Package 'hintr'

Build and start the API

Description

Build and start the API

Usage

api(
  queue_id = NULL,
  workers = 2,
  results_dir = tempdir(),
  inputs_dir = NULL,
  log_level = "info",
  health_check_interval = 0
)

Arguments

queue_id	ID of an existing queue to connect to, creates a new one if NULL
workers	Number of workers to spawn
results_dir	The dir for results to be saved to
inputs_dir	THe directory where input files are stored
log_level	The "lgr" log level to use
health_check_interval	Interval in seconds, after which the next time the redis connection is used the connection will be reset. 0 for no reconnection. This is used on cloud services where the TCP connections have an idle timeout and must be manually kept alive or restarted by the client.

Value

Running API

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Get debug output from naomi

Description

Get debug output from naomi

Usage

download_debug(
  id,
  dest = tempfile(),
  server = NULL,
  github_token = Sys.getenv("NAOMI_DOWNLOAD_DEBUG_TOKEN"),
  verbose = TRUE
)

Arguments

id	The model run id to download. This will be printed below the error message.
dest	The destination for the downloaded data. The actual data will be unpacked into a directory corresponding to the run id within this, so it is safe to use a common directory.
server	The url of the server. The default is to use the production naomi/hint/hintr instance. It is not possible to use the staging instance. You can change this if running locally.
github_token	Token with access to read hivtools org team members. Used to check you are a person with access to download debugs. Ideally don't pass this and use env var or interactive prompt instead.
verbose	Add a progress bar

Details

This uses GitHub authentication to pull the debug file. You need to

1. Make sure you are a member of the naomi-debug GitHub team

2. Generate a GitHub personal access token. Create a new fine-grained token. Set the resource owner to "hivtools" organisation. Under "Permissions" add "Members" read-only permission. And generate the token.

3. Pass the token to this function, fill in the interactive prompt or set as an environment variable "NAOMI_DOWNLOAD_DEBUG_TOKEN".

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Submit a prerun to the web app

Description

This requires VPN or RDP access to work.

Usage

hintr_submit_prerun(
  inputs,
  model_output,
  calibrate_output,
  server = "https://naomi.unaids.org",
  port = "8888",
  output_zip_path = tempfile(fileext = ".zip")
)

Arguments

inputs	The model inputs, a named list of file paths including pjnz, shape, population, survey and optionally programme and anc.
model_output	The hintr_output object from model fit
calibrate_output	The hintr_output object from calibration
server	The server URL to upload files to
port	The port the API is running on
output_zip_path	The path to save the output zip at, will use a tempfile by default

Details

This will take all model files and upload to a specified server and output the model output zip which can be saved into the ADR or uploaded into the Naomi app to view plots of model outputs.

Can use this for countries which cannot get a fit to work via the app you can prepare a model fit locally and then upload those outputs into the app.

Value

Path to the generated output zip

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