Merge pull request #449 from jembi/dev

Release 19 March 2021

metadata/configuration/concepts/1280_TB_form.csv

@@ -21,6 +21,7 @@ a196e44f-7911-4942-b586-b59cf79c202f,,,Site extrapulmonaire,Extrapulmonary site,
 41bde817-b2e0-4f58-88be-f875e7b31eed,,,Confirmé bactériologiquement,Bacteriologically Confirmed,Confirmé bactériologiquement,Bacteriologically Confirmed,Misc,N/A,,
 c1e4f600-2cdd-4ce0-a687-af76e9e20721,,,"Non confirmé, diag cliniquement","Non-confirmed, clinically diag","Non confirmé, diag cliniquement","Non-confirmed, clinically diag",Misc,N/A,,
 c4bbc310-2e01-4c6d-be90-decc1b91a800,,"Bacteriologically Confirmed;Non-confirmed, clinically diag",Confirmation MTB,MTB confirmation,Confirmation MTB,MTB confirmation,Misc,Coded,,
+6ab25a03-6ac3-45f1-aa04-af54186411e0,,Positive;Negative,Résultat Diagnostic TB,TB Diagnostic Result,Résultat Diagnostic TB,TB Diagnostic Result,Misc,Coded,,
 91884f8a-36fe-4974-85bc-6b8b5c1c9da1,,,Prélèvement,Smear,Prélèvement,Smear,Misc,N/A,,
 3f80913f-0d3e-43be-b033-324e8e351dc7,,,Xpert MTB/RIF,Xpert MTB/RIF,Xpert MTB/RIF,Xpert MTB/RIF,Misc,N/A,,
 6ad904f9-8bb2-4dfa-b3a2-579e7e798f6b,,,Test de Hain,Hain test,Test de Hain,Hain test,Misc,N/A,,
@@ -45,5 +46,5 @@ ae1baeb2-4e9b-4500-bdc8-39cd40f91715,,,Évaluation de 2 semaines,2 week assessme
 7a4d5ae7-8d76-435d-84f1-ff4248304927,,,Évaluation mensuelle planifiée,Planned monthly assessment,Évaluation mensuelle planifiée,Planned monthly assessment,Misc,N/A,,
 29c66c54-716b-4df1-adb0-db74c0c42c22,,,Autre évaluation,Other assessment,Autre évaluation,Other assessment,Misc,N/A,,
 ec81acc9-b48c-4497-9916-fe5d2bdf9193,,2 week assessment;Planned monthly assessment;Other assessment,Raison de la prochaine visite,Reason for next visit,Raison de la prochaine visite,Reason for next visit,Misc,Coded,,
-9f22febc-7826-4550-9174-3e31ae95cc2c,WHO registration group;Previously treated group;Disease site;Extrapulmonary site;MTB confirmation;Method of confirmation;Other method of confirmation;Drug resistance profile;Sub-class of drug resistance profile;MDR-TB diagnosis date;Reason for next visit,,Définition du Cas,Case Definition,Définition du Cas,Case Definition,Misc,N/A,,
+9f22febc-7826-4550-9174-3e31ae95cc2c,WHO registration group;Previously treated group;Disease site;Extrapulmonary site;MTB confirmation;TB Diagnostic Result;Method of confirmation;Other method of confirmation;Drug resistance profile;Sub-class of drug resistance profile;MDR-TB diagnosis date;Reason for next visit,,Définition du Cas,Case Definition,Définition du Cas,Case Definition,Misc,N/A,,
 3804e2cc-dd14-4879-88d2-94391853f7fb,Date baseline assessment;Screened;Cough > 2 weeks;Fever > 2 weeks;Weight Loss;Night Sweats;TB Contact;Malnutrition;TB Status;3dce13a8-c7e5-45ec-a6f0-8050fd4a2ca2;Case Definition,,Formulaire TB,TB Form,Formulaire TB,TB Form,Misc,N/A,,

metadata/reportssql/data_completeness_check_report_functions.sql

@@ -473,6 +473,7 @@ BEGIN
             "VISIT_TYPE_OPD",
             "Special OPD"
         )
+    ORDER BY v.date_started DESC
     LIMIT 1;
 
