Update december first2022

load.sh

@@ -9,4 +9,5 @@ mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/dr
 mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/run_isante_patient_status.sql
 mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/insertion_obs_by_day.sql
 mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/patient_status_arv_dml.sql
-mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/indicators_report.sql
+mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/indicators_report.sql
+mysql --protocol=tcp -h ${host} -P ${port} -u ${user} -p${pass} < ./sql_files/psychoSocialResume.sql

sql_files/drug_lookup_isanteplus.sql

@@ -54,7 +54,7 @@ LOCK TABLES `druglookup` WRITE;
 INSERT INTO `druglookup` VALUES 
 (1,1,70056,NULL,'abacavir','Abacavir (ABC)','NRTIs','300mg BID','ABC','Abacavir (ABC)','Abacavir (ABC)','300mg caplet','20mg/ml liquid','300mg comprimé','20mg/ml sirop','qd'),
 (2,2,70245,NULL,'acyclovir','Acyclovir','Other Treatments',NULL,'','Acyclovir','Acyclovir',NULL,NULL,NULL,NULL,NULL),
-(3,3,NULL, NULL,'amprenavir','Amprenavir (AMP)','Pls','1200mg BID','AMP','Amprenavir (AMP)','Amprenavir (AMP)',NULL,NULL,NULL,NULL,NULL),
+(3,3,71193, NULL,'amprenavir','Amprenavir (AMP)','Pls','1200mg BID','AMP','Amprenavir (AMP)','Amprenavir (AMP)',NULL,NULL,NULL,NULL,NULL),
 (4,4,NULL,NULL,'amprenavirPlusBostRtv','Amprenavir+BostRTV','Pls','1200mg/200mg qd','AMP+BostRTV','Amprenavir+BostRTV','Amprenavir+BostRTV',NULL,NULL,NULL,NULL,NULL),
 (5,5,71647,NUll,'atazanavir','Atazanavir (ATZN)','Pls','400mg qd','ATZN','Atazanavir (ATZN)','Atazanavir (ATZN)','150 mg qd',NULL,'150 mg qd',NULL,NULL),
 (6,6,159809,NULL,'atazanavirPlusBostRtv','Atazanavir+BostRTV','Pls','300mg/100mg qd','ATZN+BostRTV','Atazanavir+BostRTV','Atazanavir+BostRTV',NULL,NULL,NULL,NULL,NULL),

sql_files/indicators_report.sql

@@ -214,6 +214,23 @@ DROP TABLE IF EXISTS isanteplus.report_type;
 	INSERT INTO isanteplus.indicator_type (indicator_type_id,report_type_id,indicator_name_fr,
 	indicator_name_en,indicator_type_description,date_created)
 	VALUES(37,1,'Violences (physique, sexuelle)','Violence (physical, sexual) ','Violences (physique, sexuelle)', now());
+
+	/*Covid suspect 155762*/
+	INSERT INTO isanteplus.indicator_type (indicator_type_id,report_type_id,indicator_name_fr,
+	indicator_name_en,indicator_type_description,date_created)
+	VALUES(38,1,'Covid suspect','Covid suspect','Covid suspect', now());
+
+	/*Covid confirmé*/
+	INSERT INTO isanteplus.indicator_type (indicator_type_id,report_type_id,indicator_name_fr,
+	indicator_name_en,indicator_type_description,date_created)
+	VALUES(39,1,'Covid confirmé','Covid confirmé','Confirm Covid', now());
+
+	/*Cancer du Col*/
+
+	INSERT INTO isanteplus.indicator_type (indicator_type_id,report_type_id,indicator_name_fr,
+	indicator_name_en,indicator_type_description,date_created)
+	VALUES(40,1,'Cancer du Col','Cancer du Col','Cancer of Col', now());
+
 
  DELIMITER $$
 	DROP PROCEDURE IF EXISTS patient_diagnosis$$
@@ -273,8 +290,9 @@ INSERT into patient_diagnosis
 	/*Update encounter date for patient_diagnosis*/	   
 	update patient_diagnosis pdiag, openmrs.encounter enc
     SET pdiag.encounter_date = DATE(enc.encounter_datetime)
-    WHERE pdiag.location_id = enc.location_id
-          AND pdiag.encounter_id = enc.encounter_id
+    WHERE /*pdiag.location_id = enc.location_id
+          AND*/ pdiag.encounter_id = enc.encounter_id
+		  AND enc.encounter_datetime IS NOT NULL
 		  AND enc.voided = 0;
 /*Ending patient_diagnosis*/
  END$$
@@ -294,6 +312,7 @@ DELIMITER ;
 	AND pdiag.answer_concept_id = 160146
 	AND pdiag.suspected_confirmed = 159393
 	AND pdiag.voided <> 1
+	AND pdiag.encounter_date IS NOT NULL
 	ON DUPLICATE KEY UPDATE
 	last_updated_date = NOW(),
 	voided = pdiag.voided;
@@ -398,7 +417,7 @@ DELIMITER ;
 		voided = pdiag.voided;
 
