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Source code for galaxy.tool_util.verify.asserts.xml

import re
from typing import Optional

from lxml.etree import XMLSyntaxError

from galaxy.tool_util.verify import asserts
from galaxy.util import (
    asbool,
    parse_xml_string,
    unicodify,
)


[docs]def assert_is_valid_xml(output): """Simple assertion that just verifies the specified output is valid XML.""" try: parse_xml_string(output) except XMLSyntaxError as e: raise AssertionError(f"Expected valid XML, but could not parse output. {unicodify(e)}")
[docs]def assert_has_element_with_path(output, path, negate: bool = False): """Asserts the specified output has at least one XML element with a path matching the specified path argument. Valid paths are the simplified subsets of XPath implemented by lxml.etree; https://lxml.de/xpathxslt.html for more information.""" assert_xml_element(output, path, negate=negate)
[docs]def assert_has_n_elements_with_path( output, path, n: Optional[int] = None, delta: int = 0, min: Optional[int] = None, max: Optional[int] = None, negate: bool = False, ): """Asserts the specified output has exactly n elements matching the path specified.""" assert_xml_element(output, path, n=n, delta=delta, min=min, max=max, negate=negate)
[docs]def assert_element_text_matches(output, path, expression, negate: bool = False): """Asserts the text of the first element matching the specified path matches the specified regular expression.""" sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}} assert_xml_element(output, path, asserts.verify_assertions, [sub])
[docs]def assert_element_text_is(output, path, text, negate: bool = False): """Asserts the text of the first element matching the specified path matches exactly the specified text.""" assert_element_text_matches(output, path, re.escape(text) + "$", negate=negate)
[docs]def assert_attribute_matches(output, path, attribute, expression, negate: bool = False): """Asserts the specified attribute of the first element matching the specified path matches the specified regular expression.""" sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}} assert_xml_element(output, path, asserts.verify_assertions, [sub], attribute=attribute)
[docs]def assert_attribute_is(output, path, attribute, text, negate: bool = False): """Asserts the specified attribute of the first element matching the specified path matches exactly the specified text.""" assert_attribute_matches(output, path, attribute, re.escape(text) + "$", negate=negate)
[docs]def assert_element_text(output, path, verify_assertions_function, children, negate: bool = False): """Recursively checks the specified assertions against the text of the first element matching the specified path.""" assert_xml_element(output, path, verify_assertions_function, children, negate=negate)
[docs]def assert_xml_element( output, path, verify_assertions_function=None, children=None, attribute=None, all=False, n: Optional[int] = None, delta: int = 0, min: Optional[int] = None, max: Optional[int] = None, negate: bool = False, ): """ Check if path occurs in the xml. If n and delta or min and max are given also the number of occurences is checked. If there are any sub assertions then check them against - the element's text if attribute is None - the content of the attribute If all is True then the sub assertions are checked for all occurences. """ children = children or [] all = asbool(all) # assert that path is in output (the specified number of times) xml = parse_xml_string(output) asserts._util._assert_presence_number( xml, path, n, delta, min, max, negate, lambda x, p: x.find(p) is not None, lambda x, p: len(x.findall(p)), "{expected} path '{text}' in xml", "{expected} {n}+-{delta} occurrences of path '{text}' in xml", "{expected} that the number of occurences of path '{text}' in xml is in [{min}:{max}]", ) # check sub-assertions if len(children) == 0 or verify_assertions_function is None: return for occ in xml.findall(path): if attribute is None or attribute == "": content = occ.text else: content = occ.attrib[attribute] try: verify_assertions_function(content, children) except AssertionError as e: if attribute is not None and attribute != "": raise AssertionError(f"Attribute '{attribute}' on element with path '{path}': {str(e)}") else: raise AssertionError(f"Text of element with path '{path}': {str(e)}") if not all: break