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Merge branch 'master' into cr2-patches
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@Injiri
Injiri authored Aug 22, 2024
2 parents 1870c2d + 958e329 commit 2559051
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85 changes: 85 additions & 0 deletions api/src/main/java/org/openmrs/module/kenyaemr/advice/RefreshPatientFlagsOnEncounterSave.java
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/**
* 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.module.kenyaemr.advice;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.openmrs.Encounter;
import org.openmrs.Patient;
import org.openmrs.api.context.Context;
import org.openmrs.calculation.patient.PatientCalculationService;
import org.openmrs.calculation.result.CalculationResult;
import org.openmrs.module.kenyacore.calculation.CalculationManager;
import org.openmrs.module.kenyacore.calculation.PatientFlagCalculation;
import org.openmrs.module.kenyaemr.metadata.CommonMetadata;
import org.springframework.aop.AfterReturningAdvice;
import org.springframework.cache.CacheManager;

import java.lang.reflect.Method;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
* Refreshes patient flags cache from changes in patient clinical data
*/
public class RefreshPatientFlagsOnEncounterSave implements AfterReturningAdvice {
private Log log = LogFactory.getLog(this.getClass());

@Override
public void afterReturning(Object returnValue, Method method, Object[] args, Object target) throws Throwable {

if (method.getName().equals("saveEncounter")) {
Encounter enc = (Encounter) args[0];
Patient patient = enc.getPatient();

/**
* We only want to refresh data for an active visit.
* TODO: should we also limit this to Point-of-care visit?
*/
if (enc != null && enc.getVisit() != null && enc.getVisit().getStopDatetime() == null && enc.getForm() != null && (CommonMetadata._Form.TRIAGE.equalsIgnoreCase(enc.getForm().getUuid()) || CommonMetadata._Form.CLINICAL_ENCOUNTER.equalsIgnoreCase(enc.getForm().getUuid()))) {
// we can use global property to track this list for ease of management
List<String> patientFlagsToRefresh = Arrays.asList(
"EligibleForIDSRFlagsCalculation"
);
CalculationManager calculationManager = Context.getRegisteredComponent("calculationManager", CalculationManager.class);

CacheManager cacheManager = Context.getRegisteredComponent("apiCacheManager", CacheManager.class);
calculationManager.refresh();
// check if patient already has data in the cache
Map<String,String> patientFlagsMap = new HashMap<>();
if (cacheManager.getCache("patientFlagCache").get(patient.getUuid()) != null) {
patientFlagsMap = (HashMap<String, String>) cacheManager.getCache("patientFlagCache").get(patient.getUuid()).get();
}

for (PatientFlagCalculation calc : calculationManager.getFlagCalculations()) {
if (!patientFlagsToRefresh.contains(calc.getClass().getSimpleName())) {
continue;
}
try {
CalculationResult result = Context.getService(PatientCalculationService.class).evaluate(patient.getId(), calc);
if (result != null && (Boolean) result.getValue()) {
patientFlagsMap.put(calc.getClass().getSimpleName(), calc.getFlagMessage()); // add/update the flag
}
}
catch (Exception ex) {
log.error("Error updating patient flag for " + calc.getClass(), ex);
}
}
if (!patientFlagsMap.isEmpty()) {
cacheManager.getCache("patientFlagCache").put(patient.getUuid(), patientFlagsMap);
}
}
}

}

}
201 changes: 201 additions & 0 deletions ...rc/main/java/org/openmrs/module/kenyaemr/chore/MigratePatientContactPersonAttributes.java
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/**
* 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.module.kenyaemr.chore;

import org.openmrs.api.context.Context;
import org.openmrs.module.kenyacore.chore.AbstractChore;
import org.springframework.stereotype.Component;

import java.io.PrintWriter;

/**
* Migrate Patient contacts from kenyaemr_hiv_testing_patient_contact
*/
@Component("kenyaemr.chore.MigratePatientContactPersonAttributes")
public class MigratePatientContactPersonAttributes extends AbstractChore {

/**
* @see AbstractChore#perform(PrintWriter)
*/

@Override
public void perform(PrintWriter out) {

String insertPersonAttributes = "insert into person_attribute (person_id, value, person_attribute_type_id, creator, date_created, changed_by,\n" +
" date_changed, voided, voided_by, date_voided, void_reason, uuid)\n" +
" (select c.patient_id,\n" +
" case c.baseline_hiv_status when 'Negative' then 664 when 'Positive' then 703 else 1067 end,\n" +
" (select person_attribute_type_id from person_attribute_type t where uuid ='3ca03c84-632d-4e53-95ad-91f1bd9d96d6'),\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" null,\n" +
" c.date_changed,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null)\n" +
" union all\n" +
" (select c.patient_id,\n" +
" ifnull(c.living_with_patient,1067),\n" +
" (select person_attribute_type_id from person_attribute_type t where uuid = '35a08d84-9f80-4991-92b4-c4ae5903536e'),\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" null,\n" +
" c.date_changed,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null)\n" +
" union all\n" +
" (select c.patient_id,\n" +
" ifnull(c.pns_approach,1067),\n" +
" (select person_attribute_type_id from person_attribute_type t where uuid ='59d1b886-90c8-4f7f-9212-08b20a9ee8cf'),\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" null,\n" +
" c.date_changed,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null)\n" +
" union all\n" +
" (select c.patient_id,\n" +
" 1065,\n" +
" (select person_attribute_type_id from person_attribute_type t where uuid = '7c94bd35-fba7-4ef7-96f5-29c89a318fcf'),\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" null,\n" +
" c.date_changed,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null)\n" +
"union all\n" +
"(select c.patient_id,\n" +
" ifnull(c.ipv_outcome,'False'),\n" +
" (select person_attribute_type_id from person_attribute_type t where uuid = '49c543c2-a72a-4b0a-8cca-39c375c0726f'),\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" null,\n" +
" c.date_changed,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null);";

