Merge pull request #13152 from bernt-matthias/topic/xml-replace-fix-test

XML macros: add named yields, tokenized macros, tokens for attributes, and fix replacement of toplevel yield

lib/galaxy/util/xml_macros.py

@@ -1,5 +1,5 @@
 import os
-from copy import deepcopy
+from copy import copy, deepcopy
 
 from galaxy.util import parse_xml
 
@@ -17,13 +17,30 @@ def load_with_references(path):
 
     macro_paths = _import_macros(root, path)
 
+    # temporarily remove the children of the macros node
+    # and create a copy. this is done because this allows
+    # to iterate over all expand nodes of the tree
+    # that are not included in the macros node
+    macros_el = _macros_el(root)
+    if macros_el is not None:
+        macros_copy = copy(macros_el)
+        macros_el.clear()
+    else:
+        macros_copy = None
+
     # Collect tokens
-    tokens = _macros_of_type(root, 'token', lambda el: el.text or '')
+    tokens = _macros_of_type(macros_copy, 'token', lambda el: el.text or '')
     tokens = expand_nested_tokens(tokens)
 
     # Expand xml macros
-    macro_dict = _macros_of_type(root, 'xml', lambda el: XmlMacroDef(el))
+    macro_dict = _macros_of_type(macros_copy, 'xml', lambda el: XmlMacroDef(el))
     _expand_macros([root], macro_dict, tokens)
+
+    # readd the stashed children of the macros node
+    # TODO is this this really necesary? Since macro nodes are removed anyway just below.
+    if macros_copy is not None:
+        _xml_set_children(macros_el, list(macros_copy))
+
     for el in root.xpath('//macro'):
         if el.get('type') != 'template':
             # Only keep template macros
@@ -43,7 +60,8 @@ def template_macro_params(root):
     with these.
     """
     param_dict = {}
-    macro_dict = _macros_of_type(root, 'template', lambda el: el.text)
+    macros_el = _macros_el(root)
+    macro_dict = _macros_of_type(macros_el, 'template', lambda el: el.text)
     for key, value in macro_dict.items():
         param_dict[key] = value
     return param_dict
@@ -63,6 +81,10 @@ def imported_macro_paths(root):
 
 
 def _import_macros(root, path):
+    """
+    root the parsed XML tree
+    path the path to the main xml document
+    """
     xml_base_dir = os.path.dirname(path)
     macros_el = _macros_el(root)
     if macros_el is not None:
@@ -75,16 +97,14 @@ def _macros_el(root):
     return root.find('macros')
 
 
-def _macros_of_type(root, type, el_func):
-    macros_el = root.find('macros')
-    macro_dict = {}
-    if macros_el is not None:
-        macro_els = macros_el.findall('macro')
-        filtered_els = [(macro_el.get("name"), el_func(macro_el))
-                        for macro_el in macro_els
-                        if macro_el.get('type') == type]
-        macro_dict = dict(filtered_els)
-    return macro_dict
+def _macros_of_type(macros_el, type, el_func):
+    if macros_el is None:
+        return {}
+    macro_els = macros_el.findall('macro')
+    filtered_els = [(macro_el.get("name"), el_func(macro_el))
+                    for macro_el in macro_els
+                    if macro_el.get('type') == type]
+    return dict(filtered_els)
 
 
 def expand_nested_tokens(tokens):
@@ -106,6 +126,11 @@ def _expand_tokens(elements, tokens):
 
 
 def _expand_tokens_for_el(element, tokens):
+    """
+    expand tokens in element and (recursively) in its children
+    replacements of text attributes and attribute values are
+    possible
+    """
     value = element.text
     if value:
         new_value = _expand_tokens_str(element.text, tokens)
@@ -115,6 +140,11 @@ def _expand_tokens_for_el(element, tokens):
         new_value = _expand_tokens_str(value, tokens)
         if not (new_value is value):
             element.attrib[key] = new_value
+        new_key = _expand_tokens_str(key, tokens)
+        if not (new_key is key):
+            element.attrib[new_key] = element.attrib[key]
+            del element.attrib[key]
+    # recursively expand in childrens
     _expand_tokens(list(element), tokens)
 
 
@@ -125,7 +155,7 @@ def _expand_tokens_str(s, tokens):
     return s
 
 
-def _expand_macros(elements, macros, tokens):
+def _expand_macros(elements, macros, tokens, visited=None):
     if not macros and not tokens:
         return
 
@@ -134,48 +164,60 @@ def _expand_macros(elements, macros, tokens):
             expand_el = element.find('.//expand')
             if expand_el is None:
                 break
-            _expand_macro(element, expand_el, macros, tokens)
+            if visited is None:
+                v = []
+            else:
+                v = visited
+            _expand_macro(expand_el, macros, tokens, v)
 
