opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-29 17:42:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

full coverage of inputs linter

Browse Source 
and several small improvements

- lint for empty param name / type
- distinct option definition possibilities for selects and selects in
conditionals
- condtional parameter
  - check for exactly 1 conditional param (before only 0)
  - warn if boolean select param for conditional
  - warn for optional and multiple select
This commit is contained in:
Matthias Bernt
2022-01-17 11:07:48 +01:00
parent 1b5f120189
commit 96f0e72887
2 changed files with 270 additions and 60 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/tool_util/linters/inputs.py
+36 -14
View File
@@ -66,14 +66,23 @@ def lint_inputs(tool_xml, lint_ctx):
if "name" in param_attrib and "argument" in param_attrib:
if param_attrib.get("name") == _parse_name(None, param_attrib.get("argument")):
lint_ctx.warn(f"Param input [{param_name}] 'name' attribute is redundant if argument implies the same name.")
if param_name.strip() == "":
lint_ctx.error("Param input with empty name.", line=param.sourceline, xpath=tool_xml.getpath(param))
elif not is_valid_cheetah_placeholder(param_name):
lint_ctx.warn(f"Param input [{param_name}] is not a valid Cheetah placeholder.", line=param.sourceline, xpath=tool_xml.getpath(param))
# TODO lint for params with duplicated name (in inputs & outputs)
if "type" not in param_attrib:
lint_ctx.error(f"Param input [{param_name}] input with no type specified.", line=param.sourceline, xpath=tool_xml.getpath(param))
continue
elif param_attrib["type"].strip() == "":
lint_ctx.error(f"Param input [{param_name}] with empty 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, xpath=tool_xml.getpath(param))
# TODO lint for valid param type - attribute combinations
# TODO lint required attributes for valid each param type
if param_type == "data":
if "format" not in param_attrib:
@@ -89,13 +98,18 @@ def lint_inputs(tool_xml, lint_ctx):
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, xpath=tool_xml.getpath(param))
if param.getparent().tag != "conditional":
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, xpath=tool_xml.getpath(param))
else:
if len(select_options) == 0:
lint_ctx.error(f"Select parameter of a conditional [{param_name}] options have to be defined by 'option' children elements.", line=param.sourceline, xpath=tool_xml.getpath(param))
# lint dynamic options
if len(options) == 1:
filters = options[0].findall("./filter")
# lint filters
# TODO check if dataset is available for filters referring other datasets
filter_adds_options = False
for f in filters:
ftype = f.get("type", None)
@@ -113,6 +127,8 @@ def lint_inputs(tool_xml, lint_ctx):
from_parameter = options[0].get("from_parameter", None)
from_dataset = options[0].get("from_dataset", None)
from_data_table = options[0].get("from_data_table", None)
# TODO check if input param is present for from_dataset
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):
@@ -136,7 +152,7 @@ def lint_inputs(tool_xml, lint_ctx):
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, xpath=tool_xml.getpath(options[1]))
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):
@@ -174,6 +190,7 @@ def lint_inputs(tool_xml, lint_ctx):
# TODO: Validate type, much more...
# lint validators
# TODO check if dataset is available for validators referring other datasets
validators = param.findall("./validator")
for validator in validators:
vtype = validator.attrib['type']
@@ -184,13 +201,13 @@ def lint_inputs(tool_xml, lint_ctx):
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, xpath=tool_xml.getpath(validator))
if vtype == "expression" and validator.text is None:
lint_ctx.error(f"Parameter [{param_name}]: expression validator without content")
lint_ctx.error(f"Parameter [{param_name}]: expression validator without content", line=validator.sourceline, xpath=tool_xml.getpath(validator))
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, 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, 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, xpath=tool_xml.getpath(validator))
lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s)", 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, xpath=tool_xml.getpath(validator))
@@ -202,14 +219,17 @@ def lint_inputs(tool_xml, lint_ctx):
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 <param>", line=conditional.sourceline, xpath=tool_xml.getpath(conditional))
first_param = conditional.findall("param")
if len(first_param) != 1:
lint_ctx.error(f"Conditional [{conditional_name}] needs exactly one child <param> found {len(first_param)}", line=conditional.sourceline, xpath=tool_xml.getpath(conditional))
continue
first_param = first_param[0]
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.sourceline, xpath=tool_xml.getpath(first_param))
lint_ctx.error(f'Conditional [{conditional_name}] first param should have type="select" (or type="boolean" which is discouraged)', line=first_param.sourceline, xpath=tool_xml.getpath(first_param))
continue
elif first_param_type == 'boolean':
lint_ctx.warn(f'Conditional [{conditional_name}] first param of type="boolean" is discouraged, use a select', line=first_param.sourceline, xpath=tool_xml.getpath(first_param))
if first_param_type == 'select':
select_options = _find_with_attribute(first_param, 'option', 'value')
@@ -220,14 +240,15 @@ def lint_inputs(tool_xml, lint_ctx):
first_param.get('falsevalue', 'false')
]
if string_as_bool(first_param.get('optional', False)):
lint_ctx.warn(f"Conditional [{conditional_name}] test parameter cannot be optional", line=first_param.sourceline, xpath=tool_xml.getpath(first_param))
for incomp in ["optional", "multiple"]:
if string_as_bool(first_param.get(incomp, False)):
lint_ctx.warn(f'Conditional [{conditional_name}] test parameter cannot be {incomp}="true"', 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, xpath=tool_xml.getpath(conditional))
when_ids = [w.get('value') for w in whens]
when_ids = [w.get('value') for w in whens if w.get('value') is not None]
for option_id in option_ids:
if option_id not in when_ids:
@@ -241,6 +262,7 @@ def lint_inputs(tool_xml, lint_ctx):
lint_ctx.warn(f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'", line=conditional.sourceline, xpath=tool_xml.getpath(conditional))
if datasource:
# TODO only display is subtag of inputs, uihints is a separate top level tag (supporting only attrib minwidth)
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", line=tool_line, xpath=tool_path)