4884

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Build # 4884

Build Type

push

travis-ci

Committed by

dkayiwa

Commit Message

<a href="https://github.com/openmrs/openmrs-core/commit/<a class=hub.com/openmrs/openmrs-core/commit/df4621c1928148d6a3c417c9fdee4004904fb63e">df4621c19<a href="https://github.com/openmrs/openmrs-core/commit/df4621c1928148d6a3c417c9fdee4004904fb63e">&quot;&gt;Deal with active lists which have no reactions - TRUNK-5076
(cherry picked from commit </a><a class="double-link" href="https://github.com/openmrs/openmrs-core/commit/<a class="double-link" href="https://github.com/openmrs/openmrs-core/commit/4bb1770f9fcff34c916ae9a77514c582d8bcbd7c">4bb1770f9</a>">4bb1770f9</a><a href="https://github.com/openmrs/openmrs-core/commit/df4621c1928148d6a3c417c9fdee4004904fb63e">)

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2.74

/api/src/main/java/org/openmrs/util/databasechange/MigrateAllergiesChangeSet.java

/**
 * 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.util.databasechange;

import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.Statement;
import java.util.UUID;

import org.openmrs.AllergySeverity;

import liquibase.change.custom.CustomTaskChange;
import liquibase.database.Database;
import liquibase.database.jvm.JdbcConnection;
import liquibase.exception.CustomChangeException;
import liquibase.exception.SetupException;
import liquibase.exception.ValidationErrors;
import liquibase.resource.ResourceAccessor;

/**
 * Moves un voided allergies from the old active_list and active_list_allergy tables to the new
 * allergy and allergy_recation tables
 */
public class MigrateAllergiesChangeSet implements CustomTaskChange {
        
        private Integer mildConcept;
        private Integer moderateConcept;
        private Integer severeConcept;
        
        @Override
        public String getConfirmationMessage() {
                return "Successfully moved un voided allergies from old to new tables";
        }
        
        @Override
        public void setUp() throws SetupException {
                
        }
        
        @Override
        public void setFileOpener(ResourceAccessor resourceAccessor) {
                
        }
        
        @Override
        public ValidationErrors validate(Database database) {
                return null;
        }
        
        @Override
        public void execute(Database database) throws CustomChangeException {
                try {
                        loadSeverityConcepts(database);
                        
                        JdbcConnection connection = (JdbcConnection) database.getConnection();
                        
                        String sql = "select active_list_type_id from active_list_type where name = 'Allergy'";
                        Statement selectStatement = connection.createStatement();
                        ResultSet rs = selectStatement.executeQuery(sql);
                        if (!rs.next()) {
                                throw new CustomChangeException("Failed to find row with name 'Allergy' in the active_list_type");
                        }
                        int allergyTypeId = rs.getInt(1);
                        
                        sql = "insert into allergy (patient_id, coded_allergen, severity_concept_id, creator, date_created, uuid, comment, allergen_type) " +
                                        "values(?,?,?,?,?,?,?,?)";
                        PreparedStatement allergyInsertStatement = connection.prepareStatement(sql);
                        
                        sql = "insert into allergy_reaction (allergy_id, reaction_concept_id, uuid) " +
                                        "values (?,?,?)";
                        PreparedStatement reactionInsertStatement = connection.prepareStatement(sql);
                        
                        sql = "select allergy_id from allergy where uuid = ?";
                        PreparedStatement allergySelectStatement = connection.prepareStatement(sql);
                        
                        sql = "select person_id, concept_id, comments, creator, date_created, uuid, reaction_concept_id, severity, allergy_type "
                                + "from active_list al inner join active_list_allergy ala on al.active_list_id=ala.active_list_id "
                                + "where voided = 0 and active_list_type_id = " + allergyTypeId;
                        
                        selectStatement = connection.createStatement();
                        rs = selectStatement.executeQuery(sql);
                        while (rs.next()) {
                                String uuid = rs.getString("uuid");        
                                
                                //insert allergy
                                allergyInsertStatement.setInt(1, rs.getInt("person_id"));
                                allergyInsertStatement.setInt(2, rs.getInt("concept_id"));
                                
                                Integer severityConcept = null;
                                String severity = rs.getString("severity");
                                if (AllergySeverity.MILD.name().equals(severity)) {
                                        severityConcept = mildConcept;
                                }
                                else if (AllergySeverity.MODERATE.name().equals(severity)) {
                                        severityConcept = moderateConcept;
                                }
                                else if (AllergySeverity.SEVERE.name().equals(severity)) {
                                        severityConcept = severeConcept;
                                }
                                //TODO what do we do with the other severities?
                                
