diff --git a/lib/galaxy/tool_util/lint.py b/lib/galaxy/tool_util/lint.py
index c747da489450..003856cdf112 100644
--- a/lib/galaxy/tool_util/lint.py
+++ b/lib/galaxy/tool_util/lint.py
@@ -63,6 +63,20 @@ 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 +94,9 @@ 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 +112,65 @@ 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"]
+
+ @property
+ def error_messages(self):
+ return [x.message for x in self.message_list if x.level == "error"]
- def __handle_message(self, message_list, message, *args):
+ 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
diff --git a/lib/galaxy/tool_util/linters/citations.py b/lib/galaxy/tool_util/linters/citations.py
index c038b4fdd0e2..60f3527a2238 100644
--- a/lib/galaxy/tool_util/linters/citations.py
+++ b/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)
diff --git a/lib/galaxy/tool_util/linters/command.py b/lib/galaxy/tool_util/linters/command.py
index e675f92cc4ab..cd0afe744eee 100644
--- a/lib/galaxy/tool_util/linters/command.py
+++ b/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):
diff --git a/lib/galaxy/tool_util/linters/general.py b/lib/galaxy/tool_util/linters/general.py
index 5d47bd6670a1..59d0bf4b14b2 100644
--- a/lib/galaxy/tool_util/linters/general.py
+++ b/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:
@@ -72,6 +80,3 @@ def lint_general(tool_source, lint_ctx):
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)
diff --git a/lib/galaxy/tool_util/linters/help.py b/lib/galaxy/tool_util/linters/help.py
index df0a3f9b801e..be9f8ecce46b 100644
--- a/lib/galaxy/tool_util/linters/help.py
+++ b/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):
diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py
index bab58d018331..fb18cd73ecc4 100644
--- a/lib/galaxy/tool_util/linters/inputs.py
+++ b/lib/galaxy/tool_util/linters/inputs.py
@@ -46,6 +46,11 @@
def lint_inputs(tool_xml, lint_ctx):
"""Lint parameters in a tool's inputs block."""
+ # determine line to report for general problems with outputs
+ try:
+ tool_line = tool_xml.find("./tool").sourceline
+ except:
+ tool_line = 0
datasource = is_datasource(tool_xml)
inputs = tool_xml.findall("./inputs//param")
num_inputs = 0
@@ -53,21 +58,21 @@ def lint_inputs(tool_xml, lint_ctx):
num_inputs += 1
param_attrib = param.attrib
if "name" not in param_attrib and "argument" not in param_attrib:
- lint_ctx.error("Found param input with no name specified.")
+ lint_ctx.error("Found param input with no name specified.", line=param.sourceline)
continue
param_name = _parse_name(param_attrib.get("name"), param_attrib.get("argument"))
if "type" not in param_attrib:
- lint_ctx.error(f"Param input [{param_name}] input with no type specified.")
+ lint_ctx.error(f"Param input [{param_name}] input with no type specified.", line=param.sourceline)
continue
param_type = param_attrib["type"]
if not is_valid_cheetah_placeholder(param_name):
- lint_ctx.warn(f"Param input [{param_name}] is not a valid Cheetah placeholder.")
+ lint_ctx.warn(f"Param input [{param_name}] is not a valid Cheetah placeholder.", line=param.sourceline)
if param_type == "data":
if "format" not in param_attrib:
- lint_ctx.warn(f"Param input [{param_name}] with no format specified - 'data' format will be assumed.")
+ lint_ctx.warn(f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", line=param.sourceline)
elif param_type == "select":
# get dynamic/statically defined options
dynamic_options = param.get("dynamic_options", None)
@@ -77,11 +82,11 @@ def lint_inputs(tool_xml, lint_ctx):
select_options_text = [option.text.strip() if option.text is not None else option.attrib.get("value", "").capitalize() for option in select_options]
if dynamic_options is not None:
- lint_ctx.warn(f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.")
