gen3utils 0.8.3

Gen3 Library Template

gen3utils

Utils for Gen3 commons management

Install with pip

pip install gen3utils

manifest.json validation

Validate one or more manifest.json files:

gen3utils validate_manifest cdis-manifest/*/manifest.json

The validation settings can be updated by modifying this file.

etlMapping.yaml validation

Validate an etlMapping.yaml file against the dictionary URL specified in a manifest.json file:

gen3utils validate_etl_mapping etlMapping.yaml manifest.json

Portal Configuration (gitops.json) validation

Validate a gitops.json file against the dictionary URL specified in a manifest.json file and an etlMapping.yaml file. Adds a comment to a pull request listing all the errors encountered when validating against etlMapping.yaml

gen3utils validate_portal_config etlMapping.yaml manifest.json gitops.json <username>/<repository> <pull request number>

To run without making a pull request comment

gen3utils validate_portal_config etlMapping.yaml manifest.json gitops.json

Comment on a PR with any deployment changes when updating manifest services

The command requires the name of the repository, the pull request number and a GITHUB_TOKEN environment variable containing a token with read and write access to the repository. It also comments a warning if a service is pinned on a branch.

pip install gen3utils
gen3utils post_deployment_changes <username>/<repository> <pull request number>

Log parser for CTDS log pipeline

pip install gen3utils
gen3utils s3log --help
gen3utils s3log [OPTIONS] BUCKET PREFIX SCRIPT

Run SCRIPT in Gen3 logs under S3 BUCKET:PREFIX. The SCRIPT should be importable defining a method like this:

def handle_row(obj, line):
    if 1 + 1 == 2:
        return line

For example, to process logs in bucket my-commons-logs at prefix my-logs with a gen3utils/script.py file:

pip install gen3utils
gen3utils s3log my-commons-logs my-logs gen3utils.script

Running tests locally

poetry install -vv
poetry run pytest -vv ./tests