                                if (severityConcept != null) {
                                        allergyInsertStatement.setInt(3, severityConcept);
                                }
                                
                                allergyInsertStatement.setInt(4, rs.getInt("creator"));
                                allergyInsertStatement.setDate(5, rs.getDate("date_created"));
                                allergyInsertStatement.setString(6, uuid);
                                allergyInsertStatement.setString(7, rs.getString("comments"));
                                
                                String allergyType = rs.getString("allergy_type");
                                if (allergyType == null) {
                                        allergyType = "DRUG";
                                }
                                else if ("ENVIRONMENTAL".equals(allergyType)) {
                                        allergyType = "ENVIRONMENT";
                                }
                                
                                allergyInsertStatement.setString(8, allergyType);
                                
                                allergyInsertStatement.execute();
                                
                                //get inserted allergy_id
                                allergySelectStatement.setString(1, uuid);
                                ResultSet rs2 = allergySelectStatement.executeQuery();
                                rs2.next();
                                
                                //insert reaction
                                reactionInsertStatement.setInt(1, rs2.getInt(1));
                                reactionInsertStatement.setInt(2, rs.getInt("reaction_concept_id"));
                                reactionInsertStatement.setString(3, UUID.randomUUID().toString());
                                
                                //some active lists do not have reactions recorded
                                if (!rs.wasNull()) {
                                        reactionInsertStatement.execute();
                                }
                        }
                }
                catch (Exception ex) {
                        throw new CustomChangeException(ex);
                }
        }
        
        private void loadSeverityConcepts(Database database) throws Exception {
                mildConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.mild");
                moderateConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.moderate");
                severeConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.severe");
        }
        
        private Integer getConceptByGlobalProperty(Database database, String globalPropertyName) throws Exception {
                JdbcConnection connection = (JdbcConnection) database.getConnection();
                Statement stmt = connection.createStatement();
                ResultSet rs = stmt.executeQuery("SELECT property_value FROM global_property WHERE property = '" + globalPropertyName + "'");
                if (rs.next()) {
                        String uuid = rs.getString("property_value");
                        
                        rs = stmt.executeQuery("SELECT concept_id FROM concept WHERE uuid = '" + uuid + "'");
                        if (rs.next()) {
                                return rs.getInt("concept_id");
                        }
                }
                
                throw new IllegalStateException("Configuration required: " + globalPropertyName);
        }
}

