diff --git a/preview/release/drs-1.4.0/docs/index.html b/preview/release/drs-1.4.0/docs/index.html new file mode 100644 index 00000000..54e4ba5c --- /dev/null +++ b/preview/release/drs-1.4.0/docs/index.html @@ -0,0 +1,2761 @@ + + + + + + Data Repository Service + + + + + + + + + +
logo
API docs by Redocly

Data Repository Service (1.4.0)

Download OpenAPI specification:Download

GA4GH Cloud Work Stream: ga4gh-cloud@ga4gh.org License: Apache 2.0 Terms of Service

Introduction

The Data Repository Service (DRS) API provides a generic interface to data repositories so data consumers, including workflow systems, can access data objects in a single, standard way regardless of where they are stored and how they are managed. The primary functionality of DRS is to map a logical ID to a means for physically retrieving the data represented by the ID. The sections below describe the characteristics of those IDs, the types of data supported, how they can be pointed to using URIs, and how clients can use these URIs to ultimately make successful DRS API requests. This document also describes the DRS API in detail and provides information on the specific endpoints, request formats, and responses. This specification is intended for developers of DRS-compatible services and of clients that will call these DRS services.

+

The key words MUST, MUST NOT, REQUIRED, SHALL, SHALL NOT, SHOULD, SHOULD NOT, RECOMMENDED, MAY, and OPTIONAL in this document are to be interpreted as described in RFC 2119.

+

DRS API Principles

DRS IDs

Each implementation of DRS can choose its own id scheme, as long as it follows these guidelines:

+
    +
  • DRS IDs are strings made up of uppercase and lowercase letters, decimal digits, hyphen, period, underscore and tilde [A-Za-z0-9.-_~]. See RFC 3986 § 2.3.
    • +
  • DRS IDs can contain other characters, but they MUST be encoded into valid DRS IDs whenever they are used in API calls. This is because non-encoded IDs may interfere with the interpretation of the objects/{id}/access endpoint. To overcome this limitation use percent-encoding of the ID, see RFC 3986 § 2.4
    • +
  • One DRS ID MUST always return the same object data (or, in the case of a collection, the same set of objects). This constraint aids with reproducibility.
    • +
  • DRS implementations MAY have more than one ID that maps to the same object.
    • +
  • DRS version 1.x does NOT support semantics around multiple versions of an object. (For example, there’s no notion of “get latest version” or “list all versions”.) Individual implementations MAY choose an ID scheme that includes version hints.
    • +
+

DRS URIs

For convenience, including when passing content references to a WES server, we define a URI scheme for DRS-accessible content. This section documents the syntax of DRS URIs, and the rules clients follow for translating a DRS URI into a URL that they use for making the DRS API calls described in this spec.

+

There are two styles of DRS URIs, Hostname-based and Compact Identifier-based, both using the drs:// URI scheme. DRS servers may choose either style when exposing references to their content;. DRS clients MUST support resolving both styles.

+

Tip:

+
+

See Appendix: Background Notes on DRS URIs for more information on our design motivations for DRS URIs.

+
+

Hostname-based DRS URIs

+

Hostname-based DRS URIs are simpler than compact identifier-based URIs. They contain the DRS server name and the DRS ID only and can be converted directly into a fetchable URL based on a simple rule. They take the form:

+
drs://<hostname>/<id>
+
+

DRS URIs of this form mean "you can fetch the content with DRS id <id> from the DRS server at <hostname>". +For example, here are the client resolution steps if the URI is:

+
drs://drs.example.org/314159
+
+
    +
  1. The client parses the string to extract the hostname of “drs.example.org” and the id of “314159”.
    2. +
  2. The client makes a GET request to the DRS server, using the standard DRS URL syntax:
    3. +
+
GET https://drs.example.org/ga4gh/drs/v1/objects/314159
+
+

The protocol is always https and the port is always the standard 443 SSL port. It is invalid to include a different port in a DRS hostname-based URI.

+

Tip:

+
+

See the Appendix: Hostname-Based URIs for information on how hostname-based DRS URI resolution to URLs is likely to change in the future, when the DRS v2 major release happens.

+
+

Compact Identifier-based DRS URIs

+

Compact Identifier-based DRS URIs use resolver registry services (specifically, identifiers.org and n2t.net (Name-To-Thing)) to provide a layer of indirection between the DRS URI and the DRS server name — the actual DNS name of the DRS server is not present in the URI. This approach is based on the Joint Declaration of Data Citation Principles as detailed by Wimalaratne et al (2018).

+

For more information, see the document More Background on Compact Identifiers.

+

Compact Identifiers take the form:

+
drs://[provider_code/]namespace:accession
+
+

Together, provider code and the namespace are referred to as the prefix. The provider code is optional and is used by identifiers.org/n2t.net for compact identifier resolver mirrors. Both the provider_code and namespace disallow spaces or punctuation, only lowercase alphanumerical characters, underscores and dots are allowed (e.g. [A-Za-z0-9._]).

+

Tip:

+
+

See the Appendix: Compact Identifier-Based URIs for more background on Compact Identifiers and resolver registry services like identifiers.org/n2t.net (aka meta-resolvers), how to register prefixes, possible caching strategies, and security considerations.

