21763664900

Committed 06 Feb 2026 07:45PM UTC coverage: 63.49% (+0.1%) from 63.392%

Build # 21763664900

Build Type

push

github

Committed by

ibacher

Commit Message

TRUNK-6536: Replace string concatenation with query building (#5753)

Run Details

39 of 95 new or added lines in 5 files covered. (41.05%)

4 existing lines in 2 files now uncovered.

23156 of 36472 relevant lines covered (63.49%)

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1.35

/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.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();

                        int allergyTypeId;
                        try (PreparedStatement typeStmt = connection.prepareStatement(
                                        "select active_list_type_id from active_list_type where name = ?")) {
                                typeStmt.setString(1, "Allergy");
                                try (ResultSet rs = typeStmt.executeQuery()) {
                                        if (!rs.next()) {
                                                throw new CustomChangeException("Failed to find row with name 'Allergy' in the active_list_type");
                                        }
                                        allergyTypeId = rs.getInt(1);
                                }
                        }

                        try (PreparedStatement allergyInsertStatement = connection.prepareStatement(
                                        "insert into allergy (patient_id, coded_allergen, severity_concept_id, creator, date_created, uuid, comment, allergen_type) "
                                                + "values(?,?,?,?,?,?,?,?)");
                                PreparedStatement reactionInsertStatement = connection.prepareStatement(
                                        "insert into allergy_reaction (allergy_id, reaction_concept_id, uuid) "
                                                + "values (?,?,?)");
                                PreparedStatement allergySelectStatement = connection.prepareStatement(
                                        "select allergy_id from allergy where uuid = ?");
                                PreparedStatement activeListStmt = connection.prepareStatement(
                                        "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 = ?")) {

                                activeListStmt.setInt(1, allergyTypeId);
                                try (ResultSet rs = activeListStmt.executeQuery()) {
                                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);
                                        } else {
                                                allergyInsertStatement.setNull(3, java.sql.Types.INTEGER);
                                        }

                                        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);
                                        try (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();
                try (PreparedStatement gpStmt = connection.prepareStatement(
                                "SELECT property_value FROM global_property WHERE property = ?")) {
                        gpStmt.setString(1, globalPropertyName);
                        try (ResultSet rs = gpStmt.executeQuery()) {
                                if (rs.next()) {
                                        String uuid = rs.getString("property_value");

