FilesAsUserApi¶
All URIs are relative to http://localhost
| Method | HTTP request | Description |
|---|---|---|
| GetFileAsUser | GET /api/v1/as-user/files/{id}/download | Retrieve a file by ID (accession) |
| GetFileMetadataByIdAsUser | GET /api/v1/as-user/files/{id} | Retrieve file's metadata by ID (accession) |
| GetFilesMetadataAsUser | GET /api/v1/as-user/files | Retrieve file's metadata by its fields |
| HeadFileAsUser | HEAD /api/v1/as-user/files/{id}/download | Check if a file exists by ID (accession). |
GetFileAsUser¶
data.frame GetFileAsUser(id, range = var.range)
Retrieve a file by ID (accession)
Download a file by its accession.
Example¶
library(odmApi)
# Retrieve a file by ID (accession)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_range <- "bytes=0-" # character | Request a specific range of bytes to support partial downloads. Example: `bytes=0-1024` to download the first 1024 bytes. Supplying several ranges is not supported. (Optional)
api_instance <- FilesAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetFileAsUser(var_id, range = var_rangedata_file = "result.txt")
result <- api_instance$GetFileAsUser(var_id, range = var_range)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. | |
| range | character | Request a specific range of bytes to support partial downloads. Example: `bytes=0-1024` to download the first 1024 bytes. Supplying several ranges is not supported. | [optional] |
Return type¶
data.frame
Authorization¶
Access-token, Genestack-API-Token
HTTP request headers¶
- Content-Type: Not defined
- Accept: application/octet-stream
HTTP response details¶
| Status code | Description | Response headers |
|---|---|---|
| 200 | File downloaded successfully | - |
| 206 | Partial content downloaded successfully | - |
| 400 | File cannot be retrieved. | - |
| 401 | User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page). | - |
| 404 | No object exists with the given ID. | - |
| 406 | File cannot be downloaded. | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details. | - |
GetFileMetadataByIdAsUser¶
object GetFileMetadataByIdAsUser(id, include_contents = FALSE)
Retrieve file's metadata by ID (accession)
Example¶
library(odmApi)
# Retrieve file's metadata by ID (accession)
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
var_include_contents <- FALSE # character | Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response. (Optional)
api_instance <- FilesAsUserApi$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$GetFileMetadataByIdAsUser(var_id, include_contents = var_include_contentsdata_file = "result.txt")
result <- api_instance$GetFileMetadataByIdAsUser(var_id, include_contents = var_include_contents)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. | |
| include_contents | character | Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response. | [optional] [default to FALSE] |
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 | Invalid data in the request. See the error message for details. | - |
| 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 | Object with provided accession could not be found in ODM. | - |
| 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. | - |
GetFilesMetadataAsUser¶
ListResponse GetFilesMetadataAsUser(filter = var.filter, query = var.query, include_contents = FALSE, page_limit = var.page_limit, page_offset = var.page_offset)
Retrieve file's metadata by its fields
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 (\\). ## 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 retrieve all results, iterate through pages by increasing the offset in multiples of limit (e.g., offset = n * limit), until all results have been retrieved. The total number of pages can be calculated by dividing the total number of results by the limit. ## List operation This endpoint can be called without any query parameters. When called this way, it returns a list of all files metadata objects.¶
Example¶
library(odmApi)
# Retrieve file's metadata by its fields
#
# prepare function argument(s)
var_filter <- "filter_example" # character | Filter by files metadata (key-value metadata pair(s)). (Optional)
var_query <- "query_example" # character | Search for files via a full-text query over all file metadata. (Optional)
var_include_contents <- FALSE # character | Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response. (Optional)
var_page_limit <- 56 # integer | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 2000. (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 <- FilesAsUserApi$new()
# Configure API key authorization: Access-token
api_instance$api_client$api_keys["Authorization"] <- Sys.getenv("API_KEY")
# Configure API key authorization: Genestack-API-Token
# api_instance$api_client$api_keys["Genestack-API-Token"] <- Sys.getenv("API_KEY")
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
# result <- api_instance$GetFilesMetadataAsUser(filter = var_filter, query = var_query, include_contents = var_include_contents, page_limit = var_page_limit, page_offset = var_page_offsetdata_file = "result.txt")
result <- api_instance$GetFilesMetadataAsUser(filter = var_filter, query = var_query, include_contents = var_include_contents, page_limit = var_page_limit, page_offset = var_page_offset)
dput(result)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| filter | character | Filter by files metadata (key-value metadata pair(s)). | [optional] |
| query | character | Search for files via a full-text query over all file metadata. | [optional] |
| include_contents | character | Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response. | [optional] [default to FALSE] |
| page_limit | integer | Maximum number of results to return per page (see Paging above). This value must be between 0 and 2000 (inclusive). The default is 2000. | [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. | - |
| 400 | Invalid data in the request. See the error message for details. | - |
| 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. | - |
HeadFileAsUser¶
HeadFileAsUser(id)
Check if a file exists by ID (accession).
Check if a file exists by its accession. This endpoint can be used to check if a file exists and accessible before downloading it.
Example¶
library(odmApi)
# Check if a file exists by ID (accession).
#
# prepare function argument(s)
var_id <- "id_example" # character | Unique identifier (accession) of the object.
api_instance <- FilesAsUserApi$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$HeadFileAsUser(var_id)
Parameters¶
| Name | Type | Description | Notes |
|---|---|---|---|
| id | character | Unique identifier (accession) of the object. |
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 |
|---|---|---|
| 200 | File exists. Additional metadata is provided in the response headers. | - |
| 400 | File cannot be downloaded. | - |
| 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. | - |
| 406 | File cannot be downloaded. | - |
| 500 | An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to | - |