Validators¶
Classes to validate the integrity of the investigation model as well as study and assay graphs with respect to ISA-Tab format specifications.
AltamISA uses the Python warnings module for reporting validation warnings.
# Parse investigation and validate, capture warnings in `ws`.
with open("investigation.tsv", "rt") as inputf:
with warnings.catch_warnings(record=True) as warnings:
isa_inv = InvestigationReader.from_stream(input_file=inputf).read()
InvestigationValidator(isa_inv).validate()
# Iterate over all captured warnings and handle them.
for warning in warnings:
somehow_handle(warning)
Note
You can use the IsaWarning
class hierarchy for getting severity information.
Contents
altamisa.isatab.AssayValidator¶
-
class
altamisa.isatab.
AssayValidator
(investigation: altamisa.isatab.models.InvestigationInfo, study_info: altamisa.isatab.models.StudyInfo, assay_info: altamisa.isatab.models.AssayInfo, assay: altamisa.isatab.models.Assay, parent_study: altamisa.isatab.models.Study = None)[source]¶ Validator for Assay
Parameters: - investigation (models.InvestigationInfo) – The corresponding investigation model
- study_info (models.StudyInfo) – The corresponding study information
- assay_info (models.AssayInfo) – The corresponding assay information
- assay (models.Assay) – The Assay model to validate
- parent_study (models.Study) – Optional: The parent Study of the current Assay (for extended validation)
altamisa.isatab.StudyValidator¶
-
class
altamisa.isatab.
StudyValidator
(investigation: altamisa.isatab.models.InvestigationInfo, study_info: altamisa.isatab.models.StudyInfo, study: altamisa.isatab.models.Study)[source]¶ Validator for Study
Parameters: - investigation (models.InvestigationInfo) – The corresponding investigation model
- study_info (models.StudyInfo) – The corresponding study information
- study (models.Study) – The Study model to validate