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Pipestat configuration

Pipestat requires a few pieces of information to run:

  • a pipeline_name to write into, usually contained within the schema file (see below).
  • a path to the schema file that describes results that can be reported, e.g. "your/path/sample_output_schema.yaml":
    title: An example Pipestat output schema
    description: A pipeline that uses pipestat to report sample and project level results.
    type: object
    properties:
      pipeline_name: "default_pipeline_name"
      samples:
        type: object
        properties:
            result_name:
              type: string
              description: "ResultName"
    
  • backend info: either path to a YAML-formatted file or pipestat config with PostgreSQL database login credentials. Note that the config file can also contain a path to the yaml-formatted results file:
    schema_path: sample_output_schema.yaml
    #The config can contain either a results_file_path (file backend) or a databse connection (database backend)
    # results_file_path takes priority and will create a PipestatManager with a file backend
    results_file_path: results_file.yaml 
    database:
      dialect: postgresql
      driver: psycopg
      name: pipestat-test
      user: postgres
      password: pipestat-password
      host: 127.0.0.1
      port: 5432
    

Apart from that, there are many other optional configuration points that have defaults. Please refer to the environment variables reference to learn about the the optional configuration options and their meaning.

Configuration sources

Pipestat configuration can come from 3 sources, with the following priority:

  1. PipestatManager constructor
  2. Pipestat configuration file
  3. Environment variables