CDM on Synapse dedicated pool

README.md

@@ -34,12 +34,13 @@ Some of the OHDSI projects included:
 
 ## CDM Version
 
-This setup is based on the [CDM v5.4.0 for PostgreSQL](https://github.com/OHDSI/CommonDataModel/tree/main/inst/ddl/5.4/postgresql).
+This setup is based on the [CDM v5.4.0](https://github.com/OHDSI/CommonDataModel/tree/main/inst/ddl/5.4) and supports both PostgreSQL and Azure Synapse.
 
 ## Getting Started
 
 To get started, click on deploy to Azure button.
 To get more detailed instructions, please refer to the [Deployment Guide](./docs/DeploymentGuide.md).
+
 [![Deploy to Azure](https://aka.ms/deploytoazurebutton)](https://portal.azure.com/#create/Microsoft.Template/uri/https%3A%2F%2Fraw.githubusercontent.com%2Fmicrosoft%2FOHDSIonAzure%2Fv2%2Finfra%2Farm_output%2Fmain.json)
 
 ## Contributing

docs/DeploymentGuide.md

@@ -21,17 +21,18 @@ In order to deploy OHDSI on Azure, you will need the following prerequisites:
 | Region                        | The region of the resource group.                                                                             | As the resource group                                         |
 | Location                      | The location of the resources.                                                                                | Resource group location                                       |
 | Suffix                        | The suffix for the resource names.                                                                            | Unique string is being generated                              |
-| CDM Container URL             | The URL prefix or Blob container where CDM files can be downloaded from.           | <https://omoppublic.blob.core.windows.net/shared/synthea1k/> |
-| CDM SAS Token                 | The SAS token for accessing the CDM container. Leave empty if the files are available anonymously.                      | Blank                                                          |
-| Postgres OMOP CDM Database Name| The name of the PostgreSQL OMOP CDM database.                                                                 | Synthea1k                                                          |
+| CDM Container URL             | The URL prefix or Blob container where CDM files can be downloaded from.                                      | <https://omoppublic.blob.core.windows.net/shared/synthea1k/> |
+| CDM SAS Token                 | The SAS token for accessing the CDM container. Leave empty if the files are available anonymously.            | Blank                                                         |
+| OMOP CDM Database Type        | The type of database to host the CDM on. Valid values are: `PostgreSQL`, `Synapse Dedicated Pool`             | PostgreSQL                                                    |
+| OMOP CDM Database Name        | The name of the OMOP CDM database.                                                                            | synthea1k                                                     |
+| OMOP CDM Password             | The admin password for the OMOP CDM database.                                                                 | Unique password is being generated                            |
 | App Plan SKU                  | The SKU for the app plan.                                                                                     | S1                                                            |
 | Postgres SKU                  | The SKU for the PostgreSQL database.                                                                          | Standard_D2s_v3                                               |
 | Postgres Storage Size         | The storage size for the PostgreSQL database.                                                                 | 32                                                            |
 | Postgres Admin Password       | The password for the PostgreSQL admin user.                                                                   | Unique password is being generated                            |
 | Postgres WebAPI Admin Password| The password for the PostgreSQL WebAPI admin user.                                                            | Unique password is being generated                            |
 | Postgres WebAPI App Password  | The password for the PostgreSQL WebAPI app user.                                                              | Unique password is being generated                            |
-| Postgres OMOP CDM Password     | The password for the PostgreSQL OMOP CDM user.                                                                | Unique password is being generated                            |
-| Atlas Security Admin Password | The password for the Atlas security admin user.                                                                | Unique password is being generated                            |
+| Atlas Security Admin Password | The password for the Atlas security admin user.                                                               | Unique password is being generated                            |
 | Atlas Users List             | Atlas Users List              | The list of users for the Atlas system should be provided in the following format: username1,password1,username2,password2' and so on. Ensure usernames and passwords are in the correct order and do not include any additional spaces or characters between the credentials. Note that this format allows you to specify multiple sets of username-password pairs for different users. Make sure each pair is properly formatted and separated by commas. | None                                                          |None                                                          |
 | Local Debug                   | Enable local debugging mode. If enabled, it will create a Firewall rule that will enable unrestricted access to the PostgreSQL database from any location.    | false                                                         |
 

infra/main.bicep

@@ -12,7 +12,7 @@ param cdmContainerUrl string = 'https://omoppublic.blob.core.windows.net/shared/
 param cdmSasToken string = ''
 