+ lint_ctx.warn(f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.", line=param.sourceline)
# check if options are defined by exactly one possibility
if (dynamic_options is not None) + (len(options) > 0) + (len(select_options) > 0) != 1:
- lint_ctx.error(f"Select parameter [{param_name}] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.")
+ lint_ctx.error(f"Select parameter [{param_name}] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.", line=param.sourceline)
# lint dynamic options
if len(options) == 1:
@@ -91,10 +96,10 @@ def lint_inputs(tool_xml, lint_ctx):
for f in filters:
ftype = f.get("type", None)
if ftype is None:
- lint_ctx.error(f"Select parameter [{param_name}] contains filter without type.")
+ lint_ctx.error(f"Select parameter [{param_name}] contains filter without type.", line=f.sourceline)
continue
if ftype not in FILTER_TYPES:
- lint_ctx.error(f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.")
+ lint_ctx.error(f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.", line=f.sourceline)
continue
if ftype in ['add_value', 'data_meta']:
filter_adds_options = True
@@ -107,50 +112,50 @@ def lint_inputs(tool_xml, lint_ctx):
if (from_file is None and from_parameter is None
and from_dataset is None and from_data_table is None
and not filter_adds_options):
- lint_ctx.error(f"Select parameter [{param_name}] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values.")
+ lint_ctx.error(f"Select parameter [{param_name}] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values.", line=options[0].sourceline)
if from_file is not None:
- lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_file' attribute.")
+ lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_file' attribute.", line=options[0].sourceline)
if from_parameter is not None:
- lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_parameter' attribute.")
+ lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_parameter' attribute.", line=options[0].sourceline)
if from_dataset is not None and from_data_table is not None:
- lint_ctx.error(f"Select parameter [{param_name}] options uses 'from_dataset' and 'from_data_table' attribute.")
+ lint_ctx.error(f"Select parameter [{param_name}] options uses 'from_dataset' and 'from_data_table' attribute.", line=options[0].sourceline)
if options[0].get("meta_file_key", None) is not None and from_dataset is None:
- lint_ctx.error(f"Select parameter [{param_name}] 'meta_file_key' is only compatible with 'from_dataset'.")
+ lint_ctx.error(f"Select parameter [{param_name}] 'meta_file_key' is only compatible with 'from_dataset'.", line=options[0].sourceline)
if options[0].get("options_filter_attribute", None) is not None:
- lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'options_filter_attribute' attribute.")
+ lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'options_filter_attribute' attribute.", line=options[0].sourceline)
if options[0].get("transform_lines", None) is not None:
- lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'transform_lines' attribute.")
+ lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'transform_lines' attribute.", line=options[0].sourceline)
elif len(options) > 1:
- lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements")
+ lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements", line=options[1].sourceline)
# lint statically defined options
if any(['value' not in option.attrib for option in select_options]):
- lint_ctx.error(f"Select parameter [{param_name}] has option without value")
+ lint_ctx.error(f"Select parameter [{param_name}] has option without value", line=param.sourceline)
if any([option.text is None for option in select_options]):
- lint_ctx.warn(f"Select parameter [{param_name}] has option without text")
+ lint_ctx.warn(f"Select parameter [{param_name}] has option without text", line=param.sourceline)
if len(set(select_options_text)) != len(select_options_text):
- lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content")
+ lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content", line=param.sourceline)
if len({option.attrib.get("value") for option in select_options}) != len(select_options):
- lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value")
+ lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value", line=param.sourceline)
multiple = string_as_bool(param_attrib.get("multiple", "false"))
optional = string_as_bool(param_attrib.get("optional", multiple))
if param_attrib.get("display") == "checkboxes":
if not multiple:
- lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute')
+ lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute', line=param.sourceline)
if not optional:
- lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute')
+ lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute', line=param.sourceline)
if param_attrib.get("display") == "radio":
if multiple:
- lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with multiple="true"')
+ lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with multiple="true"', line=param.sourceline)
if optional:
- lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with optional="true"')
+ lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with optional="true"', line=param.sourceline)
# TODO: Validate type, much more...
# lint validators
@@ -159,36 +164,36 @@ def lint_inputs(tool_xml, lint_ctx):
vtype = validator.attrib['type']
if param_type in PARAMETER_VALIDATOR_TYPE_COMPATIBILITY:
if vtype not in PARAMETER_VALIDATOR_TYPE_COMPATIBILITY[param_type]:
- lint_ctx.error(f"Parameter [{param_name}]: validator with an incompatible type '{vtype}'")
+ lint_ctx.error(f"Parameter [{param_name}]: validator with an incompatible type '{vtype}'", line=validator.sourceline)
for attrib in ATTRIB_VALIDATOR_COMPATIBILITY:
if attrib in validator.attrib and vtype not in ATTRIB_VALIDATOR_COMPATIBILITY[attrib]:
- lint_ctx.error(f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'")
+ lint_ctx.error(f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'", line=validator.sourceline)
if vtype == "expression" and validator.text is None:
lint_ctx.error(f"Parameter [{param_name}]: expression validator without content")
if vtype not in ["expression", "regex"] and validator.text is not None:
- lint_ctx.warn(f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')")
+ lint_ctx.warn(f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')", line=validator.sourceline)
if vtype in ["in_range", "length", "dataset_metadata_in_range"] and ("min" not in validator.attrib and "max" not in validator.attrib):
- lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)")
+ lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)", line=validator.sourceline)
if vtype in ["metadata"] and ("check" not in validator.attrib and "skip" not in validator.attrib):
- lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s) {validator.attrib}")
+ lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s) {validator.attrib}", line=validator.sourceline)
if vtype in ["value_in_data_table", "value_not_in_data_table", "dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table"] and "table_name" not in validator.attrib:
- lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute")
+ lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute", line=validator.sourceline)
conditional_selects = tool_xml.findall("./inputs//conditional")
for conditional in conditional_selects:
conditional_name = conditional.get('name')
if not conditional_name:
- lint_ctx.error("Conditional without a name")
+ lint_ctx.error("Conditional without a name", line=conditional.sourceline)
if conditional.get("value_from"):
# Probably only the upload tool use this, no children elements
continue
first_param = conditional.find("param")
if first_param is None:
- lint_ctx.error(f"Conditional [{conditional_name}] has no child ")
+ lint_ctx.error(f"Conditional [{conditional_name}] has no child ", line=conditional.sourceline)
continue
first_param_type = first_param.get('type')
if first_param_type not in ['select', 'boolean']:
- lint_ctx.warn(f'Conditional [{conditional_name}] first param should have type="select" /> or type="boolean"')
+ lint_ctx.warn(f'Conditional [{conditional_name}] first param should have type="select" /> or type="boolean"', line=first_param_type.sourceline)
continue
if first_param_type == 'select':
@@ -201,37 +206,37 @@ def lint_inputs(tool_xml, lint_ctx):
]
if string_as_bool(first_param.get('optional', False)):
- lint_ctx.warn(f"Conditional [{conditional_name}] test parameter cannot be optional")
+ lint_ctx.warn(f"Conditional [{conditional_name}] test parameter cannot be optional", line=first_param_type.sourceline)
whens = conditional.findall('./when')
if any('value' not in when.attrib for when in whens):
- lint_ctx.error(f"Conditional [{conditional_name}] when without value")
+ lint_ctx.error(f"Conditional [{conditional_name}] when without value", line=conditional.sourceline)
when_ids = [w.get('value') for w in whens]
for option_id in option_ids:
if option_id not in when_ids:
- lint_ctx.warn(f"Conditional [{conditional_name}] no block found for {first_param_type} option '{option_id}'")
+ lint_ctx.warn(f"Conditional [{conditional_name}] no block found for {first_param_type} option '{option_id}'", line=conditional.sourceline)
for when_id in when_ids:
if when_id not in option_ids:
if first_param_type == 'select':
- lint_ctx.warn(f"Conditional [{conditional_name}] no found for when block '{when_id}'")
+ lint_ctx.warn(f"Conditional [{conditional_name}] no found for when block '{when_id}'", line=conditional.sourceline)
else:
- lint_ctx.warn(f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'")
+ lint_ctx.warn(f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'", line=conditional.sourceline)
if datasource:
for datasource_tag in ('display', 'uihints'):
if not any([param.tag == datasource_tag for param in inputs]):
- lint_ctx.info(f"{datasource_tag} tag usually present in data sources")
+ lint_ctx.info(f"{datasource_tag} tag usually present in data sources", line=tool_line)
if num_inputs:
- lint_ctx.info(f"Found {num_inputs} input parameters.")