     RETURN (result);

metadata/reportssql/drug_functions.sql

@@ -93,7 +93,8 @@ BEGIN
     WHERE o.voided = 0
         AND o.person_id = p_patientId
         AND o.order_id = p_orderId
-        AND c.uuid = uuidDispensedConcept;
+        AND c.uuid = uuidDispensedConcept
+    LIMIT 1;
 
     SELECT TRUE INTO retrospectiveDrugEntry
     FROM orders o
@@ -105,7 +106,8 @@ BEGIN
         AND o.date_created > calculateTreatmentEndDate(
             o.scheduled_date,
             do.duration,
-            c.uuid);
+            c.uuid)
+    LIMIT 1;
 
     RETURN (drugDispensed OR retrospectiveDrugEntry); 
 END$$ 

metadata/reportssql/index_program_functions.sql

@@ -141,14 +141,14 @@ CREATE FUNCTION getFirstIndexID(
     p_contactPatientId INT(11)) RETURNS INT(11)
     DETERMINISTIC
 BEGIN
-    DECLARE result TEXT DEFAULT 0;
+    DECLARE result INT(11);
 
     SELECT p.patient_id INTO result
     FROM patient p
     WHERE patientsAreRelated(p_contactPatientId, p.patient_id) AND
         patientIsIndex(p.patient_id)
-        ORDER BY p.date_created ASC 
-        LIMIT 1;
+    ORDER BY p.date_created ASC 
+    LIMIT 1;
 
     RETURN (result);
 END$$
@@ -191,10 +191,9 @@ BEGIN
 
     SELECT TRUE INTO result
     FROM relationship r
-    JOIN person pIndex ON (r.person_a = p_contactId AND r.person_b = pIndex.person_id) OR
-            (r.person_a = pIndex.person_id AND r.person_b = p_contactId)
-    WHERE 
-        patientIsIndex(pIndex.person_id)
+    JOIN person pIndex ON (r.person_a = p_contactId AND r.person_b = pIndex.person_id AND patientIsIndex(r.person_b)) OR
+            (r.person_a = pIndex.person_id AND r.person_b = p_contactId AND patientIsIndex(r.person_a))
+    WHERE r.voided = 0
     LIMIT 1;
 
     RETURN (result);

metadata/reportssql/testing_report_functions.sql

@@ -1806,9 +1806,7 @@ DROP FUNCTION IF EXISTS getTestingEntryPointWithinRepPeriod;
 
 DELIMITER $$
 CREATE FUNCTION getTestingEntryPointWithinRepPeriod(
-    p_patientId INT(11),
-    p_startDate DATE,
-    p_endDate DATE) RETURNS VARCHAR(50)
+    p_patientId INT(11)) RETURNS VARCHAR(50)
     DETERMINISTIC
 BEGIN
     DECLARE result VARCHAR(50);
@@ -1822,7 +1820,6 @@ BEGIN
     WHERE o.voided = 0
         AND o.person_id = p_patientId
         AND c.uuid = uuidTestingEntryPoint
-        AND o.date_created BETWEEN p_startDate AND p_endDate
     ORDER BY o.date_created DESC
     LIMIT 1;
 

metadata/reportssql/treatment_report_functions.sql

@@ -93,15 +93,15 @@ WHERE
     patientHasStartedARVTreatmentDuringOrBeforeReportingPeriod(pat.patient_id, p_endDate) AND
     IF (
         isOldPatient(pat.patient_id, p_startDate),
-        (patientOnARTDuringPartOfReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, p_minDuration, p_maxDuration) OR
+        (patientOnARTDuringPartOfReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, p_endDate, p_minDuration, p_maxDuration) OR
             patientPickedARVDrugDuringReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, p_endDate, p_minDuration, p_maxDuration)),
         patientPickedARVDrugDuringReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, p_endDate, p_minDuration, p_maxDuration)
     ) AND
     patientIsNotDead(pat.patient_id) AND
     patientIsNotLostToFollowUp(pat.patient_id) AND
     (
         patientIsNotTransferredOut(pat.patient_id) OR
-        patientOnARTDuringPartOfReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, 0, 2000)
+        patientOnARTDuringPartOfReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, p_endDate, 0, 2000)
     );
 
