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Merge pull request #12733 from bernt-matthias/topic/validator_needs_no_expression
[21.09] Fix linter: Parameter validator needs no expression
This commit is contained in:
Marius van den Beek
@@ -19,16 +19,16 @@ FILTER_TYPES = [
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ATTRIB_VALIDATOR_COMPATIBILITY = {
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"check": ["metadata"],
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"expression": ["regex", "substitute_value_in_message"],
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"expression": ["substitute_value_in_message"],
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"table_name": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "value_in_data_table", "value_not_in_data_table"],
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"filename": ["dataset_metadata_in_file"],
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"metadata_name": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "dataset_metadata_in_file"],
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"metadata_column": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "value_in_data_table", "value_not_in_data_table", "dataset_metadata_in_file options"],
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"metadata_column": ["dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "value_in_data_table", "value_not_in_data_table", "dataset_metadata_in_file"],
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"line_startswith": ["dataset_metadata_in_file"],
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"min": ["in_range", "length"],
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"max": ["in_range", "length"],
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"exclude_min": ["in_range"],
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"exclude_max": ["in_range"],
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"min": ["in_range", "length", "dataset_metadata_in_range"],
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"max": ["in_range", "length", "dataset_metadata_in_range"],
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"exclude_min": ["in_range", "dataset_metadata_in_range"],
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"exclude_max": ["in_range", "dataset_metadata_in_range"],
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"split": ["dataset_metadata_in_file"],
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"skip": ["metadata"]
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}
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@@ -132,7 +132,7 @@ def lint_inputs(tool_xml, lint_ctx):
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# lint statically defined options
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if any(['value' not in option.attrib for option in select_options]):
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lint_ctx.error(f"Select parameter [{param_name}] has option without value")
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if len(set([option.text.strip() for option in select_options])) != len(select_options):
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if len(set([option.text.strip() for option in select_options if option.text is not None])) != len(select_options):
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lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same text content")
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if len(set([option.attrib.get("value") for option in select_options])) != len(select_options):
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lint_ctx.error(f"Select parameter [{param_name}] has multiple options with the same value")
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@@ -161,14 +161,12 @@ def lint_inputs(tool_xml, lint_ctx):
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lint_ctx.error(f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'")
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if vtype == "expression" and validator.text is None:
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lint_ctx.error(f"Parameter [{param_name}]: expression validator without content")
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if vtype != "expression" and validator.text is not None:
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if vtype not in ["expression", "regex"] and validator.text is not None:
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lint_ctx.warn(f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')")
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if vtype == "regex" and "expression" not in validator.attrib:
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lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define an 'expression' attribute")
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if vtype in ["in_range", "length", "dataset_metadata_in_range"] and ("min" not in validator.attrib or "max" not in validator.attrib):
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if vtype in ["in_range", "length", "dataset_metadata_in_range"] and ("min" not in validator.attrib and "max" not in validator.attrib):
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lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)")
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if vtype in ["metadata"] and ("check" not in validator.attrib or "skip" not in validator.attrib):
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lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s)")
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if vtype in ["metadata"] and ("check" not in validator.attrib and "skip" not in validator.attrib):
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lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s) {validator.attrib}")
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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:
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lint_ctx.error(f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute")
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@@ -134,6 +134,51 @@ VALIDATOR_INCOMPATIBILITIES = """
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</tool>
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"""
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VALIDATOR_CORRECT = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
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<description>The BWA Mapper</description>
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<version_command interpreter="python">bwa.py --version</version_command>
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<inputs>
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<param name="data_param" type="data" format="data">
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<validator type="metadata" check="md1,md2" skip="md3,md4" message="cutom validation message" negate="true"/>
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<validator type="unspecified_build" message="cutom validation message" negate="true"/>
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<validator type="dataset_ok_validator" message="cutom validation message" negate="true"/>
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<validator type="dataset_metadata_in_range" min="0" max="100" exclude_min="true" exclude_max="true" message="cutom validation message" negate="true"/>
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<validator type="dataset_metadata_in_file" filename="file.tsv" metadata_column="3" split="," message="cutom validation message" negate="true"/>
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<validator type="dataset_metadata_in_data_table" table_name="datatable_name" metadata_column="3" message="cutom validation message" negate="true"/>
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</param>
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<param name="collection_param" type="collection">
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<validator type="metadata" check="md1,md2" skip="md3,md4" message="cutom validation message"/>
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<validator type="unspecified_build" message="cutom validation message"/>
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<validator type="dataset_ok_validator" message="cutom validation message"/>
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<validator type="dataset_metadata_in_range" min="0" max="100" exclude_min="true" exclude_max="true" message="cutom validation message"/>
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<validator type="dataset_metadata_in_file" filename="file.tsv" metadata_column="3" split="," message="cutom validation message"/>
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<validator type="dataset_metadata_in_data_table" table_name="datatable_name" metadata_column="3" message="cutom validation message"/>
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</param>
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<param name="text_param" type="text">
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<validator type="regex">reg.xp</validator>
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<validator type="length" min="0" max="100" message="cutom validation message"/>
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<validator type="empty_field" message="cutom validation message"/>
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<validator type="value_in_data_table" table_name="datatable_name" metadata_column="3" message="cutom validation message"/>
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<validator type="expression" message="cutom validation message">somepythonexpression</validator>
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</param>
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<param name="select_param" type="select">
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<options from_data_table="bowtie2_indexes"/>
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<validator type="no_options" negate="true"/>
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<validator type="regex" negate="true">reg.xp</validator>
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<validator type="length" min="0" max="100" message="cutom validation message" negate="true"/>
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<validator type="empty_field" message="cutom validation message" negate="true"/>
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<validator type="value_in_data_table" table_name="datatable_name" metadata_column="3" message="cutom validation message" negate="true"/>
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<validator type="expression" message="cutom validation message" negate="true">somepythonexpression</validator>
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</param>
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<param name="int_param" type="integer">
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<validator type="in_range" min="0" max="100" exclude_min="true" exclude_max="true" negate="true"/>
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<validator type="expression" message="cutom validation message">somepythonexpression</validator>
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</param>
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</inputs>
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</tool>
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"""
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# check that linter accepts format source for collection elements as means to specify format
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# and that the linter warns if format and format_source are used
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OUTPUTS_COLLECTION_FORMAT_SOURCE = """
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@@ -226,8 +271,11 @@ TESTS = [
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and "Parameter [param_name]: validator with an incompatible type 'in_range'" in x.error_messages
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and "Parameter [param_name]: 'in_range' validators need to define the 'min' or 'max' attribute(s)" in x.error_messages
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and "Parameter [param_name]: attribute 'filename' is incompatible with validator of type 'regex'" in x.error_messages
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and "Parameter [param_name]: 'regex' validators need to define an 'expression' attribute" in x.error_messages
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and len(x.warn_messages) == 1 and len(x.error_messages) == 4
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and len(x.warn_messages) == 1 and len(x.error_messages) == 3
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),
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(
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VALIDATOR_CORRECT, inputs.lint_inputs,
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lambda x: len(x.warn_messages) == 0 and len(x.error_messages) == 0
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),
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(
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OUTPUTS_COLLECTION_FORMAT_SOURCE, outputs.lint_output,
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@@ -251,6 +299,7 @@ TEST_IDS = [
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'select option definitions',
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'hazardous whitespace',
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'validator imcompatibilities',
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'validator all correct',
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'outputs collection static elements with format_source',
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'outputs discover datatsets with tool provided metadata'
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]
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