diff env/lib/python3.9/site-packages/galaxy/tool_util/verify/asserts/__init__.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/tool_util/verify/asserts/__init__.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,87 @@
+import logging
+import sys
+
+from galaxy.util import unicodify
+from galaxy.util.getargspec import getfullargspec
+
+log = logging.getLogger(__name__)
+
+assertion_module_names = ['text', 'tabular', 'xml', 'hdf5', 'archive', 'size']
+
+# Code for loading modules containing assertion checking functions, to
+# create a new module of assertion functions, create the needed python
+# source file "test/base/asserts/<MODULE_NAME>.py" and add
+# <MODULE_NAME> to the list of assertion module names defined above.
+assertion_modules = []
+for assertion_module_name in assertion_module_names:
+    full_assertion_module_name = 'galaxy.tool_util.verify.asserts.' + assertion_module_name
+    try:
+        # Dynamically import module
+        __import__(full_assertion_module_name)
+        assertion_module = sys.modules[full_assertion_module_name]
+        assertion_modules.append(assertion_module)
+    except Exception:
+        log.exception('Failed to load assertion module: %s', assertion_module_name)
+
+
+def verify_assertions(data, assertion_description_list):
+    """ This function takes a list of assertions and a string to check
+    these assertions against. """
+    for assertion_description in assertion_description_list:
+        verify_assertion(data, assertion_description)
+
+
+def verify_assertion(data, assertion_description):
+    tag = assertion_description["tag"]
+    assert_function_name = "assert_" + tag
+    assert_function = None
+    for assertion_module in assertion_modules:
+        if hasattr(assertion_module, assert_function_name):
+            assert_function = getattr(assertion_module, assert_function_name)
+
+    if assert_function is None:
+        errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag
+        raise AssertionError(errmsg)
+
+    assert_function_args = getfullargspec(assert_function).args
+    args = {}
+    for attribute, value in assertion_description["attributes"].items():
+        if attribute in assert_function_args:
+            args[attribute] = value
+
+    # Three special arguments automatically populated independently of
+    # tool XML attributes. output is passed in as the contents of the
+    # output file. verify_assertions_function is passed in as the
+    # verify_assertions function defined above, this allows
+    # recursively checking assertions on subsections of
+    # output. children is the parsed version of the child elements of
+    # the XML element describing this assertion. See
+    # assert_element_text in test/base/asserts/xml.py as an example of
+    # how to use verify_assertions_function and children in conjuction
+    # to apply assertion checking to a subset of the input. The parsed
+    # version of an elements child elements do not need to just define
+    # assertions, developers of assertion functions can also use the
+    # child elements in novel ways to define inputs the assertion
+    # checking function (for instance consider the following fictional
+    # assertion function for checking column titles of tabular output
+    # - <has_column_titles><with_name name="sequence"><with_name
+    # name="probability"></has_column_titles>.)
+    if "output" in assert_function_args:
+        # If the assert_function will have an attribute called "output"
+        # the data passed from the test to the function will be unicodified.
+        # This is because most of the assert functions are working on pure
+        # text files.
+        args["output"] = unicodify(data)
+    if "output_bytes" in assert_function_args:
+        # This will read in data as bytes and will not change it prior passing
+        # it to the assert_function
+        args["output_bytes"] = data
+
+    if "verify_assertions_function" in assert_function_args:
+        args["verify_assertions_function"] = verify_assertions
+
+    if "children" in assert_function_args:
+        args["children"] = assertion_description["children"]
+
+    # TODO: Verify all needed function arguments are specified.
+    assert_function(**args)