 	/*9 : Paludisme confirme*/
-	INSERT INTO isanteplus.indicators (indicator_id,indicator_type_id,patient_id,location_id,encounter_id,
+	/*INSERT INTO isanteplus.indicators (indicator_id,indicator_type_id,patient_id,location_id,encounter_id,
 										indicator_date,voided,created_date,last_updated_date)
 	SELECT 9,9,pdiag.patient_id, pdiag.location_id, pdiag.encounter_id, pdiag.encounter_date,
 	pdiag.voided, now(), now() FROM isanteplus.patient p, isanteplus.patient_diagnosis pdiag
@@ -409,7 +428,7 @@ DELIMITER ;
 	AND pdiag.voided <> 1
 	ON DUPLICATE KEY UPDATE
 	last_updated_date = NOW(),
-	voided = pdiag.voided;
+	voided = pdiag.voided;*/
 
 	/*10 : Paralysie flasque aigue(pfa)*/
 
@@ -784,6 +803,51 @@ DELIMITER ;
 	ON DUPLICATE KEY UPDATE
 	last_updated_date = NOW(),
 	voided = pdiag.voided;
+
+	/* 38: Covid Suspect - 155762 */
+
+	INSERT INTO isanteplus.indicators (indicator_id,indicator_type_id,patient_id,location_id,encounter_id,
+										indicator_date,voided,created_date,last_updated_date)
+	SELECT 38,38,pdiag.patient_id, pdiag.location_id, pdiag.encounter_id, pdiag.encounter_date,
+	pdiag.voided, now(), now() FROM isanteplus.patient p, isanteplus.patient_diagnosis pdiag
+	WHERE p.patient_id = pdiag.patient_id
+	AND pdiag.concept_id = 1284
+	AND pdiag.answer_concept_id = 155762
+	AND pdiag.suspected_confirmed = 159393
+	AND pdiag.voided <> 1
+	ON DUPLICATE KEY UPDATE
+	last_updated_date = NOW(),
+	voided = pdiag.voided;
+
+	/* 39: Covid Confirme - 155762 */
+
+	INSERT INTO isanteplus.indicators (indicator_id,indicator_type_id,patient_id,location_id,encounter_id,
+										indicator_date,voided,created_date,last_updated_date)
+	SELECT 39,39,pdiag.patient_id, pdiag.location_id, pdiag.encounter_id, pdiag.encounter_date,
+	pdiag.voided, now(), now() FROM isanteplus.patient p, isanteplus.patient_diagnosis pdiag
+	WHERE p.patient_id = pdiag.patient_id
+	AND pdiag.concept_id = 1284
+	AND pdiag.answer_concept_id = 155762
+	AND pdiag.suspected_confirmed = 159392
+	AND pdiag.voided <> 1
+	ON DUPLICATE KEY UPDATE
+	last_updated_date = NOW(),
+	voided = pdiag.voided;
+
+	/*CANCER DU COL*/
+
+	INSERT INTO isanteplus.indicators (indicator_id,indicator_type_id,patient_id,location_id,encounter_id,
+										indicator_date,voided,created_date,last_updated_date)
+	SELECT 40,40,pdiag.patient_id, pdiag.location_id, pdiag.encounter_id, pdiag.encounter_date,
+	pdiag.voided, now(), now() FROM isanteplus.patient p, isanteplus.patient_diagnosis pdiag
+	WHERE p.patient_id = pdiag.patient_id
+	AND pdiag.concept_id = 1284
+	AND pdiag.answer_concept_id = 116023
+	AND pdiag.voided <> 1
+	ON DUPLICATE KEY UPDATE
+	last_updated_date = NOW(),
+	voided = pdiag.voided;
+
   END$$
 DELIMITER ;
 