     RETURN (result);
@@ -139,7 +139,7 @@ WHERE
     patientIsNotLostToFollowUp(pat.patient_id) AND
     (
         patientIsNotTransferredOut(pat.patient_id) OR
-        patientOnARTDuringPartOfReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, 0, 2000)
+        patientOnARTDuringPartOfReportingPeriodAndDurationBetween(pat.patient_id, p_startDate, p_endDate, 0, 2000)
     );
 
     RETURN (result);
@@ -610,12 +610,27 @@ DELIMITER $$
 CREATE FUNCTION patientOnARTDuringPartOfReportingPeriodAndDurationBetween(
     p_patientId INT(11),
     p_startDate DATE,
+    p_endDate DATE,
     p_minDuration INT(11),
     p_maxDuration INT(11)) RETURNS TINYINT(1)
     DETERMINISTIC
 BEGIN
 
     DECLARE result TINYINT(1) DEFAULT 0;
+    DECLARE orderIdMostRecentDispense INT(11);
+
+    SELECT o.order_id INTO orderIdMostRecentDispense
+    FROM orders o
+    JOIN drug_order do ON do.order_id = o.order_id
+    JOIN concept c ON do.duration_units = c.concept_id AND c.retired = 0
+    JOIN drug d ON d.drug_id = do.drug_inventory_id AND d.retired = 0
+    WHERE o.patient_id = p_patientId AND o.voided = 0
+        AND drugIsARV(d.concept_id)
+        AND drugOrderIsDispensed(o.patient_id, o.order_id)
+        AND o.scheduled_date IS NOT NULL
+        AND o.scheduled_date <= p_endDate
+    ORDER BY o.scheduled_date
+    LIMIT 1;
 
     SELECT TRUE INTO result
     FROM orders o
@@ -633,7 +648,9 @@ BEGIN
             ) >= p_startDate
         AND o.scheduled_date IS NOT NULL
         AND calculateDurationInMonths(o.scheduled_date, do.duration,c.uuid) >= p_minDuration
-        AND calculateDurationInMonths(o.scheduled_date, do.duration,c.uuid) < p_maxDuration   
+        AND calculateDurationInMonths(o.scheduled_date, do.duration,c.uuid) < p_maxDuration
+        AND orderIdMostRecentDispense IS NOT NULL
+        AND o.order_id = orderIdMostRecentDispense
     GROUP BY o.patient_id;
 
     RETURN (result );
@@ -687,6 +704,20 @@ CREATE FUNCTION patientPickedARVDrugDuringReportingPeriodAndDurationBetween(
 BEGIN
 
     DECLARE result TINYINT(1) DEFAULT 0;
+    DECLARE orderIdMostRecentDispense INT(11);
+
+    SELECT o.order_id INTO orderIdMostRecentDispense
+    FROM orders o
+    JOIN drug_order do ON do.order_id = o.order_id
+    JOIN concept c ON do.duration_units = c.concept_id AND c.retired = 0
+    JOIN drug d ON d.drug_id = do.drug_inventory_id AND d.retired = 0
+    WHERE o.patient_id = p_patientId AND o.voided = 0
+        AND drugIsARV(d.concept_id)
+        AND drugOrderIsDispensed(o.patient_id, o.order_id)
+        AND o.scheduled_date IS NOT NULL
+        AND o.scheduled_date <= p_endDate
+    ORDER BY o.scheduled_date
+    LIMIT 1;
 
     SELECT TRUE INTO result
     FROM orders o
@@ -700,6 +731,8 @@ BEGIN
         AND o.scheduled_date BETWEEN p_startDate AND p_endDate
         AND calculateDurationInMonths(o.scheduled_date, do.duration,c.uuid) >= p_minDuration
         AND calculateDurationInMonths(o.scheduled_date, do.duration,c.uuid) < p_maxDuration
+        AND orderIdMostRecentDispense IS NOT NULL
+        AND o.order_id = orderIdMostRecentDispense
     GROUP BY o.patient_id;
 
     RETURN (result );

openmrs/apps/reports/GEORGETOWN_INDEX_TESTING_REPORT/sql/georgetownIndexTestingReport.sql

