Cronjobs Documentation

Cronjobs Documentation

The application uses Flask-Celery with Redis to manage and execute cronjobs. A separate cronjob container is responsible for scheduling these tasks, which are defined in a crontab file. The cronjobs communicate with the Flask API and can be triggered either on schedule or manually via API requests.

Cronjob Setup

The cronjobs are managed by a dedicated container containing a crontab file that schedules API requests to the Flask app. The cronjobs can also be triggered manually by sending a request to the /cronjob API endpoint.

Triggering Cronjobs

To trigger a cronjob via the API, send a request to the cronjob endpoint using the format:

parent_dict_key/nested_child_key

For example, to import biosamples, the endpoint would be:

/cronjob/biosamples/import

Current Cronjobs

Below are the currently available cronjobs and their respective API keys:

1. Biosamples

   • Import Biosamples:
     API Key: biosamples/import
     Function: biosamples.import_biosamples_from_project_names
   • Get Biosamples Derived From Parent:
     API Key: biosamples/derived_from
     Function: biosamples.get_biosamples_derived_from_parent
   • Get Biosample Parents:
     API Key: biosamples/parents
     Function: biosamples.get_biosample_parents

2. Experiments

   • Import Experiments:
     API Key: experiments/import
     Function: experiments.get_experiments_from_bioproject_accession

3. Assemblies

   • Import Assemblies by Bioproject:
     API Key: assemblies/import
     Function: assemblies.import_assemblies_by_bioproject
   • Add Blobtoolkit Link:
     API Key: assemblies/blob_link
     Function: assemblies.add_blob_link

4. Helpers

   • Handle Orphan Organisms:
     API Key: helpers/handle_orphans
     Function: taxonomy.handle_orphan_organisms
   • Add Lineage to Models:
     API Key: helpers/add_lineage
     Function: taxonomy.add_lineage

5. Geolocation

   • Create Coordinates from Local Samples:
     API Key: geo_locations/create_from_local_samples
     Function: geolocation.create_local_sample_coordinates
   • Create Coordinates from Biosamples:
     API Key: geo_locations/create_from_biosamples
     Function: geolocation.create_biosample_coordinates
   • Update All Countries:
     API Key: geo_locations/create_countries
     Function: geolocation.update_all_countries