+ lint_ctx.info(f"Found {num_inputs} input parameters.", line=tool_line)
else:
if datasource:
- lint_ctx.info("No input parameters, OK for data sources")
+ lint_ctx.info("No input parameters, OK for data sources", line=tool_line)
else:
- lint_ctx.warn("Found no input parameters.")
+ lint_ctx.warn("Found no input parameters.", line=tool_line)
def lint_repeats(tool_xml, lint_ctx):
@@ -239,9 +244,9 @@ def lint_repeats(tool_xml, lint_ctx):
repeats = tool_xml.findall("./inputs//repeat")
for repeat in repeats:
if "name" not in repeat.attrib:
- lint_ctx.error("Repeat does not specify name attribute.")
+ lint_ctx.error("Repeat does not specify name attribute.", line=repeat.sourceline)
if "title" not in repeat.attrib:
- lint_ctx.error("Repeat does not specify title attribute.")
+ lint_ctx.error("Repeat does not specify title attribute.", line=repeat.sourceline)
def _find_with_attribute(element, tag, attribute, test_value=None):
diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index a57e9a9cb38a..6f33fcb42915 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -6,27 +6,28 @@
def lint_output(tool_xml, lint_ctx):
"""Check output elements, ensure there is at least one and check attributes."""
+ # determine line to report for general problems with outputs
+ try:
+ tool_line = tool_xml.find("./tool").sourceline
+ except:
+ tool_line = 0
outputs = tool_xml.findall("./outputs")
if len(outputs) == 0:
- lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.")
+ lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.", line=tool_line)
+ return
if len(outputs) > 1:
- lint_ctx.warn("Tool contains multiple output sections, behavior undefined.")
-
+ lint_ctx.warn("Tool contains multiple output sections, behavior undefined.", line=outputs[1].sourceline)
num_outputs = 0
- if len(outputs) == 0:
- lint_ctx.warn("No outputs found")
- return
-
for output in list(outputs[0]):
if output.tag not in ["data", "collection"]:
- lint_ctx.warn(f"Unknown element found in outputs [{output.tag}]")
+ lint_ctx.warn(f"Unknown element found in outputs [{output.tag}]", line=output.sourceline)
continue
num_outputs += 1
if "name" not in output.attrib:
- lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.")
+ lint_ctx.warn("Tool output doesn't define a name - this is likely a problem.", line=output.sourceline)
else:
if not is_valid_cheetah_placeholder(output.attrib["name"]):
- lint_ctx.warn("Tool output name [%s] is not a valid Cheetah placeholder.", output.attrib["name"])
+ lint_ctx.warn("Tool output name [%s] is not a valid Cheetah placeholder.", output.attrib["name"], line=output.sourceline)
format_set = False
if __check_format(output, lint_ctx):
@@ -37,7 +38,7 @@ def lint_output(tool_xml, lint_ctx):
elif output.tag == "collection":
if "type" not in output.attrib:
- lint_ctx.warn("Collection output with undefined 'type' found.")
