceptId = :conceptId").setParameter("conceptId", i); obj = query.uniqueResult(); } cn = (ConceptNumeric) obj; return cn; } /** * @see org.openmrs.api.db.ConceptDAO#getConcepts(java.lang.String, java.util.Locale, boolean, * java.util.List, java.util.List) */ public List<Concept> getConcepts(final String name, final Locale loc, final boolean searchOnPhrase, final List<ConceptClass> classes, final List<ConceptDatatype> datatypes) throws DAOException { final Locale locale; if (loc == null) { locale = Context.getLocale(); } else { locale = loc; } LuceneQuery<ConceptName> conceptNameQuery = newConceptNameLuceneQuery(name, !searchOnPhrase, Arrays.asList(locale), false, false, classes, null, datatypes, null, null); List<ConceptName> names = conceptNameQuery.list(); List<Concept> concepts = transformNamesToConcepts(names); return concepts; } private List<Concept> transformNamesToConcepts(List<ConceptName> names) { List<Concept> concepts = new ArrayList<Concept>(); for (ConceptName name : names) { concepts.add(name.getConcept()); } return concepts; } private String newConceptNameQuery(final String name, final boolean searchKeywords, final Set<Locale> locales, final boolean searchExactLocale) { final String escapedName = LuceneQuery.escapeQuery(name); final List<String> tokenizedName = tokenizeConceptName(escapedName, locales); final StringBuilder query = new StringBuilder(); query.append("(concept.conceptMappings.conceptReferenceTerm.code:(").append(escapedName) .append(")^0.4 OR ("); final StringBuilder nameQuery = newNameQuery(tokenizedName, escapedName, searchKeywords); query.append(nameQuery); query.append(" localePreferred:true)^0.4 OR ("); query.append(nameQuery); query.append(")^0.2)"); List<String> localeQueries = new ArrayList<String>(); for (Locale locale : locales) { if (searchExactLocale) { localeQueries.add(locale.toString()); } else { String localeQuery = locale.getLanguage() + "* "; if (!StringUtils.isBlank(locale.getCountry())) { localeQuery += " OR " + locale + "^2 "; } localeQueries.add(localeQuery); } } query.append(" locale:("); query.append(StringUtils.join(localeQueries, " OR ")); query.append(")"); query.append(" voided:false"); return query.toString(); } private StringBuilder newNameQuery(final List<String> tokenizedName, final String escapedName, final boolean searchKeywords) { final StringBuilder query = new StringBuilder(); query.append("("); if (searchKeywords) { //Put exact phrase higher query.append(" name:(\"" + escapedName + "\")^0.7"); if (!tokenizedName.isEmpty()) { query.append(" OR ("); for (String token : tokenizedName) { query.append(" (name:("); //Include exact query.append(token); query.append(")^0.6 OR name:("); //Include partial query.append(token); query.append("*)^0.3 OR name:("); //Include similar query.append(token); query.append("~0.8)^0.1)"); } query.append(")^0.3"); } } else { query.append(" name:\"" + escapedName + "\""); } query.append(")"); return query; } private List<String> tokenizeConceptName(final String escapedName, final Set<Locale> locales) { List<String> words = new ArrayList<String>(); words.addAll(Arrays.asList(escapedName.trim().split(" "))); Set<String> stopWords = new HashSet<String>(); for (Locale locale : locales) { stopWords.addAll(Context.getConceptService().getConceptStopWords(locale)); } List<String> tokenizedName = new ArrayList<String>(); for (String word : words) { word = word.trim(); if (!word.isEmpty() && !stopWords.contains(word.toUpperCase())) { tokenizedName.add(word); } } return tokenizedName; } /** * gets questions for the given answer concept * * @see org.openmrs.api.db.ConceptDAO#getConceptsByAnswer(org.openmrs.Concept) */ @SuppressWarnings("unchecked") public List<Concept> getConceptsByAnswer(Concept concept) { String q = "select c from Concept c join c.answers ca where ca.answerConcept = :answer"; Query query = sessionFactory.getCurrentSession().createQuery(q); query.setParameter("answer", concept); return query.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getPrevConcept(org.openmrs.Concept) */ @SuppressWarnings("unchecked") public Concept getPrevConcept(Concept c) { Integer i = c.getConceptId(); List<Concept> concepts = sessionFactory.getCurrentSession().createCriteria(Concept.class) .add(Restrictions.lt("conceptId", i)).addOrder(Order.desc("conceptId")).setFetchSize(1).list(); if (concepts.size() < 1) { return null; } return concepts.get(0); } /** * @see org.openmrs.api.db.ConceptDAO#getNextConcept(org.openmrs.Concept) */ @SuppressWarnings("unchecked") public Concept getNextConcept(Concept c) { Integer i = c.getConceptId(); List<Concept> concepts = sessionFactory.getCurrentSession().createCriteria(Concept.class) .add(Restrictions.gt("conceptId", i)).addOrder(Order.asc("conceptId")).setMaxResults(1).list(); if (concepts.size() < 1) { return null; } return concepts.get(0); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptsWithDrugsInFormulary() */ @SuppressWarnings("unchecked") public List<Concept> getConceptsWithDrugsInFormulary() { Query query = sessionFactory.getCurrentSession() .createQuery("select distinct concept from Drug d where d.retired = false"); return query.list(); } /** * @see org.openmrs.api.db.ConceptDAO#purgeDrug(org.openmrs.Drug) */ public void purgeDrug(Drug drug) throws DAOException { sessionFactory.getCurrentSession().delete(drug); } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptProposal(org.openmrs.ConceptProposal) */ public ConceptProposal saveConceptProposal(ConceptProposal cp) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(cp); return cp; } /** * @see