+
+

For DRS Servers

+

If your DRS implementation will issue DRS URIs based on your own compact identifiers, you MUST first register a new prefix with identifiers.org (which is automatically mirrored to n2t.net). You will also need to include a provider resolver resource in this registration which links the prefix to your DRS server, so that DRS clients can get sufficient information to make a successful DRS GET request. For clarity, we recommend you choose a namespace beginning with drs.

+

For DRS Clients

+

A DRS client parses the DRS URI compact identifier components to extract the prefix and the accession, and then uses meta-resolver APIs to locate the actual DRS server. For example, here are the client resolution steps if the URI is:

+
drs://drs.42:314159
+
+
    +

  1. The client parses the string to extract the prefix of drs.42 and the accession of 314159, using the first occurrence of a colon (":") character after the initial drs:// as a delimiter. (The colon character is not allowed in a Hostname-based DRS URI, making it easy to tell them apart.)

    +
    2. +

  2. The client makes API calls to a meta-resolver to look up the URL pattern for the namespace. (See Calling Meta-Resolver APIs for Compact Identifier-Based DRS URIs for details.) The URL pattern is a string containing a {$id} parameter, such as:

    +
    3. +
+
https://drs.myexample.org/ga4gh/drs/v1/objects/{$id}
+
+
    +
  1. The client generates a DRS URL from the URL template by replacing {$id} with the accession it extracted in step 1. It then makes a GET request to the DRS server:
    2. +
+
GET https://drs.myexample.org/ga4gh/drs/v1/objects/314159
+
+
    +
  1. The client follows any HTTP redirects returned in step 3, in case the resolver goes through an extra layer of redirection.
    2. +
+

For performance reasons, DRS clients SHOULD cache the URL pattern returned in step 2, with a suggested 24 hour cache life.

+

Choosing a URI Style

+

DRS servers can choose to issue either hostname-based or compact identifier-based DRS URIs, and can be confident that compliant DRS clients will support both. DRS clients must be able to accommodate both URI types. Tradeoffs that DRS server builders, and third parties who need to cite DRS objects in datasets, workflows or elsewhere, may want to consider include:

+

Table 1: Choosing a URI Style

+ + + + + + + + + + + + + + + + + + + + + + + +
Hostname-basedCompact Identifier-based
URI DurabilityURIs are valid for as long as the server operator maintains ownership of the published DNS address. (They can of course point that address at different physical serving infrastructure as often as they would like.)URIs are valid for as long as the server operator maintains ownership of the published compact identifier resolver namespace. (They also depend on the meta-resolvers like identifiers.org/n2t.net remaining operational, which is intended to be essentially forever.)
Client EfficiencyURIs require minimal client logic, and no network requests, to resolve.URIs require small client logic, and 1-2 cacheable network requests, to resolve.
SecurityServers have full control over their own security practices.Server operators, in addition to maintaining their own security practices, should confirm they are comfortable with the resolver registry security practices, including protection against denial of service and namespace-hijacking attacks. (See the Appendix: Compact Identifier-Based URIs for more information on resolver registry security.)
+

DRS Datatypes

DRS's job is data access, period. Therefore, the DRS API supports a simple flat content model -- every DrsObject, like a file, represents a single opaque blob of bytes. DRS has no understanding of the meaning of objects and only provides simple domain-agnostic metadata. Understanding the semantics of specific object types is the responsibility of the applications that use DRS to fetch those objects (e.g. samtools for BAM files, DICOM viewers for DICOM objects).

+

Atomic Objects

+

DRS can be used to access individual objects of all kinds, simple or complex, large or small, stored in type-specific formats (e.g. BAM files, VCF files, CSV files). At the API level these are all the same; at the application level, DRS clients and servers are expected to agree on object semantics using non-DRS mechanisms, including but not limited to the GA4GH Data Connect API.

+

Compound Objects

+

DRS can also be used to access compound objects, consisting of two or more atomic objects related to each other in a well-specified way. See the Appendix: Compound Objects for suggested best practices for working with compound objects.

+

[DEPRECATED] Bundles

+

Previous versions of the DRS API spec included support for a bundle content type, which was a folder-like collection of other DRS objects (either blobs or bundles), represented by a DrsObject with a contents array. As of v1.3, bundles have been deprecated in favor of the best practices documented in the Appendix: Compound Objects. A future version of the API spec may remove bundle support entirely and/or replace bundles with a scalable approach based on the needs of our driver projects.

+

Read-only

DRS v1 is a read-only API. We expect that each implementation will define its own mechanisms and interfaces (graphical and/or programmatic) for adding and updating data.

+

Standards

The DRS API specification is written in OpenAPI and embodies a RESTful service philosophy. It uses JSON in requests and responses and standard HTTPS on port 443 for information transport. Optionally, it +supports authentication and authorization using the GA4GH Passport standard.

+

Authorization & Authentication

Making DRS Requests

The DRS implementation is responsible for defining and enforcing an authorization policy that determines which users are allowed to make which requests. GA4GH recommends that DRS implementations use an OAuth 2.0 bearer token or a GA4GH Passport, although they can choose other mechanisms if appropriate.