@@ -17,11 +17,11 @@ SELECT DISTINCT
     DATE(getProgramAttributeValueWithinReportingPeriod(p.patient_id, "2000-01-01","2100-01-01", "2dc1aafd-a708-11e6-91e9-0800270d80ce")) as "Date of Initiation",
     getPatientARTNumber(getFirstIndexID(p.patient_id)) as "Index Related ART Code",
     getPatientIdentifier(getFirstIndexID(p.patient_id)) as "Index Related Unique ID"
-FROM patient p, patient_program_attribute_history ppah, patient_program pp, program_attribute_type pat
+FROM patient p
+    LEFT JOIN patient_program pp ON pp.patient_id = p.patient_id
+    LEFT JOIN patient_program_attribute_history ppah ON ppah.patient_program_id = pp.patient_program_id
+    LEFT JOIN program_attribute_type pat ON pat.program_attribute_type_id = ppah.attribute_type_id
+        AND pat.name IN ("PROGRAM_MANAGEMENT_2_NOTIFICATION_DATE", "PROGRAM_MANAGEMENT_3_NOTIFICATION_OUTCOME")
 WHERE
-    ppah.patient_program_id = pp.patient_program_id AND
-    pp.patient_id = p.patient_id AND
-    pat.program_attribute_type_id = ppah.attribute_type_id AND
-    pat.name IN ("PROGRAM_MANAGEMENT_2_NOTIFICATION_DATE", "PROGRAM_MANAGEMENT_3_NOTIFICATION_OUTCOME") AND
     patientIsContact(p.patient_id)
 ORDER BY ppah.date_created DESC;

openmrs/apps/reports/GEORGETOWN_PATIENT_INFORMATION_REPORT/sql/georgetownPatientInformationReport.sql

@@ -18,6 +18,7 @@ SELECT
     IF(patientIsEligibleForVL(p.patient_id), "Yes", "No") as "eligibilityForVl",
     getDateLatestARVRelatedVisit(p.patient_id) as "dateOfLastVisit",
     getDateMostRecentARVAppointment(p.patient_id) as "lastAppointmentDate",
+    getPatientMostRecentProgramOutcome(p.patient_id, "en", "HIV_PROGRAM_KEY") as "hivOutcome",
     getPatientMostRecentProgramAttributeCodedValue(p.patient_id, "39202f47-a709-11e6-91e9-0800270d80ce", "en") as "transferredIn",
     IF(getPatientMostRecentProgramOutcome(p.patient_id, "en", "HIV_PROGRAM_KEY")="Transferred Out", "Yes", "No") as "transfertOut",
     IF(getObsCodedValue(p.patient_id, "211f0857-61a3-4049-9777-374c4a592453") IS NOT NULL, "True", "False") as "kp",