sql_files/insertion_obs_by_day.sql

@@ -406,17 +406,21 @@ CREATE TABLE IF NOT EXISTS patient_prescription_day (
 	AND en.visit_id=vi.visit_id
 	AND vi.voided = 0;
 	/*update test_done,date_test_done,comment_test_done for patient_laboratory*/
-	update patient_laboratory plab,isanteplus.obs_by_day ob
-	SET plab.test_done=1,plab.test_result=CASE WHEN ob.value_coded<>''
+	UPDATE patient_laboratory plab,openmrs.obs ob
+	SET plab.test_done=1,
+		plab.test_result=CASE WHEN ob.value_coded IS NOT NULL
 	   THEN ob.value_coded
-	   WHEN ob.value_numeric<>'' THEN ob.value_numeric
-	   WHEN ob.value_text<>'' THEN ob.value_text
+	   WHEN ob.value_numeric IS NOT NULL 
+	   THEN ob.value_numeric
+	   WHEN ob.value_text IS NOT NULL THEN ob.value_text
 	   END,
 	plab.date_test_done=ob.obs_datetime,
 	plab.comment_test_done=ob.comments
 	WHERE plab.test_id=ob.concept_id
 	AND plab.encounter_id=ob.encounter_id
-	AND ob.voided = 0;
+	AND ob.voided = 0
+	AND (ob.value_coded IS NOT NULL OR ob.value_numeric IS NOT NULL
+	OR ob.value_text IS NOT NULL);
 
 /*End of patient_laboratory*/
 	END$$

sql_files/isanteplusreportsddlscript.sql

@@ -837,10 +837,10 @@ ALTER TABLE isanteplus.patient_prescription
 ADD COLUMN dispensation_date DATE AFTER drug_id;
 
 ALTER TABLE isanteplus.patient_prescription
-ADD COLUMN number_day_dispense INT(11) AFTER number_day;
+ADD COLUMN number_day_dispense DOUBLE AFTER number_day;
 
 ALTER TABLE isanteplus.patient_prescription
-ADD COLUMN pills_amount_dispense INT(11) AFTER number_day_dispense;
+ADD COLUMN pills_amount_dispense DOUBLE AFTER number_day_dispense;
 
 ALTER TABLE isanteplus.patient
 ADD COLUMN isante_id varchar(50) AFTER national_id;
@@ -1217,4 +1217,21 @@ CREATE TABLE if not exists immunization_dose (
 ) ENGINE=InnoDB DEFAULT CHARSET=utf8;
 
 ALTER TABLE isanteplus.patient_prescription 
-MODIFY COLUMN number_day double;
+MODIFY COLUMN number_day double;
+
+ALTER TABLE isanteplus.patient
+ADD COLUMN date_transferred_in DATETIME AFTER transferred_in;
+
+ALTER TABLE isanteplus.patient
+ADD COLUMN date_started_arv_other_site DATETIME 
+AFTER date_transferred_in;
+/*Field modify on 17_12_2021*/
+ALTER TABLE isanteplus.patient_on_art 
+MODIFY COLUMN cervical_cancer_treatment TEXT;
+/*Field added on 19 janv 2022*/
+ALTER TABLE isanteplus.patient_dispensing
+ADD COLUMN ddp int(11) default 0 AFTER dispensation_location;
+
+ALTER TABLE patient_dispensing
+MODIFY COLUMN dose_day double;
+

sql_files/isanteplusreportsdmlscript.sql

@@ -76,26 +76,30 @@ DELIMITER $$
 			openmrs.patient_identifier_type pit set p.st_id=pi.identifier 
 			where p.patient_id=pi.patient_id 
 			AND pi.identifier_type=pit.patient_identifier_type_id
-			and pit.uuid="d059f6d0-9e42-4760-8de1-8316b48bc5f1";
+			and pit.uuid="d059f6d0-9e42-4760-8de1-8316b48bc5f1"
+			AND pi.voided <> 1;
             /*National ID*/
 			update patient p,openmrs.patient_identifier pi, 
 			openmrs.patient_identifier_type pit set p.national_id=pi.identifier 
 			where p.patient_id=pi.patient_id 
 			AND pi.identifier_type=pit.patient_identifier_type_id
-			and pit.uuid="9fb4533d-4fd5-4276-875b-2ab41597f5dd";
+			and pit.uuid="9fb4533d-4fd5-4276-875b-2ab41597f5dd"
+			AND pi.voided <> 1;
 			/*iSantePlus_ID*/
 			update patient p,openmrs.patient_identifier pi, 
 			openmrs.patient_identifier_type pit set p.identifier=pi.identifier 
 			where p.patient_id=pi.patient_id 
 			AND pi.identifier_type=pit.patient_identifier_type_id
-			and pit.uuid="05a29f94-c0ed-11e2-94be-8c13b969e334";
+			and pit.uuid="05a29f94-c0ed-11e2-94be-8c13b969e334"
+			AND pi.voided <> 1;
 
