Open sequences in Agouti for imaging

The agouti_imager function opens specified sequences in Agouti for editing and tracks which sequences have been processed.

Usage

agouti_imager(
  agouti_prj_id,
  seqID,
  skip_tracking = FALSE,
  ask = FALSE,
  email = Sys.getenv("email"),
  sheet_id = "1PcqJziXm-ZNbCi2JJliQH_FQY8YMPXNEGgYwiiP2Ws8"
)

Arguments

agouti_prj_id

The Agouti project ID.

seqID

A vector of sequence IDs to be processed.

skip_tracking

Optional. A logical value indicating whether to skip tracking processed sequences. Defaults to FALSE.

ask

boolean whether the user should be prompted per seqID if it should be done again.

email

Optional. The email address used for Google Sheets authentication. Defaults to the "email" system environment variable.

sheet_id

Optional. The Google Sheets ID for tracking processed sequences. Defaults to a predefined sheet ID.

Value

None. The function opens URLs in the default web browser and updates a tracking file.

Details

This function requires the Agouti project ID, project name, and a vector of sequence IDs. It opens each sequence in the default web browser for editing in Agouti. After processing each sequence, the user is prompted to confirm if the sequence is complete. If confirmed, the sequence ID is appended to a tracking file to avoid reprocessing in future runs. To use this function effectively, ensure that you have the Agouti project ID and the sequence IDs you wish to process. The Agouti project ID can typically be found in the URL of your Agouti project. Create a Agouti export or use an existing one to obtain the sequence IDs. A mismatch between the provided Agouti project ID and the sequence IDs may lead to errors. The function uses Google Sheets to maintain the tracking file, requiring authentication via an email address. If the email is not provided, it attempts to retrieve it from system environment variables or prompts the user for input. Make sure to have the googlesheets4 and svDialogs packages installed and properly configured for Google Sheets authentication.

Note: Ensure that you have the necessary permissions to access and modify the specified Google Sheet. Note: if a PERMISSION_DENIED or FORBIDDEN error occurs when you have the correct access to the specified Google Sheet, try the following: googlesheets4::gs4_deauth() -> googlesheets4::gs4_auth() and select option 1. After going through the authentication steps, try this function again.

See also

Other agouti: agouti_validate_ai(), depopulate_agouti_imager_seq_done(), download_dep_media(), download_seq_media(), drg_example, populate_agouti_imager_seq_done(), redo_non_tracked(), rename_ct_files()

Author

Lynn Pallemaerts

Sander Devisscher

Examples

if (FALSE) { # \dontrun{

seqID <- c("f9cfa2ac-36a5-45e0-bd84-2b3a5a234ee6",
"793b5057-90b3-47db-b400-96b2b31c9b59",
"53075b53-dd7b-41b0-b778-394f28e16268",
 "560c8d87-ec9a-43f2-adb9-d96a09f589ef",
  "7b2d6285-34af-4bd3-b9f9-40022a267ad8")

agouti_imager(agouti_prj_id = "e10e6b2b-78fc-44ad-9d66-c4d0b1dd889e",
seqID)
} # }