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openapi: 3.0.0
servers:
- url: /rnaget
info:
title: RNAget API
description: |
## Design principles
This API provides a means of retrieving data from several types of RNA experiments including:
* Feature-level expression data from RNA-seq type measurements
* Coordinate-based signal/intensity data similar to a bigwig representation
via a client/server model.
Features of this API include:
* Support for a hierarchical data model which provides the option for servers to associate expression data for discovery and retrieval
* Support for accessing subsets of expression data through slicing operations on the expression matrix and/or query filters to specify features to be included
* Support for accessing signal/intensity data by specifying a range of genomic coordinates to be included
Out of the scope of this API are:
* A means of retrieving primary (raw) read sequence data. Input samples are identified in expression output and data servers should implement additional API(s) to allow for search and retrieval of raw reads. The [htsget API](https://samtools.github.io/hts-specs/htsget.html) is designed for retrieval of read data.
* A means of retrieving reference sequences. Servers should implement additional API(s) to allow for search and retrieval of reference base sequences. The [refget API](https://samtools.github.io/hts-specs/refget.html) is designed for retrieval of references sequences.
* A means of retrieving feature annotation details. Expression matrices provide the identity of each mapped feature. Servers should implement additional API(s) to allow for search and retrieval of genomic feature annotation details.
## OpenAPI Description
An OpenAPI description of this specification is available and [describes the 1.0.0 version](rnaget-openapi.yaml). OpenAPI is an independent API description format for describing REST services and is compatible with a number of [third party tools](http://openapi.tools/).
## Compliance
Implementors can check if their RNAget implementations conform to the
specification by using our [compliance suite](https://github.com/ga4gh-rnaseq/rnaget-compliance-suite).
## Protocol essentials
All API invocations are made to a configurable HTTPS endpoint, receive URL-encoded query string parameters and HTTP headers, and return text or other allowed formatting as requested by the user. Queries containing [unsafe or reserved](https://www.ietf.org/rfc/rfc1738.txt) characters in the URL, including but not limited to "&", "/", "#", MUST encode all such characters. Successful requests result with HTTP status code 200 and have the appropriate text encoding in the response body as defined for each endpoint. The server may provide responses with chunked transfer encoding. The client and server may mutually negotiate HTTP/2 upgrade using the standard mechanism.
HTTP responses may be compressed using [RFC 2616](https://www.w3.org/Protocols/rfc2616/rfc2616-sec3.html) transfer-coding, not content-coding.
HTTP response may include a 3XX response code and Location header redirecting the client to retrieve expression data from an alternate location as specified by [RFC 7231](https://tools.ietf.org/html/rfc7231), clients SHOULD be configured to follow redirects. `302`, `303` and `307` are all valid response codes to use.
Responses from the server MUST include a Content-Type header containing the encoding for the invoked method and protocol version. Unless negotiated with the client and allowed by the server, the default encoding is:
```
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json; charset=us-ascii
```
All response objects from the server are expected to be in JSON format, regardless of the response status code, unless otherwise negotiated with the client and allowed by the server.
Object IDs are intended for persistent retrieval of their respective objects. An object ID MUST uniquely identify an object within the scope of a single data server. It is beyond the scope of this API to enforce uniqueness of ID among different data servers. IDs are strings made up of uppercase and lowercase letters, decimal digits, hypen, period, underscore and tilde [A-Za-z0-9.-_~]. See [RFC 3986 § 2.3](https://tools.ietf.org/html/rfc3986#section-2.3).
Endpoints are described as HTTPS GET methods which will be sufficient for most queries. Queries containing multiple metadata filters may approach or exceed the URL length limits. To handle these types of queries it is recommended that servers SHOULD implement parallel HTTPS POST endpoints accepting the same URL parameters as a UTF8-encoded JSON key-value dictionary.
When processing requests containing multiple filters and filters with lists of items, the data provider MUST use a logical `AND` for selecting the results to return.
