diff --git a/lib/galaxy/tool_util/lint.py b/lib/galaxy/tool_util/lint.py index 003856cdf11..aac34bb1cae 100644 --- a/lib/galaxy/tool_util/lint.py +++ b/lib/galaxy/tool_util/lint.py @@ -74,6 +74,9 @@ class LintMessage: 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 @@ class LintContext: return self.printed_linter_info = False self.message_list = [] - + # call linter lint_func(lint_target, self) # TODO: colorful emoji if in click CLI. diff --git a/lib/galaxy/tool_util/linters/citations.py b/lib/galaxy/tool_util/linters/citations.py index ecd18b21103..086172d16d0 100644 --- a/lib/galaxy/tool_util/linters/citations.py +++ b/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) diff --git a/lib/galaxy/tool_util/linters/command.py b/lib/galaxy/tool_util/linters/command.py index e7e13749678..482fe4ac70f 100644 --- a/lib/galaxy/tool_util/linters/command.py +++ b/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): diff --git a/lib/galaxy/tool_util/linters/help.py b/lib/galaxy/tool_util/linters/help.py index c557d6049e3..2667966856d 100644 --- a/lib/galaxy/tool_util/linters/help.py +++ b/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): diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py index 6a8915ec556..59d80845cd6 100644 --- a/lib/galaxy/tool_util/linters/inputs.py +++ b/lib/galaxy/tool_util/linters/inputs.py @@ -49,8 +49,10 @@ def lint_inputs(tool_xml, lint_ctx): # determine line to report for general problems with outputs try: tool_line = tool_xml.find("./tool").sourceline + tool_path = tool_xml.getpath(tool_xml.find("./tool")) except AttributeError: - tool_line = 0 + tool_line = 1 + tool_path = None datasource = is_datasource(tool_xml) inputs = tool_xml.findall("./inputs//param") num_inputs = 0 @@ -58,7 +60,7 @@ 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.", line=param.sourceline) + lint_ctx.error("Found param input with no name specified.", line=param.sourceline, xpath=tool_xml.getpath(param)) continue param_name = _parse_name(param_attrib.get("name"), param_attrib.get("argument")) if "name" in param_attrib and "argument" in param_attrib: @@ -66,16 +68,16 @@ def lint_inputs(tool_xml, lint_ctx): lint_ctx.warn(f"Param input [{param_name}] 'name' attribute is redundant if argument implies the same name.") if "type" not in param_attrib: - lint_ctx.error(f"Param input [{param_name}] input with no type specified.", line=param.sourceline) + lint_ctx.error(f"Param input [{param_name}] input with no type specified.", line=param.sourceline, xpath=tool_xml.getpath(param)) 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.", line=param.sourceline) + lint_ctx.warn(f"Param input [{param_name}] is not a valid Cheetah placeholder.", line=param.sourceline, xpath=tool_xml.getpath(param)) 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.", line=param.sourceline) + lint_ctx.warn(f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", line=param.sourceline, xpath=tool_xml.getpath(param)) elif param_type == "select": # get dynamic/statically defined options dynamic_options = param.get("dynamic_options", None) @@ -84,11 +86,11 @@ def lint_inputs(tool_xml, lint_ctx): select_options = param.findall('./option') if dynamic_options is not None: - lint_ctx.warn(f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.", line=param.sourceline) + lint_ctx.warn(f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.", line=param.sourceline, xpath=tool_xml.getpath(param)) # 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.", line=param.sourceline) + 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, xpath=tool_xml.getpath(param)) # lint dynamic options if len(options) == 1: @@ -98,10 +100,10 @@ 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.", line=f.sourceline) + lint_ctx.error(f"Select parameter [{param_name}] contains filter without type.", line=f.sourceline, xpath=tool_xml.getpath(f)) continue if ftype not in FILTER_TYPES: - lint_ctx.error(f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.", line=f.sourceline) + lint_ctx.error(f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.", line=f.sourceline, xpath=tool_xml.getpath(f)) continue if ftype in ['add_value', 'data_meta']: filter_adds_options = True @@ -114,33 +116,33 @@ 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.", line=options[0].sourceline) + 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, xpath=tool_xml.getpath(options[0])) if from_file is not None: - lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_file' attribute.", line=options[0].sourceline) + lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_file' attribute.", line=options[0].sourceline, xpath=tool_xml.getpath(options[0])) if from_parameter is not None: - lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_parameter' attribute.", line=options[0].sourceline) + lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'from_parameter' attribute.", line=options[0].sourceline, xpath=tool_xml.getpath(options[0])) 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.", line=options[0].sourceline) + lint_ctx.error(f"Select parameter [{param_name}] options uses 'from_dataset' and 'from_data_table' attribute.", line=options[0].sourceline, xpath=tool_xml.getpath(options[0])) 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'.", line=options[0].sourceline) + lint_ctx.error(f"Select parameter [{param_name}] 'meta_file_key' is only compatible with 'from_dataset'.", line=options[0].sourceline, xpath=tool_xml.getpath(options[0])) 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.", line=options[0].sourceline) + lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'options_filter_attribute' attribute.", line=options[0].sourceline, xpath=tool_xml.getpath(options[0])) if options[0].get("transform_lines", None) is