StudySPoTAsUserApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| GetStudyAsUser | GET /api/v1/as-user/studies/{id} | Retrieve a single study object by ID (accession) |
| GetStudyByVersionAsUser | GET /api/v1/as-user/studies/{id}/versions/{version} | Retrieve a single study object by ID (accession) |
| GetStudyVersionsAsUser | GET /api/v1/as-user/studies/{id}/versions | Retrieve a list of object versions by ID |
| SearchStudiesAsUser | GET /api/v1/as-user/studies | List or search for study metadata objects |
GetStudyAsUser¶
object GetStudyAsUser(id, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve a single study object by ID (accession)
Example¶
library(odmApi)
# Retrieve a single study object by ID (accession)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- StudySPoTAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetStudyAsUser(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetStudyAsUser(var_id, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fields)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. | |
| response_format | ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. | [optional] |
| returned_metadata_fields | Enum [minimal_data, extended_data_included, original_data_included] | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. | [optional] |
Return type¶
object
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is the object. | - |
| 400 | The supplied object ID is invalid. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 404 | No object exists with the given ID. | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetStudyByVersionAsUser¶
object GetStudyByVersionAsUser(id, version, response_format = var.response_format, returned_metadata_fields = var.returned_metadata_fields)
Retrieve a single study object by ID (accession)
Example¶
library(odmApi)
# Retrieve a single study object by ID (accession)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_version <- "version_example" # character | Unique version of the object.
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
api_instance <- StudySPoTAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetStudyByVersionAsUser(var_id, var_version, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fieldsdata_file = "result.txt")
result <- api_instance$GetStudyByVersionAsUser(var_id, var_version, response_format = var_response_format, returned_metadata_fields = var_returned_metadata_fields)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. | |
| version | character | Unique version of the object. | |
| response_format | ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. | [optional] |
| returned_metadata_fields | Enum [minimal_data, extended_data_included, original_data_included] | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. | [optional] |
Return type¶
object
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is the object. | - |
| 400 | The supplied object ID is invalid. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 404 | No object exists with the given ID. | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetStudyVersionsAsUser¶
array[CommitInfo] GetStudyVersionsAsUser(id)
Retrieve a list of object versions by ID
Example¶
library(odmApi)
# Retrieve a list of object versions by ID
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
api_instance <- StudySPoTAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetStudyVersionsAsUser(var_iddata_file = "result.txt")
result <- api_instance$GetStudyVersionsAsUser(var_id)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is the list of object versions. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
SearchStudiesAsUser¶
ListResponse SearchStudiesAsUser(response_format = var.response_format, filter = var.filter, query = var.query, search_specific_terms = var.search_specific_terms, returned_metadata_fields = var.returned_metadata_fields, sort = var.sort, page_limit = var.page_limit, page_offset = var.page_offset)
List or search for study metadata objects
Retrieve study metadata objects by searching/listing study metadata. ## Metadata full-text queries Single words can be supplied as is, otherwise use speech marks (\") to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (\\). ## Metadata filters Metadata filters are key-value pairs joined by an operator. The = operator matches literal values/string. The != operator matches anything except the literal value/string. The < or > operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (\"). ## Combinations Metadata queries/filters for the same parameter can be combined with &&, AND, || and OR operators, using white-space to separate out the terms and operators. Parentheses ( ) can be used for complex expressions. ## Paging For performance reasons this endpoint returns results in \"pages\" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To return all results iterate through pages using pageOffset values of n * pageLimit until the resultsExhausted response field is true. ## List operation This endpoint can be called with no query parameter. Doing so returns a list of all study objects.
Example¶
library(odmApi)
# List or search for study metadata objects
#
# prepare function argument(s)
var_response_format <- ResponseFormat$new() # ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. (Optional)
var_filter <- "filter_example" # character | Filter by study metadata (key-value metadata pair(s)). E.g. `\"Study Source\"=ArrayExpress` (Optional)
var_query <- "query_example" # character | Search for study objects via a full-text query over all study metadata fields. E.g. `\"RNA-Seq of human dendritic cells\"`. Queries matching dictionary terms are automatically expanded to include synonyms. (Optional)
var_search_specific_terms <- "search_specific_terms_example" # character | If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. For example, the search query \"Body fluid\" can be expanded to include the term \"Blood\" (a child term of \"Body fluid\") so files containing either \"Body fluid\" or \"Blood\" in their metadata will be returned in the search results. The parent-child relationship is defined by the key \"broaders\" or \"subClassOf\" in the dictionary. If the full query term is not present in a dictionary then this parameter has no effect. (Optional)
var_returned_metadata_fields <- "returned_metadata_fields_example" # character | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. (Optional)
var_sort <- "sort_example" # character | Attribute to sort by, with optional ascending/descending marker, of the form `\"[+|-]<key_name>\"`. No marker or `\"+\"` indicates ascending sort, and `\"-\"` indicates descending sort. *Default:* sort by ID in ascending order. (Optional)
var_page_limit <- 56 # integer | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). (Optional)
var_page_offset <- 56 # integer | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0. (Optional)
api_instance <- StudySPoTAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$SearchStudiesAsUser(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, returned_metadata_fields = var_returned_metadata_fields, sort = var_sort, page_limit = var_page_limit, page_offset = var_page_offsetdata_file = "result.txt")
result <- api_instance$SearchStudiesAsUser(response_format = var_response_format, filter = var_filter, query = var_query, search_specific_terms = var_search_specific_terms, returned_metadata_fields = var_returned_metadata_fields, sort = var_sort, page_limit = var_page_limit, page_offset = var_page_offset)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| response_format | ResponseFormat | Supply this parameter with the value `term_id` as part of the query to return extended information including IDs for values and dictionaries. | [optional] |
| filter | character | Filter by study metadata (key-value metadata pair(s)). E.g. `\"Study Source\"=ArrayExpress` | [optional] |
| query | character | Search for study objects via a full-text query over all study metadata fields. E.g. `\"RNA-Seq of human dendritic cells\"`. Queries matching dictionary terms are automatically expanded to include synonyms. | [optional] |
| search_specific_terms | character | If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query. For example, the search query \"Body fluid\" can be expanded to include the term \"Blood\" (a child term of \"Body fluid\") so files containing either \"Body fluid\" or \"Blood\" in their metadata will be returned in the search results. The parent-child relationship is defined by the key \"broaders\" or \"subClassOf\" in the dictionary. If the full query term is not present in a dictionary then this parameter has no effect. | [optional] |
| returned_metadata_fields | Enum [minimal_data, extended_data_included, original_data_included] | The parameter defines amount of metadata attributes to return: 1. `minimal_data` - return metadata attributes according to the default template. 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints. 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints. | [optional] |
| sort | Enum [id, creation, last_update, name, +id, +creation, +last_update, +name, -id, -creation, -last_update, -name] | Attribute to sort by, with optional ascending/descending marker, of the form `\"[+ | -]<key_name>\"`. No marker or `\"+\"` indicates ascending sort, and `\"-\"` indicates descending sort. Default: sort by ID in ascending order. |
| page_limit | integer | Maximum number of results to return. This value must be between 0 and 2000 (inclusive). | [optional] |
| page_offset | integer | Show the page {pageOffset+1} results from the start of the results. E.g. 100 will show a page of results starting from the 101st result. The default value is 0. | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json, text/tab-separated-values
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is a list of objects. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |