Add encrypted_size migration to DCS

services/dcs/README.md

@@ -299,6 +299,36 @@ The service requires the following configuration parameters:
   ```
 
 
+- **`db_version_collection`** *(string, required)*: The name of the collection containing DB version information for this service.
+
+
+  Examples:
+
+  ```json
+  "ifrsDbVersions"
+  ```
+
+
+- **`migration_wait_sec`** *(integer, required)*: The number of seconds to wait before checking the DB version again.
+
+
+  Examples:
+
+  ```json
+  5
+  ```
+
+
+  ```json
+  30
+  ```
+
+
+  ```json
+  180
+  ```
+
+
 - **`drs_server_uri`** *(string, required)*: The base of the DRS URI to access DRS objects. Has to start with 'drs://' and end with '/'.
 
 

services/dcs/config_schema.json

@@ -330,6 +330,24 @@
       "title": "Db Name",
       "type": "string"
     },
+    "db_version_collection": {
+      "description": "The name of the collection containing DB version information for this service",
+      "examples": [
+        "ifrsDbVersions"
+      ],
+      "title": "Db Version Collection",
+      "type": "string"
+    },
+    "migration_wait_sec": {
+      "description": "The number of seconds to wait before checking the DB version again",
+      "examples": [
+        5,
+        30,
+        180
+      ],
+      "title": "Migration Wait Sec",
+      "type": "integer"
+    },
     "drs_server_uri": {
       "description": "The base of the DRS URI to access DRS objects. Has to start with 'drs://' and end with '/'.",
       "examples": [
@@ -586,6 +604,8 @@
     "kafka_servers",
     "db_connection_str",
     "db_name",
+    "db_version_collection",
+    "migration_wait_sec",
     "drs_server_uri",
     "ekss_base_url",
     "presigned_url_expires_after",

services/dcs/dev_config.yaml

@@ -39,5 +39,7 @@ unstaged_download_collection: unstagedDownloadRequested
 files_to_delete_topic: file-deletions
 file_deleted_event_topic: file-downloads
 file_deleted_event_type: file_deleted
+db_version_collection: dcsDbVersions
+migration_wait_sec: 10
 auth_key: "{}"
 log_level: INFO

services/dcs/example_config.yaml

@@ -20,6 +20,7 @@ cors_allowed_methods: []
 cors_allowed_origins: []
 db_connection_str: '**********'
 db_name: dev
+db_version_collection: dcsDbVersions
 docs_url: /docs
 download_served_event_topic: file-downloads
 download_served_event_type: download_served
@@ -45,6 +46,7 @@ kafka_ssl_password: ''
 log_format: null
 log_level: INFO
 log_traceback: true
+migration_wait_sec: 10
 object_storages:
   test:
     bucket: outbox

services/dcs/openapi.yaml

@@ -206,7 +206,7 @@ info:
     \ Object Storage. \n\nThis is an implementation of the DRS standard from the Global\
     \ Alliance for Genomics and Health, please find more information at: https://github.com/ga4gh/data-repository-service-schemas"
   title: Download Controller Service
-  version: 4.0.0
+  version: 3.0.0
 openapi: 3.1.0
 paths:
   /health:

services/dcs/src/dcs/config.py

@@ -22,7 +22,6 @@
 from hexkit.config import config_from_yaml
 from hexkit.log import LoggingConfig
 from hexkit.providers.akafka import KafkaConfig
-from hexkit.providers.mongodb import MongoDbConfig
 from pydantic import Field
 
 from dcs.adapters.inbound.event_sub import (
@@ -33,6 +32,7 @@
 from dcs.adapters.outbound.daopub import OutboxDaoConfig
 from dcs.adapters.outbound.event_pub import EventPubTranslatorConfig
 from dcs.core.data_repository import DataRepositoryConfig
+from dcs.migration_logic import MigrationConfig
 
 
 class WorkOrderTokenConfig(AuthConfig):
@@ -54,7 +54,7 @@ class Config(
     DrsApiConfig,
     WorkOrderTokenConfig,
     DataRepositoryConfig,
-    MongoDbConfig,
+    MigrationConfig,
     KafkaConfig,
     EventPubTranslatorConfig,
     EventSubTranslatorConfig,

services/dcs/src/dcs/migration_logic/__init__.py

@@ -0,0 +1,34 @@
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Temporary database migration logic, copied from IFRS until added to hexkit"""
+
+from ._manager import (
+    MigrationConfig,
+    MigrationManager,
+    MigrationMap,
+    MigrationStepError,
+)
+from ._utils import Document, MigrationDefinition, Reversible, validate_doc
+
+__all__ = [
+    "Document",
+    "MigrationConfig",
+    "MigrationDefinition",
+    "MigrationManager",
+    "MigrationMap",
+    "MigrationStepError",
+    "Reversible",
+    "validate_doc",
+]