Added GP practice code to RQ038

projects/038 - O'Neill/extraction-sql/falls.sql

@@ -11,10 +11,6 @@
 --Just want the output, not the messages
 SET NOCOUNT ON;
 
--- Set the temp end date until new legal basis
-DECLARE @TEMPRQ038EndDate datetime;
-SET @TEMPRQ038EndDate = '2022-06-01';
-
 -- Build the main cohort
 --┌────────────────────────────────────────────────────┐
 --│ Define Cohort for RQ038: COVID + frailty project   │
@@ -25,32 +21,20 @@ SET @TEMPRQ038EndDate = '2022-06-01';
 --						patient who was >=60 years old on 1 Jan 2020 and have at least
 --				 		one GP recorded positive COVID test
 --            UPDATE 21/12/22 - recent SURG approved ALL patients >= 60 years
--- INPUT: A variable:
---	@TEMPRQ038EndDate - the date that we will not get records beyond
+-- INPUT: None
 
 -- OUTPUT: Temp tables as follows:
 -- #Patients - list of patient ids of the cohort
 
 ------------------------------------------------------------------------------
 
--- Only include patients who were first registered at a GP practice prior
--- to June 2022. This is 1 month before COPI expired and so acts as a buffer.
--- If we only looked at patients who first registered before July 2022, then
--- there is a chance that their data was processed after COPI expired.
-IF OBJECT_ID('tempdb..#PatientsToInclude') IS NOT NULL DROP TABLE #PatientsToInclude;
-SELECT FK_Patient_Link_ID INTO #PatientsToInclude
-FROM SharedCare.Patient_GP_History
-GROUP BY FK_Patient_Link_ID
-HAVING MIN(StartDate) < @TEMPRQ038EndDate;
-
 -- Table of all patients with a GP record
 IF OBJECT_ID('tempdb..#Patients') IS NOT NULL DROP TABLE #Patients;
 SELECT DISTINCT FK_Patient_Link_ID
 INTO #Patients
 FROM SharedCare.Patient
 WHERE FK_Reference_Tenancy_ID=2
-AND GPPracticeCode NOT LIKE 'ZZZ%'
-AND FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #PatientsToInclude);
+AND GPPracticeCode NOT LIKE 'ZZZ%';
 
 --┌───────────────┐
 --│ Year of birth │
@@ -222,7 +206,8 @@ CREATE TABLE #codessnomed (
 	[description] [varchar](255) NULL
 ) ON [PRIMARY];
 
-
+INSERT INTO #codessnomed
+VALUES ('efi-falls',1,'1912002',NULL,'Fall (event)'),('efi-falls',1,'49808004',NULL,'Old-age (finding)'),('efi-falls',1,'161898004',NULL,'Falls (finding)'),('efi-falls',1,'217082002',NULL,'Accidental fall (event)'),('efi-falls',1,'217154006',NULL,'Fall on same level from slipping, tripping or stumbling (event)'),('efi-falls',1,'271873000',NULL,'Senility (finding)'),('efi-falls',1,'279992002',NULL,'Recurrent falls (finding)'),('efi-falls',1,'298343000',NULL,'Finding related to falls (finding)'),('efi-falls',1,'298344006',NULL,'Elderly fall (finding)'),('efi-falls',1,'247541000000106',NULL,'Referral to falls service (procedure)'),('efi-falls',1,'248451000000109',NULL,'Referral to elderly falls prevention clinic (procedure)'),('efi-falls',1,'294231000000103',NULL,'Provision of telecare community alarm service (regime/therapy)'),('efi-falls',1,'501661000000103',NULL,'[D]Old age (situation)')
 
 INSERT INTO #AllCodes
 SELECT [concept], [version], [code], [description] from #codessnomed;
@@ -348,5 +333,4 @@ WHERE SuppliedCode IN (
   AND VERSION = 1
 )
 AND e.FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
-AND EventDate < @TEMPRQ038EndDate
 ORDER BY e.FK_Patient_Link_ID, e.EventDate;