## Internet Media Types Handling
When responding to a request a server MUST use the fully specified media type for that endpoint. When determining if a request is well-formed, a server MUST allow a internet type to degrade like so
- `application/vnd.ga4gh.rnaget.v1.0.0+json; charset=us-ascii`
- `application/vnd.ga4gh.rnaget.v1.0.0+json`
- `application/json`
## Errors
The server MUST respond with an appropriate HTTP status code (4xx or 5xx) when an error condition is detected. In the case of transient server errors (e.g., 503 and other 5xx status codes), the client SHOULD implement appropriate retry logic. For example, if a client sends an alphanumeric string for a parameter that is specified as unsigned integer the server MUST reply with `Bad Request`.
| Error type | HTTP status code | Description
|-------------------|------------------|-------------|
| `Bad Request` | 400 | Cannot process due to malformed request, the requested parameters do not adhere to the specification |
| `Unauthorized` | 401 | Authorization provided is invalid |
| `Not Found` | 404 | The resource requested was not found |
| `Not Acceptable` | 406 | The requested formatting is not supported by the server |
| `Not Implemented` | 501 | The specified request is not supported by the server |
## Security
The RNAget API can be used to retrieve potentially sensitive genomic data and is dependent on the implementation. Effective security measures are essential to protect the integrity and confidentiality of these data.
Sensitive information transmitted on public networks, such as access tokens and human genomic data, MUST be protected using Transport Level Security (TLS) version 1.2 or later, as specified in [RFC 5246](https://tools.ietf.org/html/rfc5246).
If the data holder requires client authentication and/or authorization, then the client's HTTPS API request MUST present an OAuth 2.0 bearer access token as specified in [RFC 6750](https://tools.ietf.org/html/rfc6750), in the Authorization request header field with the Bearer authentication scheme:
```
Authorization: Bearer [access_token]
```
Data providers SHOULD verify user identity and credentials. The policies and processes used to perform user authentication and authorization, and the means through which access tokens are issued, are beyond the scope of this API specification. GA4GH recommends the use of the OAuth 2.0 framework ([RFC 6749](https://tools.ietf.org/html/rfc6749)) for authentication and authorization. It is also recommended that implementations of this standard also implement and follow the GA4GH [Authentication and Authorization Infrastructure (AAI) standard](https://docs.google.com/document/d/1zzsuNtbNY7agPRjfTe6gbWJ3BU6eX19JjWRKvkFg1ow).
## CORS
Cross-origin resource sharing (CORS) is an essential technique used to overcome the same origin content policy seen in browsers. This policy restricts a webpage from making a request to another website and leaking potentially sensitive information. However the same origin policy is a barrier to using open APIs. GA4GH open API implementers should enable CORS to an acceptable level as defined by their internal policy. For any public API implementations should allow requests from any server.
GA4GH is publishing a [CORS best practices document](https://docs.google.com/document/d/1Ifiik9afTO-CEpWGKEZ5TlixQ6tiKcvug4XLd9GNcqo/edit?usp=sharing), which implementers should refer to for guidance when enabling CORS on public API instances.
## Possible Future API Enhancements
- Allow OR for search filters
- Report size of download file
- Matrix slicing with bool array or list of indices
## API specification change log
1.0.0 Initial release version
version: 1.0.0
contact:
name: GA4GH RNA-seq Working Group
email: ga4gh-rnaseq@ga4gh.org
license:
name: Apache 2.0
url: https://github.com/ga4gh-rnaseq/schema/blob/master/LICENSE
externalDocs:
description: Find out more about GA4GH
url: http://ga4gh.org
tags:
- name: projects
description: |
The project is the top level of the model hierarchy and contains a set of related studies. Example projects include:
* all data submitted by contributor X
* the local mirror of the European Nucleotide Archive data
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
- name: studies
description: |
The study is a set of related RNA expression values. It is assumed all samples in a study have been processed uniformly. Example studies include:
* multiple tissues from all patients enrolled in clinical trial X
* a collection of liver samples from several sources which have been uniformly reprocessed for differential analysis
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
- name: expressions
description: |
The expression is a matrix of calculated expression values.