+

Fetching DRS Objects

The DRS API allows implementers to support a variety of different content access policies, depending on what AccessMethod records they return. Implementers have a choice to make the +GET /objects/{object_id} and GET /objects/{object_id}/access/{access_id} calls open or requiring a Basic, Bearer, or Passport token (Passport requiring a POST). The following describes the +various access approaches following a successful GET/POST /objects/{object_id} request in order to them obtain access to the bytes for a given object ID/access ID:

+
    +
  • public content:
      +
    • server provides an access_url with a url and no headers
      • +
    • caller fetches the object bytes without providing any auth info
      • +
    +
    • +
  • private content that requires the caller to have out-of-band auth knowledge (e.g. service account credentials):
      +
    • server provides an access_url with a url and no headers
      • +
    • caller fetches the object bytes, passing the auth info they obtained out-of-band
      • +
    +
    • +
  • private content that requires the caller to pass an Authorization token:
      +
    • server provides an access_url with a url and headers
      • +
    • caller fetches the object bytes, passing auth info via the specified header(s)
      • +
    +
    • +
  • private content that uses an expensive-to-generate auth mechanism (e.g. a signed URL):
      +
    • server provides an access_id
      • +
    • caller passes the access_id to the /access endpoint
      • +
    • server provides an access_url with the generated mechanism (e.g. a signed URL in the url field)
      • +
    • caller fetches the object bytes from the url (passing auth info from the specified headers, if any)
      • +
    +
    • +
+

In the approaches above GA4GH Passports are not mentioned and that is on purpose. A DRS server may return a Bearer token or other platform-specific token in a header in response to a valid Bearer token or GA4GH Passport (Option 3 above). But it is not the responsibility of a DRS server to return a Passport, that is the responsibility of a Passport Broker and outside the scope of DRS.

+

DRS implementers should ensure their solutions restrict access to targets as much as possible, detect attempts to exploit through log monitoring, and they are prepared to take action if an exploit in their DRS implementation is detected.

+

Authentication

Discovery

+

The APIs to fetch DrsObjects and AccessURLs may require authorization. The authorization mode may vary between DRS objects hosted by a service. The authorization mode may vary between the APIs to fetch a DrsObject and an associated AccessURL. Implementers should indicate how to authenticate to fetch a DrsObject by implementing the OptionsOjbect API. Implementers should indicate how to authenticate to fetch an AccessURL within a DrsObject.

+

Modes

+

BasicAuth

+

A valid authorization token must be passed in the 'Authorization' header, e.g. "Basic ${token_string}"

+ + + + + + + + + + + +
Security Scheme TypeHTTP
HTTP Authorization Schemebasic
+

BearerAuth

+

A valid authorization token must be passed in the 'Authorization' header, e.g. "Bearer ${token_string}"

+ + + + + + + + + + + +
Security Scheme TypeHTTP
HTTP Authorization Schemebearer
+

PassportAuth

+

A valid authorization GA4GH Passport token must be passed in the body of a POST request

+ + + + + + + + + + + +
Security Scheme TypeHTTP
HTTP POSTtokens[]
+

Objects

Get Authorization info about a DrsObject.

Returns a list of Authorizations that can be used to determine how to authorize requests to GetObject or PostObject.

+
Authorizations:
None
path Parameters
object_id
required
string

DrsObject identifier

+

Responses

Response samples

Content type
application/json
{
  • "drs_object_id": "string",
  • "supported_types": [
    ],
  • "passport_auth_issuers": [
    ],
  • "bearer_auth_issuers": [
    ]
}

Get info about a DrsObject.

Returns object metadata, and a list of access methods that can be used to fetch object bytes.

+
Authorizations:
NoneBasicAuthBearerAuth
path Parameters
object_id
required
string

DrsObject identifier

+
query Parameters
expand
boolean

If false and the object_id refers to a bundle, then the ContentsObject array contains only those objects directly contained in the bundle. That is, if the bundle contains other bundles, those other bundles are not recursively included in the result. +If true and the object_id refers to a bundle, then the entire set of objects in the bundle is expanded. That is, if the bundle contains other bundles, then those other bundles are recursively expanded and included in the result. Recursion continues through the entire sub-tree of the bundle. +If the object_id refers to a blob, then the query parameter is ignored.

+

Responses

Response samples

Content type
application/json
{
  • "id": "string",
  • "name": "string",
  • "self_uri": "drs://drs.example.org/314159",
  • "size": 0,
  • "created_time": "2019-08-24T14:15:22Z",
  • "updated_time": "2019-08-24T14:15:22Z",
  • "version": "string",
  • "mime_type": "application/json",
  • "checksums": [
    ],
  • "access_methods": [
    ],
  • "contents": [
    ],
  • "description": "string",
  • "aliases": [
    ]
}

Get info about a DrsObject through POST'ing a Passport.

Returns object metadata, and a list of access methods that can be used to fetch object bytes. +Method is a POST to accommodate a JWT GA4GH Passport sent in the formData in order to authorize access.

