sprocket_bio.grammar

class sprocket_bio.grammar.Diagnostic

Bases: object

Represents a diagnostic to display to the user.

static error(message): Creates a new diagnostic error with the given message.

static note(message): Creates a new diagnostic node with the given message.

static warning(message): Creates a new diagnostic warning with the given message.

with_fix(fix): Sets the fix message for the diagnostic.

with_help(help)

Sets the help message for the diagnostic.

This is different from the fix message, as it only serves to provide more context to the issue, rather than a solution.

with_highlight(span)

Adds a highlight to the diagnostic.

This is equivalent to adding a label with an empty message.

The span for the highlight is expected to be for the same file as the diagnostic.

with_label(message, span)

Adds a label to the diagnostic.

The first label added is considered the primary label.

The span for the label is expected to be for the same file as the diagnostic.

with_rule(rule): Sets the rule for the diagnostic.

with_severity(severity): Sets the severity of the diagnostic.

fix: The optional fix suggestion for the diagnostic.

help: The optional help message.

labels

The labels for the diagnostic.

The first label in the collection is considered the primary label.

message: The diagnostic message.

rule: The optional rule associated with the diagnostic.

severity: The default severity of the diagnostic.

class sprocket_bio.grammar.Label(message, span)

Bases: object

Represents a label that annotates the source code.

message: The optional message of the label (may be empty).

span: The span of the label.

class sprocket_bio.grammar.Severity

Bases: object

Represents the severity of a diagnostic.

ERROR = Severity.ERROR

NOTE = Severity.NOTE

WARNING = Severity.WARNING

class sprocket_bio.grammar.Span(start, len)

Bases: object

Represents a span of source.

contains(offset): Determines if the span contains the given offset.

intersect(other)

Calculates an intersection of two spans, if one exists.

If spans are adjacent, a zero-length span is returned.

Returns None if the two spans are disjoint.

Examples

>>> Span(0, 10).intersect(Span(5, 10))
Span(5..10)

is_empty(): Determines if the span is empty.

len(): Gets the length of the span.

end: The end of the span.

start: The start of the span.

class sprocket_bio.grammar.SupportedVersion

Bases: object

Represents a supported WDL version.

The Default implementation of this type returns the most recent fully-supported ratified version of WDL.

class V1(_0)

Bases: SupportedVersion

The document version is 1.x.

has_same_major_version(other)

Returns true if the other version has the same major version as this one.

>>> from sprocket_bio.grammar.version import SupportedVersion, V1
>>> SupportedVersion.V1(V1.ZERO).has_same_major_version(SupportedVersion.V1(V1.TWO))
True

class sprocket_bio.grammar.SyntaxKind

Bases: object

Represents the kind of syntax element (node or token) in a WDL concrete syntax tree (CST).

Nodes have at least one token child and represent a syntactic construct.

Tokens are terminal and represent any span of the source.

This enumeration is a union of all supported WDL tokens and nodes.

describe()

Describes the syntax kind.

Errors

This method will throw ValueError if the SyntaxKind is symbolic (when SyntaxKind.is_symbolic() returns true).

is_keyword()

Returns whether the SyntaxKind is a keyword.

NOTE: This does not include types, see SyntaxKind.is_type().

is_operator(): Returns whether the SyntaxKind is an operator.

is_symbolic()

Returns whether the token is a symbolic SyntaxKind.

Generally speaking, symbolic SyntaxKinds have special meanings during parsing—they are not real elements of the grammar but rather an implementation detail.

is_trivia(): Returns whether the SyntaxKind is trivia.

is_type(): Returns whether the SyntaxKind is a predefined type keyword.

