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CI Tests Coverage

nmdc_automation

Goal

Demonstrate how the various stages of a series of workflows could be tracked and triggered by the runtime.

Approach

The workflows are defined in a YAML file. This describes the following for each workflow

  • Name
  • Git Repo associated with the workflow
  • Version: The current active version that should be run
  • WDL: The "top-level" WDL that should be run
  • Input Prefix: The string that should be prefixed to all of the inputs. This is a workaround because Mongo doesn't like dots in key names
  • Inputs: The array of inputs for the workflow. Not it doesn't deal with nested structures yet.

The main scheduling loop does the following:

  1. For each workflow, it gathers up all jobs and activities that match the current repo and version. This basically to figure out what is in-flight or completed that matches the current release. These records also include the trigger object that initiated the previous jobs.
  2. Using the trigger object type find all objects that could be processed.
  3. See if the trigger object exist in the query from step 1. Anything missing will generate a new job.
  4. Generate a job record for each object. Use the workflow spec to populate the inputs.

Install Dependencies

To install the environment using poetry, there are a few steps to take. If Poetry is no installed, run: pip install poetry

Once poetry is installed, you can run: poetry install

To use the environment, you can shell into the env: poetry shell

Implementation

This package is meant to be used on NMDC approvied compute instances with directories that can be accessed via https and are linked to the microbiomedata.org/data endpoint.

The main python drivers can be found in the nmdc_automation/run_process directory that contians two processes that require configurations to be supplied.

Run NMDC Workflows with corresponding omics processing records

nmdc_automation/run_process/run_worklfows.py will automate job claims, job processing, and analysis record and data object submission via the nmdc runtime-api. To submit a process that will spawn a daemon that will claim, process, and submit all jobs that have not been claimed, cd in to nmdc_automation/run_process and run python run_workflows.py watcher --config ../../configs/site_configuration_nersc.toml daemon, this will watch for omics processing records that have not been claimed and processed.

Setting up Watcher/Runner on Perlmutter:
1. After logging into nmdcda on perlmutter do ~/bin/screen.sh prod
2. /global/cfs/cdirs/m3408/squads/napacompliance
    a. check workflows.yaml
3. ./run_prod.sh or ./run.sh - pulling from nmdc and submitting to Cromwell; monitors job to see if it succeeded or failed
4. start up workers, sbatch ~/workers_perlmutter.sl
    a. sbatch -N 5 -q regular ./workers_perlmutter.sl
    b. salloc -N 1 -C cpu -q interactive -t 4:00:00
5. Cq running -> to see what jobs are still running
6. Cq meta <string> ->status of string job

Setting up Scheduler on Rancher:
1. cd /conf
2. /allow.lst is where the allow list is
3. /conf/fetch_latest_workflow_yaml.sh - fetches latest workflow from repo
4. /conf/run.sh in order to reprocess workflows.yaml
5. 'ps aux' to see what the scheduler is currently running

Run Workflow import for data processed by non NMDC workflows

nmdc_automation/run_process/run_workflows.py is designed to take in data files avilable on disk, transform them into NMDC analysis records, and submit them back to the central data store via runtime-api. This process includes minting identifers for workflow execution subclasses and data objects. Currently this process is only suitable for data processed at JGI, but with collaboration, data from other processing centers could be transformed and ingested into NMDC. To submit the import process, log into Perlmutter using the collaboration account. To run import in the root repository directory run python nmdc_automation/run_process/run_import.py import-projects import.tsv configs/import.yaml configs/site_configuration.toml, where import.tsv expects the follow format:

nucleotide_sequencing_id project_id project_path
nmdc:omprc-11-q8b9dh63 Ga0597031 /path/to/project/Ga0597031

The following need to be set in the site_configuration.toml file: api_url, url_root, client_id, client_secret.