+
Authorizations:
PassportAuth
path Parameters
object_id
required
string

DrsObject identifier

+
Request Body schema: application/json
expand
boolean

If false and the object_id refers to a bundle, then the ContentsObject array contains only those objects directly contained in the bundle. That is, if the bundle contains other bundles, those other bundles are not recursively included in the result. +If true and the object_id refers to a bundle, then the entire set of objects in the bundle is expanded. That is, if the bundle contains other bundles, then those other bundles are recursively expanded and included in the result. Recursion continues through the entire sub-tree of the bundle. +If the object_id refers to a blob, then the query parameter is ignored.

+
passports
Array of strings

the encoded JWT GA4GH Passport that contains embedded Visas. The overall JWT is signed as are the individual Passport Visas.

+

Responses

Request samples

Content type
application/json
{
  • "expand": false,
  • "passports": [
    ]
}

Response samples

Content type
application/json
{
  • "id": "string",
  • "name": "string",
  • "self_uri": "drs://drs.example.org/314159",
  • "size": 0,
  • "created_time": "2019-08-24T14:15:22Z",
  • "updated_time": "2019-08-24T14:15:22Z",
  • "version": "string",
  • "mime_type": "application/json",
  • "checksums": [
    ],
  • "access_methods": [
    ],
  • "contents": [
    ],
  • "description": "string",
  • "aliases": [
    ]
}

Get Authorization info about multiple DrsObjects.

Returns a structure that contains for each DrsObjects a list of Authorizations that can be used to determine how to authorize requests to GetObject or PostObject (or bulk equivalents).

+
Authorizations:
None
Request Body schema: application/json
bulk_object_ids
Array of strings

An array of ObjectIDs.

+

Responses

Request samples

Content type
application/json
{
  • "bulk_object_ids": [
    ]
}

Response samples

Content type
application/json
{
  • "summary": {
    },
  • "unresolved_drs_objects": [
    ],
  • "resolved_drs_object": [
    ]
}

Get info about multiple DrsObjects with an optional Passport(s).

Returns an array of object metadata, and a list of access methods that can be used to fetch objects' bytes. Currently this is limited to use passports (one or more) or a single bearer token, so make sure your bulk request is for objects that all use the same passports/token.

+
Authorizations:
PassportAuth
query Parameters
expand
boolean

If false and the object_id refers to a bundle, then the ContentsObject array contains only those objects directly contained in the bundle. That is, if the bundle contains other bundles, those other bundles are not recursively included in the result. +If true and the object_id refers to a bundle, then the entire set of objects in the bundle is expanded. That is, if the bundle contains other bundles, then those other bundles are recursively expanded and included in the result. Recursion continues through the entire sub-tree of the bundle. +If the object_id refers to a blob, then the query parameter is ignored.

+
Request Body schema: application/json
passports
Array of strings

the encoded JWT GA4GH Passport that contains embedded Visas. The overall JWT is signed as are the individual Passport Visas.

+
bulk_object_ids
Array of strings

An array of ObjectIDs.

+

Responses

Request samples

Content type
application/json
{
  • "passports": [
    ],
  • "bulk_object_ids": [
    ]
}

Response samples

Content type
application/json
{
  • "summary": {
    },
  • "unresolved_drs_objects": [
    ],
  • "resolved_drs_object": [
    ]
}

Get a URL for fetching bytes

Returns a URL that can be used to fetch the bytes of a DrsObject. +This method only needs to be called when using an AccessMethod that contains an access_id (e.g., for servers that use signed URLs for fetching object bytes).

+
Authorizations:
NoneBasicAuthBearerAuth
path Parameters
object_id
required
string

DrsObject identifier

+
access_id
required
string

An access_id from the access_methods list of a DrsObject

+

Responses

Response samples

Content type
application/json
{
  • "url": "string",
  • "headers": "Authorization: Basic Z2E0Z2g6ZHJz"
}

Get a URL for fetching bytes through POST'ing a Passport

Returns a URL that can be used to fetch the bytes of a DrsObject. +This method only needs to be called when using an AccessMethod that contains an access_id (e.g., for servers that use signed URLs for fetching object bytes). +Method is a POST to accommodate a JWT GA4GH Passport sent in the formData in order to authorize access.

+
Authorizations:
PassportAuth
path Parameters
object_id
required
string

DrsObject identifier

+
access_id
required
string

An access_id from the access_methods list of a DrsObject

+
Request Body schema: application/json
passports
Array of strings

the encoded JWT GA4GH Passport that contains embedded Visas. The overall JWT is signed as are the individual Passport Visas.

+

Responses

Request samples

Content type
application/json
{
  • "passports": [
    ]
}

Response samples

Content type
application/json
{
  • "url": "string",
  • "headers": "Authorization: Basic Z2E0Z2g6ZHJz"
}

Get URLs for fetching bytes from multiple objects with an optional Passport(s).

Returns an array of URL objects that can be used to fetch the bytes of multiple DrsObjects. +This method only needs to be called when using an AccessMethod that contains an access_id (e.g., for servers that use signed URLs for fetching object bytes). +Currently this is limited to use passports (one or more) or a single bearer token, so make sure your bulk request is for objects that all use the same passports/token.

