ghga/rts

ghga/rts repository overview

⁠Reverse Transpiler Service

Reverse Transpiler Service - A service running a REST API that serves accessioned metadata files by study ID

The service ships as the container image ghga/rts and the Helm chart rts⁠.

⁠Description

The service consumes the artifact events that carry a study's accessioned metadata as JSON, converts the metadata back into a spreadsheet workbook, and serves the workbook in .xlsx format by study ID over its REST API.

⁠Usage

The executable rts takes one of these commands:

run-rest runs the HTTP REST API
consume-events runs an event consumer listening to the configured topics
migrate-db runs the database migrations

Running a service⁠ shows how to start, build and deploy it.

⁠Configuration

The settings take the prefix rts: the environment variable RTS_HOST sets host, and the YAML file is .rts.yaml. example_config.yaml⁠ holds a complete set to adapt, and Configuration⁠ says where the service looks for them.

⁠Parameters

The service requires the following configuration parameters:

artifact_topic (string, required): Name of the event topic containing artifact events.

Examples:
```
"artifacts"
```
mongo_dsn (string, format: multi-host-uri, required): MongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/⁠. Length must be at least 1.

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

Examples:
```
"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:
```
300
```
```
600
```
```
null
```
db_version_collection (string, required): The name of the collection containing DB version information for this service.

Examples:
```
"ifrsDbVersions"
```
migration_wait_sec (integer, required): The number of seconds to wait before checking the DB version again.

Examples:
```
5
```
```
30
```
```
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:
```
null
```
```
300
```
```
600
```
```
3600
```
service_name (string): Short name of this service. Default: "rts".
service_instance_id (string, required): A string that uniquely identifies this instance across all instances of this service. This is included in log messages.

Examples:
```
"germany-bw-instance-001"
```
kafka_servers (array, required): A list of connection strings to connect to Kafka bootstrap servers.
- Items (string)
Examples:
```
[
    "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:
```
true
```
```
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:
```
1048576
```
```
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:
```
null
```
```
"gzip"
```
```
"snappy"
```
```
"lz4"
```
```
"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:
```
0
```
```
1
```
```
2
```
```
3
```
```
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:
```
true
```
```
false
```
kafka_dlq_topic (string): The name of the topic used to resolve error-causing events. Default: "dlq".

Examples:
```
"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:
```
0
```
```
1
```
```
2
```
```
3
```
```
5
```
log_level (string): The minimum log level to capture. Must be one of: "CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG", or "TRACE". Default: "INFO".
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:
```
"%(timestamp)s - %(service)s - %(level)s - %(message)s"
```
```
"%(asctime)s - Severity: %(levelno)s - %(msg)s"
```
log_traceback (boolean): Whether to include exception tracebacks in log messages. Default: true.
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:
```
5
```
```
90
```
```
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:
```
[
    "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:
```
[
    "https://example.org",
    "https://www.example.org"
]
```
cors_allowed_methods: A list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods. Default: null.
- Any of
  - array
    - Items (string)
  - null
Examples:
```
[
    "*"
]
```
cors_allowed_headers: A list of HTTP request headers that should be supported for cross-origin requests. Defaults to []. You can use ['*'] to allow all request headers. The Accept, Accept-Language, Content-Language, Content-Type and some are always allowed for CORS requests. Default: null.
- Any of
  - array
    - Items (string)
  - null
Examples:
```
[]
```
cors_exposed_headers: A list of HTTP response headers that should be exposed for cross-origin responses. Defaults to []. Note that you can NOT use ['*'] to expose all response headers. The Cache-Control, Content-Language, Content-Length, Content-Type, Expires, Last-Modified and Pragma headers are always exposed for CORS responses. Default: null.
- Any of
  - array
    - Items (string)
  - null
Examples:
```
[]
```
sheet_names (object, required): Mapping of worksheet names to display names in the workbook. Can contain additional properties.
- Additional properties (string): Length must be between 1 and 31 (inclusive).
Examples:
```
{
    "analyses": "Analysis",
    "analysis_method_supporting_files": "AnalysisMethodSupportingFile"
}
```

⁠HTTP API

The service's OpenAPI specification is in openapi.yaml⁠.

⁠Architecture and Design

This is a Python-based service following the Triple Hexagonal Architecture pattern. It uses protocol/provider pairs and dependency injection mechanisms provided by the hexkit⁠ library.

⁠License

This repository is free to use and modify according to the Apache 2.0 License⁠.

Tag summary

Recent tags

Content type

Image

Digest

sha256:01d19a5bf…

Size

60.7 MB

Last updated

about 1 hour ago

docker pull ghga/rts:15.4.0-rc.2

This week's pulls

Pulls:

2,627

Oct 26 to Nov 1

Learn more⁠