Adding Category data to Conditions table

query-connector/docker-compose.yaml

@@ -13,6 +13,8 @@ services:
       interval: 2s
       timeout: 5s
       retries: 20
+    volumes:
+      - ./data/Conditions_and_Categories_20241024.csv:/tmp/Conditions_and_Categories_20241024.csv
 
   # Next.js app with Flyway
   tefca-viewer:

query-connector/flyway/sql/V01_03__insert_hardcoded_values.sql

@@ -1,6 +1,6 @@
 INSERT INTO conditions VALUES('1','DIBBs Local Code System','Newborn Screening','20240909');
 INSERT INTO conditions VALUES('2','DIBBs Local Code System','Cancer (Leukemia)','20240909');
-INSERT INTO conditions VALUES('3','DIBBs Local Code System','Social Determinants of Health','20240909'); -- has no valuesets
+-- INSERT INTO conditions VALUES('3','DIBBs Local Code System','Social Determinants of Health','20240909'); -- has no valuesets
 
 -- Newborn Screening valueset(s)
 INSERT INTO valuesets VALUES('1_20240909','1','20240909','Newborn Screening','DIBBs','lotc');

query-connector/flyway/sql/V01_07__add_conditions_category.sql

@@ -0,0 +1,34 @@
+-- 1. Add the new 'category' column to the condition table
+ALTER TABLE conditions
+ADD COLUMN category TEXT;
+
+-- 2. Create a staging table to hold the CSV data
+CREATE TABLE IF NOT EXISTS category_data (
+    condition_name TEXT,
+    condition_code TEXT,
+    category TEXT
+);
+
+-- 3. Load the CSV data into the staging table
+COPY category_data (condition_name, condition_code, category)
+FROM '/tmp/Conditions_and_Categories_20241024.csv'
+DELIMITER ','
+CSV HEADER;
+
+-- 4. Update the condition table with the category from the staging table
+UPDATE conditions
+SET category = category_data.category
+FROM category_data
+WHERE conditions.id = category_data.condition_code;
+
+-- 5. Add hardcoded categories from DIBBs-specific additions
+UPDATE conditions
+SET category = 'Birth Defects and Infant Disorders'
+WHERE conditions.name = 'Newborn Screening';
+
+UPDATE conditions
+SET category = 'Cancer'
+WHERE conditions.name = 'Cancer (Leukemia)';
+
+-- 6. Drop the staging table after the join
+DROP TABLE category_data;