ghga/dcs

ghga

Download Controller Service - a GA4GH DRS-compliant service for delivering files from S3 encrypted a

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Download Controller Service

a GA4GH DRS-compliant service for delivering files from S3 encrypted according to the GA4GH Crypt4GH standard.

Description

This service implements the https://github.com/ga4gh/data-repository-service-schemas v1.0.0 for serving files that where encrypted according to the GA4GH Crypt4GH from S3-compatible object storages.

Thereby, only the GET /objects/{object_id} is implemented. It always returns an access_method for the object via S3. This makes the second endpoint GET /objects/{object_id}/access/{access_id} that is contained in the DRS spec unnecessary. For more details see the OpenAPI spec described below.

For authorization, a JSON web token is expected via Bearer Authentication that has a format described here.

All files that can be requested are registered in a MongoDB database owned and controlled by this service. Registration of new events happens through a Kafka event.

It serves pre-signed URLs to S3 objects located in a single so-called download bucket. If the file is not already in the bucket when the user calls the object endpoint, an event is published to request staging the file to the download bucket. The staging has to be carried out by a different service.

For more details on the events consumed and produced by this service, see the configuration.

The DRS object endpoint serves files in an encrypted fashion as described by the Crypt4GH standard, but without the evelope. A user-specific envelope can be requested from the GET /objects/{object_id}/envelopes endpoint. The actual envelope creation is delegated to another service via a RESTful call. Please see the configuration for further details.

Installation

We recommend using the provided Docker container.

A pre-built version is available at https://hub.docker.com/repository/docker/ghga/download-controller-service:

bash
docker pull ghga/download-controller-service:10.3.0

Or you can build the container yourself from the ./Dockerfile:

bash
# Execute in the repo's root dir:
docker build -t ghga/download-controller-service:10.3.0 .

For production-ready deployment, we recommend using Kubernetes, however, for simple use cases, you could execute the service using docker on a single server:

bash
# The entrypoint is preconfigured:
docker run -p 8080:8080 ghga/download-controller-service:10.3.0 --help

If you prefer not to use containers, you may install the service from source:

bash
# Execute in the repo's root dir:
pip install .

# To run the service:
dcs --help

Configuration

Parameters

The service requires the following configuration parameters:

client_exponential_backoff_max (integer): Maximum number of seconds to wait between retries when using exponential backoff retry strategies. The client timeout might need to be adjusted accordingly. Minimum: 0. Default: 60.
client_num_retries (integer): Number of times to retry failed API calls. Minimum: 0. Default: 3.
client_retry_status_codes (array): List of status codes that should trigger retrying a request. Default: [408, 429, 500, 502, 503, 504].
- Items (integer): Minimum: 0.
client_reraise_from_retry_error (boolean): Specifies if the exception wrapped in the final RetryError is reraised or the RetryError is returned as is. Default: true.
per_request_jitter (number): Max amount of jitter (in seconds) to add to each request. Minimum: 0. Default: 0.0.
retry_after_applicable_for_num_requests (integer): Amount of requests after which the stored delay from a 429 response is ignored again. Can be useful to adjust if concurrent requests are fired in quick succession. Exclusive minimum: 0. Default: 1.
http_request_timeout_seconds (number): Request timeout setting in seconds. Default: 60.0.
ekss_base_url (string, required): URL containing host and port of the EKSS endpoint to retrieve personalized envelope from.

Examples:
```
json
"http://ekss:8080/"
```
enable_opentelemetry (boolean): If set to true, this will run necessary setup code.If set to false, no setup code is run, which leaves tracing disabled. Default: false.
otel_trace_sampling_rate (number): Determines which proportion of spans should be sampled. A value of 1.0 means all and is equivalent to the previous behaviour. Setting this to 0 will result in no spans being sampled, but this does not automatically set enable_opentelemetry to False. Minimum: 0. Maximum: 1. Default: 1.0.
log_level (string): The minimum log level to capture. Must be one of: "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG", or "TRACE". Default: "INFO".
service_name (string): Default: "dcs".
service_instance_id (string, required): A string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id.

Examples:
```
json
"germany-bw-instance-001"
```

log_format: If set, will replace JSON formatting with the specified string format. If not set, has no effect. In addition to the standard attributes, the following can also be specified: timestamp, service, instance, level, correlation_id, and details. Default: null.

Any of
- string
- null

Examples:

json
"%(timestamp)s - %(service)s - %(level)s - %(message)s"

json
"%(asctime)s - Severity: %(levelno)s - %(msg)s"

log_traceback (boolean): Whether to include exception tracebacks in log messages. Default: true.
object_storages (object, required): Can contain additional properties.
- Additional properties: Refer to #/$defs/S3ObjectStorageNodeConfig.
file_deletion_request_topic (string, required): The name of the topic to receive events informing about files to delete.