org.openmrs.api.db.ConceptDAO#purgeConceptProposal(org.openmrs.ConceptProposal) */ public void purgeConceptProposal(ConceptProposal cp) throws DAOException { sessionFactory.getCurrentSession().delete(cp); return; } /** * @see org.openmrs.api.db.ConceptDAO#getAllConceptProposals(boolean) */ @SuppressWarnings("unchecked") public List<ConceptProposal> getAllConceptProposals(boolean includeCompleted) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptProposal.class); if (!includeCompleted) { crit.add(Restrictions.eq("state", OpenmrsConstants.CONCEPT_PROPOSAL_UNMAPPED)); } crit.addOrder(Order.asc("originalText")); return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptProposal(java.lang.Integer) */ public ConceptProposal getConceptProposal(Integer conceptProposalId) throws DAOException { return (ConceptProposal) sessionFactory.getCurrentSession().get(ConceptProposal.class, conceptProposalId); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptProposals(java.lang.String) */ @SuppressWarnings("unchecked") public List<ConceptProposal> getConceptProposals(String text) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptProposal.class); crit.add(Restrictions.eq("state", OpenmrsConstants.CONCEPT_PROPOSAL_UNMAPPED)); crit.add(Restrictions.eq("originalText", text)); return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getProposedConcepts(java.lang.String) */ @SuppressWarnings("unchecked") public List<Concept> getProposedConcepts(String text) throws DAOException { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptProposal.class); crit.add(Restrictions.ne("state", OpenmrsConstants.CONCEPT_PROPOSAL_UNMAPPED)); crit.add(Restrictions.eq("originalText", text)); crit.add(Restrictions.isNotNull("mappedConcept")); crit.setProjection(Projections.distinct(Projections.property("mappedConcept"))); return crit.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptSetsByConcept(org.openmrs.Concept) */ @SuppressWarnings("unchecked") public List<ConceptSet> getConceptSetsByConcept(Concept concept) { return sessionFactory.getCurrentSession().createCriteria(ConceptSet.class) .add(Restrictions.eq("conceptSet", concept)).addOrder(Order.asc("sortWeight")).list(); } /** * @see org.openmrs.api.db.ConceptDAO#getSetsContainingConcept(org.openmrs.Concept) */ @SuppressWarnings("unchecked") public List<ConceptSet> getSetsContainingConcept(Concept concept) { return sessionFactory.getCurrentSession().createCriteria(ConceptSet.class) .add(Restrictions.eq("concept", concept)).list(); } /** * returns a list of n-generations of parents of a concept in a concept set * * @param Concept current * @return List<Concept> * @throws DAOException */ @SuppressWarnings("unchecked") private List<Concept> getParents(Concept current) throws DAOException { List<Concept> parents = new Vector<Concept>(); if (current != null) { Query query = sessionFactory.getCurrentSession() .createQuery("from Concept c join c.conceptSets sets where sets.concept = ?") .setEntity(0, current); List<Concept> immed_parents = query.list(); for (Concept c : immed_parents) { parents.addAll(getParents(c)); } parents.add(current); if (log.isDebugEnabled()) { log.debug("parents found: "); for (Concept c : parents) { log.debug("id: " + c.getConceptId()); } } } return parents; } /** * @see org.openmrs.api.db.ConceptDAO#getLocalesOfConceptNames() */ public Set<Locale> getLocalesOfConceptNames() { Set<Locale> locales = new HashSet<Locale>(); Query query = sessionFactory.getCurrentSession().createQuery("select distinct locale from ConceptName"); for (Object locale : query.list()) { locales.add((Locale) locale); } return locales; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptNameTag(java.lang.Integer) */ public ConceptNameTag getConceptNameTag(Integer i) { return (ConceptNameTag) sessionFactory.getCurrentSession().get(ConceptNameTag.class, i); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptNameTagByName(java.lang.String) */ public ConceptNameTag getConceptNameTagByName(String name) { Criteria crit = sessionFactory.getCurrentSession().createCriteria(ConceptNameTag.class) .add(Restrictions.eq("tag", name)); if (crit.list().size() < 1) { return null; } return (ConceptNameTag) crit.list().get(0); } /** * @see org.openmrs.api.db.ConceptDAO#getAllConceptNameTags() */ @SuppressWarnings("unchecked") public List<ConceptNameTag> getAllConceptNameTags() { return sessionFactory.getCurrentSession().createQuery("from ConceptNameTag cnt order by cnt.tag").list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptSource(java.lang.Integer) */ public ConceptSource getConceptSource(Integer conceptSourceId) { return (ConceptSource) sessionFactory.getCurrentSession().get(ConceptSource.class, conceptSourceId); } /** * @see org.openmrs.api.db.ConceptDAO#getAllConceptSources(boolean) */ @SuppressWarnings("unchecked") public List<ConceptSource> getAllConceptSources(boolean includeRetired) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptSource.class); if (!includeRetired) { criteria.add(Restrictions.eq("retired", false)); } return criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#deleteConceptSource(org.openmrs.ConceptSource) */ public ConceptSource deleteConceptSource(ConceptSource cs) throws DAOException { sessionFactory.getCurrentSession().delete(cs); return cs; } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptSource(org.openmrs.ConceptSource) */ public ConceptSource saveConceptSource(ConceptSource conceptSource) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(conceptSource); return conceptSource; } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptNameTag(org.openmrs.ConceptNameTag) */ public ConceptNameTag saveConceptNameTag(ConceptNameTag nameTag) { if (nameTag == null) { return null; } sessionFactory.getCurrentSession().saveOrUpdate(nameTag); return nameTag; } /** * @see org.openmrs.api.db.ConceptDAO#getMaxConceptId() */ public Integer getMinConceptId() { Query query = sessionFactory.getCurrentSession().createQuery("select min(conceptId) from Concept"); return (Integer) query.