projects/038 - O'Neill/scripts/main.js

@@ -510,23 +510,46 @@ ${err}`);
         log(`There are ${newPatientIds.length} new patient ids from the database.`);
         if (newPatientIds.length > 0) {
           const newPatientIdRows = randomIdGenerator(maxPseudoId, newPatientIds);
+          log('Appending new patient ids to the lookup file...');
           fs.writeFileSync(PSEUDO_ID_FILE, '\n' + newPatientIdRows.join('\n'), { flag: 'a' });
           log(`New patient ids added to the pseudo id lookup file.`);
         }
+        return resolve();
       } else {
         log(chalk.bold(`${patientIds.length} patient ids retrived.`));
         const patientIdRows = randomIdGenerator(0, patientIds);
-        fs.writeFileSync(PSEUDO_ID_FILE, patientIdRows.join('\n'));
-        log(`Patient ids written to the pseudo id lookup file.`);
+        log('Writing new patient ids to the lookup file...');
+        const pseudoFileWriter = fs.createWriteStream(PSEUDO_ID_FILE);
+        pseudoFileWriter.on('error', function (err) {
+          throw err;
+        });
+        pseudoFileWriter.on('close', () => {
+          log(`Patient ids written to the pseudo id lookup file.`);
+          return resolve();
+        });
+        let i = 0;
+        function writeToFile() {
+          let ok = true;
+          while (ok && i < patientIdRows.length) {
+            ok = pseudoFileWriter.write(patientIdRows[i] + '\n');
+            i++;
+          }
+          if (i === patientIdRows.length) pseudoFileWriter.end();
+          else pseudoFileWriter.once('drain', writeToFile);
+        }
+        writeToFile();
+
+        // pseudoFileWriter.end();
+        // fs.writeFileSync(PSEUDO_ID_FILE, patientIdRows.join('\n'));
       }
-      return resolve();
     });
   });
 }
 
 function randomIdGenerator(start = 0, ids) {
   log('Randomly assigning ids...');
   shuffleArray(ids);
+  log('Array shuffling complete');
   return ids.map((id, i) => {
     store.highestId = start + i + 1;
     store.pseudoLookup[id] = store.highestId;

projects/038 - O'Neill/template-sql/cohort.template.sql

@@ -29,10 +29,6 @@ SET NOCOUNT ON;
 DECLARE @StartDate datetime;
 SET @StartDate = '2019-01-01';
 
--- Set the temp end date until new legal basis
-DECLARE @TEMPRQ038EndDate datetime;
-SET @TEMPRQ038EndDate = '2022-06-01';
-
 -- Build the main cohort
 --> EXECUTE query-build-rq038-cohort.sql
 
@@ -57,7 +53,8 @@ SELECT
   SuppliedCode,
   FK_Reference_SnomedCT_ID,
   FK_Reference_Coding_ID,
-  [Value]
+  [Value],
+  Units
 INTO #PatientEventData1
 FROM [SharedCare].GP_Events
 WHERE FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
@@ -74,7 +71,8 @@ SELECT
   SuppliedCode,
   FK_Reference_SnomedCT_ID,
   FK_Reference_Coding_ID,
-  [Value]
+  [Value],
+  Units
 INTO #PatientEventData2
 FROM [SharedCare].GP_Events
 WHERE FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
@@ -91,7 +89,8 @@ SELECT
   SuppliedCode,
   FK_Reference_SnomedCT_ID,
   FK_Reference_Coding_ID,
-  [Value]
+  [Value],
+  Units
 INTO #PatientEventData3
 FROM [SharedCare].GP_Events
 WHERE FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
@@ -121,8 +120,7 @@ SELECT
 INTO #PatientMedicationData1
 FROM [SharedCare].GP_Medications
 WHERE FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
-AND	SuppliedCode IN (SELECT Code FROM #AllCodes)
-AND MedicationDate < @TEMPRQ038EndDate;
+AND	SuppliedCode IN (SELECT Code FROM #AllCodes);
 -- 1m
 
 -- 2. Patients with a FK_Patient_Link_ID in our list
@@ -136,8 +134,7 @@ SELECT
 INTO #PatientMedicationData2
 FROM [SharedCare].GP_Medications
 WHERE FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
-AND	FK_Reference_Coding_ID IN (SELECT FK_Reference_Coding_ID FROM #VersionedCodeSets)
-AND MedicationDate < @TEMPRQ038EndDate;
+AND	FK_Reference_Coding_ID IN (SELECT FK_Reference_Coding_ID FROM #VersionedCodeSets);
 --29s
 