openmrs/apps/reports/GEORGETOWN_PCR_REPORT/sql/georgetownPcrReport.sql

@@ -1,15 +1,18 @@
 SELECT
     CAST(@a:=@a+1 AS CHAR) as "serialNumber",
-    getPatientIdentifier(r.person_b) as "uniquePatientId",
-    getPatientBirthdate(r.person_b) as "dateOfBirth",
-    getPatientAgeInMonthsAtDate(r.person_b, NOW()) as "ageInMonths",
-    getPatientIdentifier(r.person_a) as "motherId",
-    CONCAT(getPatientPreciseLocation(r.person_a),", ",getPatientVillage(r.person_a)) as "mothersAddress",
-    getPatientPhoneNumber(r.person_a) as "mothersContact",
-    getMostRecentTestResultDate(r.person_b,"a5239a85-6f75-4882-9b9b-60168e54b7da","9bb7b360-3790-4e1a-8aca-0d1341663040") as "resultDatePcr",
-    getTestResultWithinReportingPeriod(r.person_b,"2000-01-01","2100-01-01","a5239a85-6f75-4882-9b9b-60168e54b7da","9bb7b360-3790-4e1a-8aca-0d1341663040") as "pcrResult",
-	getProgramAttributeDateValueFromAttributeAndProgramName(r.person_b, "PROGRAM_MANAGEMENT_2_PATIENT_TREATMENT_DATE", "HIV_PROGRAM_KEY") as "artInitiationDate",
-    getObsCodedValue(r.person_b, "3447254f-501f-4b07-815c-cd0f6da98158") as "reasonOfNonInitiation"
+    getPatientIdentifier(r.person_a) as "uniquePatientId",
+    getPatientBirthdate(r.person_a) as "dateOfBirth",
+    getPatientAgeInMonthsAtDate(r.person_a, NOW()) as "ageInMonths",
+    getPatientIdentifier(r.person_b) as "motherId",
+    CONCAT(getPatientPreciseLocation(r.person_b),", ",getPatientVillage(r.person_b)) as "mothersAddress",
+    getPatientPhoneNumber(r.person_b) as "mothersContact",
+    getMostRecentTestResultDate(r.person_a,"a5239a85-6f75-4882-9b9b-60168e54b7da","9bb7b360-3790-4e1a-8aca-0d1341663040") as "resultDatePcr",
+    getTestResultWithinReportingPeriod(r.person_a,"2000-01-01","2100-01-01","a5239a85-6f75-4882-9b9b-60168e54b7da","9bb7b360-3790-4e1a-8aca-0d1341663040") as "pcrResult",
+	getProgramAttributeDateValueFromAttributeAndProgramName(r.person_a, "PROGRAM_MANAGEMENT_2_PATIENT_TREATMENT_DATE", "HIV_PROGRAM_KEY") as "artInitiationDate",
+    getObsCodedValue(r.person_a, "3447254f-501f-4b07-815c-cd0f6da98158") as "reasonOfNonInitiation"
 FROM (SELECT @a:= 0) AS a, relationship r
     JOIN relationship_type rt ON rt.relationship_type_id = r.relationship AND rt.a_is_to_b = "RELATIONSHIP_BIO_MOTHER"
-    JOIN patient_identifier pi ON pi.patient_id = r.person_a AND pi.preferred = 1;  
+    JOIN patient_identifier pi ON pi.patient_id = r.person_a AND pi.preferred = 1
+WHERE
+    getPatientAgeInMonthsAtDate(r.person_a, NOW()) <= 24 AND
+    patientHasEnrolledIntoHivProgram(r.person_b) = "Yes";

openmrs/apps/reports/GEORGETOWN_TB_REPORT/sql/georgetownTbReport.sql

@@ -8,11 +8,13 @@ SELECT
     getPatientPhoneNumber(p.patient_id) as "telephone",
     getMostRecentCodedObservation(p.patient_id,"Method of confirmation","en") as "Type of Exam",
     getDateTBPosDiagnose(p.patient_id) as "dateTBPosDiag",
+    getMostRecentCodedObservation(p.patient_id,"TB Diagnostic Result","en") as "tbDiagnosticResult",
+    getMostRecentDateObservation(p.patient_id,"MDR-TB diagnosis date") as "tbDiagnosticDate",
     getProgramAttributeDateValueFromAttributeAndProgramName(p.patient_id, "PROGRAM_MANAGEMENT_2_PATIENT_TREATMENT_DATE", "TB_PROGRAM_KEY") as "dateOfTxTbStart",
     getHIVTestDate(p.patient_id,"2000-01-01","2100-01-01") as "dateOfHivTesting",
     getHIVResult(p.patient_id,"2000-01-01","2100-01-01") as "hivTestingResult",
     getProgramAttributeDateValueFromAttributeAndProgramName(p.patient_id, "PROGRAM_MANAGEMENT_2_PATIENT_TREATMENT_DATE", "HIV_PROGRAM_KEY") as "dateOfInitiation"
 FROM patient p, (SELECT @a:= 0) AS a
 WHERE
     getDateTBPosDiagnose(p.patient_id) IS NOT NULL AND
-    getObsCodedValue(p.patient_id, "f0447183-d13f-463d-ad0f-1f45b99d97cc") LIKE "Yes%";
+    getObsCodedValue(p.patient_id, "61931c8b-0637-40f9-97dc-07796431dd3b") = "Suspected / Probable";