+
Authorizations:
PassportAuth
Request Body schema: application/json
passports
Array of strings
Array of objects

Responses

Request samples

Content type
application/json
{
  • "passports": [
    ],
  • "bulk_object_access_ids": [
    ]
}

Response samples

Content type
application/json
{
  • "summary": {
    },
  • "unresolved_drs_objects": [
    ],
  • "resolved_drs_object_access_urls": [
    ]
}

Service Info

Retrieve information about this service

Returns information about the DRS service

+

Extends the +v1.0.0 GA4GH Service Info specification +as the standardized format for GA4GH web services to self-describe.

+

According to the +service-info type registry +maintained by the Technical Alignment Sub Committee (TASC), +a DRS service MUST have:

+
    +
  • a type.group value of org.ga4gh
    • +
  • a type.artifact value of drs
    • +
+

e.g.

+
{
+    "id": "com.example.drs",
+    "description": "Serves data according to DRS specification",
+    ...
+    "type": {
+        "group": "org.ga4gh",
+        "artifact": "drs"
+    }
+    ...
+}
+
+

See the Service Registry Appendix for more information on how to register a DRS service with a service registry.

+
Authorizations:
NoneBasicAuthBearerAuth

Responses

Response samples

Content type
application/json
{
  • "id": "org.ga4gh.myservice",
  • "name": "My project",
  • "type": {
    },
  • "description": "This service provides...",
  • "organization": {},
  • "contactUrl": "mailto:support@example.com",
  • "documentationUrl": "https://docs.myservice.example.com",
  • "createdAt": "2019-06-04T12:58:19Z",
  • "updatedAt": "2019-06-04T12:58:19Z",
  • "environment": "test",
  • "version": "1.0.0",
  • "maxBulkRequestLength": 0
}

AccessMethod

type
required
string
Enum: "s3" "gs" "ftp" "gsiftp" "globus" "htsget" "https" "file"

Type of the access method.

+
object

An AccessURL that can be used to fetch the actual object bytes. Note that at least one of access_url and access_id must be provided.

+
access_id
string

An arbitrary string to be passed to the /access method to get an AccessURL. This string must be unique within the scope of a single object. Note that at least one of access_url and access_id must be provided.

+
region
string

Name of the region in the cloud service provider that the object belongs to.

+
object

When access_id is provided, authorizations provides information about how to authorize the /access method.

+
{
  • "type": "s3",
  • "access_url": {
    },
  • "access_id": "string",
  • "region": "us-east-1",
  • "authorizations": {
    }
}

AccessURL

url
required
string

A fully resolvable URL that can be used to fetch the actual object bytes.

+
headers
Array of strings

An optional list of headers to include in the HTTP request to url. These headers can be used to provide auth tokens required to fetch the object bytes.

+
{
  • "url": "string",
  • "headers": "Authorization: Basic Z2E0Z2g6ZHJz"
}

Checksum

checksum
required
string

The hex-string encoded checksum for the data

+
type
required
string

The digest method used to create the checksum. +The value (e.g. sha-256) SHOULD be listed as Hash Name String in the https://www.iana.org/assignments/named-information/named-information.xhtml#hash-alg[IANA Named Information Hash Algorithm Registry]. Other values MAY be used, as long as implementors are aware of the issues discussed in https://tools.ietf.org/html/rfc6920#section-9.4[RFC6920]. +GA4GH may provide more explicit guidance for use of non-IANA-registered algorithms in the future. Until then, if implementers do choose such an algorithm (e.g. because it's implemented by their storage provider), they SHOULD use an existing standard type value such as md5, etag, crc32c, trunc512, or sha1.

+
{
  • "checksum": "string",
  • "type": "sha-256"
}

ContentsObject

name
required
string

A name declared by the bundle author that must be used when materialising this object, overriding any name directly associated with the object itself. The name must be unique within the containing bundle. This string is made up of uppercase and lowercase letters, decimal digits, hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable filenames].

+
id
string

A DRS identifier of a DrsObject (either a single blob or a nested bundle). If this ContentsObject is an object within a nested bundle, then the id is optional. Otherwise, the id is required.

+
drs_uri
Array of strings

A list of full DRS identifier URI paths that may be used to obtain the object. These URIs may be external to this DRS instance.

+
contents
Array of objects (ContentsObject)

If this ContentsObject describes a nested bundle and the caller specified "?expand=true" on the request, then this contents array must be present and describe the objects within the nested bundle.

+
{
  • "name": "string",
  • "id": "string",
  • "drs_uri": "drs://drs.example.org/314159",
  • "contents": [
    ]
}

DrsObject

id
required
string

An identifier unique to this DrsObject

+
name
string

A string that can be used to name a DrsObject. +This string is made up of uppercase and lowercase letters, decimal digits, hyphen, period, and underscore [A-Za-z0-9.-_]. See http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282[portable filenames].

+
self_uri
required
string

A drs:// hostname-based URI, as defined in the DRS documentation, that tells clients how to access this object. +The intent of this field is to make DRS objects self-contained, and therefore easier for clients to store and pass around. For example, if you arrive at this DRS JSON by resolving a compact identifier-based DRS URI, the self_uri presents you with a hostname and properly encoded DRS ID for use in subsequent access endpoint calls.

