galaxy.tool_util.verify.asserts package

galaxy.tool_util.verify.asserts.verify_assertions(data: bytes, assertion_description_list, decompress=None)

This function takes a list of assertions and a string to check these assertions against.

galaxy.tool_util.verify.asserts.verify_assertion(data: bytes, assertion_description)

Submodules

galaxy.tool_util.verify.asserts.archive module

galaxy.tool_util.verify.asserts.archive.assert_has_archive_member(output_bytes: bytes, path: str, verify_assertions_function, children, all: Union[bool, str] = False, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Recursively checks the specified children assertions against the text of the first element matching the specified path found within the archive. Currently supported formats: .zip, .tar, .tar.gz.

galaxy.tool_util.verify.asserts.hdf5 module

galaxy.tool_util.verify.asserts.hdf5.assert_has_h5_attribute(output_bytes: bytes, key: str, value: str) → None

Asserts the specified HDF5 output has a given key-value pair as HDF5 attribute

galaxy.tool_util.verify.asserts.hdf5.assert_has_h5_keys(output_bytes: bytes, keys: str) → None

Asserts the specified HDF5 output has the given keys.

galaxy.tool_util.verify.asserts.size module

galaxy.tool_util.verify.asserts.size.assert_has_size(output_bytes: bytes, value: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts the specified output has a size of the specified value, allowing for absolute (delta) and relative (delta_frac) difference.

galaxy.tool_util.verify.asserts.tabular module

galaxy.tool_util.verify.asserts.tabular.get_first_line(output: str, comment: str) → str

get the first non-comment and non-empty line

galaxy.tool_util.verify.asserts.tabular.assert_has_n_columns(output: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, sep: str = '\t', comment: str = '', negate: Union[bool, str] = False) → None

Asserts the tabular output contains n columns. The optional sep argument specifies the column seperator used to determine the number of columns. The optional comment argument specifies comment characters

galaxy.tool_util.verify.asserts.text module

galaxy.tool_util.verify.asserts.text.assert_has_text(output: str, text: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts specified output contains the substring specified by the argument text. The exact number of occurrences can be optionally specified by the argument n

galaxy.tool_util.verify.asserts.text.assert_not_has_text(output: str, text: str) → None

Asserts specified output does not contain the substring specified by the argument text

galaxy.tool_util.verify.asserts.text.assert_has_line(output: str, line: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts the specified output contains the line specified by the argument line. The exact number of occurrences can be optionally specified by the argument n

galaxy.tool_util.verify.asserts.text.assert_has_n_lines(output: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts the specified output contains n lines allowing for a difference in the number of lines (delta) or relative differebce in the number of lines

galaxy.tool_util.verify.asserts.text.assert_has_text_matching(output: str, expression: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts the specified output contains text matching the regular expression specified by the argument expression. If n is given the assertion checks for exacly n (nonoverlapping) occurences.

galaxy.tool_util.verify.asserts.text.assert_has_line_matching(output: str, expression: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts the specified output contains a line matching the regular expression specified by the argument expression. If n is given the assertion checks for exactly n occurences.

galaxy.tool_util.verify.asserts.xml module

galaxy.tool_util.verify.asserts.xml.assert_is_valid_xml(output: str) → None

Simple assertion that just verifies the specified output is valid XML.

galaxy.tool_util.verify.asserts.xml.assert_has_element_with_path(output: str, path: str, negate: Union[bool, str] = False) → None

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.

galaxy.tool_util.verify.asserts.xml.assert_has_n_elements_with_path(output: str, path: str, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

Asserts the specified output has exactly n elements matching the path specified.

galaxy.tool_util.verify.asserts.xml.assert_element_text_matches(output: str, path: str, expression: str, negate: Union[bool, str] = False) → None

Asserts the text of the first element matching the specified path matches the specified regular expression.

galaxy.tool_util.verify.asserts.xml.assert_element_text_is(output: str, path: str, text: str, negate: Union[bool, str] = False) → None

Asserts the text of the first element matching the specified path matches exactly the specified text.

galaxy.tool_util.verify.asserts.xml.assert_attribute_matches(output: str, path: str, attribute, expression: str, negate: Union[bool, str] = False) → None

Asserts the specified attribute of the first element matching the specified path matches the specified regular expression.

galaxy.tool_util.verify.asserts.xml.assert_attribute_is(output: str, path: str, attribute: str, text, negate: Union[bool, str] = False) → None

Asserts the specified attribute of the first element matching the specified path matches exactly the specified text.

galaxy.tool_util.verify.asserts.xml.assert_element_text(output: str, path: str, verify_assertions_function, children, negate: Union[bool, str] = False) → None

Recursively checks the specified assertions against the text of the first element matching the specified path.

galaxy.tool_util.verify.asserts.xml.assert_xml_element(output: str, path: str, verify_assertions_function=None, children=None, attribute: Optional[str] = None, all: Union[bool, str] = False, n: Optional[Union[str, int]] = None, delta: Union[int, str] = 0, min: Optional[Union[str, int]] = None, max: Optional[Union[str, int]] = None, negate: Union[bool, str] = False) → None

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.