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getMaxConceptId() */ public Integer getMaxConceptId() { Query query = sessionFactory.getCurrentSession().createQuery("select max(conceptId) from Concept"); return (Integer) query.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#conceptIterator() */ public Iterator<Concept> conceptIterator() { return new ConceptIterator(); } /** * An iterator that loops over all concepts in the dictionary one at a time */ private class ConceptIterator implements Iterator<Concept> { Concept currentConcept = null; Concept nextConcept; public ConceptIterator() { final int firstConceptId = getMinConceptId(); nextConcept = getConcept(firstConceptId); } /** * @see java.util.Iterator#hasNext() */ public boolean hasNext() { return (nextConcept != null); } /** * @see java.util.Iterator#next() */ public Concept next() { if (currentConcept != null) { sessionFactory.getCurrentSession().evict(currentConcept); } currentConcept = nextConcept; nextConcept = getNextConcept(currentConcept); return currentConcept; } /** * @see java.util.Iterator#remove() */ public void remove() { throw new UnsupportedOperationException(); } } /** * @see org.openmrs.api.db.ConceptDAO#getConceptsByMapping(String, String, boolean) */ @SuppressWarnings("unchecked") public List<Concept> getConceptsByMapping(String code, String sourceName, boolean includeRetired) { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptMap.class); // make this criteria return a list of concepts criteria.setProjection(Projections.property("concept")); //join to the conceptReferenceTerm table criteria.createAlias("conceptReferenceTerm", "term"); // match the source code to the passed code if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) { criteria.add(Restrictions.eq("term.code", code).ignoreCase()); } else { criteria.add(Restrictions.eq("term.code", code)); } // join to concept reference source and match to the h17Code or source name criteria.createAlias("term.conceptSource", "source"); if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) { criteria.add(Restrictions.or(Restrictions.eq("source.name", sourceName).ignoreCase(), Restrictions.eq("source.hl7Code", sourceName).ignoreCase())); } else { criteria.add(Restrictions.or(Restrictions.eq("source.name", sourceName), Restrictions.eq("source.hl7Code", sourceName))); } criteria.createAlias("concept", "concept"); if (!includeRetired) { // ignore retired concepts criteria.add(Restrictions.eq("concept.retired", false)); } else { // sort retired concepts to the end of the list criteria.addOrder(Order.asc("concept.retired")); } // we only want distinct concepts criteria.setResultTransformer(DistinctRootEntityResultTransformer.INSTANCE); return (List<Concept>) criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptByUuid(java.lang.String) */ public Concept getConceptByUuid(String uuid) { return (Concept) sessionFactory.getCurrentSession().createQuery("from Concept c where c.uuid = :uuid") .setString("uuid", uuid).uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptClassByUuid(java.lang.String) */ public ConceptClass getConceptClassByUuid(String uuid) { return (ConceptClass) sessionFactory.getCurrentSession() .createQuery("from ConceptClass cc where cc.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } public ConceptAnswer getConceptAnswerByUuid(String uuid) { return (ConceptAnswer) sessionFactory.getCurrentSession() .createQuery("from ConceptAnswer cc where cc.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } public ConceptName getConceptNameByUuid(String uuid) { return (ConceptName) sessionFactory.getCurrentSession() .createQuery("from ConceptName cc where cc.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } public ConceptSet getConceptSetByUuid(String uuid) { return (ConceptSet) sessionFactory.getCurrentSession() .createQuery("from ConceptSet cc where cc.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } public ConceptSource getConceptSourceByUuid(String uuid) { return (ConceptSource) sessionFactory.getCurrentSession() .createQuery("from ConceptSource cc where cc.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptDatatypeByUuid(java.lang.String) */ public ConceptDatatype getConceptDatatypeByUuid(String uuid) { return (ConceptDatatype) sessionFactory.getCurrentSession() .createQuery("from ConceptDatatype cd where cd.uuid = :uuid").setString("uuid", uuid) .uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptNumericByUuid(java.lang.String) */ public ConceptNumeric getConceptNumericByUuid(String uuid) { return (ConceptNumeric) sessionFactory.getCurrentSession() .createQuery("from ConceptNumeric cn where cn.