 @description('The name of the database to create for the OMOP CDM')
-param postgresOMOPCDMDatabaseName string = 'synthea1k'
+param OMOPCDMDatabaseName string = 'synthea1k'
 
 @description('The app service plan sku')
 @allowed([
@@ -78,7 +78,7 @@ param postgresWebapiAppPassword string = uniqueString(newGuid())
 
 @secure()
 @description('The password for the postgres OMOP CDM user')
-param postgresOMOPCDMPassword string = uniqueString(newGuid())
+param OMOPCDMPassword string = uniqueString(newGuid())
 
 @secure()
 @description('The password for atlas security admin user')
@@ -91,6 +91,14 @@ param atlasUsersList string
 @description('Enables local access for debugging.')
 param localDebug bool = false
 
+@description('OMOP CDM database type')
+@allowed([
+    'PostgreSQL'
+    'Synapse Dedicated Pool'
+  ]
+)
+param cdmDbType string = 'PostgreSQL'
+
 var tenantId = subscription().tenantId
 
 @description('Creates the app service plan')
@@ -182,29 +190,46 @@ module ohdsiWebApiWebapp 'ohdsi_webapi.bicep' = {
   ]
 }
 
-@description('Creates OMOP CDM database')
-module omopCDM 'omop_cdm.bicep' = {
-  name: 'omopCDM'
+@description('Creates OMOP CDM database on Postgres')
+module omopCDMPostgres 'omop_cdm_postgres.bicep' = if (cdmDbType == 'PostgreSQL') {
+  name: 'omopCDMPostgres'
   params: {
     location: location
     keyVaultName: keyVault.name
     cdmContainerUrl: cdmContainerUrl
     cdmSasToken: cdmSasToken
     postgresAtlasDatabaseName: atlasDatabase.outputs.postgresWebApiDatabaseName
-    postgresOMOPCDMDatabaseName: postgresOMOPCDMDatabaseName
+    postgresOMOPCDMDatabaseName: OMOPCDMDatabaseName
     postgresAdminPassword: postgresAdminPassword
     postgresWebapiAdminPassword: postgresWebapiAdminPassword
-    postgresOMOPCDMPassword: postgresOMOPCDMPassword
+    postgresOMOPCDMPassword: OMOPCDMPassword
     postgresServerName: atlasDatabase.outputs.postgresServerName
     ohdsiWebapiUrl: ohdsiWebApiWebapp.outputs.ohdsiWebapiUrl
   }
-
   dependsOn: [
     ohdsiWebApiWebapp
     atlasDatabase
   ]
 }
 