not None: - lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'transform_lines' attribute.", line=options[0].sourceline) + lint_ctx.warn(f"Select parameter [{param_name}] options uses deprecated 'transform_lines' attribute.", line=options[0].sourceline, xpath=tool_xml.getpath(options[0])) elif len(options) > 1: - lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements", line=options[1].sourceline) + lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements", line=options[1].sourceline, xpath=tool_xml.getpath(options[1])) # 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", line=param.sourceline) + lint_ctx.error(f"Select parameter [{param_name}] has option without value", line=param.sourceline, xpath=tool_xml.getpath(param)) if any(option.text is None for option in select_options): - lint_ctx.warn(f"Select parameter [{param_name}] has option without text", line=param.sourceline) + lint_ctx.warn(f"Select parameter [{param_name}] has option without text", line=param.sourceline, xpath=tool_xml.getpath(param)) select_options_texts = list() select_options_values = list() @@ -153,22 +155,22 @@ def lint_inputs(tool_xml, lint_ctx): select_options_texts.append((text, option.attrib.get("selected", "false"))) select_options_values.append((value, option.attrib.get("selected", "false"))) if len(set(select_options_texts)) != len(select_options_texts): - lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content", line=param.sourceline) + lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content", line=param.sourceline, xpath=tool_xml.getpath(param)) if len(set(select_options_values)) != len(select_options_values): - lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value", line=param.sourceline) + lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value", line=param.sourceline, xpath=tool_xml.getpath(param)) 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', line=param.sourceline) + lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute', line=param.sourceline, xpath=tool_xml.getpath(param)) if not optional: - lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute', line=param.sourceline) + lint_ctx.error(f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute', line=param.sourceline, xpath=tool_xml.getpath(param)) if param_attrib.get("display") == "radio": if multiple: - lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with multiple="true"', line=param.sourceline) + lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with multiple="true"', line=param.sourceline, xpath=tool_xml.getpath(param)) if optional: - lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with optional="true"', line=param.sourceline) + lint_ctx.error(f'Select [{param_name}] display="radio" is incompatible with optional="true"', line=param.sourceline, xpath=tool_xml.getpath(param)) # TODO: Validate type, much more... # lint validators @@ -177,36 +179,36 @@ 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}'", line=validator.sourceline) + lint_ctx.error(f"Parameter [{param_name}]: validator with an incompatible type '{vtype}'", line=validator.sourceline, xpath=tool_xml.getpath(validator)) 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}'", line=validator.sourceline) + lint_ctx.error(f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'", line=validator.sourceline, xpath=tool_xml.getpath(validator)) 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}')", line=validator.sourceline) + lint_ctx.warn(f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')", line=validator.sourceline, xpath=tool_xml.getpath(validator)) 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)", line=validator.sourceline) + lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)", line=validator.sourceline, xpath=tool_xml.getpath(validator)) 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}", line=validator.sourceline) + lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s) {validator.attrib}", line=validator.sourceline, xpath=tool_xml.getpath(validator)) 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", line=validator.sourceline) + lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute", line=validator.sourceline, xpath=tool_xml.getpath(validator)) 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", line=conditional.sourceline) + lint_ctx.error("Conditional without a name", line=conditional.sourceline, xpath=tool_xml.getpath(conditional)) 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 ", line=conditional.sourceline) + lint_ctx.error(f"Conditional [{conditional_name}] has no child ", line=conditional.sourceline, xpath=tool_xml.getpath(conditional)) 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"', line=first_param_type.sourceline) + lint_ctx.warn(f'Conditional [{conditional_name}] first param should have type="select" /> or type="boolean"', line=first_param.sourceline, xpath=tool_xml.getpath(first_param)) continue if first_param_type == 'select': @@ -219,37 +221,37 @@ 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", line=first_param_type.sourceline) + lint_ctx.warn(f"Conditional [{conditional_name}] test parameter cannot be optional", line=first_param.sourceline, xpath=tool_xml.getpath(first_param)) 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", line=conditional.sourceline) + lint_ctx.error(f"Conditional [{conditional_name}] when without value", line=conditional.sourceline, xpath=tool_xml.getpath(conditional)) 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}'", line=conditional.sourceline) + lint_ctx.warn(f"Conditional [{conditional_name}] no block found for {first_param_type} option '{option_id}'", line=conditional.sourceline, xpath=tool_xml.getpath(conditional)) 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