##### Expression metadata
This describes a set of minimal metadata appropriate for several types of RNA experiments. The purpose is to define a common naming scheme for metadata to enable client software to have some expectation of data fields for improved interoperability. These definitions are not intended to be a comprehensive set of metadata and defining such a universal set is beyond the scope of this effort.
Where possible details are incorporated by reference. This is to reduce the final size of matrix files, support existing metadata standards and support server-defined metadata fields.
All field names are presented here in camel case. Parsers should treat field names as case-insensitive and any white space contained in the field names should be ignored:
sampleID == sampleid == Sample ID != sample_id
All fields are optional. Fields that utilize an ontology term assume both an id and a label. Later implementations will utilize schemablocks and/or Phenopackets as referenced entities.
| Metadata Field | Description
|------------------|-------------|
| sampleID | an identifier for the biological specimen the experiment was conducted on. This id MUST uniquely identify the sample within the scope of the server |
| assayType | the type of experiment performed (ex. RNA-seq, ATAC-seq, ChIP-seq, DNase-Hypersensitivity, methylation profiling, histone profiling, microRNA profiling, transcription profiling, WGS) |
| samplePrepProtocol | reference to a resource or webpage describing the protocol used to obtain and prepare the sample |
| libraryPrepProtocol | reference to a resource or webpage describing the protocol used to prepare the library for sequencing |
| annotation | a reference to the specific annotation used for quantifying the reads |
| analysisPipeline | reference to a resource or webpage describing the analysis protocol. This description should include a full listing of all software used including the exact version and command line options used. If containerized software is used a reference to the specific containers should be included. The GA4GH [Tool Registry Service](https://github.com/ga4gh/tool-registry-service-schemas) is a resource for discovering and registering genomic tools and workflows. |
| cellTypeID | a cell type term ID |
| cellTypeLabel | a cell type term label from the [CL ontology](http://www.ontobee.org/ontology/CL) |
| phenotypeID | phenotype ID applicable to the sample |
| phenotypeLabel | phenotype term (recommended ontologies: [Human Phenotype Ontology](http://www.human-phenotype-ontology.org/), [NCIT](http://www.obofoundry.org/ontology/ncit.html), or [ICD](https://www.icd10data.com/)) |
| sexID | sex ID of the organism providing the sample |
| sexTerm | sex label of the organism providing the sample [PATO 47 term](http://purl.obolibrary.org/obo/PATO_0000047) |
| organismID | organism ID for the sample origin |
| organismlabel | organism label for the sample origin [NCBITaxon](http://www.obofoundry.org/ontology/ncbitaxon.html) |
| tissueID | tissue ID of origin or organism part of origin |
| tissueLabel | tissue Label of origin or organism part of origin (recommended to use [Uberon](http://www.obofoundry.org/ontology/uberon.html) |
| cellLineID | ID of cell line |
| cellLineLabel | Label of [cell line](http://www.ontobee.org/ontology/CLO) |
For metadata ID values it is recommended that implementors use the `id:label` CURIE notation as described in [Identifiers and CURIEs](https://schemablocks.org/standards/identifiers-curies.html)
#### Example metadata using CURIE
| Metadata Field | Value
|------------------|------------------|
| `organismID` | `NCBITaxon:9606` |
| `organismLabel` | `human` |
##### The meaning of zero
Microarray and image-based RNA-seq (Seq-FISH etc.) have a dependency on probes which may not have 100% coverage of the annotation reference. The consequence is that some features which show zero expression may not necessarily have a truly zero expression. This idea can be extended further in the context of submitted data as well as potentially access restricted data. The result is that a zero value can indicate one of several states:
1. _Not measured_ - not measured at all and value is not available
2. _Not supplied_ - measured but not provided to the data repository
3. _Restricted access_ - measured but require further authentication to view
4. _Not applicable_ - measurement does not apply to the sample
If applicable, the `NaN` value MUST be used to indicate these states.
