add xpath

lib/galaxy/tool_util/lint.py

@@ -74,6 +74,9 @@ def __str__(self):
         rval = f".. {self.level.upper()}: {self.message}"
         if self.line is not None:
             rval += f" (line {self.line})"
+        if self.xpath is not None:
+            rval += f" [{self.xpath}]"
+
         return rval
 
 
@@ -95,7 +98,7 @@ def lint(self, name, lint_func, lint_target):
             return
         self.printed_linter_info = False
         self.message_list = []
-        
+
         # call linter
         lint_func(lint_target, self)
         # TODO: colorful emoji if in click CLI.

lib/galaxy/tool_util/linters/citations.py

@@ -10,30 +10,32 @@ def lint_citations(tool_xml, lint_ctx):
     root = tool_xml.getroot()
     if root is not None:
         root_line = root.sourceline
+        root_xpath = tool_xml.getpath(root)
     else:
         root_line = 1
+        root_xpath = None
     citations = root.findall("citations")
     if len(citations) > 1:
-        lint_ctx.error("More than one citation section found, behavior undefined.", line=citations[1].sourceline)
+        lint_ctx.error("More than one citation section found, behavior undefined.", line=citations[1].sourceline, xpath=tool_xml.getpath(citations[1]))
         return
 
     if len(citations) == 0:
-        lint_ctx.warn("No citations found, consider adding citations to your tool.", line=root_line)
+        lint_ctx.warn("No citations found, consider adding citations to your tool.", line=root_line, xpath=root_xpath)
         return
 
     valid_citations = 0
     for citation in citations[0]:
         if citation.tag != "citation":
-            lint_ctx.warn(f"Unknown tag discovered in citations block [{citation.tag}], will be ignored.", line=citation.sourceline)
+            lint_ctx.warn(f"Unknown tag discovered in citations block [{citation.tag}], will be ignored.", line=citation.sourceline, xpath=tool_xml.getpath(citation))
             continue
         citation_type = citation.attrib.get("type")
         if citation_type not in ('bibtex', 'doi'):
-            lint_ctx.warn(f"Unknown citation type discovered [{citation_type}], will be ignored.", line=citation.sourceline)
+            lint_ctx.warn(f"Unknown citation type discovered [{citation_type}], will be ignored.", line=citation.sourceline, xpath=tool_xml.getpath(citation))
             continue
         if citation.text is None or not citation.text.strip():
-            lint_ctx.error(f'Empty {citation_type} citation.', line=citation.sourceline)
+            lint_ctx.error(f'Empty {citation_type} citation.', line=citation.sourceline, xpath=tool_xml.getpath(citation))
             continue
         valid_citations += 1
 
     if valid_citations > 0:
-        lint_ctx.valid(f"Found {valid_citations} likely valid citations.", line=root_line)
+        lint_ctx.valid(f"Found {valid_citations} likely valid citations.", line=root_line, xpath=root_xpath)

lib/galaxy/tool_util/linters/command.py

@@ -10,20 +10,22 @@ def lint_command(tool_xml, lint_ctx):
     root = tool_xml.getroot()
     if root is not None:
         root_line = root.sourceline
+        root_path = tool_xml.getpath(root)
     else:
         root_line = 1
+        root_path = None
     commands = root.findall("command")
     if len(commands) > 1:
-        lint_ctx.error("More than one command tag found, behavior undefined.", line=commands[1].sourceline)
+        lint_ctx.error("More than one command tag found, behavior undefined.", line=commands[1].sourceline, xpath=tool_xml.getpath(commands[1]))
         return
 
     if len(commands) == 0:
-        lint_ctx.error("No command tag found, must specify a command template to execute.", line=root_line)
+        lint_ctx.error("No command tag found, must specify a command template to execute.", line=root_line, xpath=root_path)
         return
 
     command = get_command(tool_xml)
     if "TODO" in command:
-        lint_ctx.warn("Command template contains TODO text.", line=command.sourceline)
+        lint_ctx.warn("Command template contains TODO text.", line=command.sourceline, xpath=tool_xml.getpath(command))
 
     command_attrib = command.attrib
     interpreter_type = None
@@ -33,14 +35,14 @@ def lint_command(tool_xml, lint_ctx):
         elif key == "detect_errors":
             detect_errors = value
             if detect_errors not in ["default", "exit_code", "aggressive"]:
-                lint_ctx.warn(f"Unknown detect_errors attribute [{detect_errors}]", line=command.sourceline)
+                lint_ctx.warn(f"Unknown detect_errors attribute [{detect_errors}]", line=command.sourceline, xpath=tool_xml.getpath(command))
 
     interpreter_info = ""
     if interpreter_type:
         interpreter_info = f" with interpreter of type [{interpreter_type}]"
     if interpreter_type:
-        lint_ctx.info("Command uses deprecated 'interpreter' attribute.", line=command.sourceline)
-    lint_ctx.info(f"Tool contains a command{interpreter_info}.", line=command.sourceline)
+        lint_ctx.info("Command uses deprecated 'interpreter' attribute.", line=command.sourceline, xpath=tool_xml.getpath(command))
+    lint_ctx.info(f"Tool contains a command{interpreter_info}.", line=command.sourceline, xpath=tool_xml.getpath(command))
 
 
 def get_command(tool_xml):

lib/galaxy/tool_util/linters/help.py

@@ -11,33 +11,34 @@ def lint_help(tool_xml, lint_ctx):
     root = tool_xml.getroot()
     if root is not None:
         root_line = root.sourceline
-    else
+        root_path = tool_xml.getpath(root)
+    else:
         root_line = 1
-
+        root_path = None
     helps = root.findall("help")
     if len(helps) > 1:
-        lint_ctx.error("More than one help section found, behavior undefined.", line=helps[1].sourceline)
+        lint_ctx.error("More than one help section found, behavior undefined.", line=helps[1].sourceline, xpath=tool_xml.getpath(helps[1]))
         return
 
     if len(helps) == 0:
-        lint_ctx.warn("No help section found, consider adding a help section to your tool.", line=root_line)
+        lint_ctx.warn("No help section found, consider adding a help section to your tool.", line=root_line, xpath=root_path)
         return
 
     help = helps[0].text or ''
     if not help.strip():
-        lint_ctx.warn("Help section appears to be empty.", line=helps[0].sourceline)
+        lint_ctx.warn("Help section appears to be empty.", line=helps[0].sourceline, xpath=tool_xml.getpath(helps[0]))
         return
 
-    lint_ctx.valid("Tool contains help section.", line=root_line)
+    lint_ctx.valid("Tool contains help section.", line=helps[0].sourceline, xpath=tool_xml.getpath(helps[0]))
     invalid_rst = rst_invalid(help)
 
     if "TODO" in help:
-        lint_ctx.warn("Help contains TODO text.", line=helps[0].sourceline)
+        lint_ctx.warn("Help contains TODO text.", line=helps[0].sourceline, xpath=tool_xml.getpath(helps[0]))
 
     if invalid_rst:
-        lint_ctx.warn(f"Invalid reStructuredText found in help - [{invalid_rst}].", line=helps[0].sourceline)
+        lint_ctx.warn(f"Invalid reStructuredText found in help - [{invalid_rst}].", line=helps[0].sourceline, xpath=tool_xml.getpath(helps[0]))
     else:
-        lint_ctx.valid("Help contains valid reStructuredText.", line=helps[0].sourceline)
+        lint_ctx.valid("Help contains valid reStructuredText.", line=helps[0].sourceline, xpath=tool_xml.getpath(helps[0]))
 
 
 def rst_invalid(text):