 -- 3. Patients with a FK_Reference_SnomedCT_ID in our list
@@ -151,8 +148,7 @@ SELECT
 INTO #PatientMedicationData3
 FROM [SharedCare].GP_Medications
 WHERE FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
-AND	FK_Reference_SnomedCT_ID IN (SELECT FK_Reference_SnomedCT_ID FROM #VersionedSnomedSets)
-AND MedicationDate < @TEMPRQ038EndDate;
+AND	FK_Reference_SnomedCT_ID IN (SELECT FK_Reference_SnomedCT_ID FROM #VersionedSnomedSets);
 
 IF OBJECT_ID('tempdb..#PatientMedicationData') IS NOT NULL DROP TABLE #PatientMedicationData;
 SELECT * INTO #PatientMedicationData FROM #PatientMedicationData1
@@ -184,32 +180,34 @@ CREATE INDEX medData ON #PatientMedicationData (SuppliedCode) INCLUDE (FK_Patien
 
 
 
---> EXECUTE query-get-closest-value-to-date.sql code-set:bmi version:2 temp-table-name:#PostStartBMI date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:bmi version:2 temp-table-name:#PreStartBMI date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:systolic-blood-pressure version:1 temp-table-name:#PostStartSBP date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:systolic-blood-pressure version:1 temp-table-name:#PreStartSBP date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:diastolic-blood-pressure version:1 temp-table-name:#PostStartDBP date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:diastolic-blood-pressure version:1 temp-table-name:#PreStartDBP date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:egfr version:1 temp-table-name:#PostStartEGFR date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:egfr version:1 temp-table-name:#PreStartEGFR date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:hba1c version:2 temp-table-name:#PostStartHBA1C date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:hba1c version:2 temp-table-name:#PreStartHBA1C date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:vitamin-d version:1 temp-table-name:#PostStartVitD date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:vitamin-d version:1 temp-table-name:#PreStartVitD date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:bmi version:2 temp-table-name:#PostStartBMI date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:bmi version:2 temp-table-name:#PreStartBMI date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:systolic-blood-pressure version:1 temp-table-name:#PostStartSBP date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:systolic-blood-pressure version:1 temp-table-name:#PreStartSBP date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:diastolic-blood-pressure version:1 temp-table-name:#PostStartDBP date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:diastolic-blood-pressure version:1 temp-table-name:#PreStartDBP date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:egfr version:1 temp-table-name:#PostStartEGFR date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:egfr version:1 temp-table-name:#PreStartEGFR date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:hba1c version:2 temp-table-name:#PostStartHBA1C date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:hba1c version:2 temp-table-name:#PreStartHBA1C date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:vitamin-d version:1 temp-table-name:#PostStartVitD date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:vitamin-d version:1 temp-table-name:#PreStartVitD date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
 
---> EXECUTE query-get-closest-value-to-date.sql code-set:haemoglobin version:1 temp-table-name:#PostStartHb date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:haemoglobin version:1 temp-table-name:#PreStartHb date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:white-blood-cells version:1 temp-table-name:#PostStartWBC date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:white-blood-cells version:1 temp-table-name:#PreStartWBC date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:platelets version:1 temp-table-name:#PostStartPlatelets date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:platelets version:1 temp-table-name:#PreStartPlatelets date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:alkaline-phosphatase version:1 temp-table-name:#PostStartAlkalinePhosphatase date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:alkaline-phosphatase version:1 temp-table-name:#PreStartAlkalinePhosphatase date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:corrected-calcium version:1 temp-table-name:#PostStartCorrectedCalcium date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
---> EXECUTE query-get-closest-value-to-date.sql code-set:corrected-calcium version:1 temp-table-name:#PreStartCorrectedCalcium date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:haemoglobin version:1 temp-table-name:#PostStartHb date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:haemoglobin version:1 temp-table-name:#PreStartHb date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:white-blood-cells version:1 temp-table-name:#PostStartWBC date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:white-blood-cells version:1 temp-table-name:#PreStartWBC date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:platelets version:1 temp-table-name:#PostStartPlatelets date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:platelets version:1 temp-table-name:#PreStartPlatelets date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:alkaline-phosphatase version:1 temp-table-name:#PostStartAlkalinePhosphatase date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:alkaline-phosphatase version:1 temp-table-name:#PreStartAlkalinePhosphatase date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:corrected-calcium version:1 temp-table-name:#PostStartCorrectedCalcium date:2020-01-01 comparison:>= all-patients:false gp-events-table:#PatientEventData
+--> EXECUTE query-get-closest-value-to-date.sql unit:% min-value:0 max-value:100000 code-set:corrected-calcium version:1 temp-table-name:#PreStartCorrectedCalcium date:2020-01-01 comparison:< all-patients:false gp-events-table:#PatientEventData
 
