From 3472b80b3508cf2d669b3184f24f0ef3c2fb21d2 Mon Sep 17 00:00:00 2001
From: Ryan Crichton <ryan@jembi.org>
Date: Mon, 4 Dec 2023 09:48:44 +0200
Subject: [PATCH] Add improved examples for reporting pipeline

---
 .../importer/config/clickhouseTables.js       | 56 ++++++++++++++-----
 kafka-mapper-consumer/fhir-mapping.json       | 24 +++++++-
 2 files changed, 66 insertions(+), 14 deletions(-)

diff --git a/analytics-datastore-clickhouse/importer/config/clickhouseTables.js b/analytics-datastore-clickhouse/importer/config/clickhouseTables.js
index 8c3ba4e7..ab9767a9 100644
--- a/analytics-datastore-clickhouse/importer/config/clickhouseTables.js
+++ b/analytics-datastore-clickhouse/importer/config/clickhouseTables.js
@@ -1,22 +1,52 @@
-const CLUSTERED_MODE = process.env.CLUSTERED_MODE || 'true';
+const CLUSTERED_MODE = process.env.CLUSTERED_MODE || "true";
 
 const queries =
   Boolean(CLUSTERED_MODE) === true
     ? [
-        `CREATE TABLE default_table(
-			createdAt Date,
-			updatedAt Date
-		) 
-		ENGINE=MergeTree
-		ORDER BY tuple();`,
+        `CREATE TABLE patient_example(
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					goldenId String,
+					patientGivenName String,
+					patientFamilyName String,
+				) 
+				ENGINE=MergeTree
+				ORDER BY tuple();`,
+        `CREATE TABLE observation_example(
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					observationValue Double,
+					patientId String,
+				) 
+				ENGINE=MergeTree
+				ORDER BY tuple();`,
       ]
     : [
-        `CREATE TABLE default.default_table ON CLUSTER '{cluster}' (
-			createdAt Date,
-			updatedAt Date
-		)
-		ENGINE = ReplicatedMergeTree('/clickhouse/tables/{cluster}/{shard}/{table}', '{replica}')
-		ORDER BY tuple();`,
+        `CREATE TABLE patient_example ON CLUSTER '{cluster}' (
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					goldenId String,
+					patientGivenName String,
+					patientFamilyName String,
+				) 
+				ENGINE = ReplicatedMergeTree('/clickhouse/tables/{cluster}/{shard}/{table}', '{replica}')
+				ORDER BY tuple();`,
+        `CREATE TABLE observation_example ON CLUSTER '{cluster}' (
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					observationValue Double,
+					patientId String,
+				) 
+				ENGINE = ReplicatedMergeTree('/clickhouse/tables/{cluster}/{shard}/{table}', '{replica}')
+				ORDER BY tuple();`,
       ];
 
 module.exports = queries;
diff --git a/kafka-mapper-consumer/fhir-mapping.json b/kafka-mapper-consumer/fhir-mapping.json
index 943ed02f..e15d482f 100644
--- a/kafka-mapper-consumer/fhir-mapping.json
+++ b/kafka-mapper-consumer/fhir-mapping.json
@@ -3,8 +3,12 @@
     "resourceType": "Patient",
     "tableMappings": [
       {
-        "targetTable": "patient",
+        "targetTable": "patient_example",
         "columnMappings": [
+          {
+            "columnName": "goldenId",
+            "fhirPath": "Patient.link.where(type='refer').other.reference.replace('Patient/', '')"
+          },
           {
             "columnName": "patientGivenName",
             "fhirPath": "Patient.name.given"
@@ -16,5 +20,23 @@
         ]
       }
     ]
+  },
+  {
+    "resourceType": "Observation",
+    "tableMappings": [
+      {
+        "targetTable": "observation_example",
+        "columnMappings": [
+          {
+            "columnName": "observationValue",
+            "fhirPath": "Observation.valueQuantity.value"
+          },
+          {
+            "columnName": "patientId",
+            "fhirPath": "Observation.subject.reference.replace('Patient/', '')"
+          }
+        ]
+      }
+    ]
   }
 ]