resolve merge conflicts

Scripts/NDWH/C&T FACT TABLES/load_FactNCDs.sql

@@ -0,0 +1,168 @@
+IF OBJECT_ID(N'[NDWH].[dbo].[FactNCD]', N'U') IS NOT NULL 
+	DROP TABLE [NDWH].[dbo].[FactNCD]
+
+GO
+
+BEGIN
+
+with ncd_source_data as (
+    select 
+        *
+    from (
+            select 
+                distinct 
+                case 
+                    when value = 'Alzheimers Disease and other Dementias' then 'Alzheimer''s Disease and other Dementias' 
+                    else value 
+                end as value,
+                PatientPKHash,
+                PatientPK,               
+                SiteCode              
+            from ODS.dbo.CT_AllergiesChronicIllness  as chronic  
+                cross apply STRING_SPLIT(chronic.ChronicIllness, '|')
+            ) as chronic 
+            pivot(
+                count(value)
+                for value IN (
+                    "Alzheimers Disease and other Dementias",
+                    "Alzheimer's Disease and other Dementias",
+                    "Arthritis",
+                    "Asthma",
+                    "Cancer",
+                    "Cardiovascular diseases",
+                    "Chronic Hepatitis",
+                    "Chronic Kidney Disease",
+                    "Chronic Obstructive Pulmonary Disease(COPD)",
+                    "Chronic Renal Failure",
+                    "Cystic Fibrosis",
+                    "Deafness and Hearing Impairment",
+                    "Diabetes",
+                    "Endometriosis",
+                    "Epilepsy",
+                    "Glaucoma",
+                    "Heart Disease",
+                    "Hyperlipidaemia",
+                    "Hypertension",
+                    "Hypothyroidism",
+                    "Mental illness",
+                    "Multiple Sclerosis",
+                    "Obesity",
+                    "Osteoporosis",
+                    "Sickle Cell Anaemia",
+                    "Thyroid disease"
+                )
+            ) as pivot_table
+),
+MFL_partner_agency_combination as (
+	select 
+		distinct MFL_Code,
+		SDP,
+	    SDP_Agency as Agency 
+	from ODS.dbo.All_EMRSites 
+),
+diabetes_tests_ordering as (
+    /* get all Diabetes tests and order by date*/
+    SELECT 
+        ROW_NUMBER() OVER (PARTITION BY PatientPKHash, Sitecode ORDER BY OrderedbyDate DESC) AS RowNum,
+        PatientPKHash,
+        SiteCode,
+        TestName,
+        TRY_CAST(TestResult AS NUMERIC(18, 2)) AS NumericTestResult
+    FROM ODS.dbo.CT_PatientLabs
+    WHERE 
+        TestName in ('HgB', 'HbsAg', 'HBA1C') 
+            or TestName in ('FBS', 'Blood Sugar')
+
+),
+latest_diabetes_test as  (
+ select 
+    *
+ from diabetes_tests_ordering where RowNum = 1
+),
+latest_diabetes_test_controlled as (
+    /* get all last Diabetes tests that are within the controlled range*/
+    select 
+        * 
+    from latest_diabetes_test
+    where (TestName IN ('HgB', 'HbsAg', 'HBA1C') AND NumericTestResult <= 6.5)
+        or (TestName IN ('FBS', 'Blood Sugar') AND NumericTestResult < 7.0)
+),
+visits_ordering as (
+    select 
+        PatientPKHash,
+        PatientPK,               
+        SiteCode,
+        VisitDate,
+        row_number() over (partition by PatientPK, Sitecode order by VisitDate desc) as rank
+    from ODS.dbo.CT_AllergiesChronicIllness as chronic
+),
+age_as_of_last_visit as (
+    select 
+        visits_ordering.PatientPKHash,
+        visits_ordering.PatientPK,               
+        visits_ordering.SiteCode,
+        datediff(yy, patient.DOB, coalesce(visits_ordering.VisitDate, getdate() )) As  AgeLastVisit
+    from visits_ordering
