LinkageAsCuratorApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| DeleteLinkAsCurator | DELETE /api/v1/as-curator/links | Deletes existing links matching the specified criteria. |
| GetDataTypesAsCurator | GET /api/v1/as-curator/data-types | Lists all available data types. |
| GetDataTypesLinksAsCurator | GET /api/v1/as-curator/data-types/links | List all possible links between data types that match the specified criteria. |
| GetLinksByIdsAsCurator | POST /api/v1/as-curator/links/get-batch | Finds existing links by passing many IDs. Pagination goes through all links matched the criteria. |
| GetLinksByParamsAsCurator | GET /api/v1/as-curator/links | Finds existing links matching the specified criteria. |
| SaveLinksAsCurator | POST /api/v1/as-curator/links | Creates new links between objects. |
DeleteLinkAsCurator¶
DeleteLinkAsCurator(first_id, second_id, first_type = var.first_type, second_type = var.second_type)
Deletes existing links matching the specified criteria.
This method should be used in case you want to delete the links of an object. Please, keep in mind that deleting a link between Study and Sample will not delete a link between corresponding Sample and it’s signal.
Example¶
library(odmApi)
# Deletes existing links matching the specified criteria.
#
# prepare function argument(s)
var_first_id <- "first_id_example" # character | Object ID (accession) (e.g. accession of study)
var_second_id <- "second_id_example" # character | Object ID (accession) (e.g. accession of study)
var_first_type <- "first_type_example" # character | Type of the object (e.g. study) (Optional)
var_second_type <- "second_type_example" # character | Type of the object (e.g. study) (Optional)
api_instance <- LinkageAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
api_instance$DeleteLinkAsCurator(var_first_id, var_second_id, first_type = var_first_type, second_type = var_second_type)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| first_id | character | Object ID (accession) (e.g. accession of study) | |
| second_id | character | Object ID (accession) (e.g. accession of study) | |
| first_type | character | Type of the object (e.g. study) | [optional] |
| second_type | character | Type of the object (e.g. study) | [optional] |
Return type¶
void (empty response body)
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: Not defined
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 204 | Link has been successfully deleted. | - |
| 400 | Invalid data in request. | - |
| 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 links were found. | - |
| 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. | - |
GetDataTypesAsCurator¶
set[character] GetDataTypesAsCurator()
Lists all available data types.
This endpoint is for instructional uses and can be used to get the latest list of Data Types.
Example¶
library(odmApi)
# Lists all available data types.
#
api_instance <- LinkageAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetDataTypesAsCurator(data_file = "result.txt")
result <- api_instance$GetDataTypesAsCurator()
dput(result)
Parameters¶
This endpoint does not need any parameter.
Return type¶
set[character]
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is a list of objects. | - |
| 400 | Entities cannot be retrieved. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetDataTypesLinksAsCurator¶
set[SourceTypePair] GetDataTypesLinksAsCurator(type = var.type)
List all possible links between data types that match the specified criteria.
This endpoint should be used for instructional needs, and can be used in order to get the links between the Data Types.
Example¶
library(odmApi)
# List all possible links between data types that match the specified criteria.
#
# prepare function argument(s)
var_type <- "type_example" # character | Return only links with the specified data type. (Optional)
api_instance <- LinkageAsCuratorApi$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$GetDataTypesLinksAsCurator(type = var_typedata_file = "result.txt")
result <- api_instance$GetDataTypesLinksAsCurator(type = var_type)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| type | character | Return only links with the specified data type. | [optional] |
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 a list of objects. | - |
| 400 | Entities cannot be retrieved. | - |
| 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. | - |
GetLinksByIdsAsCurator¶
ListResponse GetLinksByIdsAsCurator(request = var.request)
Finds existing links by passing many IDs. Pagination goes through all links matched the criteria.
Please make sure to use that endpoint for batch calls only. You are not allowed to pass 'mixed' objects. e.g. Studies and Samples at the same time. Please always specify firstType.
Example¶
library(odmApi)
# Finds existing links by passing many IDs. Pagination goes through all links matched the criteria.
#
# prepare function argument(s)
var_request <- BatchOfIds$new("firstType_example", c("firstIds_example"), 123, 123) # BatchOfIds | (Optional)
api_instance <- LinkageAsCuratorApi$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$GetLinksByIdsAsCurator(request = var_requestdata_file = "result.txt")
result <- api_instance$GetLinksByIdsAsCurator(request = var_request)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| request | BatchOfIds | [optional] |
Return type¶
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: application/json
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | The request was successful. The returned value is a list of objects. | - |
| 400 | Entities cannot be retrieved. | - |
| 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. | - |
GetLinksByParamsAsCurator¶
ListResponse GetLinksByParamsAsCurator(first_id, first_type = var.first_type, second_id = var.second_id, second_type = var.second_type, offset = 0, limit = 1000)
Finds existing links matching the specified criteria.
Please make sure that this endpoint should be used only for getting all links to a specific object. In case you specify both firstId and secondId an expected answer would be true for existing links and false for no link between the objects.
Example¶
library(odmApi)
# Finds existing links matching the specified criteria.
#
# prepare function argument(s)
var_first_id <- "first_id_example" # character | Object ID (accession) (e.g. accession of study)
var_first_type <- "first_type_example" # character | Type of the object (e.g. study) (Optional)
var_second_id <- "second_id_example" # character | Object ID (accession) (e.g. accession of study) (Optional)
var_second_type <- "second_type_example" # character | Type of the object (e.g. study) (Optional)
var_offset <- 0 # integer | Param says to skip that many links before beginning to return links. (Optional)
var_limit <- 1000 # integer | Param says to limit the count of returned links. (Optional)
api_instance <- LinkageAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetLinksByParamsAsCurator(var_first_id, first_type = var_first_type, second_id = var_second_id, second_type = var_second_type, offset = var_offset, limit = var_limitdata_file = "result.txt")
result <- api_instance$GetLinksByParamsAsCurator(var_first_id, first_type = var_first_type, second_id = var_second_id, second_type = var_second_type, offset = var_offset, limit = var_limit)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| first_id | character | Object ID (accession) (e.g. accession of study) | |
| first_type | character | Type of the object (e.g. study) | [optional] |
| second_id | character | Object ID (accession) (e.g. accession of study) | [optional] |
| second_type | character | Type of the object (e.g. study) | [optional] |
| offset | integer | Param says to skip that many links before beginning to return links. | [optional] [default to 0] |
| limit | integer | Param says to limit the count of returned links. | [optional] [default to 1000] |
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 a list of objects. | - |
| 400 | Entities cannot be retrieved. | - |
| 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. | - |
SaveLinksAsCurator¶
SaveLinksAsCurator(links = var.links)
Creates new links between objects.
This method should be used only in case you need to create links between 2 objects. Links are created both ways (e.g. when linking Object A to Object B it can be done both ways, by linking firstType to secondType and vice versa).
Example¶
library(odmApi)
# Creates new links between objects.
#
# prepare function argument(s)
var_links <- c(Link$new("firstId_example", "firstType_example", "secondId_example", "secondType_example")) # array[Link] | (Optional)
api_instance <- LinkageAsCuratorApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
api_instance$SaveLinksAsCurator(links = var_links)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| links | list( Link ) | [optional] |
Return type¶
void (empty response body)
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: application/json
- Accept: Not defined
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | Links were updated or not modified. | - |
| 201 | At least one new link has been created.Some other links might have been updated or not modified. | - |
| 400 | Invalid data in request. | - |
| 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). | - |
| 409 | Link cannot be created due to conflict with existing link | - |
| 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. | - |