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptProposalByUuid(java.lang.String) */ public ConceptProposal getConceptProposalByUuid(String uuid) { return (ConceptProposal) sessionFactory.getCurrentSession() .createQuery("from ConceptProposal cp where cp.uuid = :uuid").setString("uuid", uuid) .uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getDrugByUuid(java.lang.String) */ public Drug getDrugByUuid(String uuid) { return (Drug) sessionFactory.getCurrentSession().createQuery("from Drug d where d.uuid = :uuid") .setString("uuid", uuid).uniqueResult(); } public DrugIngredient getDrugIngredientByUuid(String uuid) { return (DrugIngredient) sessionFactory.getCurrentSession() .createQuery("from DrugIngredient d where d.uuid = :uuid").setString("uuid", uuid).uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptUuids() */ public Map<Integer, String> getConceptUuids() { Map<Integer, String> ret = new HashMap<Integer, String>(); Query q = sessionFactory.getCurrentSession().createQuery("select conceptId, uuid from Concept"); List<Object[]> list = q.list(); for (Object[] o : list) { ret.put((Integer) o[0], (String) o[1]); } return ret; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptDescriptionByUuid(java.lang.String) */ public ConceptDescription getConceptDescriptionByUuid(String uuid) { return (ConceptDescription) sessionFactory.getCurrentSession() .createQuery("from ConceptDescription cd where cd.uuid = :uuid").setString("uuid", uuid) .uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptNameTagByUuid(java.lang.String) */ public ConceptNameTag getConceptNameTagByUuid(String uuid) { return (ConceptNameTag) sessionFactory.getCurrentSession() .createQuery("from ConceptNameTag cnt where cnt.uuid = :uuid").setString("uuid", uuid) .uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptMapsBySource(ConceptSource) */ @SuppressWarnings("unchecked") public List<ConceptMap> getConceptMapsBySource(ConceptSource conceptSource) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptMap.class); criteria.createAlias("conceptReferenceTerm", "term"); criteria.add(Restrictions.eq("term.conceptSource", conceptSource)); return (List<ConceptMap>) criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptSourceByName(java.lang.String) */ public ConceptSource getConceptSourceByName(String conceptSourceName) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptSource.class, "source"); criteria.add(Restrictions.eq("source.name", conceptSourceName)); return (ConceptSource) criteria.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getSavedConceptDatatype(org.openmrs.Concept) */ public ConceptDatatype getSavedConceptDatatype(Concept concept) { SQLQuery sql = sessionFactory.getCurrentSession() .createSQLQuery("select datatype.* from " + "concept_datatype datatype, " + "concept concept " + "where " + "datatype.concept_datatype_id = concept.datatype_id " + "and concept.concept_id=:conceptId") .addEntity(ConceptDatatype.class); sql.setInteger("conceptId", concept.getConceptId()); return (ConceptDatatype) sql.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getSavedConceptName(org.openmrs.ConceptName) */ @Override public ConceptName getSavedConceptName(ConceptName conceptName) { sessionFactory.getCurrentSession().refresh(conceptName); return conceptName; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptStopWords(java.util.Locale) */ public List<String> getConceptStopWords(Locale locale) throws DAOException { locale = (locale == null ? Context.getLocale() : locale); Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptStopWord.class); criteria.setProjection(Projections.property("value")); criteria.add(Restrictions.eq("locale", locale)); return (List<String>) criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptStopWord(org.openmrs.ConceptStopWord) */ public ConceptStopWord saveConceptStopWord(ConceptStopWord conceptStopWord) throws DAOException { if (conceptStopWord != null) { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptStopWord.class); criteria.add(Restrictions.eq("value", conceptStopWord.getValue())); criteria.add(Restrictions.eq("locale", conceptStopWord.getLocale())); List<ConceptStopWord> stopWordList = criteria.list(); if (!stopWordList.isEmpty()) { throw new DAOException("Duplicate ConceptStopWord Entry"); } sessionFactory.getCurrentSession().saveOrUpdate(conceptStopWord); } return conceptStopWord; } /** * @see org.openmrs.api.db.ConceptDAO#deleteConceptStopWord(java.lang.Integer) */ public void deleteConceptStopWord(Integer conceptStopWordId) throws DAOException { if (conceptStopWordId == null) { throw new DAOException("conceptStopWordId is null"); } Object csw = sessionFactory.getCurrentSession().createCriteria(ConceptStopWord.class) .add(Restrictions.eq("conceptStopWordId", conceptStopWordId)).uniqueResult(); if (csw == null) { throw new DAOException("Concept Stop Word not found or already deleted"); } sessionFactory.getCurrentSession().delete(csw); } /** * @see org.openmrs.api.db.ConceptDAO#getAllConceptStopWords() */ public List<ConceptStopWord> getAllConceptStopWords() { return sessionFactory.getCurrentSession().createCriteria(ConceptStopWord.class).list(); } /** * @see ConceptService#getCountOfDrugs(String, Concept, boolean, boolean, boolean) */ public Long getCountOfDrugs(String drugName, Concept concept, boolean searchKeywords, boolean searchDrugConceptNames, boolean includeRetired) throws DAOException { LuceneQuery<Drug> drugsQuery = newDrugQuery(drugName, searchKeywords, searchDrugConceptNames, Context.getLocale(), false, concept, includeRetired); if (drugsQuery == null) { return 0L; } return drugsQuery.resultSize(); } /** * @should return a drug if either the drug name or concept name matches the phase not both * @should return distinct drugs * @should return a drug, if phrase match concept_name No need to match both concept_name and * drug_name * @should return drug when phrase match drug_name even searchDrugConceptNames is false * @should return a drug if phrase match drug_name No need to match both concept_name