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
- name: continuous
description: Continuous is a matrix of coordinate range based signal data
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
- name: projectModel
x-displayName: The Project Model
description: |
<SchemaDefinition schemaRef="#/components/schemas/project" />
- name: studyModel
x-displayName: The Study Model
description: |
<SchemaDefinition schemaRef="#/components/schemas/study" />
- name: filterModel
x-displayName: The Filter Model
description: |
<SchemaDefinition schemaRef="#/components/schemas/filter" />
- name: ticketModel
x-displayName: The Ticket Model
description: |
<SchemaDefinition schemaRef="#/components/schemas/ticket" />
x-tagGroups:
- name: Interface
tags:
- projects
- studies
- expressions
- continuous
- name: Models
tags:
- projectModel
- studyModel
- filterModel
- ticketModel
paths:
"/projects/{projectId}":
get:
tags:
- projects
summary: Get a single project by ID
description: Returns the project matching the provided ID
operationId: getProjectById
parameters:
- name: projectId
in: path
description: ID of project to return
required: true
schema:
type: string
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: "#/components/schemas/project"
"400":
description: Invalid ID supplied
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"404":
description: Project not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:project
/projects:
get:
tags:
- projects
summary: Returns a list of projects matching filters
description: Get a list of projects matching filters
operationId: getProjects
parameters:
- $ref: "#/components/parameters/versionParam"
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/project"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:project
/projects/filters:
get:
tags:
- projects
summary: Returns filters for project searches
description: To support flexible search this provides a means of discovering the search filters supported by the data provider.
operationId: getProjectFilters
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/filter"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:project
"/studies/{studyId}":
get:
tags:
- studies
summary: Get a single study by ID
description: Returns the study matching the provided ID
operationId: getStudyById
parameters:
- name: studyId
in: path
description: ID of study to return
required: true
schema:
type: string
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: "#/components/schemas/study"
"400":
description: Invalid ID supplied
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"404":
description: Study not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:study
/studies:
get:
tags:
- studies
summary: Returns a list of studies matching filters
description: Get a list of studies matching filters
operationId: getStudies
parameters:
- $ref: "#/components/parameters/versionParam"
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/study"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:study
/studies/filters:
get:
tags:
- studies
summary: Returns filters for study searches
description: To support flexible search this provides a means of discovering the search filters supported by the data provider.
operationId: getStudyFilters
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/filter"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:study
"/expressions/{expressionId}/ticket":
get:
tags:
- expressions
summary: Get specific expression data ticket
description: Returns a ticket to download a single specified expression matrix
operationId: getExpressionTicketById
parameters:
- name: expressionId
in: path
description: ID of expression to return
required: true
schema:
type: string
- $ref: "#/components/parameters/sampleIDListParam"
- $ref: "#/components/parameters/featureIDListParam"
- $ref: "#/components/parameters/featureNameListParam"
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: "#/components/schemas/ticket"
"400":
description: Invalid ID supplied
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"404":
description: Expression not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:expression
"/expressions/{expressionId}/bytes":
get:
tags:
- expressions
summary: Get specific expression data file
description: Returns a single specified expression matrix
operationId: getExpressionFileById
parameters:
- name: expressionId
in: path
description: ID of expression to return
required: true
schema:
type: string
- $ref: "#/components/parameters/sampleIDListParam"
- $ref: "#/components/parameters/featureIDListParam"
- $ref: "#/components/parameters/featureNameListParam"
responses:
"200":
description: successful operation
content:
application/octet-stream:
schema:
type: string
format: binary
application/vnd.loom:
schema:
type: string
format: binary
text/tab-separated-values:
schema:
type: string
format: binary
"400":
description: Invalid ID supplied
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"404":
description: Expression not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:expression
/expressions/ticket:
get:
tags:
- expressions
summary: Get a ticket to download expression data
description: Returns a download ticket for expression data matching filters
