provide more context for lint context

line number and xpath

lib/galaxy/tool_util/lint.py

@@ -63,6 +63,19 @@ def lint_xml_with(lint_context, tool_xml, extra_modules=None):
     return lint_tool_source_with(lint_context, tool_source, extra_modules=extra_modules)
 
 
+class LintMessage:
+    def __init__(self, level, message, line, xpath=None):
+        self.level = level
+        self.message = message
+        self.line = line
+        self.xpath = xpath
+
+    def __str__(self):
+        rval = f".. {self.level.upper()}: {self.message}"
+        if self.line is not None:
+            rval += f" (line {self.line})"
+        return rval
+
 # TODO: Nothing inherently tool-y about LintContext and in fact
 # it is reused for repositories in planemo. Therefore, it should probably
 # be moved to galaxy.util.lint.
@@ -80,10 +93,9 @@ def lint(self, name, lint_func, lint_target):
         if name in self.skip_types:
             return
         self.printed_linter_info = False
-        self.valid_messages = []
-        self.info_messages = []
-        self.warn_messages = []
-        self.error_messages = []
+        self.message_list = []
+
+        # call linter
         lint_func(lint_target, self)
         # TODO: colorful emoji if in click CLI.
         if self.error_messages:
@@ -99,41 +111,65 @@ def print_linter_info():
             self.printed_linter_info = True
             print(f"Applying linter {name}... {status}")
 
-        for message in self.error_messages:
+        for message in self.message_list:
+            if message.level != "error":
+                continue
             self.found_errors = True
             print_linter_info()
-            print(f".. ERROR: {message}")
+            print(f"{message}")
 
         if self.level != LEVEL_ERROR:
-            for message in self.warn_messages:
+            for message in self.message_list:
+                if message.level != "warning":
+                    continue
                 self.found_warns = True
                 print_linter_info()
-                print(f".. WARNING: {message}")
+                print(f"{message}")
 
         if self.level == LEVEL_ALL:
-            for message in self.info_messages:
+            for message in self.message_list:
+                if message.level != "info":
+                    continue
                 print_linter_info()
-                print(f".. INFO: {message}")
-            for message in self.valid_messages:
+                print(f"{message}")
+            for message in self.message_list:
+                if message.level != "check":
+                    continue
                 print_linter_info()
-                print(f".. CHECK: {message}")
+                print(f"{message}")
+
+    @property
+    def valid_messages(self):
+        return [x.message for x in self.message_list if x.level == "check"]
+
+    @property
+    def info_messages(self):
+        return [x.message for x in self.message_list if x.level == "info"]
+
+    @property
+    def warn_messages(self):
+        return [x.message for x in self.message_list if x.level == "warning"]
 
-    def __handle_message(self, message_list, message, *args):
+    @property
+    def error_messages(self):
+        return [x.message for x in self.message_list if x.level == "error"]
+
+    def __handle_message(self, level, message, line, xpath, *args):
         if args:
             message = message % args
-        message_list.append(message)
+        self.message_list.append(LintMessage(level=level, message=message, line=line, xpath=xpath))
 
-    def valid(self, message, *args):
-        self.__handle_message(self.valid_messages, message, *args)
+    def valid(self, message, line=None, xpath=None, *args):
+        self.__handle_message("check", message, line, xpath, *args)
 
-    def info(self, message, *args):
-        self.__handle_message(self.info_messages, message, *args)
+    def info(self, message, line=None, xpath=None, *args):
+        self.__handle_message("info", message, line, xpath, *args)
 
-    def error(self, message, *args):
-        self.__handle_message(self.error_messages, message, *args)
+    def error(self, message, line=None, xpath=None, *args):
+        self.__handle_message("error", message, line, xpath, *args)
 