and * drug_name */ @SuppressWarnings("unchecked") @Override public List<Drug> getDrugs(String drugName, Concept concept, boolean searchKeywords, boolean searchDrugConceptNames, boolean includeRetired, Integer start, Integer length) throws DAOException { LuceneQuery<Drug> drugsQuery = newDrugQuery(drugName, searchKeywords, searchDrugConceptNames, Context.getLocale(), false, concept, includeRetired); if (drugsQuery == null) { return Collections.emptyList(); } return drugsQuery.listPart(start, length).getList(); } private LuceneQuery<Drug> newDrugQuery(String drugName, boolean searchKeywords, boolean searchDrugConceptNames, Locale locale, boolean exactLocale, Concept concept, boolean includeRetired) { if (StringUtils.isBlank(drugName) && concept == null) { return null; } if (locale == null) { locale = Context.getLocale(); } StringBuilder query = new StringBuilder(); if (!StringUtils.isBlank(drugName)) { List<String> tokenizedName = Arrays.asList(drugName.trim().split("\\+")); String escapedName = LuceneQuery.escapeQuery(drugName); query.append("("); query.append(newNameQuery(tokenizedName, escapedName, searchKeywords)); query.append(")^0.3 OR drugReferenceMaps.conceptReferenceTerm.code:(\"").append(escapedName) .append("\")^0.6"); } if (concept != null) { query.append(" OR concept.conceptId:(").append(concept.getConceptId()).append(")^0.1"); } else if (searchDrugConceptNames) { LuceneQuery<ConceptName> conceptNameQuery = newConceptNameLuceneQuery(drugName, searchKeywords, Arrays.asList(locale), exactLocale, includeRetired, null, null, null, null, null); List<Object> conceptIds = conceptNameQuery.listProjection("concept.conceptId"); if (!conceptIds.isEmpty()) { CollectionUtils.transform(conceptIds, new Transformer() { @Override public Object transform(Object input) { return ((Object[]) input)[0].toString(); } }); //The default Lucene clauses limit is 1024. We arbitrarily chose to use 512 here as it does not make sense to return more hits by concept name anyway. int maxSize = (conceptIds.size() < 512) ? conceptIds.size() : 512; query.append(" OR concept.conceptId:(") .append(StringUtils.join(conceptIds.subList(0, maxSize), " OR ")).append(")^0.1"); } } LuceneQuery<Drug> drugsQuery = LuceneQuery.newQuery(Drug.class, sessionFactory.getCurrentSession(), query.toString()); if (!includeRetired) { drugsQuery.include("retired", false); } return drugsQuery; } /** * @see ConceptDAO#getConcepts(String, List, boolean, List, List, List, List, Concept, Integer, * Integer) */ @Override public List<ConceptSearchResult> getConcepts(final String phrase, final List<Locale> locales, final boolean includeRetired, final List<ConceptClass> requireClasses, final List<ConceptClass> excludeClasses, final List<ConceptDatatype> requireDatatypes, final List<ConceptDatatype> excludeDatatypes, final Concept answersToConcept, final Integer start, final Integer size) throws DAOException { LuceneQuery<ConceptName> query = newConceptNameLuceneQuery(phrase, true, locales, false, includeRetired, requireClasses, excludeClasses, requireDatatypes, excludeDatatypes, answersToConcept); ListPart<ConceptName> names = query.listPart(start, size); List<ConceptSearchResult> results = new ArrayList<ConceptSearchResult>(); for (ConceptName name : names.getList()) { results.add(new ConceptSearchResult(phrase, name.getConcept(), name)); } return results; } @Override public Integer getCountOfConcepts(final String phrase, List<Locale> locales, boolean includeRetired, List<ConceptClass> requireClasses, List<ConceptClass> excludeClasses, List<ConceptDatatype> requireDatatypes, List<ConceptDatatype> excludeDatatypes, Concept answersToConcept) throws DAOException { LuceneQuery<ConceptName> query = newConceptNameLuceneQuery(phrase, true, locales, false, includeRetired, requireClasses, excludeClasses, requireDatatypes, excludeDatatypes, answersToConcept); Long size = query.resultSize(); return size.intValue(); } private LuceneQuery<ConceptName> newConceptNameLuceneQuery(final String phrase, boolean searchKeywords, List<Locale> locales, boolean searchExactLocale, boolean includeRetired, List<ConceptClass> requireClasses, List<ConceptClass> excludeClasses, List<ConceptDatatype> requireDatatypes, List<ConceptDatatype> excludeDatatypes, Concept answersToConcept) { final StringBuilder query = new StringBuilder(); if (!StringUtils.isBlank(phrase)) { final Set<Locale> searchLocales; if (locales == null) { searchLocales = new HashSet<Locale>(Arrays.asList(Context.getLocale())); } else { searchLocales = new HashSet<Locale>(locales); } query.append(newConceptNameQuery(phrase, searchKeywords, searchLocales, searchExactLocale)); } LuceneQuery<ConceptName> luceneQuery = LuceneQuery .newQuery(ConceptName.class, sessionFactory.getCurrentSession(), query.toString()) .include("concept.conceptClass.conceptClassId", transformToIds(requireClasses)) .exclude("concept.conceptClass.conceptClassId", transformToIds(excludeClasses)) .include("concept.datatype.conceptDatatypeId", transformToIds(requireDatatypes)) .exclude("concept.datatype.conceptDatatypeId", transformToIds(excludeDatatypes)); if (answersToConcept != null) { Collection<ConceptAnswer> answers = answersToConcept.getAnswers(false); if (answers != null && !answers.isEmpty()) { List<Integer> ids = new ArrayList<Integer>(); for (ConceptAnswer conceptAnswer : answersToConcept.getAnswers(false)) { ids.add(conceptAnswer.getAnswerConcept().getId()); } luceneQuery.include("concept.conceptId", ids.toArray(new Object[0])); } } if (!includeRetired) { luceneQuery.include("concept.retired", false); } luceneQuery.skipSame("concept.conceptId"); return