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Package eido Documentation

Project configuration

Class EidoValidationError

Object was not validated successfully according to schema.

def __init__(self, message, errors_by_type)

Initialize self. See help(type(self)) for accurate signature.

def validate_project(project, schema)

Validate a project object against a schema

Parameters:

  • project (peppy.Project): a project object to validate
  • schema (str | dict): schema dict to validate against or a path to onefrom the error. Useful when used ith large projects
def validate_sample(project, sample_name, schema)

Validate the selected sample object against a schema

Parameters:

  • project (peppy.Project): a project object to validate
  • sample_name (str | int): name or index of the sample to validate
  • schema (str | dict): schema dict to validate against or a path to one
def validate_config(project, schema)

Validate the config part of the Project object against a schema

Parameters:

  • project (peppy.Project): a project object to validate
  • schema (str | dict): schema dict to validate against or a path to one
def read_schema(schema)

Safely read schema from YAML-formatted file.

If the schema imports any other schemas, they will be read recursively.

Parameters:

  • schema (str | Mapping): path to the schema fileor schema in a dict form

Returns:

  • list[dict]: read schemas

Raises:

  • TypeError: if the schema arg is neither a Mapping nor a file path orif the 'imports' sections in any of the schemas is not a list
def inspect_project(p, sample_names=None, max_attr=10)

Print inspection info: Project or, if sample_names argument is provided, matched samples

Parameters:

  • p (peppy.Project): project to inspect
  • sample_names (Iterable[str]): list of samples to inspect
  • max_attr (int): max number of sample attributes to display
def get_available_pep_filters()

Get a list of available target formats

Returns:

  • List[str]: a list of available formats
def convert_project(prj, target_format, plugin_kwargs=None)

Convert a peppy.Project object to a selected format

Parameters:

  • prj (peppy.Project): a Project object to convert
  • plugin_kwargs (dict): kwargs to pass to the plugin function
  • target_format (str): the format to convert the Project object to

Raises:

  • EidoFilterError: if the requested filter is not defined
def validate_input_files(project, schemas, sample_name=None)

Determine which of the required and optional files are missing.

The names of the attributes that are required and/or deemed as inputs are sourced from the schema, more specifically from required_files and files sections in samples section: - If any of the required files are missing, this function raises an error. - If any of the optional files are missing, the function raises a warning. Note, this function also performs Sample object validation with jsonschema.

Parameters:

  • project (peppy.Project): project that defines the samples to validate
  • schema (str | dict): schema dict to validate against or a path to one
  • sample_name (str | int): name or index of the sample to validate. If None,validate all samples in the project

Raises:

  • PathAttrNotFoundError: if any required sample attribute is missing
def get_input_files_size(sample, schema)

Determine which of this Sample's required attributes/files are missing and calculate sizes of the files (inputs).

The names of the attributes that are required and/or deemed as inputs are sourced from the schema, more specifically from required_input_attrs and input_attrs sections in samples section. Note, this function does perform actual Sample object validation with jsonschema.

Parameters:

  • sample (peppy.Sample): sample to investigate
  • schema (list[dict] | str): schema dict to validate against or a path to one

Returns:

  • dict: dictionary with validation data, i.e missing,required_inputs, all_inputs, input_file_size

Raises:

  • ValidationError: if any required sample attribute is missing

Version Information: eido v0.2.1, generated by lucidoc v0.4.4