ABANDONED = SyntaxKind.ABANDONED

ACCESS_EXPR_NODE = SyntaxKind.ACCESS_EXPR_NODE

ADDITION_EXPR_NODE = SyntaxKind.ADDITION_EXPR_NODE

AFTER_KEYWORD = SyntaxKind.AFTER_KEYWORD

ALIAS_KEYWORD = SyntaxKind.ALIAS_KEYWORD

ARRAY_TYPE_KEYWORD = SyntaxKind.ARRAY_TYPE_KEYWORD

ARRAY_TYPE_NODE = SyntaxKind.ARRAY_TYPE_NODE

ASSIGNMENT = SyntaxKind.ASSIGNMENT

ASTERISK = SyntaxKind.ASTERISK

AS_KEYWORD = SyntaxKind.AS_KEYWORD

BOOLEAN_TYPE_KEYWORD = SyntaxKind.BOOLEAN_TYPE_KEYWORD

BOUND_DECL_NODE = SyntaxKind.BOUND_DECL_NODE

CALL_AFTER_NODE = SyntaxKind.CALL_AFTER_NODE

CALL_ALIAS_NODE = SyntaxKind.CALL_ALIAS_NODE

CALL_EXPR_NODE = SyntaxKind.CALL_EXPR_NODE

CALL_INPUT_ITEM_NODE = SyntaxKind.CALL_INPUT_ITEM_NODE

CALL_KEYWORD = SyntaxKind.CALL_KEYWORD

CALL_STATEMENT_NODE = SyntaxKind.CALL_STATEMENT_NODE

CALL_TARGET_NODE = SyntaxKind.CALL_TARGET_NODE

CLOSE_BRACE = SyntaxKind.CLOSE_BRACE

CLOSE_BRACKET = SyntaxKind.CLOSE_BRACKET

CLOSE_HEREDOC = SyntaxKind.CLOSE_HEREDOC

CLOSE_PAREN = SyntaxKind.CLOSE_PAREN

COLON = SyntaxKind.COLON

COMMA = SyntaxKind.COMMA

COMMAND_KEYWORD = SyntaxKind.COMMAND_KEYWORD

COMMAND_SECTION_NODE = SyntaxKind.COMMAND_SECTION_NODE

COMMENT = SyntaxKind.COMMENT

CONDITIONAL_STATEMENT_CLAUSE_NODE = SyntaxKind.CONDITIONAL_STATEMENT_CLAUSE_NODE

CONDITIONAL_STATEMENT_NODE = SyntaxKind.CONDITIONAL_STATEMENT_NODE

DIRECTORY_TYPE_KEYWORD = SyntaxKind.DIRECTORY_TYPE_KEYWORD

DIVISION_EXPR_NODE = SyntaxKind.DIVISION_EXPR_NODE

DOT = SyntaxKind.DOT

DOUBLE_QUOTE = SyntaxKind.DOUBLE_QUOTE

ELSE_KEYWORD = SyntaxKind.ELSE_KEYWORD

ENUM_CHOICE_NODE = SyntaxKind.ENUM_CHOICE_NODE

ENUM_DEFINITION_NODE = SyntaxKind.ENUM_DEFINITION_NODE

ENUM_KEYWORD = SyntaxKind.ENUM_KEYWORD

ENUM_TYPE_PARAMETER_NODE = SyntaxKind.ENUM_TYPE_PARAMETER_NODE

ENV_KEYWORD = SyntaxKind.ENV_KEYWORD

EQUAL = SyntaxKind.EQUAL

EQUALITY_EXPR_NODE = SyntaxKind.EQUALITY_EXPR_NODE

EXCLAMATION = SyntaxKind.EXCLAMATION

EXPONENTIATION = SyntaxKind.EXPONENTIATION

EXPONENTIATION_EXPR_NODE = SyntaxKind.EXPONENTIATION_EXPR_NODE

FALSE_KEYWORD = SyntaxKind.FALSE_KEYWORD

FILE_TYPE_KEYWORD = SyntaxKind.FILE_TYPE_KEYWORD

FLOAT = SyntaxKind.FLOAT

FLOAT_TYPE_KEYWORD = SyntaxKind.FLOAT_TYPE_KEYWORD

FROM_KEYWORD = SyntaxKind.FROM_KEYWORD

GREATER = SyntaxKind.GREATER

GREATER_EQUAL = SyntaxKind.GREATER_EQUAL

GREATER_EQUAL_EXPR_NODE = SyntaxKind.GREATER_EQUAL_EXPR_NODE

GREATER_EXPR_NODE = SyntaxKind.GREATER_EXPR_NODE

HINTS_KEYWORD = SyntaxKind.HINTS_KEYWORD

IDENT = SyntaxKind.IDENT

