Eido: Project Metadata Validator

Common errors

• jsonschema.exceptions.ValidationError: '...' is not valid under any of the given schemas

  cause The data in your project configuration or sample table does not conform to the specified JSON schema. This error is directly from the underlying `jsonschema` library, which `eido` uses.
  fix Carefully compare your project's `config.yaml` and `sample_table.csv` (or equivalent) against the `project_schema.yaml`. Pay attention to data types, required fields, enum values, and allowed patterns. The error message often includes details about the specific failing validation condition.

• FileNotFoundError: [Errno 2] No such file or directory: 'your_schema.yaml'

  cause The path provided for your project configuration, sample table, or schema file is incorrect or the file does not exist at the specified location.
  fix Double-check the file paths passed to `peppy.Project()` and `eido.validate_project()`. Ensure the files exist and are accessible from where your script is running. Use absolute paths or verify your current working directory.

• AttributeError: 'NoneType' object has no attribute 'get' (or similar error when accessing project attributes)

  cause This usually indicates that `peppy.Project()` failed to load your project configuration correctly, resulting in a `Project` object that is either `None` or incomplete. `eido` then tries to access non-existent attributes of this invalid project object.
  fix Inspect your `config.yaml` for syntax errors (e.g., incorrect YAML formatting, missing required sections). Ensure `peppy` can parse your project configuration independently before passing it to `eido`. Check `peppy`'s documentation for valid project structures and common parsing issues.

Warnings

• breaking In `v0.2.3`, several internal keys/attributes used in schema definition or project configuration were renamed: `files_key` to `sizing`, `required_files_key` to `tangible_key`, and `_samples` to `samples`. This may break existing PEP configurations or custom schemas.
  Fix: Update project schemas and configurations to use the new key names (`sizing`, `tangible_key`, `samples`). Review `peppy` and `eido` documentation for updated schema requirements.
• breaking The `--exclude-case` option was removed from the CLI in `v0.2.2`. Users relying on this command-line argument will find their scripts failing.
  Fix: Remove `--exclude-case` from CLI calls. If case-insensitive validation is still required, check `jsonschema` documentation for equivalent options or implement custom pre-processing.
• gotcha Eido is primarily designed to validate `peppy.Project` and `peppy.Sample` objects. While it uses JSON Schema internally, directly passing arbitrary Python dictionaries to `validate_project` or `validate_sample` will likely fail unless the dictionary mimics the structure of a `peppy` object.
  Fix: For generic dictionary validation, consider using the `jsonschema` library directly. If you need `eido`'s schema discovery or specialized PEP validation, ensure your data is wrapped in a `peppy.Project` or `peppy.Sample` object. Refer to `peppy` documentation for creating project objects.

Install

• pip install eido Install latest version

Imports

• validate_project

  from eido import validate_project

• validate_sample

  from eido import validate_sample

• validate_config

  from eido import validate_config

Quickstart

This quickstart demonstrates how to use eido to validate a peppy Project object against a JSON schema. It involves creating temporary config and schema files, loading them with `peppy`, and then invoking `eido.validate_project` for both a valid and an intentionally invalid project.

import os
import peppy
import eido
import yaml
from jsonschema import ValidationError

# Create a dummy project config file
config_content = """
project_name: MyTestProject
output_dir: output/
samples:
  - sample_name: sample1
    file_path: data/sample1.txt
    organism: human
  - sample_name: sample2
    file_path: data/sample2.txt
    organism: mouse
"""

# Create a dummy schema file
schema_content = """
type: object
properties:
  project_name: { type: string }
  output_dir: { type: string }
  samples:
    type: array
    items:
      type: object
      properties:
        sample_name: { type: string }
        file_path: { type: string }
        organism: { type: string, enum: [human, mouse, rat] }
      required: [sample_name, file_path, organism]
required: [project_name, samples]
"""

config_file = "_eido_test_config.yaml"
schema_file = "_eido_test_schema.yaml"

try:
    # Write dummy files
    with open(config_file, 'w') as f:
        f.write(config_content)
    with open(schema_file, 'w') as f:
        f.write(schema_content)

    # Load the project using peppy
    project = peppy.Project(config_file)

    # Validate the project using eido
    print(f"Attempting to validate project '{project.name}'...")
    eido.validate_project(project, schema_file)
    print("Project validated successfully!")

    # Example of validation failure (optional, for demonstration)
    print("\n--- Demonstrating a validation failure ---")
    bad_config_content = """
project_name: AnotherProject
samples:
  - sample_name: invalid_sample
    organism: alien # 'alien' is not in enum
"""
    bad_config_file = "_eido_bad_config.yaml"
    with open(bad_config_file, 'w') as f:
        f.write(bad_config_content)
    bad_project = peppy.Project(bad_config_file)
    try:
        print("Attempting to validate a project with invalid organism...")
        eido.validate_project(bad_project, schema_file)
        print("Unexpected: Validation passed for bad project!")
    except ValidationError as e:
        print(f"Caught expected validation error: {e.message}")

finally:
    # Clean up dummy files
    if os.path.exists(config_file):
        os.remove(config_file)
    if os.path.exists(schema_file):
        os.remove(schema_file)
    if os.path.exists(bad_config_file):
        os.remove(bad_config_file)