Examples:
```
json
"file-deletion-requests"
```
file_deletion_request_type (string, required): The type used for events indicating that a request to delete a file has been received.

Examples:
```
json
"file_deletion_requested"
```

file_internally_registered_topic (string, required): Name of the topic used for events indicating that a file has been registered for download.

Examples:

json
"file-registrations"

json
"file-registrations-internal"

file_internally_registered_type (string, required): The type used for event indicating that that a file has been registered for download.

Examples:
```
json
"file_internally_registered"
```
files_to_stage_topic (string, required): Name of the topic used for events indicating that a download was requested for a file that is not yet available in the outbox.

Examples:
```
json
"file-staging-requests"
```
files_to_stage_type (string, required): The type used for non-staged file request events.

Examples:
```
json
"file_staging_requested"
```
file_registered_for_download_topic (string, required): Name of the topic used for events indicating that a file has been registered by the DCS for download.

Examples:
```
json
"file-registrations"
```
```
json
"file-registrations-download"
```
file_registered_for_download_type (string, required): The type used for event indicating that a file has been registered by the DCS for download.

Examples:
```
json
"file_registered_for_download"
```
file_deleted_topic (string, required): Name of the topic used for events indicating that a file has been deleted.

Examples:
```
json
"file-deletions"
```
file_deleted_type (string, required): The type used for events indicating that a file has been deleted.

Examples:
```
json
"file_deleted"
```
download_served_topic (string, required): Name of the topic used for events indicating that a download of a specified file happened.

Examples:
```
json
"file-downloads"
```
download_served_type (string, required): The type used for event indicating that a download of a specified file happened.

Examples:
```
json
"download_served"
```
kafka_servers (array, required): A list of connection strings to connect to Kafka bootstrap servers.
- Items (string)
Examples:
```
json
[
    "localhost:9092"
]
```
kafka_security_protocol (string): Protocol used to communicate with brokers. Valid values are: PLAINTEXT, SSL. Must be one of: "PLAINTEXT" or "SSL". Default: "PLAINTEXT".
kafka_ssl_cafile (string): Certificate Authority file path containing certificates used to sign broker certificates. If a CA is not specified, the default system CA will be used if found by OpenSSL. Default: "".
kafka_ssl_certfile (string): Optional filename of client certificate, as well as any CA certificates needed to establish the certificate's authenticity. Default: "".
kafka_ssl_keyfile (string): Optional filename containing the client private key. Default: "".
kafka_ssl_password (string, format: password, write-only): Optional password to be used for the client private key. Default: "".
generate_correlation_id (boolean): A flag, which, if False, will result in an error when inbound requests don't possess a correlation ID. If True, requests without a correlation ID will be assigned a newly generated ID in the correlation ID middleware function. Default: true.

Examples:
```
json
true
```
```
json
false
```
kafka_max_message_size (integer): The largest message size that can be transmitted, in bytes, before compression. Only services that have a need to send/receive larger messages should set this. When used alongside compression, this value can be set to something greater than the broker's message.max.bytes field, which effectively concerns the compressed message size. Exclusive minimum: 0. Default: 1048576.

Examples:
```
json
1048576
```
```
json
16777216
```
kafka_compression_type: The compression type used for messages. Valid values are: None, gzip, snappy, lz4, and zstd. If None, no compression is applied. This setting is only relevant for the producer and has no effect on the consumer. If set to a value, the producer will compress messages before sending them to the Kafka broker. If unsure, zstd provides a good balance between speed and compression ratio. Default: null.
- Any of
  - string: Must be one of: "gzip", "snappy", "lz4", or "zstd".
  - null
Examples:
```
json
null
```
```
json
"gzip"
```
```
json
"snappy"
```
```
json
"lz4"
```
```
json
"zstd"
```
kafka_max_retries (integer): The maximum number of times to immediately retry consuming an event upon failure. Works independently of the dead letter queue. Minimum: 0. Default: 0.

Examples:
```
json
0
```
```
json
1
```
```
json
2
```
```
json
3
```
```
json
5
```
kafka_enable_dlq (boolean): A flag to toggle the dead letter queue. If set to False, the service will crash upon exhausting retries instead of publishing events to the DLQ. If set to True, the service will publish events to the DLQ topic after exhausting all retries. Default: false.

Examples:
```
json
true
```
```
json
false
```
kafka_dlq_topic (string): The name of the topic used to resolve error-causing events. Default: "dlq".

