List of Hub Settings (Incomplete & Work in Progress)

This document is for documenting current available settings (in config.py and config_hub.py in various projects). It is incomplete. Anyone is welcome to add more information.

VERSION_URLS

Type: List[Union[str, Dict[str, str]]]

List of URLs where BioThings Release information JSON documents can be downloaded.

If an element is a dict, then it must have a "name" field indicating its name, and a "url" that points to the JSON document.

If an element is a str then the "name" is extracted from the URL, using the name of the "directory" where the JSON document resides, e.g. the URL "https://biothings-releases.s3.amazonaws.com/mytaxon-mytaxonomy/versions.json" will be assigned a name of "mytaxon-mytaxonomy".

STANDALONE_CONFIG

Type: Dict[str, Dict]

Controls the "Releases" tab in the BioThings Studio Web App.

The "_default" key must be present.

Keys reflect the "name" field of elements in VERSION_URLS, which specifies the settings for Elasticsearch used to install a data release specified in the previous section with a matching name. If the key does not exist, information from "_default" will be used to create the helper classes.

For each of the dictionaries, the following keys are used:

"es_host"

Type: str

Defines the initial/seed host used to establish the connection to the Elasticsearch cluster.

"index"

Type: str

Defines the index/alias that the snapshots will be restored to (destination of installation).

"auth"

Type: Dict[str, Any]

Optional, defines credentials used to authenticate to Elasticsearch cluster. If set, two keys, "type" and "properties" need to be present. The value which "type" points to must be of type str. Currently the following authentication types are supported.

If this is not present in individual items, the one from "_default" will be used; to unset the default, set this to None.

"aws"

Signs requests to AWS managed search (OpenSearch). The three following keys are required "access_id", "secret_key", "region" in the "properties" field, which has a value type of dict. The "service" is assumed to be "es". Note that the role/user associated with the ID must be able to create repositories on the target cluster, and also capable of passing roles.

"http"

Uses HTTP Basic Authentication (see RFC 7235 and RFC 7617, and Elasticsearch Docs). The "properties" field contains a dictionary with keys "username", which refers to the user-id, and "password".

"repo_settings"

Type: dict

Optional, defines additional repository settings to add when creating the snapshot repository. It will be used to update the settings field when creating a repository (see the release JSON format and related Elasticsearch documentation).

If this is not present in individual items, the one from "_default" will be used; to unset the default, set this to None.

Example: Having this

{
    'repo_settings': {'role_arn': 'arn:aws:iam::1234567890:role/ExampleRole'}
}

will result in

{
  "type": "s3",
  "settings": {
    ...,
    "role_arn": "arn:aws:iam::1234567890:role/ExampleRole"
  }
}

when creating the repository. Setting/overwriting the settings defined in the release JSON.

"index_settings"

Type: dict

Not yet implemented.

Optional, defines index settings to change when restoring a snapshot. See related Elasticsearch documentation

The default will not be consulted if this is not present in individual items.