Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/planemo/xml/validation.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
---|---|
date | Sat, 02 May 2020 07:14:21 -0400 |
parents | |
children |
line wrap: on
line source
"""Module describing abstractions for validating XML content.""" import abc import subprocess from collections import namedtuple from galaxy.tool_util.deps.commands import which from galaxy.util import unicodify try: from lxml import etree except ImportError: etree = None XMLLINT_COMMAND = "xmllint --noout --schema {0} {1} 2>&1" INSTALL_VALIDATOR_MESSAGE = ("This feature requires an external dependency " "to function, pleaes install xmllint (e.g 'brew " "install libxml2' or 'apt-get install " "libxml2-utils'.") class XsdValidator(object): """Class allowing validation of XML files against XSD schema.""" __metaclass__ = abc.ABCMeta @abc.abstractmethod def validate(self, schema_path, target_path): """Validate ``target_path`` against ``schema_path``. :return type: ValidationResult """ @abc.abstractmethod def enabled(self): """Return True iff system has dependencies for this validator. :return type: bool """ ValidationResult = namedtuple("ValidationResult", ["passed", "output"]) class LxmlValidator(XsdValidator): """Validate XSD files using lxml library.""" def validate(self, schema_path, target_path): try: xsd_doc = etree.parse(schema_path) xsd = etree.XMLSchema(xsd_doc) xml = etree.parse(target_path) passed = xsd.validate(xml) return ValidationResult(passed, xsd.error_log) except etree.XMLSyntaxError as e: return ValidationResult(False, unicodify(e)) def enabled(self): return etree is not None class XmllintValidator(XsdValidator): """Validate XSD files with the external tool xmllint.""" def validate(self, schema_path, target_path): command = XMLLINT_COMMAND.format(schema_path, target_path) p = subprocess.Popen(command, stdout=subprocess.PIPE, shell=True) stdout, _ = p.communicate() passed = p.returncode == 0 return ValidationResult(passed, stdout) def enabled(self): return bool(which("xmllint")) VALIDATORS = [LxmlValidator(), XmllintValidator()] def get_validator(require=True): """Return a :class:`XsdValidator` object based on available dependencies.""" for validator in VALIDATORS: if validator.enabled(): return validator if require: raise Exception(INSTALL_VALIDATOR_MESSAGE) return None __all__ = ( "get_validator", "XsdValidator", )