                                        try (PreparedStatement conceptStmt = connection.prepareStatement(
                                                        "SELECT concept_id FROM concept WHERE uuid = ?")) {
                                                conceptStmt.setString(1, uuid);
                                                try (ResultSet conceptRs = conceptStmt.executeQuery()) {
                                                        if (conceptRs.next()) {
                                                                return conceptRs.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.util.UUID;
15
16	import org.openmrs.AllergySeverity;
17
18	import liquibase.change.custom.CustomTaskChange;
19	import liquibase.database.Database;
20	import liquibase.database.jvm.JdbcConnection;
21	import liquibase.exception.CustomChangeException;
22	import liquibase.exception.SetupException;
23	import liquibase.exception.ValidationErrors;
24	import liquibase.resource.ResourceAccessor;
25
26	/**
27	* Moves un voided allergies from the old active_list and active_list_allergy tables to the new
28	* allergy and allergy_recation tables
29	*/
30	public class MigrateAllergiesChangeSet implements CustomTaskChange {	1✔
31
32	private Integer mildConcept;
33	private Integer moderateConcept;
34	private Integer severeConcept;
35
36	@Override
37	public String getConfirmationMessage() {
38	return "Successfully moved un voided allergies from old to new tables";	×
39	}
40
41	@Override
42	public void setUp() throws SetupException {
43
44	}	×
45
46	@Override
47	public void setFileOpener(ResourceAccessor resourceAccessor) {
48
49	}	×
50
51	@Override
52	public ValidationErrors validate(Database database) {
53	return null;	×
54	}
55
56	@Override
57	public void execute(Database database) throws CustomChangeException {
58	try {
59	loadSeverityConcepts(database);	×
60
61	JdbcConnection connection = (JdbcConnection) database.getConnection();	×
62
63	int allergyTypeId;
NEW 64	try (PreparedStatement typeStmt = connection.prepareStatement(	×
65	"select active_list_type_id from active_list_type where name = ?")) {
NEW 66	typeStmt.setString(1, "Allergy");	×
NEW 67	try (ResultSet rs = typeStmt.executeQuery()) {	×
NEW 68	if (!rs.next()) {	×
NEW 69	throw new CustomChangeException("Failed to find row with name 'Allergy' in the active_list_type");	×
70	}
NEW 71	allergyTypeId = rs.getInt(1);	×
72	}
73	}
74
NEW 75	try (PreparedStatement allergyInsertStatement = connection.prepareStatement(	×
76	"insert into allergy (patient_id, coded_allergen, severity_concept_id, creator, date_created, uuid, comment, allergen_type) "
77	+ "values(?,?,?,?,?,?,?,?)");
NEW 78	PreparedStatement reactionInsertStatement = connection.prepareStatement(	×
79	"insert into allergy_reaction (allergy_id, reaction_concept_id, uuid) "
80	+ "values (?,?,?)");
NEW 81	PreparedStatement allergySelectStatement = connection.prepareStatement(	×
82	"select allergy_id from allergy where uuid = ?");
NEW 83	PreparedStatement activeListStmt = connection.prepareStatement(	×
84	"select person_id, concept_id, comments, creator, date_created, uuid, reaction_concept_id, severity, allergy_type "
85	+ "from active_list al inner join active_list_allergy ala on al.active_list_id=ala.active_list_id "
86	+ "where voided = 0 and active_list_type_id = ?")) {
87
NEW 88	activeListStmt.setInt(1, allergyTypeId);	×
NEW 89	try (ResultSet rs = activeListStmt.executeQuery()) {	×
NEW 90	while (rs.next()) {	×
NEW 91	String uuid = rs.getString("uuid");	×
92
93	//insert allergy
NEW 94	allergyInsertStatement.setInt(1, rs.getInt("person_id"));	×
NEW 95	allergyInsertStatement.setInt(2, rs.getInt("concept_id"));	×
96
NEW 97	Integer severityConcept = null;	×
NEW 98	String severity = rs.getString("severity");	×
NEW 99	if (AllergySeverity.MILD.name().equals(severity)) {	×
NEW 100	severityConcept = mildConcept;	×
101	}
NEW 102	else if (AllergySeverity.MODERATE.name().equals(severity)) {	×
NEW 103	severityConcept = moderateConcept;	×
104	}
NEW 105	else if (AllergySeverity.SEVERE.name().equals(severity)) {	×
NEW 106	severityConcept = severeConcept;	×
107	}
108	//TODO what do we do with the other severities?
109
NEW 110	if (severityConcept != null) {	×
NEW 111	allergyInsertStatement.setInt(3, severityConcept);	×
112	} else {
NEW 113	allergyInsertStatement.setNull(3, java.sql.Types.INTEGER);	×
114	}
115
NEW 116	allergyInsertStatement.setInt(4, rs.getInt("creator"));	×
NEW 117	allergyInsertStatement.setDate(5, rs.getDate("date_created"));	×
NEW 118	allergyInsertStatement.setString(6, uuid);	×
NEW 119	allergyInsertStatement.setString(7, rs.getString("comments"));	×
120
NEW 121	String allergyType = rs.getString("allergy_type");	×
NEW 122	if (allergyType == null) {	×
NEW 123	allergyType = "DRUG";	×
124	}
NEW 125	else if ("ENVIRONMENTAL".equals(allergyType)) {	×
NEW 126	allergyType = "ENVIRONMENT";	×
127	}
128
NEW 129	allergyInsertStatement.setString(8, allergyType);	×
130
NEW 131	allergyInsertStatement.execute();	×
132
133	//get inserted allergy_id
NEW 134	allergySelectStatement.setString(1, uuid);	×
NEW 135	try (ResultSet rs2 = allergySelectStatement.executeQuery()) {	×
NEW 136	rs2.next();	×
137
138	//insert reaction
NEW 139	reactionInsertStatement.setInt(1, rs2.getInt(1));	×
140	}
NEW 141	reactionInsertStatement.setInt(2, rs.getInt("reaction_concept_id"));	×
NEW 142	reactionInsertStatement.setString(3, UUID.randomUUID().toString());	×
143
144	//some active lists do not have reactions recorded
NEW 145	if (!rs.wasNull()) {	×
NEW 146	reactionInsertStatement.execute();	×
147	}
UNCOV 148	}	×
149	}
150	}
151	}
152	catch (Exception ex) {	×
153	throw new CustomChangeException(ex);	×
154	}	×
155	}	×
156
157	private void loadSeverityConcepts(Database database) throws Exception {
158	mildConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.mild");	×
159	moderateConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.moderate");	×
160	severeConcept = getConceptByGlobalProperty(database, "allergy.concept.severity.severe");	×
161	}	×
162
163	private Integer getConceptByGlobalProperty(Database database, String globalPropertyName) throws Exception {
164	JdbcConnection connection = (JdbcConnection) database.getConnection();	×
NEW 165	try (PreparedStatement gpStmt = connection.prepareStatement(	×
166	"SELECT property_value FROM global_property WHERE property = ?")) {
NEW 167	gpStmt.setString(1, globalPropertyName);	×
NEW 168	try (ResultSet rs = gpStmt.executeQuery()) {	×
NEW 169	if (rs.next()) {	×
NEW 170	String uuid = rs.getString("property_value");	×
171
NEW 172	try (PreparedStatement conceptStmt = connection.prepareStatement(	×
173	"SELECT concept_id FROM concept WHERE uuid = ?")) {
NEW 174	conceptStmt.setString(1, uuid);	×
NEW 175	try (ResultSet conceptRs = conceptStmt.executeQuery()) {	×
NEW 176	if (conceptRs.next()) {	×
NEW 177	return conceptRs.getInt("concept_id");	×
178	}
179	}
180	}
181	}
182	}
183	}
184
185	throw new IllegalStateException("Configuration required: " + globalPropertyName);	×
186	}
187	}

openmrs / openmrs-core / 21763664900

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