Drop Synapse schemas (#3599)

* Drop schemas

* Add mixin

* Lint and checks

* Lint fixes

* Lint fixes

templates/workspace_services/ohdsi/porter.yaml

@@ -1,7 +1,7 @@
 ---
 schemaVersion: 1.0.0
 name: tre-workspace-service-ohdsi
-version: 0.1.94
+version: 0.2.0
 description: "An OHDSI workspace service"
 registry: azuretre
 dockerfile: Dockerfile.tmpl
@@ -70,6 +70,7 @@ mixins:
       clientVersion: 1.4.6
   - az:
       clientVersion: 2.37.0
+  - exec
 
 outputs:
   - name: connection_uri
@@ -130,6 +131,14 @@ install:
         - name: webapi_uri
         - name: authentication_callback_uri
         - name: is_exposed_externally
+  - exec:
+      description: "Init Synapse Schemas"
+      command: ./synapse_runner.sh
+      envs:
+        DATA_SOURCE_CONFIG: ${ bundle.parameters.data_source_config }
+        DATA_SOURCE_DIAMONS: ${ bundle.parameters.data_source_daimons }
+        TRE_RESOURCE_ID: ${ bundle.parameters.id }
+        SCRIPT_PATH: sql/init_synapse_schemas.sql
 upgrade:
   - az:
       description: "Set Azure Cloud Environment"
@@ -183,3 +192,11 @@ uninstall:
         storage_account_name: ${ bundle.parameters.tfstate_storage_account_name }
         container_name: ${ bundle.parameters.tfstate_container_name }
         key: tre-workspace-service-ohdsi-${ bundle.parameters.id }
+  - exec:
+      description: "Drop Synapse Schemas"
+      command: ./synapse_runner.sh
+      envs:
+        DATA_SOURCE_CONFIG: ${ bundle.parameters.data_source_config }
+        DATA_SOURCE_DIAMONS: ${ bundle.parameters.data_source_daimons }
+        TRE_RESOURCE_ID: ${ bundle.parameters.id }
+        SCRIPT_PATH: sql/drop_synapse_schemas.sql

templates/workspace_services/ohdsi/sql/drop_synapse_schemas.sql

@@ -0,0 +1,30 @@
+/****** Copy Data ******/
+CREATE TABLE #tbl
+WITH
+( DISTRIBUTION = ROUND_ROBIN
+)
+AS
+SELECT  ROW_NUMBER() OVER(ORDER BY (SELECT NULL)) AS Sequence
+,       [name]
+,       'DROP TABLE ' + N'$(RESULTS_SCHEMA_NAME)' + '.' + name AS sql_code
+FROM    sys.tables
+WHERE schema_id = (select schema_id from sys.schemas where name = N'$(RESULTS_SCHEMA_NAME)')
+;
+
+DECLARE @nbr_statements INT = (SELECT COUNT(*) FROM #tbl)
+,       @i INT = 1
+;
+
+WHILE   @i <= @nbr_statements
+BEGIN
+    DECLARE @sql_code NVARCHAR(4000) = (SELECT sql_code FROM #tbl WHERE Sequence = @i);
+    EXEC    sp_executesql @sql_code;
+    SET     @i +=1;
+END
+
+DROP TABLE #tbl;
+
+/****** Drop Schemas ******/
+
+DROP SCHEMA [$(RESULTS_SCHEMA_NAME)];
+DROP SCHEMA [$(TEMP_SCHEMA_NAME)];