+@description('Creates OMOP CDM database on Synapse')
+module omopCDMSynapse 'omop_cdm_synapse.bicep' = if (cdmDbType == 'Synapse Dedicated Pool') {
+  name: 'omopCDMSynapse'
+  params: {
+    location: location
+    suffix: suffix
+    keyVaultName: keyVault.name
+    cdmContainerUrl: cdmContainerUrl
+    cdmSasToken: cdmSasToken    
+    databaseName: OMOPCDMDatabaseName
+    sqlAdminPassword: OMOPCDMPassword
+    ohdsiWebapiUrl: ohdsiWebApiWebapp.outputs.ohdsiWebapiUrl
+  }
+  dependsOn: [
+    ohdsiWebApiWebapp
+  ]
+}
+
 @description('Creates the ohdsi atlas UI')
 module atlasUI 'ohdsi_atlas_ui.bicep' = {
   name: 'atlasUI'
@@ -294,7 +319,7 @@ resource deplymentAddDataSource 'Microsoft.Resources/deploymentScripts@2020-10-0
     environmentVariables: [
       {
         name: 'CONNECTION_STRING'
-        secureValue: 'jdbc:postgresql://${atlasDatabase.outputs.postgresServerFullyQualifiedDomainName}:5432/${postgresOMOPCDMDatabaseName}?user=postgres_admin&password=${postgresOMOPCDMPassword}&sslmode=require'
+        secureValue: cdmDbType == 'PostgreSQL' ? 'jdbc:postgresql://${atlasDatabase.outputs.postgresServerFullyQualifiedDomainName}:5432/${OMOPCDMDatabaseName}?user=postgres_admin&password=${OMOPCDMPassword}&sslmode=require' : omopCDMSynapse.outputs.OmopCdmJdbcConnectionString
       }
       {
         name: 'OHDSI_WEBAPI_PASSWORD'
@@ -310,7 +335,7 @@ resource deplymentAddDataSource 'Microsoft.Resources/deploymentScripts@2020-10-0
       }
       {
         name: 'DIALECT'
-        value: 'postgresql'
+        value: cdmDbType == 'PostgreSQL' ? 'postgresql' : 'synapse'
       }
       {
         name: 'SOURCE_NAME'
@@ -346,6 +371,7 @@ resource deplymentAddDataSource 'Microsoft.Resources/deploymentScripts@2020-10-0
   dependsOn: [
     deploymentAtlasSecurity
     ohdsiWebApiWebapp
-    omopCDM
+    omopCDMPostgres
+    omopCDMSynapse
   ]
 }

infra/omop_cdm.bicep → infra/omop_cdm_postgres.bicep

@@ -49,6 +49,7 @@ var postgresWebapiAdminUsername = 'ohdsi_admin_user'
 var postgresAdminUsername = 'postgres_admin'
 var postgresOMOPCDMJDBCConnectionString = 'jdbc:postgresql://${postgresServer.properties.fullyQualifiedDomainName}:5432/${postgresOMOPCDMDatabaseName}?user=${postgresOMOPCDMUsername}&password=${postgresOMOPCDMPassword}&sslmode=require'
 
+
 // Get the postgres server
 resource postgresServer 'Microsoft.DBforPostgreSQL/flexibleServers@2022-12-01' existing = {
   name: postgresServerName
@@ -152,16 +153,20 @@ resource deploymentScript 'Microsoft.Resources/deploymentScripts@2020-10-01' = {
         name: 'POSTGRES_OMOP_TEMP_SCHEMA_NAME'
         value: postgresOMOPTempSchemaName
       }
+      {
+        name: 'OHDSI_WEBAPI_URL'
+        value: ohdsiWebapiUrl
+      }
       {
         name: 'SQL_create_omop_schemas'
-        value: loadTextContent('sql/create_omop_schemas.sql')
+        value: loadTextContent('sql/create_omop_schemas_postgres.sql')
       }
       {
-        name: 'SQL_create_achilles_schema'
-        value: loadTextContent('sql/create_achilles_schema.sql')
+        name: 'SQL_create_achilles_tables'
+        value: loadTextContent('sql/create_achilles_tables_postgres.sql')
       }
     ]
-    scriptContent: loadTextContent('scripts/create_omop_cdm.sh')
+    scriptContent: loadTextContent('scripts/create_omop_cdm_postgres.sh')
     supportingScriptUris: [
       'https://raw.githubusercontent.com/OHDSI/CommonDataModel/main/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql'
       'https://raw.githubusercontent.com/OHDSI/CommonDataModel/main/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_constraints.sql'
@@ -175,3 +180,5 @@ resource deploymentScript 'Microsoft.Resources/deploymentScripts@2020-10-01' = {
     }
   }
 }
+
+output OmopCdmJdbcConnectionString string = postgresOMOPCDMJDBCConnectionString