docs/SRAApi.md
In sdgamboa/omicidxClientR: R Package Client for OmicIDX
SRAApi
All URIs are relative to http://localhost
Method | HTTP request | Description
------------- | ------------- | -------------
ExperimentByAccessionSraExperimentsAccessionGet | GET /sra/experiments/{accession} | Experiment By Accession
ExperimentsForSampleSraSamplesAccessionExperimentsGet | GET /sra/samples/{accession}/experiments | Experiments For Sample
ExperimentsForStudySraStudiesAccessionExperimentsGet | GET /sra/studies/{accession}/experiments | Experiments For Study
ExperimentsSraExperimentsGet | GET /sra/experiments | Experiments
MappingSraFieldsEntityGet | GET /sra/fields/{entity} | Mapping
RunByAccessionSraRunsAccessionGet | GET /sra/runs/{accession} | Run By Accession
RunsForExperimentSraExperimentsAccessionRunsGet | GET /sra/experiments/{accession}/runs | Runs For Experiment
RunsForSampleSraSamplesAccessionRunsGet | GET /sra/samples/{accession}/runs | Runs For Sample
RunsForStudySraStudiesAccessionRunsGet | GET /sra/studies/{accession}/runs | Runs For Study
RunsSraRunsGet | GET /sra/runs | Runs
SampleByAccessionSraSamplesAccessionGet | GET /sra/samples/{accession} | Sample By Accession
SamplesForStudySraStudiesAccessionSamplesGet | GET /sra/studies/{accession}/samples | Samples For Study
SamplesSraSamplesGet | GET /sra/samples | Samples
StudiesSraStudiesGet | GET /sra/studies | Studies
StudyByAccessionSraStudiesAccessionGet | GET /sra/studies/{accession} | Study By Accession
ExperimentByAccessionSraExperimentsAccessionGet
AnyType ExperimentByAccessionSraExperimentsAccessionGet(accession, include.fields=[], exclude.fields=[])
Experiment 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.
#Experiment By Accession
api.instance <- SRAApi$new()
result <- api.instance$ExperimentByAccessionSraExperimentsAccessionGet(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
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 | - |
ExperimentsForSampleSraSamplesAccessionExperimentsGet
AnyType ExperimentsForSampleSraSamplesAccessionExperimentsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Experiments For Sample
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Experiments For Sample
api.instance <- SRAApi$new()
result <- api.instance$ExperimentsForSampleSraSamplesAccessionExperimentsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []]
size | integer| | [optional] [default to 10]
cursor | character| | [optional]
Return type
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 | - |
ExperimentsForStudySraStudiesAccessionExperimentsGet
AnyType ExperimentsForStudySraStudiesAccessionExperimentsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Experiments For Study
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Experiments For Study
api.instance <- SRAApi$new()
result <- api.instance$ExperimentsForStudySraStudiesAccessionExperimentsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []]
size | integer| | [optional] [default to 10]
cursor | character| | [optional]
Return type
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 | - |
ExperimentsSraExperimentsGet
ResponseModel ExperimentsSraExperimentsGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Experiments
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.
#Experiments
api.instance <- SRAApi$new()
result <- api.instance$ExperimentsSraExperimentsGet(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
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 | - |
MappingSraFieldsEntityGet
AnyType MappingSraFieldsEntityGet(entity)
Mapping
Example
library(omicidxClientR)
var.entity <- 'entity_example' # character |
#Mapping
api.instance <- SRAApi$new()
result <- api.instance$MappingSraFieldsEntityGet(var.entity)
dput(result)
Parameters
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
entity | Enum [studies, runs, experiments, samples] | |
Return type
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 | - |
RunByAccessionSraRunsAccessionGet
AnyType RunByAccessionSraRunsAccessionGet(accession, include.fields=[], exclude.fields=[])
Run 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.
#Run By Accession
api.instance <- SRAApi$new()
result <- api.instance$RunByAccessionSraRunsAccessionGet(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
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 | - |
RunsForExperimentSraExperimentsAccessionRunsGet
AnyType RunsForExperimentSraExperimentsAccessionRunsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Runs For Experiment
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Runs For Experiment
api.instance <- SRAApi$new()
result <- api.instance$RunsForExperimentSraExperimentsAccessionRunsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []]
size | integer| | [optional] [default to 10]
cursor | character| | [optional]
Return type
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 | - |
RunsForSampleSraSamplesAccessionRunsGet
AnyType RunsForSampleSraSamplesAccessionRunsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Runs For Sample
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Runs For Sample
api.instance <- SRAApi$new()
result <- api.instance$RunsForSampleSraSamplesAccessionRunsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []]
size | integer| | [optional] [default to 10]
cursor | character| | [optional]
Return type
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 | - |
RunsForStudySraStudiesAccessionRunsGet
AnyType RunsForStudySraStudiesAccessionRunsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Runs For Study
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Runs For Study
api.instance <- SRAApi$new()
result <- api.instance$RunsForStudySraStudiesAccessionRunsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []]
size | integer| | [optional] [default to 10]
cursor | character| | [optional]
Return type
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 | - |
RunsSraRunsGet
ResponseModel RunsSraRunsGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Runs
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.
