docs/V0Api.md

In Bioconductor/hcamatrixapi: R Package Client for HCA Matrix Service

V0Api

All URIs are relative to https://$

Method | HTTP request | Description ------------- | ------------- | ------------- MatrixLambdasApiV0CoreGetFormats | GET /v0/matrix/formats | Returns supported output formats. MatrixLambdasApiV0CoreGetMatrix | GET /v0/matrix/{request_id} | Retrieve the status, and result if available, of a matrix query request. MatrixLambdasApiV0CorePostMatrix | POST /v0/matrix | Submit a matrix query request.

MatrixLambdasApiV0CoreGetFormats

array[V0MatrixFormat] MatrixLambdasApiV0CoreGetFormats()

Returns supported output formats.

Returns the list of expression matrix formats that can be requested from this service.

Example

library(hcamatrixapi)


#Returns supported output formats.
api.instance <- V0Api$new()
result <- api.instance$MatrixLambdasApiV0CoreGetFormats()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[V0MatrixFormat]

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Success | - |

MatrixLambdasApiV0CoreGetMatrix

V0MatrixGetResponse MatrixLambdasApiV0CoreGetMatrix(request.id)

Retrieve the status, and result if available, of a matrix query request.

Returns the status, and URI of the result if available, of a matrix query request. The status of a request can be 'Complete', 'In Progress' or 'Failed'. If the request is 'Complete', the matrix_location field will be populated with a URL to download the matrix. If the request 'Failed', the error message will be available in the message field.

Example

library(hcamatrixapi)

var.request.id <- 'request.id_example' # character | The request ID generated by a POST request.

#Retrieve the status, and result if available, of a matrix query request.
api.instance <- V0Api$new()
result <- api.instance$MatrixLambdasApiV0CoreGetMatrix(var.request.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- request.id | character| The request ID generated by a POST request. |

Return type

V0MatrixGetResponse

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Request found | - | | 404 | Request not found | - |

MatrixLambdasApiV0CorePostMatrix

V0MatrixPostResponse MatrixLambdasApiV0CorePostMatrix(v0.matrix.request=var.v0.matrix.request)

Submit a matrix query request.

Prepares a single expression matrix combining all expression matrices belonging to the specified analysis bundles. On success, this request will asynchronously start a job to prepare the expression matrix and return with the request ID of the job. The request ID can be used to retrieve the status and results of the job from the GET endpoint.

Example

library(hcamatrixapi)

var.v0.matrix.request <- v0_MatrixRequest$new(list("bundle_fqids_example"), "bundle_fqids_url_example", v0_MatrixFormat$new()) # V0MatrixRequest | Use either bundle_fqids or bundle_fqids_url to specify input analysis bundles; bundle_fqids expects a list of fully-qualified IDs (bundle_uuid.bundle_version); bundle_fqids_url expects a URL that serves a Data Browser download manifest TSV file. Use the format field to specify the desired file format of the output expression matrix. Supported format values are 'loom', 'csv' and 'mtx'.

#Submit a matrix query request.
api.instance <- V0Api$new()
result <- api.instance$MatrixLambdasApiV0CorePostMatrix(v0.matrix.request=var.v0.matrix.request)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- v0.matrix.request | V0MatrixRequest| Use either bundle_fqids or bundle_fqids_url to specify input analysis bundles; bundle_fqids expects a list of fully-qualified IDs (bundle_uuid.bundle_version); bundle_fqids_url expects a URL that serves a Data Browser download manifest TSV file. Use the format field to specify the desired file format of the output expression matrix. Supported format values are 'loom', 'csv' and 'mtx'. | [optional]

Return type

V0MatrixPostResponse

Authorization

No authorization required

HTTP request headers

• Content-Type: application/json
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 202 | Matrix request accepted | - | | 400 | Bad request | - |

Bioconductor/hcamatrixapi documentation built on Nov. 6, 2019, 12:10 a.m.