1	/**
2	* This Source Code Form is subject to the terms of the Mozilla Public License,
3	* v. 2.0. If a copy of the MPL was not distributed with this file, You can
4	* obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
5	* the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
6	*
7	* Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
8	* graphic logo is a trademark of OpenMRS Inc.
9	*/
10	package org.openmrs.util.databasechange;
11
12	import java.sql.PreparedStatement;
13	import java.sql.ResultSet;
14	import java.sql.Statement;
15	import java.util.UUID;
16
17	import org.openmrs.AllergySeverity;
18
19	import liquibase.change.custom.CustomTaskChange;
20	import liquibase.database.Database;
21	import liquibase.database.jvm.JdbcConnection;
22	import liquibase.exception.CustomChangeException;
23	import liquibase.exception.SetupException;
24	import liquibase.exception.ValidationErrors;
25	import liquibase.resource.ResourceAccessor;
26
27	/**
28	* Moves un voided allergies from the old active_list and active_list_allergy tables to the new
29	* allergy and allergy_recation tables
30	*/
31	public class MigrateAllergiesChangeSet implements CustomTaskChange {	1✔
32
33	private Integer mildConcept;
34	private Integer moderateConcept;
35	private Integer severeConcept;
36
37	@Override
38	public String getConfirmationMessage() {
39	return "Successfully moved un voided allergies from old to new tables";	×
40	}
41
42	@Override
43	public void setUp() throws SetupException {
44
45	}	×
46
47	@Override
48	public void setFileOpener(ResourceAccessor resourceAccessor) {
49
50	}	×
51
52	@Override
53	public ValidationErrors validate(Database database) {
54	return null;	1✔
55	}
56
57	@Override
58	public void execute(Database database) throws CustomChangeException {
59	try {
60	loadSeverityConcepts(database);	×
61
62	JdbcConnection connection = (JdbcConnection) database.getConnection();	×
63
64	String sql = "select active_list_type_id from active_list_type where name = 'Allergy'";	×
65	Statement selectStatement = connection.createStatement();	×
66	ResultSet rs = selectStatement.executeQuery(sql);	×
67	if (!rs.next()) {	×
68	throw new CustomChangeException("Failed to find row with name 'Allergy' in the active_list_type");	×
69	}
70	int allergyTypeId = rs.getInt(1);	×
71
72	sql = "insert into allergy (patient_id, coded_allergen, severity_concept_id, creator, date_created, uuid, comment, allergen_type) " +	×
73	"values(?,?,?,?,?,?,?,?)";
74	PreparedStatement allergyInsertStatement = connection.prepareStatement(sql);	×
75
76	sql = "insert into allergy_reaction (allergy_id, reaction_concept_id, uuid) " +	×
77	"values (?,?,?)";
78	PreparedStatement reactionInsertStatement = connection.prepareStatement(sql);	×
79
80	sql = "select allergy_id from allergy where uuid = ?";	×
81	PreparedStatement allergySelectStatement = connection.prepareStatement(sql);	×
82
83	sql = "select person_id, concept_id, comments, creator, date_created, uuid, reaction_concept_id, severity, allergy_type "	×
84	+ "from active_list al inner join active_list_allergy ala on al.active_list_id=ala.active_list_id "
85	+ "where voided = 0 and active_list_type_id = " + allergyTypeId;
86
87	selectStatement = connection.createStatement();	×
88	rs = selectStatement.executeQuery(sql);	×
89	while (rs.next()) {	×
90	String uuid = rs.getString("uuid");	×
91
92	//insert allergy
93	allergyInsertStatement.setInt(1, rs.getInt("person_id"));	×
94	allergyInsertStatement.setInt(2, rs.getInt("concept_id"));	×
95
96	Integer severityConcept = null;	×
97	String severity = rs.getString("severity");	×
98	if (AllergySeverity.MILD.name().equals(severity)) {	×
99	severityConcept = mildConcept;	×
100	}
101	else if (AllergySeverity.MODERATE.name().equals(severity)) {	×
102	severityConcept = moderateConcept;	×
103	}
104	else if (AllergySeverity.SEVERE.name().equals(severity)) {	×
105	severityConcept = severeConcept;	×
106	}
107	//TODO what do we do with the other severities?
108
109	if (severityConcept != null) {	×
110	allergyInsertStatement.setInt(3, severityConcept);	×
111	}
112
113	allergyInsertStatement.setInt(4, rs.getInt("creator"));	×
114	allergyInsertStatement.setDate(5, rs.getDate("date_created"));	×
115	allergyInsertStatement.setString(6, uuid);	×
116	allergyInsertStatement.setString(7, rs.getString("comments"));	×
117
118	String allergyType = rs.getString("allergy_type");	×
119	if (allergyType == null) {	×
120	allergyType = "DRUG";	×
121	}
122	else if ("ENVIRONMENTAL".equals(allergyType)) {	×
123	allergyType = "ENVIRONMENT";	×
124	}
125
126	allergyInsertStatement.setString(8, allergyType);	×
127
128	allergyInsertStatement.execute();	×
129
130	//get inserted allergy_id
131	allergySelectStatement.setString(1, uuid);	×
132	ResultSet rs2 = allergySelectStatement.executeQuery();	×
133	rs2.next();	×
134
135	//insert reaction
136	reactionInsertStatement.setInt(1, rs2.getInt(1));	×
137	reactionInsertStatement.setInt(2, rs.getInt("reaction_concept_id"));	×
138	reactionInsertStatement.setString(3, UUID.randomUUID().toString());	×
139
140	//some active lists do not have reactions recorded
141	if (!rs.wasNull()) {	×
142	reactionInsertStatement.execute();	×
143	}
144	}	×
145	}
146	catch (Exception ex) {	×
147	throw new CustomChangeException(ex);	×
148	}	×
149	}	×
150
151	private void loadSeverityConcepts(Database database) throws Exception {
152	mildConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.mild");	×
153	moderateConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.moderate");	×
154	severeConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.severe");	×
155	}	×
156
157	private Integer getConceptByGlobalProperty(Database database, String globalPropertyName) throws Exception {
158	JdbcConnection connection = (JdbcConnection) database.getConnection();	×
159	Statement stmt = connection.createStatement();	×
160	ResultSet rs = stmt.executeQuery("SELECT property_value FROM global_property WHERE property = '" + globalPropertyName + "'");	×
161	if (rs.next()) {	×
162	String uuid = rs.getString("property_value");	×
163
164	rs = stmt.executeQuery("SELECT concept_id FROM concept WHERE uuid = '" + uuid + "'");	×
165	if (rs.next()) {	×
166	return rs.getInt("concept_id");	×
167	}
168	}
169
170	throw new IllegalStateException("Configuration required: " + globalPropertyName);	×
171	}
172	}

openmrs / openmrs-core / 4884

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