operationId: getExpressionTicket
parameters:
- name: format
in: query
description: Data format to return
required: true
schema:
type: string
- $ref: "#/components/parameters/projectIDParam"
- $ref: "#/components/parameters/studyIDParam"
- $ref: "#/components/parameters/versionParam"
- $ref: "#/components/parameters/sampleIDListParam"
- $ref: "#/components/parameters/featureIDListParam"
- $ref: "#/components/parameters/featureNameListParam"
responses:
"200":
description: Successful operation
content:
application/json:
schema:
$ref: "#/components/schemas/ticket"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:expression
/expressions/bytes:
get:
tags:
- expressions
summary: Download expression data matching filters
description: Returns an expression data file matching filters
operationId: getExpressionFile
parameters:
- name: format
in: query
description: Data format to return
required: true
schema:
type: string
- $ref: "#/components/parameters/projectIDParam"
- $ref: "#/components/parameters/studyIDParam"
- $ref: "#/components/parameters/versionParam"
- $ref: "#/components/parameters/sampleIDListParam"
- $ref: "#/components/parameters/featureIDListParam"
- $ref: "#/components/parameters/featureNameListParam"
responses:
"200":
description: Successful operation
content:
application/octet-stream:
schema:
type: string
format: binary
application/vnd.loom:
schema:
type: string
format: binary
text/tab-separated-values:
schema:
type: string
format: binary
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:expression
/expressions/formats:
get:
tags:
- expressions
summary: Get output formats
description: |
The response is a list of the supported data formats as a JSON formatted object unless an alternative formatting supported by the server is requested. A data provider may use any internal storage format that they wish with no restrictions from this API. To support development of interoperable clients, it is recommended that data providers MUST support at least 1 of the following common output formats:
* Tab delimited text (.tsv)
* [Loom](https://linnarssonlab.org/loompy/format/index.html) (.loom)
A Tab delimited file can have any number of comment lines beginning with `#` for storing metadata. There should be one header row following the comments. Feature (genes/transcripts) names and/or ID fields should be the first columns of the header row and have the `string` type. All following columns are for the samples and will have 32-bit `float` values in each row.
##### Example .tsv file
```
# Example tsv file
geneID geneName sample1 sample2
ENSG00000000003 TSPAN6 12.4 15.6
```
A Loom format file will have a 32-bit `float` matrix for the expression values with samples on the column axis and features on the row axis. Associated metadata can be stored as row and column attributes as described by loom specification.
operationId: getExpressionFormats
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
type: string
"404":
description: Format list not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:expression
/expressions/filters:
get:
tags:
- expressions
summary: Returns filters for expression searches
description: To support flexible search this provides a means of discovering the search filters supported by the data provider.
operationId: getExpressionFilters
parameters:
- name: type
in: query
description: one of `feature` or `sample` reflecting which axis to request
filters for. If blank, both will be returned
required: false
schema:
type: string
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/filter"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:expression
"/continuous/{continuousId}/ticket":
get:
tags:
- continuous
summary: Get specific continuous data ticket
description: Returns a ticket to download a single specified continuous matrix
operationId: getContinuousTicketById
parameters:
- name: continuousId
in: path
description: ID of continuous matrix to return
required: true
schema:
type: string
- $ref: "#/components/parameters/chrParam"
- $ref: "#/components/parameters/startParam"
- $ref: "#/components/parameters/endParam"
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: "#/components/schemas/ticket"
"400":
description: Invalid ID supplied
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"404":
description: Continuous matrix not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:continuous
"/continuous/{continuousId}/bytes":
get:
tags:
- continuous
summary: Get specific continuous data file
description: Returns a single specified continuous matrix
operationId: getContinuousFileById
parameters:
- name: continuousId
in: path
description: ID of continuous matrix to return
required: true
schema:
type: string
- $ref: "#/components/parameters/chrParam"
- $ref: "#/components/parameters/startParam"
- $ref: "#/components/parameters/endParam"
responses:
"200":
description: successful operation
content:
application/octet-stream:
schema:
type: string
format: binary
application/vnd.loom:
schema:
type: string
format: binary
text/tab-separated-values:
schema:
type: string
format: binary
"400":
description: Invalid ID supplied
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"404":
description: Continuous matrix not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:continuous