#Runs
api.instance <- SRAApi$new()
result <- api.instance$RunsSraRunsGet(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
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 | - |
SampleByAccessionSraSamplesAccessionGet
AnyType SampleByAccessionSraSamplesAccessionGet(accession, include.fields=[], exclude.fields=[])
Sample 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.
#Sample By Accession
api.instance <- SRAApi$new()
result <- api.instance$SampleByAccessionSraSamplesAccessionGet(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
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 | - |
SamplesForStudySraStudiesAccessionSamplesGet
AnyType SamplesForStudySraStudiesAccessionSamplesGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Samples For Study
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Samples For Study
api.instance <- SRAApi$new()
result <- api.instance$SamplesForStudySraStudiesAccessionSamplesGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []]
size | integer| | [optional] [default to 10]
cursor | character| | [optional]
Return type
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 | - |
SamplesSraSamplesGet
ResponseModel SamplesSraSamplesGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Samples
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.
#Samples
api.instance <- SRAApi$new()
result <- api.instance$SamplesSraSamplesGet(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
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 | - |
StudiesSraStudiesGet
ResponseModel StudiesSraStudiesGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Studies
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.
#Studies
api.instance <- SRAApi$new()
result <- api.instance$StudiesSraStudiesGet(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
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 | - |
StudyByAccessionSraStudiesAccessionGet
AnyType StudyByAccessionSraStudiesAccessionGet(accession, include.fields=[], exclude.fields=[])
Study 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.
#Study By Accession
api.instance <- SRAApi$new()
result <- api.instance$StudyByAccessionSraStudiesAccessionGet(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
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.
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SRAApi
All URIs are relative to http://localhost
Method | HTTP request | Description ------------- | ------------- | ------------- ExperimentByAccessionSraExperimentsAccessionGet | GET /sra/experiments/{accession} | Experiment By Accession ExperimentsForSampleSraSamplesAccessionExperimentsGet | GET /sra/samples/{accession}/experiments | Experiments For Sample ExperimentsForStudySraStudiesAccessionExperimentsGet | GET /sra/studies/{accession}/experiments | Experiments For Study ExperimentsSraExperimentsGet | GET /sra/experiments | Experiments MappingSraFieldsEntityGet | GET /sra/fields/{entity} | Mapping RunByAccessionSraRunsAccessionGet | GET /sra/runs/{accession} | Run By Accession RunsForExperimentSraExperimentsAccessionRunsGet | GET /sra/experiments/{accession}/runs | Runs For Experiment RunsForSampleSraSamplesAccessionRunsGet | GET /sra/samples/{accession}/runs | Runs For Sample RunsForStudySraStudiesAccessionRunsGet | GET /sra/studies/{accession}/runs | Runs For Study RunsSraRunsGet | GET /sra/runs | Runs SampleByAccessionSraSamplesAccessionGet | GET /sra/samples/{accession} | Sample By Accession SamplesForStudySraStudiesAccessionSamplesGet | GET /sra/studies/{accession}/samples | Samples For Study SamplesSraSamplesGet | GET /sra/samples | Samples StudiesSraStudiesGet | GET /sra/studies | Studies StudyByAccessionSraStudiesAccessionGet | GET /sra/studies/{accession} | Study By Accession
ExperimentByAccessionSraExperimentsAccessionGet
AnyType ExperimentByAccessionSraExperimentsAccessionGet(accession, include.fields=[], exclude.fields=[])
Experiment 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.
#Experiment By Accession
api.instance <- SRAApi$new()
result <- api.instance$ExperimentByAccessionSraExperimentsAccessionGet(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
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 | - |
ExperimentsForSampleSraSamplesAccessionExperimentsGet
AnyType ExperimentsForSampleSraSamplesAccessionExperimentsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Experiments For Sample
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Experiments For Sample
api.instance <- SRAApi$new()
result <- api.instance$ExperimentsForSampleSraSamplesAccessionExperimentsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []] size | integer| | [optional] [default to 10] cursor | character| | [optional]
Return type
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 | - |
ExperimentsForStudySraStudiesAccessionExperimentsGet
AnyType ExperimentsForStudySraStudiesAccessionExperimentsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Experiments For Study
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Experiments For Study
api.instance <- SRAApi$new()
result <- api.instance$ExperimentsForStudySraStudiesAccessionExperimentsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []] size | integer| | [optional] [default to 10] cursor | character| | [optional]
Return type
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 | - |
ExperimentsSraExperimentsGet
ResponseModel ExperimentsSraExperimentsGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Experiments
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.
