Package index • abba

All functions

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_batch_job(): Create a Batch API or Job file template
submit_k8s_yaml(): Submit a job profile for execution on a Kubernetes cluster