 
-def _expand_macro(element, expand_el, macros, tokens):
+def _expand_macro(expand_el, macros, tokens, visited):
     macro_name = expand_el.get('macro')
     assert macro_name is not None, "Attempted to expand macro with no 'macro' attribute defined."
+
+    # check for cycles in the nested macro expansion
+    assert macro_name not in visited, f"Cycle in nested macros: already expanded {visited} can't expand '{macro_name}' again"
+    visited.append(macro_name)
+
     assert macro_name in macros, f"No macro named {macro_name} found, known macros are {', '.join(macros.keys())}."
     macro_def = macros[macro_name]
-    expanded_elements = deepcopy(macro_def.elements)
-
+    expanded_elements = deepcopy(macro_def.element)
     _expand_yield_statements(expanded_elements, expand_el)
 
-    # Recursively expand contained macros.
-    _expand_macros(expanded_elements, macros, tokens)
     macro_tokens = macro_def.macro_tokens(expand_el)
     if macro_tokens:
         _expand_tokens(expanded_elements, macro_tokens)
 
+    # Recursively expand contained macros.
+    _expand_macros(expanded_elements, macros, tokens, visited)
     _xml_replace(expand_el, expanded_elements)
+    del visited[-1]
 
 
 def _expand_yield_statements(macro_def, expand_el):
-    yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')]
-
-    expand_el_children = list(expand_el)
-
+    """
+    Modifies the macro_def element by replacing
+    1. all named yield tags by the content of the corresponding token tags
+       - token tags need to be direct children of the expand
+       - processed in order of definition of the token tags
+    2. all unnamed yield tags by the non-token children of the expand tag
+    """
+    # replace named yields
+    for token_el in expand_el.findall('./token'):
+        name = token_el.attrib.get("name", None)
+        assert name is not None, "Found unnamed token" + str(token_el.attrib)
+        yield_els = [yield_el for yield_el in macro_def.findall(f".//yield[@name='{name}']")]
+        assert len(yield_els) > 0, f"No named yield found for named token {name}"
+        token_el_children = list(token_el)
+        for yield_el in yield_els:
+            _xml_replace(yield_el, token_el_children)
+
+    # replace unnamed yields
+    yield_els = [yield_el for yield_el in macro_def.findall('.//yield')]
+    expand_el_children = [c for c in expand_el if c.tag != "token"]
     for yield_el in yield_els:
         _xml_replace(yield_el, expand_el_children)
 
-    # Replace yields at the top level of a macro, seems hacky approach
-    replace_yield = True
-    while replace_yield:
-        for i, macro_def_el in enumerate(macro_def):
-            if macro_def_el.tag == "yield":
-                for target in expand_el_children:
-                    i += 1
-                    macro_def.insert(i, target)
-                macro_def.remove(macro_def_el)
-                continue
-
-        replace_yield = False
-
 
 def _load_macros(macros_el, xml_base_dir):
     macros = []
@@ -225,7 +267,6 @@ def _load_imported_macros(macros_el, xml_base_dir):
         file_macros, current_macro_paths = _load_macro_file(import_path, xml_base_dir)
         macros.extend(file_macros)
         macro_paths.extend(current_macro_paths)
-
     return macros, macro_paths
 
 
@@ -270,9 +311,25 @@ def _xml_replace(query, targets):
 
 
 class XmlMacroDef:
+    """
+    representation of a (Galaxy) XML macro
 
+    stores the root element of the macro and the parameters.
+    each parameter is represented as pair containing
+    - the quote character, default '@'
+    - parameter name
+
+    parameter names can be given as comma separated list using the
+    `token` attribute or as attributes `token_XXX` (where `XXX` is the name).
+    The former option should be used to specify required attributes of the
+    macro and the latter for optional attributes if the macro (the value of
+    `token_XXX is used as default value).
+
+    TODO: `token_quote` forbids `"quote"` as character name of optional
+    parameters
+    """
     def __init__(self, el):
-        self.elements = list(el)
+        self.element = el
         parameters = {}
         tokens = []
         token_quote = "@"
@@ -290,12 +347,17 @@ def __init__(self, el):
         self.parameters = parameters
 
     def macro_tokens(self, expand_el):
+        """
+        get a dictionary mapping token names to values. The names are the
+        parameter names surrounded by the quote character. Values are taken
+        from the expand_el if absent default values of optional parameters are
+        used.
+        """
         tokens = {}
         for key, (wrap_char, default_val) in self.parameters.items():
             token_value = expand_el.attrib.get(key, default_val)
             if token_value is REQUIRED_PARAMETER:
-                message = "Failed to expand macro - missing required parameter [%s]."
-                raise ValueError(message % key)
+                raise ValueError(f"Failed to expand macro - missing required parameter [{key}].")
             token_name = f"{wrap_char}{key.upper()}{wrap_char}"
             tokens[token_name] = token_value
         return tokens