+ lint_ctx.warn("Collection output with undefined 'type' found.", line=output.sourceline)
if "structured_like" in output.attrib and "inherit_format" in output.attrib:
format_set = True
for sub in output:
@@ -47,9 +48,9 @@ def lint_output(tool_xml, lint_ctx):
format_set = True
if not format_set:
- lint_ctx.warn(f"Tool {output.tag} output {output.attrib.get('name', 'with missing name')} doesn't define an output format.")
+ lint_ctx.warn(f"Tool {output.tag} output {output.attrib.get('name', 'with missing name')} doesn't define an output format.", line=output.sourceline)
- lint_ctx.info("%d outputs found.", num_outputs)
+ lint_ctx.info(f"{num_outputs} outputs found.", line=outputs[0].sourceline)
def __check_format(node, lint_ctx, allow_ext=False):
@@ -59,7 +60,7 @@ def __check_format(node, lint_ctx, allow_ext=False):
return true (node defines format/ext) / false (else)
"""
if "format_source" in node.attrib and ("ext" in node.attrib or "format" in node.attrib):
- lint_ctx.warn(f"Tool {node.tag} output {node.attrib.get('name', 'with missing name')} should use either format_source or format/ext")
+ lint_ctx.warn(f"Tool {node.tag} output {node.attrib.get('name', 'with missing name')} should use either format_source or format/ext", line=node.sourceline)
if "format_source" in node.attrib:
return True
# if allowed (e.g. for discover_datasets), ext takes precedence over format
@@ -69,7 +70,7 @@ def __check_format(node, lint_ctx, allow_ext=False):
if fmt is None:
fmt = node.attrib.get("format")
if fmt == "input":
- lint_ctx.warn(f"Using format='input' on {node.tag}, format_source attribute is less ambiguous and should be used instead.")
+ lint_ctx.warn(f"Using format='input' on {node.tag}, format_source attribute is less ambiguous and should be used instead.", line=node.sourceline)
return fmt is not None
diff --git a/lib/galaxy/tool_util/linters/stdio.py b/lib/galaxy/tool_util/linters/stdio.py
index 1c5268267d74..801ce233f0e3 100644
--- a/lib/galaxy/tool_util/linters/stdio.py
+++ b/lib/galaxy/tool_util/linters/stdio.py
@@ -4,19 +4,25 @@
def lint_stdio(tool_source, lint_ctx):
tool_xml = getattr(tool_source, "xml_tree", None)
+ # determine line to report for general problems with stdio
+ try:
+ tool_line = tool_xml.find("./tool").sourceline
+ except:
+ tool_line = 0
+
stdios = tool_xml.findall("./stdio") if tool_xml else []
if not stdios:
command = get_command(tool_xml) if tool_xml else None
if command is None or not command.get("detect_errors"):
if tool_source.parse_profile() <= "16.01":
- lint_ctx.info("No stdio definition found, tool indicates error conditions with output written to stderr.")
+ lint_ctx.info("No stdio definition found, tool indicates error conditions with output written to stderr.", line=tool_line)
else:
- lint_ctx.info("No stdio definition found, tool indicates error conditions with non-zero exit codes.")
+ lint_ctx.info("No stdio definition found, tool indicates error conditions with non-zero exit codes.", line=tool_line)
return
if len(stdios) > 1:
- lint_ctx.error("More than one stdio tag found, behavior undefined.")
+ lint_ctx.error("More than one stdio tag found, behavior undefined.", line=stdios[1].sourceline)
return
stdio = stdios[0]
@@ -28,16 +34,16 @@ def lint_stdio(tool_source, lint_ctx):
else:
message = "Unknown stdio child tag discovered [%s]. "
message += "Valid options are exit_code and regex."
- lint_ctx.warn(message % child.tag)
+ lint_ctx.warn(message % child.tag, line=child.sourceline)
def _lint_exit_code(child, lint_ctx):
for key in child.attrib.keys():
if key not in ["description", "level", "range"]:
- lint_ctx.warn(f"Unknown attribute [{key}] encountered on exit_code tag.")
