diff env/lib/python3.9/site-packages/galaxy/util/xml_macros.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/util/xml_macros.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,310 @@
+import os
+from copy import deepcopy
+
+from galaxy.util import parse_xml
+
+REQUIRED_PARAMETER = object()
+
+
+def load_with_references(path):
+    """Load XML documentation from file system and preprocesses XML macros.
+
+    Return the XML representation of the expanded tree and paths to
+    referenced files that were imported (macros).
+    """
+    tree = raw_xml_tree(path)
+    root = tree.getroot()
+
+    macro_paths = _import_macros(root, path)
+
+    # Collect tokens
+    tokens = _macros_of_type(root, '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))
+    _expand_macros([root], macro_dict, tokens)
+    for el in root.xpath('//macro'):
+        if el.get('type') != 'template':
+            # Only keep template macros
+            el.getparent().remove(el)
+    _expand_tokens_for_el(root, tokens)
+    return tree, macro_paths
+
+
+def load(path):
+    tree, _ = load_with_references(path)
+    return tree
+
+
+def template_macro_params(root):
+    """
+    Look for template macros and populate param_dict (for cheetah)
+    with these.
+    """
+    param_dict = {}
+    macro_dict = _macros_of_type(root, 'template', lambda el: el.text)
+    for key, value in macro_dict.items():
+        param_dict[key] = value
+    return param_dict
+
+
+def raw_xml_tree(path):
+    """ Load raw (no macro expansion) tree representation of XML represented
+    at the specified path.
+    """
+    tree = parse_xml(path, strip_whitespace=False, remove_comments=True)
+    return tree
+
+
+def imported_macro_paths(root):
+    macros_el = _macros_el(root)
+    return _imported_macro_paths_from_el(macros_el)
+
+
+def _import_macros(root, path):
+    xml_base_dir = os.path.dirname(path)
+    macros_el = _macros_el(root)
+    if macros_el is not None:
+        macro_els, macro_paths = _load_macros(macros_el, xml_base_dir)
+        _xml_set_children(macros_el, macro_els)
+        return macro_paths
+
+
+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 expand_nested_tokens(tokens):
+    for token_name in tokens.keys():
+        for current_token_name, current_token_value in tokens.items():
+            if token_name in current_token_value:
+                if token_name == current_token_name:
+                    raise Exception("Token '%s' cannot contain itself" % token_name)
+                tokens[current_token_name] = current_token_value.replace(token_name, tokens[token_name])
+    return tokens
+
+
+def _expand_tokens(elements, tokens):
+    if not tokens or elements is None:
+        return
+
+    for element in elements:
+        _expand_tokens_for_el(element, tokens)
+
+
+def _expand_tokens_for_el(element, tokens):
+    value = element.text
+    if value:
+        new_value = _expand_tokens_str(element.text, tokens)
+        if not (new_value is value):
+            element.text = new_value
+    for key, value in element.attrib.items():
+        new_value = _expand_tokens_str(value, tokens)
+        if not (new_value is value):
+            element.attrib[key] = new_value
+    _expand_tokens(list(element), tokens)
+
+
+def _expand_tokens_str(s, tokens):
+    for key, value in tokens.items():
+        if key in s:
+            s = s.replace(key, value)
+    return s
+
+
+def _expand_macros(elements, macros, tokens):
+    if not macros and not tokens:
+        return
+
+    for element in elements:
+        while True:
+            expand_el = element.find('.//expand')
+            if expand_el is None:
+                break
+            _expand_macro(element, expand_el, macros, tokens)
+
+
+def _expand_macro(element, expand_el, macros, tokens):
+    macro_name = expand_el.get('macro')
+    assert macro_name is not None, "Attempted to expand macro with no 'macro' attribute defined."
+    assert macro_name in macros, f"No macro named {macro_name} found, known marcos are {', '.join(macros.keys())}."
