Sk/queries

.gitignore

@@ -11,6 +11,7 @@ wheels/
 
 # IDEs
 .idea/
+.vscode/
 
 # settings files (should not be in the source tree anyway, but just in case)
 *.env

sql_scripts/README.md

@@ -0,0 +1,33 @@
+# Notes on putting together the EHR needed
+
+## Goal
+
+The ultimate aim is to have one csv per patient per day which looks roughly like
+
+ | DateTimeRecorded | Temperature | noradrenaline | etc  | Secretions | etc | Placementinstant | RemovalInstant | TubeSize | etc |Units | Comments |
+| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| 08/08/2026 00:00:15 | 36.4 |  |  |  |  | | | | | |
+| 08/08/2026 00:00:16 |  | 1 | | | | | | | | mg/L |  |
+| 08/08/2026 00:00:17 |  |  |  | None |  | | | | | |
+| 08/08/2026 00:02:18 |  |  |  |  |  | 07/08/2026 | |8mm | | |
+| 08/08/2026 00:00:15 | 38.5 |  |  |  |  | | | | | | Doctors alerted |
+
+*Note: The insertion date for a tube may well be earlier than the day on which it is recorded as these seem to get populated during the nightly update to caboodle.*
+
+## Current scripts
+
+| script | arguments | record | location of script in repo | database | 
+|- | --- | --- |- | --- |
+| mrn_based_on_bed_and_datetime.sql | location string | csn |waveform-controller/src/sql | star |
+| get_hospital_visit_id.sql| csn | hospital_visit_id | waveform-controller/sql_scripts| star |
+| flow_sheet_values.sql| hospital_visit_id/today/yesterday | part of table above | waveform-controller/sql_scripts| star |
+| airway.sql | csn/today/yesterday | part of the table above | waveform-controller/sql_scripts | caboodle |
+| sputum_secretions.sql | csn/today/yesterday | part of the table above | waveform-controller/sql_scripts | caboodle |
+
+## Unfinished scripts
+
+lab_results.sql need dealing with in the same way as flow_sheet_values
+
+lab_test_names.sql forms part of the above query but is useful for exploring
+
+We need scripts for any of the items in the a tracker that have not yet been covered.

sql_scripts/airway.sql

@@ -0,0 +1,20 @@
+
+SELECT
+lda._CreationInstant as DateTimeRecorded,
+lda.PlacementInstant,
+lda.RemovalInstant,
+fvf.Value AS TubeSize     
+
+FROM FilteredAccess.LdaFact lda
+JOIN FilteredAccess.FlowsheetValueFact fvf ON fvf.LdaKey = lda.LdaKey
+JOIN FilteredAccess.FlowsheetRowDim frd ON frd.FlowsheetRowKey = fvf.FlowsheetRowKey
+JOIN FilteredAccess.EncounterFact enc ON enc.EncounterKey = lda.InitialEncounterKey
+
+WHERE
+fvf.FlowsheetRowEpicId ='1120100079'                      
+AND enc.Type != 'Anaesthesia'
+AND frd.DisplayName like 'Single Lumen Tube Size'
+--and enc.PatientDurableKey = '1782941'
+
+AND lda._CreationInstant BETWEEN  %(yesterday)s AND %(today)s
+AND enc.EncounterEpicCsn = %(csn)

sql_scripts/flow_sheet_values.sql

@@ -0,0 +1,35 @@
+--get the flow sheet values for the particular visit on a particular day
+--  the flow sheet numbers are recorded as id_in_application in the visit_observation_type table
+--  Temperature       6
+--  Noradrenalin      3040102622
+--  Metaraminol       12946
+
+SELECT
+    vo.observation_datetime AS DateTimeRecorded,
+
+    (array_agg(vo.value_as_real) FILTER (
+        WHERE vt.id_in_application = '6'
+    ))[1] AS "Temperature",
+
+    (array_agg(vo.value_as_real) FILTER (
+        WHERE vt.id_in_application = '3040102622'
+    ))[1] AS "Noradrenaline",
+
+    (array_agg(vo.value_as_real) FILTER (
+        WHERE vt.id_in_application = '12946'
+    ))[1] AS "Metaraminol",
+
+    vo.unit AS Units,
+    vo.comment AS Comments
+
+FROM star.visit_observation AS vo
+
+LEFT JOIN star.visit_observation_type AS vt
+    ON vo.visit_observation_type_id = vt.visit_observation_type_id
+
+WHERE vt.id_in_application IN ('6', '3040102622', '12946')
+AND vo.valid_from BETWEEN %(yesterday)s AND %(today)s
+AND vo.hospital_visit_id = %(hospital_visit_id)s
+
+GROUP BY DateTimeRecorded, Units, vo.comment
+

sql_scripts/get_hospital_visit_id.sql

@@ -0,0 +1,7 @@
+<!-- Retrieve the hospital_visit_id associated with the csn value applied to this function -->
+
+
+select hospital_visit_id from star.hospital_visit  as hv
+where  hv.encounter = %(csn)s  -- note the CSN must be in quotes                      
+
+

sql_scripts/lab_results.sql

@@ -0,0 +1,24 @@
+-- This selects the values are units of lab tests
+-- 1011      CRP
+-- 722790196 CRP
+-- 390793054 WCC
+-- 390793057 WCC
+-- 390793060 WCC
+
+select
+r.result_last_modified_datetime as date,
+(select name from star.lab_test_definition as ltd
+where ltd.lab_test_definition_id = r.lab_test_definition_id) as name,
+r.value_as_real as value,
+r.units,
+r.abnormal_flag,
+r.comment
+
+
+from star.lab_result as r
+join star.lab_order as o
+on r.lab_order_id = o.lab_order_id
+where o.hospital_visit_id = 'xx'
+and r.result_status  like 'FINAL'
+and r.lab_test_definition_id in ('1001', '390793054', '390793057', '390793060', '722790196')
+

sql_scripts/lab_test_names.sql

@@ -0,0 +1,5 @@
+select lab_test_definition_id as id,
+       name,
+       standardised_vocabulary as vocab
+from star.lab_test_definition as ltd
+where ltd.lab_test_definition_id in ('1001', '390793054', '390793057', '390793060', '722790196')

sql_scripts/sputum_secretions.sql

@@ -0,0 +1,25 @@
+<- Retrieved the information about sputum and secretions >
+
+SELECT
+fv.TakenInstant AS 'DateTimeRecorded',
+CASE 
+WHEN fsd.FlowsheetRowEpicId = '451120' 
+THEN fv.Value 
+END 
+AS 'Secretions'  ,
+CASE 
+WHEN fsd.FlowsheetRowEpicId = '302600' 
+THEN fv.Value 
+END 
+AS 'Sputum'  ,
+fv.Comment AS Comments
+
+FROM FilteredAccess.FlowsheetValueFact fv 
+INNER JOIN FilteredAccess.FlowsheetRowDim fsd ON fv.FlowsheetRowKey = fsd.FlowsheetRowKey
+INNER JOIN FilteredAccess.EncounterFact enc ON fv.EncounterKey = enc.EncounterKey
+
+WHERE
+(fsd.FlowsheetRowEpicId = '451120' OR 
+fsd.FlowsheetRowEpicId ='302600')
+AND fv.TakenInstant BETWEEN %(yesterday)s AND %(today)s
+AND enc.EncounterEpicCsn = %(csn)