-    def warn(self, message, *args):
-        self.__handle_message(self.warn_messages, message, *args)
+    def warn(self, message, line=None, xpath=None, *args):
+        self.__handle_message("warning", message, line, xpath, *args)
 
     def failed(self, fail_level):
         found_warns = self.found_warns

lib/galaxy/tool_util/linters/citations.py

@@ -10,26 +10,26 @@ def lint_citations(tool_xml, lint_ctx):
     root = tool_xml.getroot()
     citations = root.findall("citations")
     if len(citations) > 1:
-        lint_ctx.error("More than one citation section found, behavior undefined.")
+        lint_ctx.error("More than one citation section found, behavior undefined.", line=citations[1].sourceline)
         return
 
     if len(citations) == 0:
-        lint_ctx.warn("No citations found, consider adding citations to your tool.")
+        lint_ctx.warn("No citations found, consider adding citations to your tool.", line=root.sourceline)
         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.")
+            lint_ctx.warn(f"Unknown tag discovered in citations block [{citation.tag}], will be ignored.", line=citation.sourceline)
             continue
         citation_type = citation.attrib.get("type")
         if citation_type not in ('bibtex', 'doi'):
-            lint_ctx.warn("Unknown citation type discovered [%s], will be ignored.", citation_type)
+            lint_ctx.warn(f"Unknown citation type discovered [{citation_type}], will be ignored.", line=citation.sourceline)
             continue
         if citation.text is None or not citation.text.strip():
-            lint_ctx.error(f'Empty {citation_type} citation.')
+            lint_ctx.error(f'Empty {citation_type} citation.', line=citation.sourceline)
             continue
         valid_citations += 1
 
     if valid_citations > 0:
-        lint_ctx.valid("Found %d likely valid citations.", valid_citations)
+        lint_ctx.valid(f"Found {valid_citations} likely valid citations.", line=root.sourceline)

lib/galaxy/tool_util/linters/command.py

@@ -10,16 +10,16 @@ def lint_command(tool_xml, lint_ctx):
     root = tool_xml.getroot()
     commands = root.findall("command")
     if len(commands) > 1:
-        lint_ctx.error("More than one command tag found, behavior undefined.")
+        lint_ctx.error("More than one command tag found, behavior undefined.", line=commands[1].sourceline)
         return
 
     if len(commands) == 0:
-        lint_ctx.error("No command tag found, must specify a command template to execute.")
+        lint_ctx.error("No command tag found, must specify a command template to execute.", line=root.sourceline)
         return
 
     command = get_command(tool_xml)
     if "TODO" in command:
-        lint_ctx.warn("Command template contains TODO text.")
+        lint_ctx.warn("Command template contains TODO text.", line=command.sourceline)
 
     command_attrib = command.attrib
     interpreter_type = None
@@ -29,14 +29,14 @@ 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}]")
+                lint_ctx.warn(f"Unknown detect_errors attribute [{detect_errors}]", line=command.sourceline)
 
     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.")
-    lint_ctx.info(f"Tool contains a command{interpreter_info}.")
+        lint_ctx.info("Command uses deprecated 'interpreter' attribute.", line=command.sourceline)
+    lint_ctx.info(f"Tool contains a command{interpreter_info}.", line=command.sourceline)
 
 
 def get_command(tool_xml):

lib/galaxy/tool_util/linters/general.py

@@ -27,39 +27,47 @@
 
 def lint_general(tool_source, lint_ctx):
     """Check tool version, name, and id."""
+    # determine line to report for general problems with outputs
+    tool_xml = getattr(tool_source, "xml_tree", None)
+    try:
+        tool_line = tool_xml.find("./tool").sourceline
+    except:
+        tool_line = 0
     version = tool_source.parse_version() or ''
     parsed_version = packaging.version.parse(version)
     if not version:
-        lint_ctx.error(ERROR_VERSION_MSG)
+        lint_ctx.error(ERROR_VERSION_MSG, line=tool_line)
     elif isinstance(parsed_version, packaging.version.LegacyVersion):
-        lint_ctx.warn(WARN_VERSION_MSG % version)
+        lint_ctx.warn(WARN_VERSION_MSG % version, line=tool_line)
     elif version != version.strip():
-        lint_ctx.warn(WARN_WHITESPACE_MSG % ('Tool version', version))
+        lint_ctx.warn(WARN_WHITESPACE_MSG % ('Tool version', version), line=tool_line)
     else:
-        lint_ctx.valid(VALID_VERSION_MSG % version)
+        lint_ctx.valid(VALID_VERSION_MSG % version, line=tool_line)
 