+    macro_def = macros[macro_name]
+    expanded_elements = deepcopy(macro_def.elements)
+
+    _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)
+
+    _xml_replace(expand_el, expanded_elements)
+
+
+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)
+
+    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 = []
+    # Import macros from external files.
+    imported_macros, macro_paths = _load_imported_macros(macros_el, xml_base_dir)
+    macros.extend(imported_macros)
+    # Load all directly defined macros.
+    macros.extend(_load_embedded_macros(macros_el, xml_base_dir))
+    return macros, macro_paths
+
+
+def _load_embedded_macros(macros_el, xml_base_dir):
+    macros = []
+
+    macro_els = []
+    # attribute typed macro
+    if macros_el is not None:
+        macro_els = macros_el.findall("macro")
+    for macro in macro_els:
+        if 'type' not in macro.attrib:
+            macro.attrib['type'] = 'xml'
+        macros.append(macro)
+
+    # type shortcuts (<xml> is a shortcut for <macro type="xml",
+    # likewise for <template>.
+    typed_tag = ['template', 'xml', 'token']
+    for tag in typed_tag:
+        macro_els = []
+        if macros_el is not None:
+            macro_els = macros_el.findall(tag)
+        for macro_el in macro_els:
+            macro_el.attrib['type'] = tag
+            macro_el.tag = 'macro'
+            macros.append(macro_el)
+
+    return macros
+
+
+def _load_imported_macros(macros_el, xml_base_dir):
+    macros = []
+    macro_paths = []
+
+    for tool_relative_import_path in _imported_macro_paths_from_el(macros_el):
+        import_path = \
+            os.path.join(xml_base_dir, tool_relative_import_path)
+        macro_paths.append(import_path)
+        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
+
+
+def _imported_macro_paths_from_el(macros_el):
+    imported_macro_paths = []
+    macro_import_els = []
+    if macros_el is not None:
+        macro_import_els = macros_el.findall("import")
+    for macro_import_el in macro_import_els:
+        raw_import_path = macro_import_el.text
+        imported_macro_paths.append(raw_import_path)
+    return imported_macro_paths
+
+
+def _load_macro_file(path, xml_base_dir):
+    tree = parse_xml(path, strip_whitespace=False)
+    root = tree.getroot()
+    return _load_macros(root, xml_base_dir)
+
+
+def _xml_set_children(element, new_children):
+    for old_child in element:
+        element.remove(old_child)
+    for i, new_child in enumerate(new_children):
+        element.insert(i, new_child)
+
+
+def _xml_replace(query, targets):
+    parent_el = query.find('..')
+    matching_index = -1
+    # for index, el in enumerate(parent_el.iter('.')):  ## Something like this for newer implementation
+    for index, el in enumerate(list(parent_el)):
+        if el == query:
+            matching_index = index
+            break
+    assert matching_index >= 0
+    current_index = matching_index
+    for target in targets:
+        current_index += 1
+        parent_el.insert(current_index, deepcopy(target))
+    parent_el.remove(query)
+
+
+class XmlMacroDef:
+
+    def __init__(self, el):
+        self.elements = list(el)
+        parameters = {}
+        tokens = []
+        token_quote = "@"
+        for key, value in el.attrib.items():
+            if key == "token_quote":
+                token_quote = value
+            if key == "tokens":
+                for token in value.split(","):
+                    tokens.append((token, REQUIRED_PARAMETER))
+            elif key.startswith("token_"):
+                token = key[len("token_"):]
+                tokens.append((token, value))
+        for name, default in tokens:
+            parameters[name] = (token_quote, default)
+        self.parameters = parameters
+
+    def macro_tokens(self, expand_el):
+        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)
+            token_name = f"{wrap_char}{key.upper()}{wrap_char}"
+            tokens[token_name] = token_value
+        return tokens
+
+
+__all__ = (
+    "imported_macro_paths",
+    "load",
+    "load_with_references",
+    "raw_xml_tree",
+    "template_macro_params",
+)