+    inner join ODS.dbo.CT_Patient as patient on patient.PatientPKHash = visits_ordering.PatientPKHash 
+	and patient.SiteCode = visits_ordering.SiteCode
+    where rank = 1
+)
+select
+    Factkey = IDENTITY(INT, 1, 1),
+    patient.PatientKey,
+    facility.FacilityKey,
+    partner.PartnerKey,
+    agency.AgencyKey,
+    age_group.AgeGroupKey,
+    ncd_source_data."Alzheimer's Disease and other Dementias",
+    ncd_source_data."Arthritis",
+    ncd_source_data."Asthma",
+    ncd_source_data."Cancer",
+    ncd_source_data."Cardiovascular diseases",
+    ncd_source_data."Chronic Hepatitis",
+    ncd_source_data."Chronic Kidney Disease",
+    ncd_source_data."Chronic Obstructive Pulmonary Disease(COPD)",
+    ncd_source_data."Chronic Renal Failure",
+    ncd_source_data."Cystic Fibrosis",
+    ncd_source_data."Deafness and Hearing Impairment",
+    ncd_source_data."Diabetes",
+    ncd_source_data."Endometriosis",
+    ncd_source_data."Epilepsy",
+    ncd_source_data."Glaucoma",
+    ncd_source_data."Heart Disease",
+    ncd_source_data."Hyperlipidaemia",
+    ncd_source_data."Hypertension",
+    ncd_source_data."Hypothyroidism",
+    ncd_source_data."Mental illness",
+    ncd_source_data."Multiple Sclerosis",
+    ncd_source_data."Obesity",
+    ncd_source_data."Osteoporosis",
+    ncd_source_data."Sickle Cell Anaemia",
+    ncd_source_data."Thyroid disease",
+    case when latest_diabetes_test.PatientPKHash is not null then 1 else 0 end as ScreenedDiabetes,
+    case when latest_diabetes_test_controlled.PatientPKHash is not null then 1 else 0 end as IsDiabetesControlledAtLastTest,
+    coalesce(visit.ScreenedBPLastVisit,0) as ScreenedBPLastVisit,
+    coalesce(visit.IsBPControlledAtLastVisit, 0) as IsBPControlledAtLastVisit
+into NDWH.dbo.FactNCD
+from ncd_source_data
+left join latest_diabetes_test on latest_diabetes_test.PatientPKHash = ncd_source_data.PatientPKHash
+    and latest_diabetes_test.SiteCode = ncd_source_data.SiteCode
+left join latest_diabetes_test_controlled on latest_diabetes_test_controlled.PatientPKHash = ncd_source_data.PatientPKHash
+    and latest_diabetes_test_controlled.SiteCode = ncd_source_data.SiteCode
+left join NDWH.dbo.DimPatient as patient on patient.PatientPKHash = ncd_source_data.PatientPKHash
+    and patient.SiteCode = ncd_source_data.SiteCode
+left join ODS.dbo.Intermediate_LastVisitDate as visit on visit.PatientPK = ncd_source_data.PatientPK
+    and visit.SiteCode = ncd_source_data.SiteCode
+left join age_as_of_last_visit on age_as_of_last_visit.PatientPKHash = ncd_source_data.PatientPKHash
+    and age_as_of_last_visit.SiteCode = ncd_source_data.SiteCode
+left join NDWH.dbo.DimFacility as facility on facility.MFLCode = ncd_source_data.SiteCode
+left join MFL_partner_agency_combination on MFL_partner_agency_combination.MFL_Code = ncd_source_data.SiteCode
+left join NDWH.dbo.DimPartner as partner on partner.PartnerName = MFL_partner_agency_combination.SDP
+left join NDWH.dbo.DimAgency as agency on agency.AgencyName = MFL_partner_agency_combination.Agency
+left join NDWH.dbo.DimAgeGroup as age_group on age_group.Age = age_as_of_last_visit.AgeLastVisit;
+
+
+
+alter table NDWH.dbo.FactNCD add primary key(FactKey);
+
+END

Scripts/ODS/data_quality/CT_cleaning_scripts/clean_CT_allergies_chronic_illness.sql

@@ -1,11 +1,3 @@
--- clean ChronicIllness
-UPDATE [ODS].[DBO].[CT_AllergiesChronicIllness] 
-    SET ChronicIllness = lkp_chronic_illness.target_name
-FROM [ODS].[DBO].[CT_AllergiesChronicIllness] AS allergies_chronic_illness
-INNER JOIN ods.dbo.lkp_chronic_illness ON lkp_chronic_illness.source_name = allergies_chronic_illness.ChronicIllness
-
-GO
-
 -- clean ChronicOnsetDate
 UPDATE [ODS].[DBO].[CT_AllergiesChronicIllness] 
     SET ChronicOnsetDate = NULL