luceneQuery; } private String[] transformToIds(final List<? extends OpenmrsObject> items) { if (items == null || items.isEmpty()) { return new String[0]; } String[] ids = new String[items.size()]; for (int i = 0; i < items.size(); i++) { ids[i] = items.get(i).getId().toString(); } return ids; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptMapTypes(boolean, boolean) */ @SuppressWarnings("unchecked") @Override public List<ConceptMapType> getConceptMapTypes(boolean includeRetired, boolean includeHidden) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptMapType.class); if (!includeRetired) { criteria.add(Restrictions.eq("retired", false)); } if (!includeHidden) { criteria.add(Restrictions.eq("isHidden", false)); } List<ConceptMapType> conceptMapTypes = criteria.list(); Collections.sort(conceptMapTypes, new ConceptMapTypeComparator()); return conceptMapTypes; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptMapType(java.lang.Integer) */ @Override public ConceptMapType getConceptMapType(Integer conceptMapTypeId) throws DAOException { return (ConceptMapType) sessionFactory.getCurrentSession().get(ConceptMapType.class, conceptMapTypeId); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptMapTypeByUuid(java.lang.String) */ @Override public ConceptMapType getConceptMapTypeByUuid(String uuid) throws DAOException { return (ConceptMapType) sessionFactory.getCurrentSession() .createQuery("from ConceptMapType cmt where cmt.uuid = :uuid").setString("uuid", uuid) .uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptMapTypeByName(java.lang.String) */ @Override public ConceptMapType getConceptMapTypeByName(String name) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptMapType.class); criteria.add(Restrictions.ilike("name", name, MatchMode.EXACT)); return (ConceptMapType) criteria.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptMapType(org.openmrs.ConceptMapType) */ @Override public ConceptMapType saveConceptMapType(ConceptMapType conceptMapType) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(conceptMapType); return conceptMapType; } /** * @see org.openmrs.api.db.ConceptDAO#deleteConceptMapType(org.openmrs.ConceptMapType) */ @Override public void deleteConceptMapType(ConceptMapType conceptMapType) throws DAOException { sessionFactory.getCurrentSession().delete(conceptMapType); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTerms(boolean) */ @SuppressWarnings("unchecked") @Override public List<ConceptReferenceTerm> getConceptReferenceTerms(boolean includeRetired) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTerm.class); if (!includeRetired) { criteria.add(Restrictions.eq("retired", false)); } return criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTerm(java.lang.Integer) */ @Override public ConceptReferenceTerm getConceptReferenceTerm(Integer conceptReferenceTermId) throws DAOException { return (ConceptReferenceTerm) sessionFactory.getCurrentSession().get(ConceptReferenceTerm.class, conceptReferenceTermId); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTermByUuid(java.lang.String) */ @Override public ConceptReferenceTerm getConceptReferenceTermByUuid(String uuid) throws DAOException { return (ConceptReferenceTerm) sessionFactory.getCurrentSession() .createQuery("from ConceptReferenceTerm crt where crt.uuid = :uuid").setString("uuid", uuid) .uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTermsBySource(ConceptSource) */ @SuppressWarnings("unchecked") @Override public List<ConceptReferenceTerm> getConceptReferenceTermsBySource(ConceptSource conceptSource) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTerm.class); criteria.add(Restrictions.eq("conceptSource", conceptSource)); return (List<ConceptReferenceTerm>) criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTermByName(java.lang.String, * org.openmrs.ConceptSource) */ @SuppressWarnings("rawtypes") @Override public ConceptReferenceTerm getConceptReferenceTermByName(String name, ConceptSource conceptSource) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTerm.class); criteria.add(Restrictions.ilike("name", name, MatchMode.EXACT)); criteria.add(Restrictions.eq("conceptSource", conceptSource)); List terms = criteria.list(); if (terms.size() == 0) { return null; } else if (terms.size() > 1) { throw new APIException("ConceptReferenceTerm.foundMultipleTermsWithNameInSource", new Object[] { name, conceptSource.getName() }); } return (ConceptReferenceTerm) terms.get(0); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTermByCode(java.lang.String, * org.openmrs.ConceptSource) */ @SuppressWarnings("rawtypes") @Override public ConceptReferenceTerm getConceptReferenceTermByCode(String code, ConceptSource conceptSource) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTerm.class); criteria.add(Restrictions.eq("code", code)); criteria.add(Restrictions.eq("conceptSource", conceptSource)); List terms = criteria.list(); if (terms.size() == 0) { return null; } else if (terms.size() > 1) { throw new APIException("ConceptReferenceTerm.foundMultipleTermsWithCodeInSource", new Object[] { code, conceptSource.getName() }); } return (ConceptReferenceTerm) terms.get(0); } /** * @see org.openmrs.api.db.ConceptDAO#saveConceptReferenceTerm(org.openmrs.ConceptReferenceTerm) */ @Override public ConceptReferenceTerm saveConceptReferenceTerm(ConceptReferenceTerm conceptReferenceTerm) throws DAOException { sessionFactory.getCurrentSession().saveOrUpdate(conceptReferenceTerm); return conceptReferenceTerm; } /** * @see org.openmrs.api.db.ConceptDAO#deleteConceptReferenceTerm(org.openmrs.ConceptReferenceTerm) */ @Override public void deleteConceptReferenceTerm(ConceptReferenceTerm conceptReferenceTerm) throws DAOException { sessionFactory.getCurrentSession().delete(conceptReferenceTerm); } /** * @see org.openmrs.api.db.ConceptDAO#getCountOfConceptReferenceTerms(String, ConceptSource, boolean) */ @Override public Long getCountOfConceptReferenceTerms(String query, ConceptSource conceptSource, boolean includeRetired) throws DAOException { Criteria criteria = createConceptReferenceTermCriteria(query, conceptSource, includeRetired); criteria.setProjection(Projections.rowCount()); return (Long) criteria.uniqueResult(); } /** * @see org.openmrs.api.db.ConceptDAO#getConceptReferenceTerms(String, ConceptSource, Integer, * Integer, boolean) */ @SuppressWarnings("unchecked") @Override public List<ConceptReferenceTerm> getConceptReferenceTerms(String query, ConceptSource conceptSource, Integer start, Integer length, boolean includeRetired) throws APIException { Criteria criteria = createConceptReferenceTermCriteria(query, conceptSource, includeRetired); if (start != null) { criteria.setFirstResult(start); } if (length != null && length > 0) { criteria.setMaxResults(length); } return criteria.list(); } /** * @param query * @param includeRetired * @return */ private Criteria createConceptReferenceTermCriteria(String query, ConceptSource conceptSource, boolean includeRetired) { Criteria searchCriteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTerm.class); if (conceptSource != null) { searchCriteria.add(Restrictions.eq("conceptSource", conceptSource)); } if (!includeRetired) { searchCriteria.add(Restrictions.eq("retired", false)); } if (query != null) { searchCriteria.add(Restrictions.or(Restrictions.ilike("name", query, MatchMode.ANYWHERE), Restrictions.ilike("code", query, MatchMode.ANYWHERE))); } return searchCriteria; } /** * @see org.openmrs.api.db.ConceptDAO#getReferenceTermMappingsTo(ConceptReferenceTerm) */ @SuppressWarnings("unchecked") @Override public List<ConceptReferenceTermMap> getReferenceTermMappingsTo(ConceptReferenceTerm term) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTermMap.class); criteria.add(Restrictions.eq("termB", term)); return criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#isConceptReferenceTermInUse(org.openmrs.ConceptReferenceTerm) */ @Override public boolean isConceptReferenceTermInUse(ConceptReferenceTerm term) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptMap.class); criteria.add(Restrictions.eq("conceptReferenceTerm", term)); criteria.setProjection(Projections.rowCount()); if ((Long) criteria.uniqueResult() > 0) { return true; } criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTermMap.class); criteria.add(Restrictions.eq("termB", term)); criteria.setProjection(Projections.rowCount()); return (Long) criteria.uniqueResult() > 0; } /** * @see org.openmrs.api.db.ConceptDAO#isConceptMapTypeInUse(org.openmrs.ConceptMapType) */ @Override public boolean isConceptMapTypeInUse(ConceptMapType mapType) throws DAOException { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptMap.class); criteria.add(Restrictions.eq("conceptMapType", mapType)); criteria.setProjection(Projections.rowCount()); if ((Long) criteria.uniqueResult() > 0) { return true; } criteria = sessionFactory.getCurrentSession().createCriteria(ConceptReferenceTermMap.class); criteria.add(Restrictions.eq("conceptMapType", mapType)); criteria.setProjection(Projections.rowCount()); return (Long) criteria.uniqueResult() > 0; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptsByName(java.lang.String, java.util.Locale, * java.lang.Boolean) */ @Override public List<Concept> getConceptsByName(final String name, final Locale locale, final Boolean exactLocale) { List<Locale> locales = new ArrayList<Locale>(); if (locale == null) { locales.add(Context.getLocale()); } else { locales.add(locale); } boolean searchExactLocale = (exactLocale == null) ? false : exactLocale; LuceneQuery<ConceptName> conceptNameQuery = newConceptNameLuceneQuery(name, true, locales, searchExactLocale, false, null, null, null, null, null); List<ConceptName> names = conceptNameQuery.list(); final List<Concept> concepts = transformNamesToConcepts(names); return concepts; } /** * @see org.openmrs.api.db.ConceptDAO#getConceptByName(java.lang.String) */ @Override public Concept getConceptByName(final String name) { Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptName.class); Locale locale = Context.getLocale(); Locale language = new Locale(locale.getLanguage() + "%"); criteria.add(Restrictions.or(Restrictions.eq("locale", locale), Restrictions.like("locale", language))); if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) { criteria.add(Restrictions.ilike("name", name)); } else { criteria.add(Restrictions.eq("name", name)); } criteria.add(Restrictions.eq("voided", false)); criteria.createAlias("concept", "concept"); criteria.add(Restrictions.eq("concept.retired", false)); @SuppressWarnings("unchecked") List<ConceptName> list = criteria.list(); if (list.size() == 1) { return list.get(0).getConcept(); } else { log.warn("Multiple concepts found for '" + name + "'"); List<Concept> concepts = transformNamesToConcepts(list); for (Concept concept : concepts) { for (ConceptName conceptName : concept.getNames(locale)) { if (conceptName.getName().equalsIgnoreCase(name)) { return concept; } } for (ConceptName indexTerm : concept.getIndexTermsForLocale(locale)) { if (indexTerm.getName().equalsIgnoreCase(name)) { return concept; } } } } return null; } /** * @see