Context.getAdministrationService().executeSQL(insertPersonAttributes, false);
out.println("Completed inserting person attributes for the contact");

String createPatientContactEncounters = "insert into encounter (encounter_type, patient_id, location_id, form_id, encounter_datetime, creator, date_created,\n" +
" voided, voided_by, date_voided, void_reason, changed_by, date_changed, visit_id, uuid)\n" +
" (select (select encounter_type_id from encounter_type where uuid='de1f9d67-b73e-4e1b-90d0-036166fc6995'),\n" +
" c.patient_id,\n" +
" null,\n" +
" 44,\n" +
" c.date_created,\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" c.changed_by,\n" +
" c.date_changed,\n" +
" null,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null);";

Context.getAdministrationService().executeSQL(createPatientContactEncounters, false);
out.println("Completed creating encounters for migrated patient contacts");

String insertRelationship = "insert into relationship\n" +
"(person_a, relationship, person_b, start_date, end_date, creator, date_created, date_changed, changed_by, voided,\n" +
" voided_by, date_voided, void_reason, uuid) (select c.patient_related_to,\n" +
" (case c.relationship_type\n" +
" when 970 then 3\n" +
" when 971 then 3\n" +
" when 1528 then 3\n" +
" when 972 then 2\n" +
" when 5617 then 6\n" +
" when 163565 then 7\n" +
" when 162221 then 8\n" +
" when 157351 then 9\n" +
" when 166606 then 12 end) as relationship,\n" +
" c.patient_id,\n" +
" c.date_created,\n" +
" null,\n" +
" c.changed_by,\n" +
" c.date_created,\n" +
" null,\n" +
" c.changed_by,\n" +
" c.voided,\n" +
" c.voided_by,\n" +
" c.date_voided,\n" +
" c.voided_reason,\n" +
" uuid()\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null\n" +
" AND NOT EXISTS (SELECT 1\n" +
" FROM relationship r\n" +
" WHERE r.person_a = c.patient_related_to\n" +
" AND r.relationship = CASE\n" +
" WHEN c.relationship_type = 970\n" +
" THEN 3\n" +
" WHEN c.relationship_type = 971\n" +
" THEN 3\n" +
" WHEN c.relationship_type = 1528\n" +
" THEN 3\n" +
" WHEN c.relationship_type = 972\n" +
" THEN 2\n" +
" WHEN c.relationship_type = 5617\n" +
" THEN 6\n" +
" WHEN c.relationship_type = 163565\n" +
" THEN 7\n" +
" WHEN c.relationship_type = 162221\n" +
" THEN 8\n" +
" WHEN c.relationship_type = 157351\n" +
" THEN 9\n" +
" WHEN c.relationship_type = 166606\n" +
" THEN 12\n" +
" END\n" +
" AND r.person_b = c.patient_id\n" +
" and r.voided = 0) group by patient_id,patient_related_to,relationship);";

Context.getAdministrationService().executeSQL(insertRelationship, false);
out.println("Completed migrating relationships");


String updatePhysicalAddress = "update person_address a inner join (select patient_id, physical_address\n" +
" from kenyaemr_hiv_testing_patient_contact c\n" +
" where c.patient_id is not null) c on a.person_id = c.patient_id\n" +
"set a.address1 = c.physical_address\n" +
"where a.address1 is null;";

Context.getAdministrationService().executeSQL(updatePhysicalAddress, false);
out.println("Completed updating physical address");

}
}
4 changes: 3 additions & 1 deletion api/src/main/java/org/openmrs/module/kenyaemr/metadata/CommonMetadata.java
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Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ public static final class _PersonAttributeType {
public static final String PNS_PATIENT_CONTACT_BASELINE_HIV_STATUS = "3ca03c84-632d-4e53-95ad-91f1bd9d96d6";
public static final String PNS_PATIENT_CONTACT_LIVING_WITH_PATIENT= "35a08d84-9f80-4991-92b4-c4ae5903536e";
public static final String PNS_PATIENT_CONTACT_REGISTRATION_SOURCE= "7c94bd35-fba7-4ef7-96f5-29c89a318fcf";

public static final String PNS_PATIENT_CONTACT_IPV_OUTCOME= "49c543c2-a72a-4b0a-8cca-39c375c0726f";

}

Expand Down Expand Up @@ -425,6 +425,8 @@ public void install() {
String.class, null, false, 4.5, _PersonAttributeType.PNS_PATIENT_CONTACT_LIVING_WITH_PATIENT));
install(personAttributeType("Contact registration from PNS", "Contact registration source from PNS",
String.class, null, false, 4.5, _PersonAttributeType.PNS_PATIENT_CONTACT_REGISTRATION_SOURCE));
install(personAttributeType("Contact IPV Outcome", "Contact IPV Outcome",
String.class, null, false, 4.5, _PersonAttributeType.PNS_PATIENT_CONTACT_IPV_OUTCOME));

// Provider attribute types.
install(providerAttributeType("Primary Facility", "Default facility for a provider", LocationDatatype.class, "", 0, 9999 , _ProviderAttributeType.PRIMARY_FACILITY));
Expand Down
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