#Experiments
api.instance <- SRAApi$new()
result <- api.instance$ExperimentsSraExperimentsGet(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
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 | - |
MappingSraFieldsEntityGet
AnyType MappingSraFieldsEntityGet(entity)
Mapping
Example
library(omicidxClientR)
var.entity <- 'entity_example' # character |
#Mapping
api.instance <- SRAApi$new()
result <- api.instance$MappingSraFieldsEntityGet(var.entity)
dput(result)
Parameters
Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- entity | Enum [studies, runs, experiments, samples] | |
Return type
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 | - |
RunByAccessionSraRunsAccessionGet
AnyType RunByAccessionSraRunsAccessionGet(accession, include.fields=[], exclude.fields=[])
Run 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.
#Run By Accession
api.instance <- SRAApi$new()
result <- api.instance$RunByAccessionSraRunsAccessionGet(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
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 | - |
RunsForExperimentSraExperimentsAccessionRunsGet
AnyType RunsForExperimentSraExperimentsAccessionRunsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Runs For Experiment
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Runs For Experiment
api.instance <- SRAApi$new()
result <- api.instance$RunsForExperimentSraExperimentsAccessionRunsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []] size | integer| | [optional] [default to 10] cursor | character| | [optional]
Return type
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 | - |
RunsForSampleSraSamplesAccessionRunsGet
AnyType RunsForSampleSraSamplesAccessionRunsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Runs For Sample
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Runs For Sample
api.instance <- SRAApi$new()
result <- api.instance$RunsForSampleSraSamplesAccessionRunsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []] size | integer| | [optional] [default to 10] cursor | character| | [optional]
Return type
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 | - |
RunsForStudySraStudiesAccessionRunsGet
AnyType RunsForStudySraStudiesAccessionRunsGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Runs For Study
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Runs For Study
api.instance <- SRAApi$new()
result <- api.instance$RunsForStudySraStudiesAccessionRunsGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []] size | integer| | [optional] [default to 10] cursor | character| | [optional]
Return type
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 | - |
RunsSraRunsGet
ResponseModel RunsSraRunsGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Runs
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.
#Runs
api.instance <- SRAApi$new()
result <- api.instance$RunsSraRunsGet(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
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 | - |
SampleByAccessionSraSamplesAccessionGet
AnyType SampleByAccessionSraSamplesAccessionGet(accession, include.fields=[], exclude.fields=[])
Sample 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.
#Sample By Accession
api.instance <- SRAApi$new()
result <- api.instance$SampleByAccessionSraSamplesAccessionGet(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
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 | - |
SamplesForStudySraStudiesAccessionSamplesGet
AnyType SamplesForStudySraStudiesAccessionSamplesGet(accession, include.fields=[], exclude.fields=[], size=10, cursor=var.cursor)
Samples For Study
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.
var.size <- 10 # integer |
var.cursor <- 'cursor_example' # character |
#Samples For Study
api.instance <- SRAApi$new()
result <- api.instance$SamplesForStudySraStudiesAccessionSamplesGet(var.accession, include.fields=var.include.fields, exclude.fields=var.exclude.fields, size=var.size, cursor=var.cursor)
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 []] size | integer| | [optional] [default to 10] cursor | character| | [optional]
Return type
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 | - |
SamplesSraSamplesGet
ResponseModel SamplesSraSamplesGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Samples
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.
#Samples
api.instance <- SRAApi$new()
result <- api.instance$SamplesSraSamplesGet(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
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 | - |
StudiesSraStudiesGet
ResponseModel StudiesSraStudiesGet(q=var.q, size=10, cursor=var.cursor, facet.size=10, include.fields=[], exclude.fields=[], facets=[])
Studies
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.
#Studies
api.instance <- SRAApi$new()
result <- api.instance$StudiesSraStudiesGet(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
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 | - |
StudyByAccessionSraStudiesAccessionGet
AnyType StudyByAccessionSraStudiesAccessionGet(accession, include.fields=[], exclude.fields=[])
Study 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.
#Study By Accession
api.instance <- SRAApi$new()
result <- api.instance$StudyByAccessionSraStudiesAccessionGet(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
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 | - |
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