IF_EXPR_NODE = SyntaxKind.IF_EXPR_NODE

IF_KEYWORD = SyntaxKind.IF_KEYWORD

IMPORT_ALIAS_NODE = SyntaxKind.IMPORT_ALIAS_NODE

IMPORT_KEYWORD = SyntaxKind.IMPORT_KEYWORD

IMPORT_MEMBERS_NODE = SyntaxKind.IMPORT_MEMBERS_NODE

IMPORT_MEMBER_NODE = SyntaxKind.IMPORT_MEMBER_NODE

IMPORT_STATEMENT_NODE = SyntaxKind.IMPORT_STATEMENT_NODE

INDEX_EXPR_NODE = SyntaxKind.INDEX_EXPR_NODE

INEQUALITY_EXPR_NODE = SyntaxKind.INEQUALITY_EXPR_NODE

INPUT_KEYWORD = SyntaxKind.INPUT_KEYWORD

INPUT_SECTION_NODE = SyntaxKind.INPUT_SECTION_NODE

INTEGER = SyntaxKind.INTEGER

INT_TYPE_KEYWORD = SyntaxKind.INT_TYPE_KEYWORD

IN_KEYWORD = SyntaxKind.IN_KEYWORD

LESS = SyntaxKind.LESS

LESS_EQUAL = SyntaxKind.LESS_EQUAL

LESS_EQUAL_EXPR_NODE = SyntaxKind.LESS_EQUAL_EXPR_NODE

LESS_EXPR_NODE = SyntaxKind.LESS_EXPR_NODE

LITERAL_ARRAY_NODE = SyntaxKind.LITERAL_ARRAY_NODE

LITERAL_BOOLEAN_NODE = SyntaxKind.LITERAL_BOOLEAN_NODE

LITERAL_COMMAND_TEXT = SyntaxKind.LITERAL_COMMAND_TEXT

LITERAL_FLOAT_NODE = SyntaxKind.LITERAL_FLOAT_NODE

LITERAL_HINTS_ITEM_NODE = SyntaxKind.LITERAL_HINTS_ITEM_NODE

LITERAL_HINTS_NODE = SyntaxKind.LITERAL_HINTS_NODE

LITERAL_INPUT_ITEM_NODE = SyntaxKind.LITERAL_INPUT_ITEM_NODE

LITERAL_INPUT_NODE = SyntaxKind.LITERAL_INPUT_NODE

LITERAL_INTEGER_NODE = SyntaxKind.LITERAL_INTEGER_NODE

LITERAL_MAP_ITEM_NODE = SyntaxKind.LITERAL_MAP_ITEM_NODE

LITERAL_MAP_NODE = SyntaxKind.LITERAL_MAP_NODE

LITERAL_NONE_NODE = SyntaxKind.LITERAL_NONE_NODE

LITERAL_NULL_NODE = SyntaxKind.LITERAL_NULL_NODE

LITERAL_OBJECT_ITEM_NODE = SyntaxKind.LITERAL_OBJECT_ITEM_NODE

LITERAL_OBJECT_NODE = SyntaxKind.LITERAL_OBJECT_NODE

LITERAL_OUTPUT_ITEM_NODE = SyntaxKind.LITERAL_OUTPUT_ITEM_NODE

LITERAL_OUTPUT_NODE = SyntaxKind.LITERAL_OUTPUT_NODE

LITERAL_PAIR_NODE = SyntaxKind.LITERAL_PAIR_NODE

LITERAL_STRING_NODE = SyntaxKind.LITERAL_STRING_NODE

LITERAL_STRING_TEXT = SyntaxKind.LITERAL_STRING_TEXT

LITERAL_STRUCT_ITEM_NODE = SyntaxKind.LITERAL_STRUCT_ITEM_NODE

LITERAL_STRUCT_NODE = SyntaxKind.LITERAL_STRUCT_NODE

LOGICAL_AND = SyntaxKind.LOGICAL_AND

LOGICAL_AND_EXPR_NODE = SyntaxKind.LOGICAL_AND_EXPR_NODE

LOGICAL_NOT_EXPR_NODE = SyntaxKind.LOGICAL_NOT_EXPR_NODE

LOGICAL_OR = SyntaxKind.LOGICAL_OR

LOGICAL_OR_EXPR_NODE = SyntaxKind.LOGICAL_OR_EXPR_NODE

MAP_TYPE_KEYWORD = SyntaxKind.MAP_TYPE_KEYWORD

MAP_TYPE_NODE = SyntaxKind.MAP_TYPE_NODE

MAX = SyntaxKind.MAX

METADATA_ARRAY_NODE = SyntaxKind.METADATA_ARRAY_NODE

METADATA_OBJECT_ITEM_NODE = SyntaxKind.METADATA_OBJECT_ITEM_NODE

