R: Batch Execution of R Programs on 'Kubernetes', 'SLURM', and 'Posit Workbench'

# Batch Execution of R Programs on 'Kubernetes', 'SLURM', and 'Posit Workbench'

## Documentation for package ‘abba’ version 0.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

abba_get_batch_log | Send GET request to get logs of all jobs in a batch
abba_get_batch_status | Send GET request to get batch job statuses
abba_get_job_log | Send GET request to get logs of specified Jobs
abba_get_job_status | Send GET request to get job status
abba_get_k8s_batch_log_local | Return list of logs for jobs that are marked with a given batch ID
abba_get_k8s_batch_status_local | Get status of all jobs in a batch
abba_get_k8s_job_log_local | Get log for every job specified in an input vector/list
abba_get_k8s_job_status_local | Get status of all pods that belong to a job
abba_rslauncher_get_job_status_local | Get Workbench job status for a given vector/list of job IDs
abba_rslauncher_get_job_succeeded_local | Check whether Workbench jobs have been fully executed.
abba_rslauncher_submit_job_local | Create a job for executing an R program
abba_rslauncher_submit_logrx_job_local | Execute programs via logrx
abba_rslauncher_watch_job_local | Periodically poll Workbench jobs for status and return their IDs when all job statuses arrive at 'Finished' state
abba_slurm_get_job_log | Return job log for each submitted job ID
abba_slurm_get_job_status | Return descriptive job status for slurm jobs
abba_slurm_get_job_succeeded | Check whether SLURM jobs have been fully executed.
abba_slurm_submit_job | Submit R program as a SLURM job
abba_slurm_watch_job | Watch SLURM job, periodically polling its execution status.
abba_submit_and_get_log | Send job and poll for status. This function sends multiple requests so it won't time out on heavy jobs
abba_submit_batch | Submit programs for execution in order defined by structure of input list. Programs inside sublists will be executed in parallel, and sublists themselves would be submitted sequentially.
abba_submit_batch_and_get_results | Submit programs for execution in order defined by structure of input list.
abba_submit_job | Send POST request to submit-job endpoint
abba_submit_k8s_job_and_poll_local | Submit a job profile for execution on a Kubernetes cluster and poll for completion
abba_submit_k8s_job_local | Submit an R program for execution on a Kubernetes cluster
abba_wait_for_batch_log | Monitor batch status and retrieve its log when the all jobs in batch finish running
abba_wait_for_job_log | Monitor job status and retrieve its log when the job finishes running
abba_watch_k8s_batch_local | Watch a K8S batch that has been submitted to Workbench, periodically polling it's execution status.
abba_watch_k8s_job_local | Watch a K8S job that has been submitted to Workbench, periodically polling it's execution status.
calculate_run_group | Calculate run_group variable using inputs and outputs of programs supplied by user
create_batch_api | Create a Batch API or Job file template
create_batch_job | Create a Batch API or Job file template
submit_k8s_yaml | Submit a job profile for execution on a Kubernetes cluster