 --> EXECUTE query-patient-number-of-records.sql
 
+--> EXECUTE query-patient-practice-and-ccg.sql
+
 -- Get patient list of those with COVID death within 28 days of positive test
 IF OBJECT_ID('tempdb..#COVIDDeath') IS NOT NULL DROP TABLE #COVIDDeath;
 SELECT DISTINCT FK_Patient_Link_ID 
@@ -230,8 +228,9 @@ SELECT
   town.TownsendScoreHigherIsMoreDeprived,
   town.TownsendQuintileHigherIsMoreDeprived,
   lsoa.LSOA_Code AS LSOA,
-  CASE WHEN pl.DeathDate < @TEMPRQ038EndDate THEN YEAR(pl.DeathDate) ELSE NULL END AS YearOfDeath,
-  CASE WHEN pl.DeathDate < @TEMPRQ038EndDate THEN MONTH(pl.DeathDate) ELSE NULL END AS MonthOfDeath,
+  practice.GPPracticeCode,
+  CASE WHEN pl.DeathDate IS NOT NULL THEN YEAR(pl.DeathDate) ELSE NULL END AS YearOfDeath,
+  CASE WHEN pl.DeathDate IS NOT NULL THEN MONTH(pl.DeathDate) ELSE NULL END AS MonthOfDeath,
   covid.FirstCovidPositiveDate, admission.FirstAdmissionPost1stCOVIDTest, los.LengthOfStay1stAdmission1stCOVIDTest,
   covid.SecondCovidPositiveDate, admission.FirstAdmissionPost2ndCOVIDTest, los.LengthOfStay1stAdmission2ndCOVIDTest,
   covid.ThirdCovidPositiveDate, admission.FirstAdmissionPost3rdCOVIDTest, los.LengthOfStay1stAdmission3rdCOVIDTest,
@@ -352,4 +351,5 @@ LEFT OUTER JOIN #PostStartAlkalinePhosphatase phosphatasePost ON phosphatasePost
 LEFT OUTER JOIN #PreStartAlkalinePhosphatase phosphatase ON phosphatase.FK_Patient_Link_ID = pat.FK_Patient_Link_ID
 LEFT OUTER JOIN #PostStartCorrectedCalcium calciumPost ON calciumPost.FK_Patient_Link_ID = pat.FK_Patient_Link_ID
 LEFT OUTER JOIN #PreStartCorrectedCalcium calcium ON calcium.FK_Patient_Link_ID = pat.FK_Patient_Link_ID
-LEFT OUTER JOIN #GPRecordCount gpRecord ON gpRecord.FK_Patient_Link_ID = pat.FK_Patient_Link_ID
+LEFT OUTER JOIN #GPRecordCount gpRecord ON gpRecord.FK_Patient_Link_ID = pat.FK_Patient_Link_ID
+LEFT OUTER JOIN #PatientPractice practice ON practice.FK_Patient_Link_ID = pat.FK_Patient_Link_ID

projects/038 - O'Neill/template-sql/efi.template.sql

@@ -11,10 +11,6 @@
 --Just want the output, not the messages
 SET NOCOUNT ON;
 
--- Set the temp end date until new legal basis
-DECLARE @TEMPRQ038EndDate datetime;
-SET @TEMPRQ038EndDate = '2022-06-01';
-
 -- Build the main cohort
 --> EXECUTE query-build-rq038-cohort.sql
 

projects/038 - O'Neill/template-sql/falls.template.sql

@@ -11,10 +11,6 @@
 --Just want the output, not the messages
 SET NOCOUNT ON;
 
--- Set the temp end date until new legal basis
-DECLARE @TEMPRQ038EndDate datetime;
-SET @TEMPRQ038EndDate = '2022-06-01';
-
 -- Build the main cohort
 --> EXECUTE query-build-rq038-cohort.sql
 
@@ -43,5 +39,4 @@ WHERE SuppliedCode IN (
   AND VERSION = 1
 )
 AND e.FK_Patient_Link_ID IN (SELECT FK_Patient_Link_ID FROM #Patients)
-AND EventDate < @TEMPRQ038EndDate
 ORDER BY e.FK_Patient_Link_ID, e.EventDate;