diff env/lib/python3.9/site-packages/planemo/commands/cmd_normalize.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/planemo/commands/cmd_normalize.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,98 @@
+"""Module describing the planemo ``normalize`` command."""
+from xml.etree import ElementTree
+
+import click
+from galaxy.tool_util.linters.xml_order import TAG_ORDER
+from galaxy.tool_util.loader import (
+    load_tool,
+    raw_tool_xml_tree,
+)
+
+from planemo import options
+from planemo.cli import command_function
+
+
[e-mail]('normalize')
[e-mail]_tool_arg()
[e-mail](
+    "--expand_macros",
+    is_flag=True,
+    help=("Expand macros while normalizing tool XML - useful to see how "
+          "macros are evaluated.")
+)
[e-mail](
+    "--skip_reorder",
+    is_flag=True,
+    help=("Planemo will reorder top-level tool blocks according to tool "
+          "development best practices as part of this command, this flag "
+          "will disable that behavior.")
+)
[e-mail](
+    "--skip_reindent",
+    is_flag=True,
+    help=("Planemo will reindent the XML according to tool development "
+          "best practices as part of this command, this flag will disable "
+          "that behavior.")
+)
+@command_function
+def cli(ctx, path, expand_macros=False, **kwds):
+    """Generate normalized tool XML from input.
+
+    This will break the formatting of your tool and is currently only intended
+    for viewing macro expansions for for use with XSD validation (see
+    https://github.com/JeanFred/Galaxy-XSD for instance). Please do not use
+    the output as is - it frequently makes tool less readable not more.
+
+    The top-level blocks will be reordered and whitespace fixed according to
+    the tool development best practices outlined on the Galaxy wiki.
+
+    \b
+        % # Print normalized version of tool.
+        % planemo normalize tool.xml
+        <tool>
+        ...
+        % # Print a variant of tool with all macros expanded out, useful for
+        % # debugging complex macros.
+        % planemo normalize --expand_macros tool.xml
+        <tool>
+        ...
+    """
+    if expand_macros:
+        tree = load_tool(path)
+    else:
+        tree = raw_tool_xml_tree(path)
+
+    root = tree.getroot()
+    if not kwds.get("skip_reorder", False):
+        last_index = len(TAG_ORDER)
+        data = []
+        for elem in root:
+            tag = elem.tag
+            if tag in TAG_ORDER:
+                key = TAG_ORDER.index(tag)
+            else:
+                key = last_index
+                last_index += 1
+            data.append((key, elem))
+        data.sort()
+        root[:] = [item[-1] for item in data]
+    if not kwds.get("skip_reindent", False):
+        _indent(root)
+    ElementTree.dump(root)
+
+
+def _indent(elem, level=0):
+    # http://stackoverflow.com/questions/749796/pretty-printing-xml-in-python
+    i = "\n" + level * "    "
+    if len(elem):
+        if not elem.text or not elem.text.strip():
+            elem.text = i + "    "
+        if not elem.tail or not elem.tail.strip():
+            elem.tail = i
+        for elem in elem:
+            _indent(elem, level + 1)
+        if not elem.tail or not elem.tail.strip():
+            elem.tail = i
+    else:
+        if level and (not elem.tail or not elem.tail.strip()):
+            elem.tail = i