org.openmrs.api.db.ConceptDAO#getDefaultConceptMapType() */ @Override public ConceptMapType getDefaultConceptMapType() throws DAOException { FlushMode previousFlushMode = sessionFactory.getCurrentSession().getFlushMode(); sessionFactory.getCurrentSession().setFlushMode(FlushMode.MANUAL); try { //Defaults to same-as if the gp is not set. String defaultConceptMapType = Context.getAdministrationService() .getGlobalProperty(OpenmrsConstants.GP_DEFAULT_CONCEPT_MAP_TYPE); if (defaultConceptMapType == null) { throw new DAOException("The default concept map type is not set. You need to set the '" + OpenmrsConstants.GP_DEFAULT_CONCEPT_MAP_TYPE + "' global property."); } ConceptMapType conceptMapType = getConceptMapTypeByName(defaultConceptMapType); if (conceptMapType == null) { throw new DAOException("The default concept map type (name: " + defaultConceptMapType + ") does not exist! You need to set the '" + OpenmrsConstants.GP_DEFAULT_CONCEPT_MAP_TYPE + "' global property."); } return conceptMapType; } finally { sessionFactory.getCurrentSession().setFlushMode(previousFlushMode); } } /** * @see org.openmrs.api.db.ConceptDAO#isConceptNameDuplicate(org.openmrs.ConceptName) */ @Override public boolean isConceptNameDuplicate(ConceptName name) { if (name.isVoided()) { return false; } if (name.getConcept() != null) { if (name.getConcept().isRetired()) { return false; } //If it is not a default name for a concept if (!name.getConcept().getName(name.getLocale()).equals(name)) { return false; } } Criteria criteria = sessionFactory.getCurrentSession().createCriteria(ConceptName.class); criteria.add(Restrictions.eq("voided", false)); criteria.add(Restrictions.or(Restrictions.eq("locale", name.getLocale()), Restrictions.eq("locale", new Locale(name.getLocale().getLanguage())))); if (Context.getAdministrationService().isDatabaseStringComparisonCaseSensitive()) { criteria.add(Restrictions.eq("name", name.getName()).ignoreCase()); } else { criteria.add(Restrictions.eq("name", name.getName())); } List<ConceptName> candidateNames = criteria.list(); for (ConceptName candidateName : candidateNames) { if (candidateName.getConcept().isRetired()) { continue; } if (candidateName.getConcept().equals(name.getConcept())) { continue; } //If it is a default name for a concept if (candidateName.getConcept().getName(candidateName.getLocale()).equals(candidateName)) { return true; } } return false; } /** * @see ConceptDAO#getDrugs(String, java.util.Locale, boolean, boolean) */ @Override public List<Drug> getDrugs(String searchPhrase, Locale locale, boolean exactLocale, boolean includeRetired) { LuceneQuery<Drug> drugQuery = newDrugQuery(searchPhrase, true, true, locale, exactLocale, null, includeRetired); return drugQuery.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getDrugsByMapping(String, ConceptSource, Collection, * boolean) */ @Override public List<Drug> getDrugsByMapping(String code, ConceptSource conceptSource, Collection<ConceptMapType> withAnyOfTheseTypes, boolean includeRetired) throws DAOException { Criteria criteria = createSearchDrugByMappingCriteria(code, conceptSource, includeRetired); // match with any of the supplied collection of conceptMapTypes if (withAnyOfTheseTypes.size() > 0) { criteria.add(Restrictions.in("map.conceptMapType", withAnyOfTheseTypes)); } //check whether retired on not retired drugs return (List<Drug>) criteria.list(); } /** * @see org.openmrs.api.db.ConceptDAO#getDrugs */ @Override public Drug getDrugByMapping(String code, ConceptSource conceptSource, Collection<ConceptMapType> withAnyOfTheseTypesOrOrderOfPreference) throws DAOException { Criteria criteria = createSearchDrugByMappingCriteria(code, conceptSource, true); // match with any of the supplied collection or order of preference of conceptMapTypes if (withAnyOfTheseTypesOrOrderOfPreference.size() > 0) { for (ConceptMapType conceptMapType : withAnyOfTheseTypesOrOrderOfPreference) { criteria.add(Restrictions.eq("map.conceptMapType", conceptMapType)); List<Drug> drugs = criteria.list(); if (drugs.size() > 1) { throw new DAOException("There are multiple matches for the highest-priority ConceptMapType"); } else if (drugs.size() == 1) { return drugs.get(0); } //reset for the next execution to avoid unwanted AND clauses on every found map type criteria = createSearchDrugByMappingCriteria(code, conceptSource, true); } } else { List<Drug> drugs = criteria.list(); if (drugs.size() > 1) { throw new DAOException("There are multiple matches for the highest-priority ConceptMapType"); } else if (drugs.size() == 1) { return drugs.get(0); } } return null; } private Criteria createSearchDrugByMappingCriteria(String code, ConceptSource conceptSource, boolean includeRetired) { Criteria searchCriteria = sessionFactory.getCurrentSession().createCriteria(Drug.class, "drug"); searchCriteria.setResultTransformer(DistinctRootEntityResultTransformer.INSTANCE); //join to the drugReferenceMap table searchCriteria.createAlias("drug.drugReferenceMaps", "map"); if (code != null || conceptSource != null) { // join to the conceptReferenceTerm table searchCriteria.createAlias("map.conceptReferenceTerm", "term"); } // match the source code to the passed code if (code != null) { searchCriteria.add(Restrictions.eq("term.code", code)); } // match the conceptSource to the passed in concept source, null accepted if (conceptSource != null) { searchCriteria.add(Restrictions.eq("term.conceptSource", conceptSource)); } //check whether retired or not retired drugs if (!includeRetired) { searchCriteria.add(Restrictions.eq("drug.retired", false)); } return searchCriteria; } }