Examples:
```
json
"dlq"
```
kafka_retry_backoff (integer): The number of seconds to wait before retrying a failed event. The backoff time is doubled for each retry attempt. Minimum: 0. Default: 0.

Examples:
```
json
0
```
```
json
1
```
```
json
2
```
```
json
3
```
```
json
5
```
mongo_dsn (string, format: multi-host-uri, required): MongoDB connection string. Might include credentials. For more information see: [***] Length must be at least 1.

Examples:
```
json
"mongodb://localhost:27017"
```
db_name (string, required): Name of the database located on the MongoDB server.

Examples:
```
json
"my-database"
```
mongo_timeout: Timeout in seconds for API calls to MongoDB. The timeout applies to all steps needed to complete the operation, including server selection, connection checkout, serialization, and server-side execution. When the timeout expires, PyMongo raises a timeout exception. If set to None, the operation will not time out (default MongoDB behavior). Default: null.
- Any of
  - integer: Exclusive minimum: 0.
  - null
Examples:
```
json
300
```
```
json
600
```
```
json
null
```
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
```
migration_max_wait_sec: The maximum number of seconds to wait for migrations to complete before raising an error. Default: null.
- Any of
  - integer
  - null
Examples:
```
json
null
```
```
json
300
```
```
json
600
```
```
json
3600
```
download_bucket_cache_timeout (integer): Time in days since last access after which a file present in the download bucket should be unstaged and has to be requested from permanent storage again for the next request. Default: 7.

Examples:
```
json
7
```
```
json
30
```
drs_server_uri (string, required): The base of the DRS URI to access DRS objects. Has to start with 'drs://' and end with '/'.

Examples:
```
json
"drs://localhost:8080/"
```
staging_speed (integer): When trying to access a DRS object that is not yet in the download bucket, assume that this many megabytes can be staged per second. Default: 100.

Examples:
```
json
100
```
```
json
500
```
retry_after_min (integer): When trying to access a DRS object that is not yet in the download bucket, wait at least this number of seconds before trying again. Default: 5.

Examples:
```
json
5
```
```
json
10
```
retry_after_max (integer): When trying to access a DRS object that is not yet in the download bucket, wait at most this number of seconds before trying again. Default: 300.

Examples:
```
json
30
```
```
json
300
```
presigned_url_expires_after (integer, required): Expiration time in seconds for presigned URLS. Positive integer required. Exclusive minimum: 0.

Examples:
```
json
30
```
```
json
60
```

auth_key (string, required): The GHGA internal public key for validating the token signature.

Examples:

json
"{\"crv\": \"P-256\", \"kty\": \"EC\", \"x\": \"...\", \"y\": \"...\"}"

auth_algs (array): A list of all algorithms used for signing GHGA internal tokens. Default: ["ES256"].
- Items (string)
auth_check_claims (object): A dict of all GHGA internal claims that shall be verified. Can contain additional properties. Default: {"work_type": null, "file_id": null, "user_public_crypt4gh_key": null, "iat": null, "exp": null}.
auth_map_claims (object): A mapping of claims to attributes in the GHGA auth context. Can contain additional properties. Default: {}.
- Additional properties (string)
host (string): IP of the host. Default: "127.0.0.1".
port (integer): Port to expose the server on the specified host. Default: 8080.
auto_reload (boolean): A development feature. Set to True to automatically reload the server upon code changes. Default: false.
workers (integer): Number of workers processes to run. Default: 1.
timeout_keep_alive (integer): The time in seconds to keep an idle connection open for subsequent requests before closing it. This value should be higher than the timeout used by any client or reverse proxy to avoid premature connection closures. Default: 90.

Examples:
```
json
5
```
```
json
90
```
```
json
5400
```
api_root_path (string): Root path at which the API is reachable. This is relative to the specified host and port. Default: "".
openapi_url (string): Path to get the openapi specification in JSON format. This is relative to the specified host and port. Default: "/openapi.json".
docs_url (string): Path to host the swagger documentation. This is relative to the specified host and port. Default: "/docs".
cors_allowed_origins: A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin. Default: null.
- Any of
  - array
    - Items (string)
  - null
Examples:
```
json
[
    "https://example.org",
    "https://www.example.org"
]
```
cors_allow_credentials: Indicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified. Default: null.
- Any of
  - boolean
  - null
Examples:
```
json
[
```


> This README is longer than Docker Hub's 25000-character overview limit, so it has been cut short here. Read the rest on GitHub: https://github.com/ghga-de/ghga/blob/main/services/dcs/README.md

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ghga/dcs

Download Controller Service - a GA4GH DRS-compliant service for delivering files from S3 encrypted a

Download Controller Service

Description

Installation

Configuration

Parameters

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mirrors 不生效