     name = tool_source.parse_name()
     if not name:
-        lint_ctx.error(ERROR_NAME_MSG)
+        lint_ctx.error(ERROR_NAME_MSG, line=tool_line)
     elif name != name.strip():
-        lint_ctx.warn(WARN_WHITESPACE_MSG % ('Tool name', name))
+        lint_ctx.warn(WARN_WHITESPACE_MSG % ('Tool name', name), line=tool_line)
     else:
-        lint_ctx.valid(VALID_NAME_MSG % name)
+        lint_ctx.valid(VALID_NAME_MSG % name, line=tool_line)
 
     tool_id = tool_source.parse_id()
     if not tool_id:
-        lint_ctx.error(ERROR_ID_MSG)
+        lint_ctx.error(ERROR_ID_MSG, line=tool_line)
     else:
-        lint_ctx.valid(VALID_ID_MSG % tool_id)
+        lint_ctx.valid(VALID_ID_MSG % tool_id, line=tool_line)
+    if re.search(r"\s", tool_id):
+        lint_ctx.warn(WARN_ID_WHITESPACE_MSG % tool_id, line=tool_line)
 
     profile = tool_source.parse_profile()
     profile_valid = PROFILE_PATTERN.match(profile) is not None
     if not profile_valid:
-        lint_ctx.error(PROFILE_INVALID_MSG)
+        lint_ctx.error(PROFILE_INVALID_MSG, line=tool_line)
     elif profile == "16.01":
-        lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG)
+        lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG, line=tool_line)
     else:
-        lint_ctx.valid(PROFILE_INFO_SPECIFIED_MSG % profile)
+        lint_ctx.valid(PROFILE_INFO_SPECIFIED_MSG % profile, line=tool_line)
 
     requirements, containers = tool_source.parse_requirements_and_containers()
     for r in requirements:
@@ -71,7 +79,4 @@ def lint_general(tool_source, lint_ctx):
             # Warn requirement attributes with leading/trailing whitespace:
             elif r.version != r.version.strip():
                 lint_ctx.warn(
-                    WARN_WHITESPACE_MSG % ('Requirement version', r.version))
-
-    if re.search(r"\s", tool_id):
-        lint_ctx.warn(WARN_ID_WHITESPACE_MSG % tool_id)
+                    WARN_WHITESPACE_MSG % ('Requirement version', r.version))

lib/galaxy/tool_util/linters/help.py

@@ -7,31 +7,32 @@
 
 def lint_help(tool_xml, lint_ctx):
     """Ensure tool contains exactly one valid RST help block."""
+    # determine line to report for general problems with outputs
     root = tool_xml.getroot()
     helps = root.findall("help")
     if len(helps) > 1:
-        lint_ctx.error("More than one help section found, behavior undefined.")
+        lint_ctx.error("More than one help section found, behavior undefined.", line=helps[1].sourceline)
         return
 
     if len(helps) == 0:
-        lint_ctx.warn("No help section found, consider adding a help section to your tool.")
+        lint_ctx.warn("No help section found, consider adding a help section to your tool.", line=root.sourceline)
         return
 
     help = helps[0].text or ''
     if not help.strip():
-        lint_ctx.warn("Help section appears to be empty.")
+        lint_ctx.warn("Help section appears to be empty.", line=helps[0].sourceline)
         return
 
-    lint_ctx.valid("Tool contains help section.")
+    lint_ctx.valid("Tool contains help section.", line=root.sourceline)
     invalid_rst = rst_invalid(help)
 
     if "TODO" in help:
-        lint_ctx.warn("Help contains TODO text.")
+        lint_ctx.warn("Help contains TODO text.", line=helps[0].sourceline)
 
     if invalid_rst:
-        lint_ctx.warn(f"Invalid reStructuredText found in help - [{invalid_rst}].")
+        lint_ctx.warn(f"Invalid reStructuredText found in help - [{invalid_rst}].", line=helps[0].sourceline)
     else:
-        lint_ctx.valid("Help contains valid reStructuredText.")
+        lint_ctx.valid("Help contains valid reStructuredText.", line=helps[0].sourceline)
 
 
 def rst_invalid(text):