attachments {CytobankAPI}

Attachment Endpoints

Description

Interact with attachments using these endpoints. Only FCS files can be analyzed in Cytobank, but any file can be uploaded as an attachment. Exported PDFs, statistics, and files also automatically attach themselves to the Experiment they are exported from. Learn more about attachments in Cytobank.

Usage

## S4 method for signature 'UserSession'
attachments.delete(
  UserSession,
  experiment_id,
  attachment_id,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
attachments.download(
  UserSession,
  experiment_id,
  attachment_id,
  directory = getwd(),
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession'
attachments.download_zip(
  UserSession,
  experiment_id,
  attachment_id,
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession'
attachments.list(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
attachments.show(
  UserSession,
  experiment_id,
  attachment_id,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
attachments.update(
  UserSession,
  attachment,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
attachments.upload(
  UserSession,
  experiment_id,
  file_path,
  output = "default",
  timeout = UserSession@long_timeout
)

Arguments

UserSession

Cytobank UserSession object

experiment_id

integer representing an experiment ID

attachment_id

integer representing an attachment ID

timeout

integer representing the request timeout time in seconds [optional]

directory

character representing a specific directory to which the file will be downloaded (optional ending directory slash), if left empty, the default will be the current working directory [optional]

output

character representing the output format [optional]
- attachments.list, attachments.show, attachments.update : ("default", "raw")

attachment

dataframe representing an attachment (can retrieve via the attachments.show endpoint)

file_path

character representing a file path

Details

attachments.delete Permanently delete an attachment.

attachments.download Download an attachment from an experiment.

attachments.download_zip Download all or a select set of attachments as a zip file from an experiment. The download link of the zip file will be sent to the user's registered email address.

attachments.list List all attachments from an experiment. Outputs a dataframe [default] or raw list with all fields present.
- Optional output parameter, specify one of the following: ("default", "raw")

attachments.show Show attachment details from an experiment.
- Optional output parameter, specify one of the following: ("default", "raw")

attachments.update Update an attachment description from an experiment.

attachments.upload Upload an attachment to an experiment.
- Optional output parameter, specify one of the following: ("default", "raw")

Examples

## Not run: # Authenticate via username/password
cyto_session <- authenticate(site="premium", username="cyril_cytometry", password="cytobank_rocks!")
Authenticate via auth_token
cyto_session <- authenticate(site="premium", auth_token="my_secret_auth_token")

## End(Not run)
## Not run: attachments.delete(cyto_session, 22, attachment_id=2)

## Not run: # Download an attachment to the current working directory
attachments.download(cyto_session, 22)

# Download an attachment to a new directory
attachments.download(cyto_session, 22, directory="/my/new/download/directory/")

## End(Not run)
## Not run: # Download the all attachment files as a zip file
attachments.download_zip(cyto_session, experiment_id=22)

# Download a select set of attachment files as a zip file
attachments.download_zip(cyto_session, experiment_id=22, attachment_id=2)

## End(Not run)
## Not run: # Dataframe of all attachments with all fields present
attachments.list(cyto_session, 22)

# Raw list of all attachments with all fields present
attachments.list(cyto_session, 22, output="raw")

## End(Not run)
## Not run: attachments.show(cyto_session, 22, attachment_id=2)

## Not run: attachments.update(cyto_session, attachment=cyto_attachment)

## Not run: attachments.upload(cyto_session, 22, file_path="/path/to/my_attachment.txt")