 			/*isante_id*/
 			update patient p,openmrs.patient_identifier pi, 
 			openmrs.patient_identifier_type pit set p.isante_id = pi.identifier 
 			where p.patient_id=pi.patient_id 
 			AND pi.identifier_type=pit.patient_identifier_type_id
-			and pit.uuid="0e0c7cc2-3491-4675-b705-746e372ff346";
+			and pit.uuid="0e0c7cc2-3491-4675-b705-746e372ff346"
+			AND pi.voided <> 1;
 
 			/* update location_id for patients*/
 				update patient p,
@@ -121,7 +125,9 @@ DELIMITER $$
 			FROM openmrs.location l, openmrs.location_attribute la, openmrs.location_attribute_type lat
 			WHERE l.location_id = la.location_id
 			AND la.attribute_type_id = lat.location_attribute_type_id
-			AND lat.uuid = "0e52924e-4ebb-40ba-9b83-b198b532653b";
+			AND lat.uuid = "0e52924e-4ebb-40ba-9b83-b198b532653b"
+			ON DUPLICATE KEY UPDATE
+			name=l.name;
 
 			update isanteplus.patient p, isanteplus.location l SET site_code = l.isante_location_id
 			WHERE p.location_id = l.location_id;
@@ -190,7 +196,7 @@ DELIMITER $$
             AND ob.concept_id = 165210
             AND (o.value_text is not null AND o.value_text <> '');
 
-			/* update patient with vih status */
+			/* update patient with vih_status when patient has a HIV form*/
 
 			UPDATE patient p, openmrs.encounter en, openmrs.encounter_type ent
 			SET p.vih_status=1
@@ -200,6 +206,18 @@ DELIMITER $$
 			 OR ent.uuid='349ae0b4-65c1-4122-aa06-480f186c8350'
 			 OR ent.uuid='33491314-c352-42d0-bd5d-a9d0bffc9bf1')
 			AND en.voided = 0;
+			/*Update vih_status WHEN patient has a laboratory form WITH
+			   HIV test positive*/
+			UPDATE patient p, openmrs.encounter en, openmrs.encounter_type ent, openmrs.obs o
+			SET p.vih_status=1
+			WHERE p.patient_id = en.patient_id AND en.encounter_type = ent.encounter_type_id
+            AND en.encounter_id = o.encounter_id
+            AND en.patient_id = o.person_id
+			AND ent.uuid = 'f037e97b-471e-4898-a07c-b8e169e0ddc4'
+            AND o.concept_id IN (1040,1042)
+            AND o.value_coded = 703
+			AND en.voided <> 1
+            ANd o.voided <> 1;
 			/*Update for vih_status = 1 where the patient has a labs test hiv positive*/
 			/*UPDATE patient p, openmrs.encounter en, openmrs.obs ob
 			SET p.vih_status=1
@@ -272,6 +290,21 @@ DELIMITER $$
 			AND o.concept_id  = 159936
 			AND o.value_coded = 5622;
 
