XSD Updates

.gitmodules

@@ -1,6 +1,3 @@
-[submodule "planemo/xml/xsd/tool"]
-	path = planemo/xml/xsd/tool
-	url = https://github.com/JeanFred/Galaxy-XSD
 [submodule "planemo/cwl/cwl2script"]
 	path = planemo/cwl/cwl2script
 	url = https://github.com/common-workflow-language/cwl2script.git

planemo/lint.py

@@ -14,15 +14,15 @@
 from planemo.xml import validation
 
 
-def lint_dois(root, lint_ctx):
-    dois = find_dois_for_xml(root)
+def lint_dois(tool_xml, lint_ctx):
+    dois = find_dois_for_xml(tool_xml)
     for publication in dois:
         is_doi(publication, lint_ctx)
 
 
-def find_dois_for_xml(root):
+def find_dois_for_xml(tool_xml):
     dois = []
-    for element in root.root.findall("citations"):
+    for element in tool_xml.getroot().findall("citations"):
         for citation in list(element):
             if citation.tag == 'citation' and citation.attrib.get('type', '') == 'doi':
                 dois.append(citation.text)

planemo/linters/doi.py

@@ -3,5 +3,5 @@
 import planemo.lint
 
 
-def lint_tool_dois(root, lint_ctx):
-    planemo.lint.lint_dois(root, lint_ctx)
+def lint_tool_dois(tool_xml, lint_ctx):
+    planemo.lint.lint_dois(tool_xml, lint_ctx)

planemo/linters/xsd.py

@@ -10,19 +10,19 @@
 TOOL_XSD = os.path.join(XSDS_PATH, "tool", "galaxy.xsd")
 
 
-def lint_tool_xsd(root, lint_ctx):
+def lint_tool_xsd(tool_xml, lint_ctx):
     """Write a temp file out and lint it."""
     with tempfile.NamedTemporaryFile() as tf:
-        _clean_root(root).write(tf.name)
+        _clean_root(tool_xml).write(tf.name)
         planemo.lint.lint_xsd(lint_ctx, TOOL_XSD, tf.name)
 
 
-def _clean_root(root):
+def _clean_root(tool_xml):
     """XSD assumes macros have been expanded, so remove them."""
-    clean_root = copy.deepcopy(root)
+    clean_tool_xml = copy.deepcopy(tool_xml)
     to_remove = []
-    for macros_el in clean_root.findall("macros"):
+    for macros_el in clean_tool_xml.getroot().findall("macros"):
         to_remove.append(macros_el)
     for macros_el in to_remove:
-        clean_root.getroot().remove(macros_el)
-    return clean_root
+        clean_tool_xml.getroot().remove(macros_el)
+    return clean_tool_xml