docs/BiosampleApi.md

In sdgamboa/omicidxClientR: R Package Client for OmicIDX

BiosampleApi

All URIs are relative to http://localhost

Method | HTTP request | Description ------------- | ------------- | ------------- BiosampleByAccessionBiosampleSamplesAccessionGet | GET /biosample/samples/{accession} | Biosample By Accession BiosamplesBiosampleSamplesGet | GET /biosample/samples | Biosamples MappingBiosampleFieldsEntityGet | GET /biosample/fields/{entity} | Mapping

BiosampleByAccessionBiosampleSamplesAccessionGet

AnyType BiosampleByAccessionBiosampleSamplesAccessionGet(accession, include.fields=[], exclude.fields=[])

Biosample By Accession

Example

library(omicidxClientR)

var.accession <- 'accession_example' # character | An accession for lookup
var.include.fields <- list("inner_example") # array[character] | Fields to include in results. The default is to all fields (*)
var.exclude.fields <- list("inner_example") # array[character] | Fields to exclude from results. The default is to not exclude any fields. 

#Biosample By Accession
api.instance <- BiosampleApi$new()
result <- api.instance$BiosampleByAccessionBiosampleSamplesAccessionGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- accession | character| An accession for lookup | include.fields | list( character )| Fields to include in results. The default is to all fields (*) | [optional] [default to []] exclude.fields | list( character )| Fields to exclude from results. The default is to not exclude any fields. | [optional] [default to []]

Return type

AnyType

Authorization

No authorization required

HTTP request headers

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

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Response | - | | 422 | Validation Error | - |

BiosamplesBiosampleSamplesGet

ResponseModel BiosamplesBiosampleSamplesGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])

Biosamples

Example

library(omicidxClientR)

var.q <- 'cancer' # character | The query, using [lucene query syntax](https://lucene.apache.org/core/3_6_0/queryparsersyntax.html)
var.size <- 10 # integer | 
var.cursor <- 'cursor_example' # character | The cursor is used to scroll through results. For a query with more results than `size`, the result will include `cursor` in the result json. Use that value here and re-issue the query. The next set or results will be returned. When no more results are available, the `cursor` will again be empty in the result json.
var.facet.size <- 10 # integer | The maximum number of records returned for each facet. This has no effect unless one or more facets are specified.
var.include.fields <- list("inner_example") # array[character] | Fields to include in results. The default is to all fields (*)
var.exclude.fields <- list("inner_example") # array[character] | Fields to exclude from results. The default is to not exclude any fields. 
var.facets <- list("inner_example") # array[character] | A list of strings identifying fields for faceted search results. Simple term faceting is used here, meaning that fields that are short text and repeated across records will be binned and counted.

#Biosamples
api.instance <- BiosampleApi$new()
result <- api.instance$BiosamplesBiosampleSamplesGet(q=var.q, size=var.size, cursor=var.cursor, facet.size=var.facet.size, include.fields=var.include.fields, exclude.fields=var.exclude.fields, facets=var.facets)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- q | character| The query, using lucene query syntax | [optional] size | integer| | [optional] [default to 10] cursor | character| The cursor is used to scroll through results. For a query with more results than `size`, the result will include `cursor` in the result json. Use that value here and re-issue the query. The next set or results will be returned. When no more results are available, the `cursor` will again be empty in the result json. | [optional] facet.size | integer| The maximum number of records returned for each facet. This has no effect unless one or more facets are specified. | [optional] [default to 10] include.fields | list( character )| Fields to include in results. The default is to all fields (*) | [optional] [default to []] exclude.fields | list( character )| Fields to exclude from results. The default is to not exclude any fields. | [optional] [default to []] facets | list( character )| A list of strings identifying fields for faceted search results. Simple term faceting is used here, meaning that fields that are short text and repeated across records will be binned and counted. | [optional] [default to []]

Return type

ResponseModel

Authorization

No authorization required

HTTP request headers

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

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Response | - | | 422 | Validation Error | - |

MappingBiosampleFieldsEntityGet

AnyType MappingBiosampleFieldsEntityGet(entity)

Mapping

Example

library(omicidxClientR)

var.entity <- 'entity_example' # character | 

#Mapping
api.instance <- BiosampleApi$new()
result <- api.instance$MappingBiosampleFieldsEntityGet(var.entity)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- entity | character| |

Return type

AnyType

Authorization

No authorization required

HTTP request headers

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

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successful Response | - | | 422 | Validation Error | - |

sdgamboa/omicidxClientR documentation built on Dec. 22, 2021, 11:12 p.m.