+
size
required
integer <int64>

For blobs, the blob size in bytes. +For bundles, the cumulative size, in bytes, of items in the contents field.

+
created_time
required
string <date-time>

Timestamp of content creation in RFC3339. +(This is the creation time of the underlying content, not of the JSON object.)

+
updated_time
string <date-time>

Timestamp of content update in RFC3339, identical to created_time in systems that do not support updates. (This is the update time of the underlying content, not of the JSON object.)

+
version
string

A string representing a version. +(Some systems may use checksum, a RFC3339 timestamp, or an incrementing version number.)

+
mime_type
string

A string providing the mime-type of the DrsObject.

+
required
Array of objects (Checksum) non-empty

The checksum of the DrsObject. At least one checksum must be provided. +For blobs, the checksum is computed over the bytes in the blob. +For bundles, the checksum is computed over a sorted concatenation of the checksums of its top-level contained objects (not recursive, names not included). The list of checksums is sorted alphabetically (hex-code) before concatenation and a further checksum is performed on the concatenated checksum value. +For example, if a bundle contains blobs with the following checksums: +md5(blob1) = 72794b6d +md5(blob2) = 5e089d29 +Then the checksum of the bundle is: +md5( concat( sort( md5(blob1), md5(blob2) ) ) ) += md5( concat( sort( 72794b6d, 5e089d29 ) ) ) += md5( concat( 5e089d29, 72794b6d ) ) += md5( 5e089d2972794b6d ) += f7a29a04

+
Array of objects (AccessMethod) non-empty

The list of access methods that can be used to fetch the DrsObject. +Required for single blobs; optional for bundles.

+
Array of objects (ContentsObject)

If not set, this DrsObject is a single blob. +If set, this DrsObject is a bundle containing the listed ContentsObject s (some of which may be further nested).

+
description
string

A human readable description of the DrsObject.

+
aliases
Array of strings

A list of strings that can be used to find other metadata about this DrsObject from external metadata sources. These aliases can be used to represent secondary accession numbers or external GUIDs.

+
{
  • "id": "string",
  • "name": "string",
  • "self_uri": "drs://drs.example.org/314159",
  • "size": 0,
  • "created_time": "2019-08-24T14:15:22Z",
  • "updated_time": "2019-08-24T14:15:22Z",
  • "version": "string",
  • "mime_type": "application/json",
  • "checksums": [
    ],
  • "access_methods": [
    ],
  • "contents": [
    ],
  • "description": "string",
  • "aliases": [
    ]
}

Error

msg
string

A detailed error message.

+
status_code
integer

The integer representing the HTTP status code (e.g. 200, 404).

+
{
  • "msg": "string",
  • "status_code": 0
}

Motivation

+ + + + +
+ Data sharing requires portable data, consistent with the FAIR data principles (findable, accessible, interoperable, reusable). Today’s researchers and clinicians are surrounded by potentially useful data, but often need bespoke tools and processes to work with each dataset. Today’s data publishers don’t have a reliable way to make their data useful to all (and only) the people they choose. And today’s data controllers are tasked with implementing standard controls of non-standard mechanisms for data access. + + + + Figure 1: there’s an ocean of data, with many different tools to drink from it, but no guarantee that any tool will work with any subset of the data + +
+ + + + + + +
+ We need a standard way for data producers to make their data available to data consumers, that supports the control needs of the former and the access needs of the latter. And we need it to be interoperable, so anyone who builds access tools and systems can be confident they’ll work with all the data out there, and anyone who publishes data can be confident it will work with all the tools out there. + + + + Figure 2: by defining a standard Data Repository API, and adapting tools to use it, every data publisher can now make their data useful to every data consumer + +
+ + + + + + +
+ We envision a world where: +
    +
  • + there are many many data consumers, working in research and in care, who can use the tools of their choice to access any and all data that they have permission to see +
    • +
  • + there are many data access tools and platforms, supporting discovery, visualization, analysis, and collaboration +
    • +
  • + there are many data repositories, each with their own policies and characteristics, which can be accessed by a variety of tools +
    • +
  • + there are many data publishing tools and platforms, supporting a variety of data lifecycles and formats +
    • +
  • + there are many many data producers, generating data of all types, who can use the tools of their choice to make their data as widely available as is appropriate +
    • +
+ 		+ + + Figure 3: a standard Data Repository API enables an ecosystem of data producers and consumers + +
+ +

This spec defines a standard Data Repository Service (DRS) API (“the yellow box”), to enable that ecosystem of data producers and consumers. Our goal is that the only thing data consumers need to know about a data repo is "here’s the DRS endpoint to access it", and the only thing data publishers need to know to tap into the world of consumption tools is "here’s how to tell it where my DRS endpoint lives".

+

Federation

The world’s biomedical data is controlled by groups with very different policies and restrictions on where their data lives and how it can be accessed. A primary purpose of DRS is to support unified access to disparate and distributed data. (As opposed to the alternative centralized model of "let’s just bring all the data into one single data repository”, which would be technically easier but is no more realistic than “let’s just bring all the websites into one single web host”.)