templates/workspace_services/ohdsi/synapse_runner.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+set -o errexit
+set -o pipefail
+set -o nounset
+
+if [[ -z ${DATA_SOURCE_CONFIG:-} ]] || [[ -z ${DATA_SOURCE_DIAMONS:-} ]]; then
+  printf 'No data source or daimons configured.'
+  exit 0
+else
+  # Parse Data source
+  ds_config="$(echo "$DATA_SOURCE_CONFIG" | base64 --decode)"
+  ds_daimons="$(echo "$DATA_SOURCE_DIAMONS" | base64 --decode)"
+  dialect="$(jq -r '.dialect' <<< "$ds_config")"
+
+  if [[ $dialect != "Azure Synapse" ]]; then
+    printf 'Not a Synapse data source, no action required.'
+    exit 0
+  fi
+
+  origin_results_schema_name="$(jq -r '.daimon_results' <<< "$ds_daimons")"
+  origin_temp_schema_name="$(jq -r '.daimon_temp' <<< "$ds_daimons")"
+  if [[ -z $origin_results_schema_name ]] || [[ -z $origin_temp_schema_name ]]; then
+    printf 'Results and temp schemas are not configured.'
+    exit 0
+  fi
+
+  # Parse required info
+  admin_user="$(jq -r '.username' <<< "$ds_config")"
+  jdbc_connection_string="$(jq -r '.connection_string' <<< "$ds_config")"
+  synapse_server="$([[ $jdbc_connection_string =~ jdbc:sqlserver://(.*):1433 ]] &&  echo "${BASH_REMATCH[1]}")"
+  synapse_db="$([[ $jdbc_connection_string =~ database=(.*)(;user) ]] &&  echo "${BASH_REMATCH[1]}")"
+  origin_results_schema_name="$(jq -r '.daimon_results' <<< "$ds_daimons")"
+  origin_temp_schema_name="$(jq -r '.daimon_temp' <<< "$ds_daimons")"
+  parsed_resource_id="$(echo "$TRE_RESOURCE_ID" | tr - _ )"
+  results_schema_name="${origin_results_schema_name}_${parsed_resource_id}"
+  temp_schema_name="${origin_temp_schema_name}_${parsed_resource_id}"
+
+  # Export password as required by sqlcmd tool
+  # shellcheck disable=SC2155
+  export SQLCMDPASSWORD="$(jq -r '.password' <<< "$ds_config")"
+
+  printf 'Execute Synapse SQL script'
+  sqlcmd -U "${admin_user}" -S "${synapse_server}" -d "${synapse_db}" -W -v RESULTS_SCHEMA_NAME="${results_schema_name}" -v TEMP_SCHEMA_NAME="${temp_schema_name}" -v ORIGIN_RESULTS_SCHEMA_NAME="${origin_results_schema_name}" -i "${SCRIPT_PATH}"
+  printf 'Execute Synapse SQL script: done.'
+  exit 0
+fi

templates/workspace_services/ohdsi/terraform/data_source.tf

@@ -31,22 +31,3 @@ resource "terraform_data" "add_data_source" {
 
   depends_on = [terraform_data.deployment_atlas_security]
 }
-
-resource "terraform_data" "init_synapse_schemas" {
-  count = local.is_synapse_data_source && local.daimon_results != null && local.daimon_temp != null ? 1 : 0
-
-  provisioner "local-exec" {
-    environment = {
-      ADMIN_USERNAME             = local.data_source_config.username
-      ADMIN_USER_PASSWORD        = local.data_source_config.password
-      SCHEMA_NAME                = local.short_service_id
-      SQL_FILE_PATH              = "../sql/init_results_and_temp_schemas.sql"
-      SYNAPSE_SERVER             = tostring(regex("(?:jdbc:sqlserver://)(.*)(:?:1433)", local.data_source_config.connection_string)[0])
-      SYNAPSE_DATABASE           = tostring(regex("(?:database=)(.*)(:?;user)", local.data_source_config.connection_string)[0])
-      RESULTS_SCHEMA_NAME        = local.results_schema_name
-      TEMP_SCHEMA_NAME           = local.temp_schema_name
-      ORIGIN_RESULTS_SCHEMA_NAME = local.data_source_daimons.daimon_results
-    }
-    command = "../scripts/synapse_runner.sh"
-  }
-}