/continuous/ticket:
get:
tags:
- continuous
summary: Get a ticket to download continuous data
description: Returns a download ticket for continuous data matching filters
operationId: getContinuousTicket
parameters:
- name: format
in: query
description: Data format to return
required: true
schema:
type: string
- $ref: "#/components/parameters/projectIDParam"
- $ref: "#/components/parameters/studyIDParam"
- $ref: "#/components/parameters/versionParam"
- $ref: "#/components/parameters/sampleIDListParam"
- $ref: "#/components/parameters/chrParam"
- $ref: "#/components/parameters/startParam"
- $ref: "#/components/parameters/endParam"
responses:
"200":
description: Successful operation
content:
application/json:
schema:
$ref: "#/components/schemas/ticket"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:continuous
/continuous/bytes:
get:
tags:
- continuous
summary: Download continuous data matching filters
description: Returns a continuous data file matching filters
operationId: getContinuousFile
parameters:
- name: format
in: query
description: Data format to return
required: true
schema:
type: string
- $ref: "#/components/parameters/projectIDParam"
- $ref: "#/components/parameters/studyIDParam"
- $ref: "#/components/parameters/versionParam"
- $ref: "#/components/parameters/sampleIDListParam"
- $ref: "#/components/parameters/chrParam"
- $ref: "#/components/parameters/startParam"
- $ref: "#/components/parameters/endParam"
responses:
"200":
description: Successful operation
content:
application/octet-stream:
schema:
type: string
format: binary
application/vnd.loom:
schema:
type: string
format: binary
text/tab-separated-values:
schema:
type: string
format: binary
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:continuous
/continuous/formats:
get:
tags:
- continuous
summary: Get output formats
description: |
The response is a list of the supported data formats as a JSON formatted object unless an alternative formatting supported by the server is requested. A data provider may use any internal storage format that they wish with no restrictions from this API. To support development of interoperable clients, it is recommended that data providers MUST support at least 1 of the following common output formats:
* Tab delimited text (.tsv)
* [Loom](https://linnarssonlab.org/loompy/format/index.html) (.loom)
A Tab delimited file can have any number of comment lines beginning with `#` for storing metadata. The first line of the tsv file will be a tab-delimited list beginning with `#labels` and containing the labels for text fields in the main matrix. The second line of the tsv file will be a tab-delimited list containing 2 items: `#range` and the range in the form chr?:start-stop where the start coordinate is zero-based, inclusive and the stop coordinate is zero-based, exclusive. Any additional comments may follow these 2 lines. The data matrix follows the comment block. Sample names and/or ID fields should be the first columns of the header row, be in the same order as listed in the `#labels` comment and have the `string` type. All coordinates in the continuous range described in the `#range` comment will be in the following columns with each base position in its own column. The coordinate columns will contain 32-bit `float` values in each row corresponding to the measured signal value at that coordinante for the sample corresponding to that row.
##### Example .tsv file
```
#labels sampleID sampleName
#range chr1:1000000-1000002
# assembly GRCh38-V29-male
12003-L1 12003-human-liver-4 12.4 15.6
```
A Loom format file will have a 32-bit `float` matrix for the signal values with coordinates on the column axis and samples on the row axis. Associated metadata can be stored as row and column attributes as described by the loom specification.
operationId: getContinuousFormats
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
type: string
"404":
description: Format list not found
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:continuous
/continuous/filters:
get:
tags:
- continuous
summary: Returns filters for continuous searches
description: To support flexible search this provides a means of discovering the search filters supported by the data provider.
operationId: getContinuousFilters
responses:
"200":
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/filter"
"400":
description: The requested data format is not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"406":
description: Requested formatting not supported
content:
application/json:
schema:
$ref: "#/components/schemas/error"
"501":
description: The specified request is not supported by the server
content:
application/json:
schema:
$ref: "#/components/schemas/error"
security:
- rnaget_auth:
- read:continuous
components:
securitySchemes:
rnaget_auth:
type: oauth2
flows:
implicit:
authorizationUrl: http://ga4gh.org/oauth/dialog
scopes:
read:expression: read expression data
read:continuous: read continuous data
read:project: read information about projects
read:study: read information about studies
read:info: read general info
schemas:
project:
type: object
description: The project is the top level of the model hierarchy and contains one or more studies.