+			/*Date des premiers soins dans cet établissement*/
+			update patient p, openmrs.obs o, openmrs.concept c
+			SET p.date_transferred_in = o.value_datetime
+			WHERE p.patient_id = o.person_id
+			AND o.concept_id = c.concept_id
+			AND c.uuid = 'd9885523-a923-474b-88df-f3294d422c3c'
+			AND o.value_datetime IS NOT NULL;
+
+			/*Date début des ARV dans l’établissement de référence*/
+			update patient p, openmrs.obs o
+			SET p.date_started_arv_other_site = o.value_datetime
+			WHERE p.patient_id = o.person_id
+			AND o.concept_id  = 159599
+			AND o.value_datetime IS NOT NULL;
+
 			/*End of DML queries*/
 		END$$
 DELIMITER ;
@@ -395,7 +428,16 @@ DELIMITER $$
 	WHERE patdisp.encounter_id=ob.encounter_id
 	AND ob.concept_id=1755
 	AND ob.value_coded=1065
-	AND ob.voided = 0;	
+	AND ob.voided = 0;
+	/*UPDATE ddp field for patient on DDP, ddp=1065 for patient on DDP
+	 and ddp = 0 for patient not on DDP*/
+	UPDATE patient_dispensing patdisp, openmrs.obs ob, openmrs.concept c 
+	SET patdisp.ddp = 1065
+	WHERE patdisp.encounter_id = ob.encounter_id
+	AND ob.concept_id = c.concept_id
+	AND c.uuid = 'c2aacdc8-156e-4527-8934-a8fb94162419'
+	AND ob.value_coded = 1065
+	AND ob.voided = 0; 
 	/* Update on patient_dispensing where the drug is a ARV drug */
 	UPDATE patient_dispensing pdis, (SELECT ad.drug_id FROM arv_drugs ad) B
 		   SET pdis.arv_drug = 1065
@@ -851,16 +893,20 @@ DELIMITER $$
 	AND vi.voided = 0;
 	/*update test_done,date_test_done,comment_test_done for patient_laboratory*/
 	UPDATE patient_laboratory plab,openmrs.obs ob
-	SET plab.test_done=1,plab.test_result=CASE WHEN ob.value_coded IS NULL
+	SET plab.test_done=1,
+		plab.test_result=CASE WHEN ob.value_coded IS NOT NULL
 	   THEN ob.value_coded
-	   WHEN ob.value_numeric<>'' THEN ob.value_numeric
-	   WHEN ob.value_text<>'' THEN ob.value_text
+	   WHEN ob.value_numeric IS NOT NULL 
+	   THEN ob.value_numeric
+	   WHEN ob.value_text IS NOT NULL THEN ob.value_text
 	   END,
 	plab.date_test_done=ob.obs_datetime,
 	plab.comment_test_done=ob.comments
 	WHERE plab.test_id=ob.concept_id
 	AND plab.encounter_id=ob.encounter_id
-	AND ob.voided = 0;
+	AND ob.voided = 0
+	AND (ob.value_coded IS NOT NULL OR ob.value_numeric IS NOT NULL
+	OR ob.value_text IS NOT NULL);
 
 	/*update order_destination for patient_laboratory*/
 	UPDATE patient_laboratory plab,openmrs.obs ob

sql_files/patient_status_arv_dml.sql

@@ -1287,8 +1287,8 @@ AND CONVERT(pati.dose, SIGNED INTEGER) = 8 AND voided <> 1;
 		DROP PROCEDURE IF EXISTS calling_patient_alert$$
 		CREATE PROCEDURE calling_patient_alert()
 		BEGIN
-			call isanteplus_patient_alert();
 			call alert_viral_load();
+			call isanteplus_patient_alert();
 			call isanteplus_patient_immunization();
 		END$$
 	DELIMITER ;

sql_files/psychoSocialResume.sql

@@ -0,0 +1,28 @@
+ /*Resume iSante PsychoSocial forms*/
+	USE isanteplus;  
+	  DROP TABLE IF EXISTS comprehension;
+	  CREATE TABLE IF NOT EXISTS comprehension(
+		comprehension_id INT(11) AUTO_INCREMENT,
+		patient_id INT(11),
+		isante_id VARCHAR(11),
+		visitDate VARCHAR(10),
+		visit_date DATE,
+		compRemarks LONGTEXT,
+		obstaclesRemarks LONGTEXT,
+		barriersToApptsText VARCHAR(255),
+		barriersToHomeVisitsText VARCHAR(255),
+		CONSTRAINT pk_comprehension_isanteplus PRIMARY KEY (comprehension_id)
+	  )ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+	  INSERT INTO comprehension(patient_id,isante_id,visitDate,compRemarks,
+			obstaclesRemarks,barriersToApptsText,barriersToHomeVisitsText)
+	  SELECT p.patient_id, c.patientID, 
+		concat(c.visitDateDd,'-',c.visitDateMm,'-',c.visitDateYy),c.compRemarks,
+	  c.obstaclesRemarks,c.barriersToApptsText, c.barriersToHomeVisitsText
+		FROM isanteplus.patient p, itech.comprehension c
+	WHERE p.isante_id = c.patientID
+	AND ((c.compRemarks IS NOT NULL OR c.compRemarks <> '')
+		OR (c.obstaclesRemarks IS NOT NULL OR c.obstaclesRemarks <> '')
+		OR (c.barriersToApptsText IS NOT NULL OR c.barriersToApptsText <> '')
+		OR (c.barriersToHomeVisitsText IS NOT NULL OR c.barriersToHomeVisitsText <> '')
+	)