+

In a DRS-enabled world, tool builders don’t have to worry about where the data their tools operate on lives — they can count on DRS to give them access. And tool users only need to know which DRS server is managing the data they need, and whether they have permission to access it; they don’t have to worry about how to physically get access to, or (worse) make a copy of the data. For example, if I have appropriate permissions, I can run a pooled analysis where I run a single tool across data managed by different DRS servers, potentially in different locations.

+

Working With Compound Objects

Compound Objects

The DRS API supports access to data objects, with each DrsObject representing a single opaque blob of bytes. Much content (e.g. VCF files) is well represented as a single atomic DrsObject. Some content, however (e.g. DICOM images) is best represented as a compound object consisting of a structured collection of atomic DrsObjects. In both cases, DRS isn't aware of the semantics of the objects it serves -- understanding those semantics is the responsibility of the applications that call DRS.

+

Common examples of compound objects in biomedicine include:

+
    +
  • BAM+BAI genomic reads, with a small index (the BAI object) to large data (the BAM object), each object using a well-defined file format.
    • +
  • DICOM images, with a contents object pointing to one or more raw image objects, each containing pixels from different aspects of a single logical biomedical image (e.g. different z-coordinates)
    • +
  • studies, with a single table of contents listing multiple objects of various types that were generated together and are meant to be processed together
    • +
+

Best Practice: Manifests

As with atomic objects, DRS applications and servers are expected to agree on the semantics of compound objects using non-DRS mechanisms. The recommended best practice for representing a particular compound object type is:

+
    +
  1. Define a manifest file syntax, which contains the DRS IDs of the constituent atomic objects, plus type-specific information about the relationship between those constituents.
      +
    • Manifest file syntax isn't prescribed by the spec, but we expect they will often be JSON files.
      • +
    • For example, for a BAM+BAI pair the manifest file could contain two key-value pairs mapping the type of each constituent file to its DRS ID.
      • +
    +
    2. +
  2. Make manifest objects and their constituent objects available using standard DRS mechanisms -- each object is referenced via its own DRS ID, just like any other atomic object.
      +
    • For example, for a BAM+BAI pair, there would be three DRS IDs -- one for the manifest, one for the BAM, and one for the BAI.
      • +
    +
    3. +
  3. Document the expected client logic for processing compound objects of interest. This logic typically consists of using standard DRS mechanisms to fetch the manifest, parsing its syntax, extracting the DRS IDs of constituent objects, and using standard DRS mechanisms to fetch the constituents as needed.
      +
    • In some cases the application will always want to fetch all of the constituents; in other cases it may want to initially fetch a subset, and only fetch the others on demand. For example, a DICOM image viewer may only want to fetch the layers that are being rendered.
      • +
    +
    4. +
+

Background Notes on DRS URIs

Design Motivation

DRS URIs are aligned with the FAIR data principles and the Joint Declaration of Data Citation Principles — both hostname-based and compact identifier-based URIs provide globally unique, machine-resolvable, persistent identifiers for data.

+
    +
  • We require all URIs to begin with drs:// as a signal to humans and systems consuming these URIs that the response they will ultimately receive, after transforming the URI to a fetchable URL, will be a DRS JSON packet. This signal differentiates DRS URIs from the wide variety of other entities (HTML documents, PDFs, ontology notes, etc.) that can be represented by compact identifiers.
    • +
  • We support hostname-based URIs because of their simplicity and efficiency for server and client implementers.
    • +
  • We support compact identifier-based URIs, and the meta-resolver services of identifiers.org and n2t.net (Name-to-Thing), because of the wide adoption of compact identifiers in the research community. as detailed by Wimalaratne et al (2018) in "Uniform resolution of compact identifiers for biomedical data."
    • +
+

Compact Identifier-Based URIs

Note: Identifiers.org/n2t.net API Changes

+

The examples below show the current API interactions with n2t.net and identifiers.org which may change over time. Please refer to the documentation from each site for the most up-to-date information. We will make best efforts to keep the DRS specification current but DRS clients MUST maintain their ability to use either the identifiers.org or n2t.net APIs to resolve compact identifier-based DRS URIs.

+

Registering a DRS Server on a Meta-Resolver

See the documentation on the n2t.net and identifiers.org meta-resolvers for adding your own compact identifier type and registering your DRS server as a resolver. You can register new prefixes (or mirrors by adding resource provider codes) for free using a simple online form. For more information see More Background on Compact Identifiers.

+

Calling Meta-Resolver APIs for Compact Identifier-Based DRS URIs

Clients resolving Compact Identifier-based URIs need to convert a prefix (e.g. “drs.42”) into a URL pattern. They can do so by calling either the identifiers.org or the n2t.net API, since the two meta-resolvers keep their mapping databases in sync.

+

Calling the identifiers.org API as a Client

+

It takes two API calls to get the URL pattern.