+ lint_ctx.warn(f"Unknown attribute [{key}] encountered on exit_code tag.", line=child.sourceline)
def _lint_regex(child, lint_ctx):
for key in child.attrib.keys():
if key not in ["description", "level", "match", "source"]:
- lint_ctx.warn(f"Unknown attribute [{key}] encountered on regex tag.")
+ lint_ctx.warn(f"Unknown attribute [{key}] encountered on regex tag.", line=child.sourceline)
diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index 05f419834eff..76738fbd444e 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -4,13 +4,22 @@
# Misspelled so as not be picked up by nosetests.
def lint_tsts(tool_xml, lint_ctx):
+ # determine line to report for general problems with tests
+ try:
+ tests_line = tool_xml.find("./tool").sourceline
+ except:
+ tests_line = 0
+ try:
+ tests_line = tool_xml.find("./tests").sourceline
+ except:
+ pass
+
tests = tool_xml.findall("./tests/test")
datasource = is_datasource(tool_xml)
-
if not tests and not datasource:
- lint_ctx.warn("No tests found, most tools should define test cases.")
+ lint_ctx.warn("No tests found, most tools should define test cases.", line=tool_xml.sourceline)
elif datasource:
- lint_ctx.info("No tests found, that should be OK for data_sources.")
+ lint_ctx.info("No tests found, that should be OK for data_sources.", line=tests_line)
num_valid_tests = 0
for test in tests:
@@ -30,7 +39,7 @@ def lint_tsts(tool_xml, lint_ctx):
for param in test.findall("param"):
name = param.attrib.get("name", None)
if not name:
- lint_ctx.error("Found test param tag without a name defined.")
+ lint_ctx.error("Found test param tag without a name defined.", line=param.sourceline)
continue
name = name.split("|")[-1]
xpaths = [f"@name='{name}'",
@@ -48,7 +57,7 @@ def lint_tsts(tool_xml, lint_ctx):
found = True
break
if not found:
- lint_ctx.error(f"Test param {name} not found in the inputs")
+ lint_ctx.error(f"Test param {name} not found in the inputs", line=param.sourceline)
output_data_names, output_collection_names = _collect_output_names(tool_xml)
found_output_test = False
@@ -56,30 +65,30 @@ def lint_tsts(tool_xml, lint_ctx):
found_output_test = True
name = output.attrib.get("name", None)
if not name:
- lint_ctx.warn("Found output tag without a name defined.")
+ lint_ctx.warn("Found output tag without a name defined.", line=output.sourceline)
else:
if name not in output_data_names:
- lint_ctx.error(f"Found output tag with unknown name [{name}], valid names [{output_data_names}]")
+ lint_ctx.error(f"Found output tag with unknown name [{name}], valid names [{output_data_names}]", line=output.sourceline)
for output_collection in test.findall("output_collection"):
found_output_test = True
name = output_collection.attrib.get("name", None)
if not name:
- lint_ctx.warn("Found output_collection tag without a name defined.")
+ lint_ctx.warn("Found output_collection tag without a name defined.", line=output_collection.sourceline)
else:
if name not in output_collection_names:
- lint_ctx.warn(f"Found output_collection tag with unknown name [{name}], valid names [{output_collection_names}]")
+ lint_ctx.warn(f"Found output_collection tag with unknown name [{name}], valid names [{output_collection_names}]", line=output_collection.sourceline)
has_test = has_test or found_output_test
if not has_test:
- lint_ctx.warn("No outputs or expectations defined for tests, this test is likely invalid.")
+ lint_ctx.warn("No outputs or expectations defined for tests, this test is likely invalid.", line=test.sourceline)
else:
num_valid_tests += 1
if num_valid_tests or datasource:
- lint_ctx.valid("%d test(s) found.", num_valid_tests)
+ lint_ctx.valid(f"{num_valid_tests} test(s) found.", line=tests_line)
else:
- lint_ctx.warn("No valid test(s) found.")
+ lint_ctx.warn("No valid test(s) found.", line=tests_line)
def _collect_output_names(tool_xml):