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galaxy.tool_util.verify.asserts package

galaxy.tool_util.verify.asserts.verify_assertions(data, assertion_description_list)

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

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

Submodules

galaxy.tool_util.verify.asserts.archive module

galaxy.tool_util.verify.asserts.archive.assert_has_archive_member(output_bytes, path, verify_assertions_function, children)

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, key, value)

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, keys)

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, value, delta=0)

Asserts the specified output has a size of the specified value

galaxy.tool_util.verify.asserts.tabular module

galaxy.tool_util.verify.asserts.tabular.get_first_line(output)

galaxy.tool_util.verify.asserts.tabular.assert_has_n_columns(output, n, sep='\t')

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

galaxy.tool_util.verify.asserts.text module

galaxy.tool_util.verify.asserts.text.assert_has_text(output, text)

Asserts specified output contains the substring specified by the argument text.

galaxy.tool_util.verify.asserts.text.assert_not_has_text(output, text)

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

galaxy.tool_util.verify.asserts.text.assert_has_line(output, line)

Asserts the specified output contains the line specified the argument line.

galaxy.tool_util.verify.asserts.text.assert_has_n_lines(output, n)

Asserts the specified output contains n lines.

galaxy.tool_util.verify.asserts.text.assert_has_text_matching(output, expression)

Asserts the specified output contains text matching the regular expression specified by the argument expression.

galaxy.tool_util.verify.asserts.text.assert_has_line_matching(output, expression)

Asserts the specified output contains a line matching the regular expression specified by the argument expression.

galaxy.tool_util.verify.asserts.xml module

galaxy.tool_util.verify.asserts.xml.to_xml(output)

galaxy.tool_util.verify.asserts.xml.xml_find_text(output, path)

galaxy.tool_util.verify.asserts.xml.xml_find(output, path)

galaxy.tool_util.verify.asserts.xml.assert_is_valid_xml(output)

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

galaxy.tool_util.verify.asserts.xml.assert_has_element_with_path(output, path)

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; http://effbot.org/zone/element-xpath.htm for more information.

galaxy.tool_util.verify.asserts.xml.assert_has_n_elements_with_path(output, path, n)

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

galaxy.tool_util.verify.asserts.xml.assert_element_text_matches(output, path, expression)

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, path, text)

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, path, attribute, expression)

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, path, attribute, text)

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, path, verify_assertions_function, children)

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