https://github.com/uwrit/leaf-scripts
Collection of useful scripts for bootstrapping and managing a Leaf instance.
https://github.com/uwrit/leaf-scripts
Last synced: about 1 year ago
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Collection of useful scripts for bootstrapping and managing a Leaf instance.
- Host: GitHub
- URL: https://github.com/uwrit/leaf-scripts
- Owner: uwrit
- License: bsd-3-clause
- Created: 2019-04-10T18:26:29.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2023-04-17T22:57:06.000Z (about 3 years ago)
- Last Synced: 2025-02-08T12:13:17.860Z (over 1 year ago)
- Language: TSQL
- Size: 1.68 MB
- Stars: 8
- Watchers: 6
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Leaf Scripts
Creating Leaf Concepts manually can be done quickly using the Leaf Admin Panel, but certain types of Concepts are best created by SQL script. Here are a few examples of how to do so.
These example assume that you have an active [UMLS license](https://uts.nlm.nih.gov/license.html) and a database named `UMLS` on the same server as your Leaf application database. Note that ICD10 diagnoses are used just as an example, and you can apply this pattern to ICD9, CPT, LOINC and other coding systems just as easily.
Alternatively, for convenience you can use the scripts in the [concepts/ontologies](https://github.com/uwrit/leaf-scripts/tree/master/concepts/ontologies) folder to generate the ontologies directly and skip the process of creating temp tables.
## ICD10 diagnoses using UMLS
You can find the full example script used here wrapped as a stored procedure at https://github.com/uwrit/leaf-scripts/blob/master/concepts/sp_InsertConceptsFromUMLS.sql.
1) Use the example [sp_GetOntologyFromUMLS](https://github.com/uwrit/leaf-scripts/blob/master/concepts/sp_GetOntologyFromUMLS.sql) stored procedure to populate a temporary table (or create the table directly using the [ICD10CM.sql](https://github.com/uwrit/leaf-scripts/tree/master/concepts/ontologies/ICD10CM.sql) script):
```sql
CREATE TABLE #Output
(
AUI NVARCHAR(20) NULL,
ParentAUI NVARCHAR(20) NULL,
MinCode NVARCHAR(20) NULL,
MaxCode NVARCHAR(20) NULL,
CodeCount INT NULL,
OntologyType NVARCHAR(20) NULL,
SqlSetWhere NVARCHAR(1000) NULL,
UiDisplayName NVARCHAR(1000) NULL
)
INSERT INTO #Output
EXEC dbo.sp_GetConceptOntologyFromUMLS 'ICD10CM'
```
Output:
| AUI | ParentAUI | MinCode | MaxCode | CodeCount | OntologyType | SqlSetWhere | UiDisplayName |
| --------- | --------- | ------- | ------- | --------- | ------------ | ---------------------------- | ------------- |
| A20... | NULL | A00.0 | Z99.89 | 69823 | ICD10CM | BETWEEN 'A00.0' AND 'Z99.89' | ICD-10-CM... |
| A18... | A17... | A02.29 | A02.29 | 1 | ICD10CM | = 'A02.29' | Salmonella... |
| A17... | A174... | A41.81 | A41.89 | 2 | ICD10CM | IN ('A41.81','A41.89') | Sepsis... |
Each row contains a reference to its parent row via `ParentAUI`, and a SQL expression in `SqlSetWhere` which we can plug into our datamodel by prepending our column names.
2) Find the diagnosis `SQL Set` ID and insert the hierarchical UMLS rows into the `app.Concept` table:
```sql
DECLARE @SqlSetId INT = (SELECT TOP (1) S.Id FROM app.ConceptSqlSet S WHERE S.SqlSetFrom = 'dbo.diagnosis')
INSERT INTO app.Concept
(
[ExternalId]
,[ExternalParentId]
,[IsPatientCountAutoCalculated]
,[IsNumeric]
,[IsParent]
,[IsRoot]
,[IsSpecializable]
,[SqlSetId]
,[SqlSetWhere]
,[UiDisplayName]
,[UiDisplayText]
,[AddDateTime]
,[ContentLastUpdateDateTime]
)
SELECT
[ExternalId] = 'UMLS_AUI:' + O.AUI
,[ExternalParentId] = 'UMLS_AUI:' + O.ParentAUI
,[IsPatientCountAutoCalculated] = 1
,[IsNumeric] = 0
,[IsParent] = CASE WHEN EXISTS (SELECT 1 FROM #Output O2 WHERE O.AUI = O2.ParentAUI) THEN 1 ELSE 0 END
,[IsRoot] = CASE WHEN ParentAUI IS NULL THEN 1 ELSE 0 END
,[IsSpecializable] = 0
,[SqlSetId] = @SqlSetId
,[SqlSetWhere] = '@.CodingSystem = ''ICD10'' AND @.Code ' + O.SqlSetWhere
,[UiDisplayName] = O.uiDisplayName
,[UiDisplayText] = 'Had diagnosis of ' + O.UiDisplayName
,[AddDateTime] = GETDATE()
,[ContentLastUpdateDateTime] = GETDATE()
FROM #Output O
WHERE NOT EXISTS (SELECT 1
FROM app.Concept c
WHERE 'UMLS_AUI:' + o.AUI = c.ExternalID)
```
Note that above in
```
,[SqlSetWhere] = '@.CodingSystem = ''ICD10'' AND @.Code ' + O.SqlSetWhere
```
The example assumes a hypothetical diagnosis table structure in your clinical database like:
| PatientId | CodingSystem | Code | ... |
| --------- | ------------ | ----- | --- |
| A | ICD10 | E11.2 | |
| B | ICD10 | T34.5 | |
| C | ICD10 | S09.1 | |
Your clinical database columns will likely differ, so tailor this section appropriately for your data.
3) Update the `app.Concept.ParentId` values using the `ExternalId` and `ExternalParentIds`:
```sql
UPDATE app.Concept
SET ParentId = p.Id
FROM app.Concept c
INNER JOIN (SELECT p.Id, p.ParentId, p.ExternalId
FROM app.Concept p) p
ON c.ExternalParentID = p.ExternalID
WHERE EXISTS (SELECT 1 FROM #Output o WHERE 'UMLS_AUI:' + o.AUI = c.ExternalId)
```
And that's it! You'll likely want to have the Leaf Admin Panel open and inspect/tweak these after running the script to make sure everything looks as expected.
You can use this general pattern to insert diagnosis, procedure, LOINC, or other codes.