properties:
id:
type: string
description: A unique identifier assigned to this object
example: c2fe2aa6ad3043108bd88a30fc0303da
version:
type: string
description: Version number of the object
example: 1.0
name:
type: string
description: Short, readable name
example: Demo Project
description:
type: string
description: Detailed description of the object
example: This is a small project to demo API funtions
required:
- id
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
study:
type: object
description: The study is a container for one or more related RNA expression matrices.
properties:
id:
type: string
description: A unique identifier assigned to this object
example: c4cf910c9ae54832902c954cb439e30c
version:
type: string
description: Version number of the object
example: 1.0
name:
type: string
description: Short, readable name
example: Demo Study
description:
type: string
description: Detailed description of the object
example: This study is part of the demo project
parentProjectID:
type: string
description: ID of the project containing the study
example: c2fe2aa6ad3043108bd88a30fc0303da
genome:
type: string
description: Name of the reference genome build used for aligning samples in the study
example: human GRCh38
required:
- id
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
filter:
type: object
description: Implementation defined parameter to use for filtering collections
properties:
filter:
type: string
description: A unique name for the filter for use in query URLs
example: tissue
fieldType:
type: string
description: The dataType (string, float, etc.) of the filter
example: string
description:
type: string
description: Detailed description of the filter
example: tissue of origin
values:
type: array
items:
type: string
example: liver
description: List of supported values for the filter
required:
- filter
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
ticket:
type: object
description: URL and type for data files
properties:
version:
type: string
description: Version number of the object
example: 1.0
fileType:
type: string
description: "Type of file. Examples include: loom, tsv"
example: loom
studyID:
type: string
description: ID of containing study
example: c4cf910c9ae54832902c954cb439e30c
url:
type: string
description: An `https:` URL to download file
units:
type: string
description: "Units for the values. Examples include: TPM, FPKM, counts"
headers:
type: object
description: 'For HTTPS URLs, the server may supply a JSON object containing one or more string key-value pairs which the client MUST supply verbatim as headers with any request to the URL. For example, if headers is `{"Authorization": "Bearer xxxx"}`, then the client must supply the header `Authorization: Bearer xxxx` with the HTTPS request to the URL.'
md5:
type: string
description: MD5 digest of the file
required:
- url
- units
externalDocs:
description: Find out more
url: https://github.com/ga4gh-rnaseq/schema
error:
type: object
description: General API error model
properties:
message:
type: string
description: Error message details
parameters:
versionParam:
name: version
in: query
description: version to filter by
required: false
schema:
type: string
example:
1.0
projectIDParam:
name: projectID
in: query
description: project to filter by
required: false
schema:
type: string
example:
9c0eba51095d3939437e220db196e27b
studyIDParam:
name: studyID
in: query
description: study to filter by
required: false
schema:
type: string
example:
c4cf910c9ae54832902c954cb439e30c
sampleIDListParam:
name: sampleIDList
in: query
description: return only values for listed sampleIDs
required: false
style: form
explode: false
schema:
type: array
items:
type: string
featureIDListParam:
name: featureIDList
in: query
description: return only values for listed feature IDs
required: false
style: form
explode: false
schema:
type: array
items:
type: string
featureNameListParam:
name: featureNameList
in: query
description: return only values for listed features
required: false
style: form
explode: false
schema:
type: array
items:
type: string
chrParam:
name: chr
in: query
description: The refererence to which start and end apply in the form chr? where ? is the specific ID of the chromosome (ex. chr1, chrX).
required: false
schema:
type: string
example:
chr10
startParam:
name: start
in: query
description: The start position of the range on the sequence, 0-based, inclusive.
required: false
schema:
type: integer
format: int32
minimum: 0
endParam:
name: end
in: query
description: The end position of the range on the sequence, 0-based, exclusive.
required: false
schema:
type: integer
format: int32
minimum: 0
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