openmrs/apps/reports/GEORGETOWN_TESTING_REPORT/sql/georgetownTestingReport.sql

@@ -13,7 +13,7 @@ SELECT
     getHIVResult(p.patient_id,"#startDate#", "#endDate#") as "result",
     DATE(getProgramAttributeValueWithinReportingPeriod(p.patient_id, "2000-01-01", "2100-12-31", "2dc1aafd-a708-11e6-91e9-0800270d80ce")) as "dateOfArtInitiation",
     getObsCodedValue(p.patient_id, "3447254f-501f-4b07-815c-cd0f6da98158") as "reasonOfNonInitiation",
-    IF(wasHIVTestDoneInANCVisitWithinRepPeriod(p.patient_id, "#startDate#", "#endDate#"),"PMTCT [ANC1-only]",getTestingEntryPointWithinRepPeriod(p.patient_id, "#startDate#", "#endDate#")) as "facilityEntryPoint",
+    IF(wasHIVTestDoneInANCVisitWithinRepPeriod(p.patient_id, "#startDate#", "#endDate#"),"PMTCT [ANC1-only]",getTestingEntryPointWithinRepPeriod(p.patient_id)) as "facilityEntryPoint",
     getHIVTestDate(p.patient_id,"#startDate#", "#endDate#") as "dateFinalResultProvidedToPatient"
 FROM patient p, (SELECT @a:= 0) AS a
 WHERE getHIVTestDate(p.patient_id, "#startDate#", "#endDate#") IS NOT NULL;

report-testing-framework/data/backup-openmrs.sql

@@ -1685,6 +1685,25 @@ LOCK TABLES `concept_name_tag` WRITE;
 /*!40000 ALTER TABLE `concept_name_tag` ENABLE KEYS */;
 UNLOCK TABLES;
 
+DROP TABLE IF EXISTS `patient_program_attribute_history`;
+CREATE TABLE `patient_program_attribute_history` (
+  `patient_program_attribute_history_id` int(11) NOT NULL AUTO_INCREMENT,
+  `patient_program_id` int(11) NOT NULL,
+  `attribute_type_id` int(11) NOT NULL,
+  `value_reference` text NOT NULL,
+  `uuid` char(38) NOT NULL,
+  `creator` int(11) NOT NULL,
+  `date_created` datetime NOT NULL,
+  PRIMARY KEY (`patient_program_attribute_history_id`),
+  UNIQUE KEY `uuid` (`uuid`),
+  KEY `patient_program_attribute_history_programid_fk` (`patient_program_id`),
+  KEY `patient_program_attribute_history_attributetype_fk` (`attribute_type_id`),
+  KEY `patient_program_attribute_history_creator_fk` (`creator`),
+  CONSTRAINT `patient_program_attribute_history_attributetype_fk` FOREIGN KEY (`attribute_type_id`) REFERENCES `program_attribute_type` (`program_attribute_type_id`),
+  CONSTRAINT `patient_program_attribute_history_creator_fk` FOREIGN KEY (`creator`) REFERENCES `users` (`user_id`),
+  CONSTRAINT `patient_program_attribute_history_programid_fk` FOREIGN KEY (`patient_program_id`) REFERENCES `patient_program` (`patient_program_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=55 DEFAULT CHARSET=utf8;
+
 --
 -- Table structure for table `concept_name_tag_map`
 --
@@ -13247,9 +13266,7 @@ DELIMITER ;
 /*!50003 SET sql_mode              = 'NO_ENGINE_SUBSTITUTION' */ ;
 DELIMITER ;;
 CREATE DEFINER=`root`@`localhost` FUNCTION `getTestingEntryPointWithinRepPeriod`(
-    p_patientId INT(11),
-    p_startDate DATE,
-    p_endDate DATE) RETURNS varchar(50) CHARSET utf8
+    p_patientId INT(11)) RETURNS varchar(50) CHARSET utf8
     DETERMINISTIC
 BEGIN
     DECLARE result VARCHAR(50);
@@ -13263,7 +13280,6 @@ BEGIN
     WHERE o.voided = 0
         AND o.person_id = p_patientId
         AND c.uuid = uuidTestingEntryPoint
-        AND o.date_created BETWEEN p_startDate AND p_endDate
     ORDER BY o.date_created DESC
     LIMIT 1;