+
    +
  1. The client makes a GET request to identifiers.org to find information about the prefix:
    2. +
+
GET https://registry.api.identifiers.org/restApi/namespaces/search/findByPrefix?prefix=drs.42
+
+

This request returns a JSON structure including various URLs containing an embedded namespace id, such as:

+
"namespace" : {
+  "href":"https://registry.api.identifiers.org/restApi/namespaces/1234"
+}
+
+
    +
  1. The client extracts the namespace id (in this example 1234), and uses it to make a second GET request to identifiers.org to find information about the namespace:
    2. +
+
GET https://registry.api.identifiers.org/restApi/resources/search/findAllByNamespaceId?id=1234
+
+

This request returns a JSON structure including an urlPattern field, whose value is a URL pattern containing a ${id} parameter, such as:

+
"urlPattern" : "https://drs.myexample.org/ga4gh/drs/v1/objects/{$id}"
+
+

Calling the n2t.net API as a Client

+

It takes one API call to get the URL pattern.

+

The client makes a GET request to n2t.net to find information about the namespace. (Note the trailing colon.)

+
GET https://n2t.net/drs.42:
+
+

This request returns a text structure including a redirect field, whose value is a URL pattern containing an $id parameter, such as:

+
redirect: https://drs.myexample.org/ga4gh/drs/v1/objects/$id
+
+

Caching with Compact Identifiers

Identifiers.org/n2t.net compact identifier resolver records do not change frequently. This reality is useful for caching resolver records and their URL patterns for performance reasons. Builders of systems that use compact identifier-based DRS URIs should cache prefix resolver records from identifiers.org/n2t.net and occasionally refresh the records (such as every 24 hours). This approach will reduce the burden on these community services since we anticipate many DRS URIs will be regularly resolved in workflow systems. Alternatively, system builders may decide to directly mirror the registries themselves, instructions are provided on the identifiers.org/n2t.net websites.

+

Security with Compact Identifiers

As mentioned earlier, identifiers.org/n2t.net performs some basic verification of new prefixes and provider code mirror registrations on their sites. However, builders of systems that consume and resolve DRS URIs may have certain security compliance requirements and regulations that prohibit relying on an external site for resolving compact identifiers. In this case, systems under these security and compliance constraints may wish to whitelist certain compact identifier resolvers and/or vet records from identifiers.org/n2t.net before enabling in their systems.

+

Accession Encoding to Valid DRS IDs

The compact identifier format used by identifiers.org/n2t.net does not percent-encode reserved URI characters but, instead, relies on the first ":" character to separate prefix from accession. Since these accessions can contain any characters, and characters like "/" will interfere with DRS API calls, you must percent encode the accessions extracted from DRS compact identifier-based URIs when using as DRS IDs in subsequent DRS GET requests. An easy way for a DRS client to handle this is to get the initial DRS object JSON response from whatever redirects the compact identifier resolves to, then look for the self_uri in the JSON, which will give you the correctly percent-encoded DRS ID for subsequent DRS API calls such as the access method.

+

Additional Examples

For additional examples, see the document More Background on Compact Identifiers.

+

Hostname-Based URIs

Encoding DRS IDs

In hostname-based DRS URIs, the ID is always percent-encoded to ensure special characters do not interfere with subsequent DRS endpoint calls. As such, ":" is not allowed in the URI and is a convenient way of differentiating from a compact identifier-based DRS URI. Also, if a given DRS service implementation uses compact identifier accessions as their DRS IDs, they must be percent encoded before using them as DRS IDs in hostname-based DRS URIs and subsequent GET requests to a DRS service endpoint.

+

GA4GH Service Registry

The GA4GH Service Registry API specification allows information about GA4GH-compliant web services, including DRS services, to be aggregated into registries and made available via a standard API. The following considerations should be followed when registering DRS services within a service registry.

+
    +
  • The DRS service attributes returned by /service-info (i.e. id, name, description, etc.) should have the same values as the registry entry for that service.
    • +
  • The value of the type object's artifact property should be drs (i.e. the same as it appears in service-info)
    • +
  • Each entry in a Service Registry must have a url, indicating the base URL to the web service. For DRS services, the registered url must include everything up to +the standardized /ga4gh/drs/v1 path. Clients should be able to assume that:
      +
    • Adding /ga4gh/drs/v1/objects/{object_id} to the registered url will hit the DrsObject endpoint
      • +
    • Adding /ga4gh/drs/v1/service-info to the registered url will hit the Service Info endpoint
      • +
    +
    • +
+

Example listing of a DRS API registration from a service registry's /services endpoint:

+
[
+    {
+        "id": "com.example.drs",
+        "name": "Example DRS API",
+        "type": {
+            "group": "org.ga4gh",
+            "artifact": "drs",
+            "version": "1.4.0"
+        },
+        "description": "The Data Repository Service (DRS) API ...",
+        "organization": {
+            "id": "com.example",
+            "name": "Example Company"
+        },
+        "contactUrl": "mailto:support@example.com",
+        "documentationUrl": "https://docs.example.com/docs/drs",
+        "createdAt": "2021-08-09T00:00:00Z",
+        "updatedAt": "2021-08-09T12:30:00Z",
+        "environment": "production",
+        "version": "1.13.4",
+        "url": "https://drs-service.example.com"
+    }
+]
+
+
+ + + + \ No newline at end of file