bedhost

bedhost is a Python FastAPI module for the API that powers BEDbase. It needs a path to the bedbase configuration file, which can be provided either via -c/--config argument or read from $BEDBASE_CONFIG environment variable.

Introduction

You can find the formal OpenAPI documentation and interactive interface at https://api.bedbase.org/v1/docs. This document provides more conceptual introduction and explanations to how to use the API effectively.

General API organization

Data types

BEDbase stores two types of data, which we call records. They are 1. BEDs, and 2. BEDsets. BEDsets are simply collections of BEDs. Each record in the database is either a BED or a BEDset.

Endpoint organization

The endpoints are divided into 3 groups:

1. /bed endpoints are used to interact with metadata for BED records.
2. /bedset endpoints are used to interact with metadata for BEDset records.
3. /objects endpoints are used to download metadata and get URLs to retrieve the underlying data itself. These endpoints implement the GA4GH DRS standard.

Therefore, to get information and statistics about BED or BEDset records, or what is contained in the database, look through the /bed and /bedset endpoints. But if you need to write a tool that gets the actual underlying files, then you'll need to use the /objects endpoints. The type of identifiers used in each case differ.

Record identifiers vs. object identifiers

Each record has an identifier. For example, 0000120fe8c5334bb0ce759dfcf06c3b is a BED identifier. You can use this identifier for the metadata endpoints. To download files, you'll need something slightly different -- you need an object identifier. This is because each BED record includes multiple files, such as the original BED file, the BigBed file, analysis plots, and so on. To download a file, you will construct what we call the object_id, which identifies the specific file.

How to construct object identifiers

Object IDs take the form <record_type>.<record_identifier>.<result_id>. An example of an object_id for a BED file is bed.0000120fe8c5334bb0ce759dfcf06c3b.bed_file

So, you can get information about this object like this:

GET https://api.bedbase.org/v1/objects/bed.0000120fe8c5334bb0ce759dfcf06c3b.bed_file

Or, you can get a URL to download the actual file with:

GET https://api.bedbase.org/v1/objects/bed.0000120fe8c5334bb0ce759dfcf06c3b.bed_file/access/http