METADATA_OBJECT_NODE = SyntaxKind.METADATA_OBJECT_NODE

METADATA_SECTION_NODE = SyntaxKind.METADATA_SECTION_NODE

META_KEYWORD = SyntaxKind.META_KEYWORD

MINUS = SyntaxKind.MINUS

MODULO_EXPR_NODE = SyntaxKind.MODULO_EXPR_NODE

MULTIPLICATION_EXPR_NODE = SyntaxKind.MULTIPLICATION_EXPR_NODE

NAME_REF_EXPR_NODE = SyntaxKind.NAME_REF_EXPR_NODE

NEGATION_EXPR_NODE = SyntaxKind.NEGATION_EXPR_NODE

NONE_KEYWORD = SyntaxKind.NONE_KEYWORD

NOT_EQUAL = SyntaxKind.NOT_EQUAL

NULL_KEYWORD = SyntaxKind.NULL_KEYWORD

OBJECT_KEYWORD = SyntaxKind.OBJECT_KEYWORD

OBJECT_TYPE_KEYWORD = SyntaxKind.OBJECT_TYPE_KEYWORD

OBJECT_TYPE_NODE = SyntaxKind.OBJECT_TYPE_NODE

OPEN_BRACE = SyntaxKind.OPEN_BRACE

OPEN_BRACKET = SyntaxKind.OPEN_BRACKET

OPEN_HEREDOC = SyntaxKind.OPEN_HEREDOC

OPEN_PAREN = SyntaxKind.OPEN_PAREN

OUTPUT_KEYWORD = SyntaxKind.OUTPUT_KEYWORD

OUTPUT_SECTION_NODE = SyntaxKind.OUTPUT_SECTION_NODE

PAIR_TYPE_KEYWORD = SyntaxKind.PAIR_TYPE_KEYWORD

PAIR_TYPE_NODE = SyntaxKind.PAIR_TYPE_NODE

PARAMETER_METADATA_SECTION_NODE = SyntaxKind.PARAMETER_METADATA_SECTION_NODE

PARAMETER_META_KEYWORD = SyntaxKind.PARAMETER_META_KEYWORD

PARENTHESIZED_EXPR_NODE = SyntaxKind.PARENTHESIZED_EXPR_NODE

PERCENT = SyntaxKind.PERCENT

PLACEHOLDER_DEFAULT_OPTION_NODE = SyntaxKind.PLACEHOLDER_DEFAULT_OPTION_NODE

PLACEHOLDER_NODE = SyntaxKind.PLACEHOLDER_NODE

PLACEHOLDER_OPEN = SyntaxKind.PLACEHOLDER_OPEN

PLACEHOLDER_SEP_OPTION_NODE = SyntaxKind.PLACEHOLDER_SEP_OPTION_NODE

PLACEHOLDER_TRUE_FALSE_OPTION_NODE = SyntaxKind.PLACEHOLDER_TRUE_FALSE_OPTION_NODE

PLUS = SyntaxKind.PLUS

PRIMITIVE_TYPE_NODE = SyntaxKind.PRIMITIVE_TYPE_NODE

QUESTION_MARK = SyntaxKind.QUESTION_MARK

REQUIREMENTS_ITEM_NODE = SyntaxKind.REQUIREMENTS_ITEM_NODE

REQUIREMENTS_KEYWORD = SyntaxKind.REQUIREMENTS_KEYWORD

REQUIREMENTS_SECTION_NODE = SyntaxKind.REQUIREMENTS_SECTION_NODE

ROOT_NODE = SyntaxKind.ROOT_NODE

RUNTIME_ITEM_NODE = SyntaxKind.RUNTIME_ITEM_NODE

RUNTIME_KEYWORD = SyntaxKind.RUNTIME_KEYWORD

RUNTIME_SECTION_NODE = SyntaxKind.RUNTIME_SECTION_NODE

SCATTER_KEYWORD = SyntaxKind.SCATTER_KEYWORD

SCATTER_STATEMENT_NODE = SyntaxKind.SCATTER_STATEMENT_NODE

SINGLE_QUOTE = SyntaxKind.SINGLE_QUOTE

SLASH = SyntaxKind.SLASH

STRING_TYPE_KEYWORD = SyntaxKind.STRING_TYPE_KEYWORD

STRUCT_DEFINITION_NODE = SyntaxKind.STRUCT_DEFINITION_NODE

STRUCT_KEYWORD = SyntaxKind.STRUCT_KEYWORD

SUBTRACTION_EXPR_NODE = SyntaxKind.SUBTRACTION_EXPR_NODE

SYMBOLIC_MODULE_PATH_NODE = SyntaxKind.SYMBOLIC_MODULE_PATH_NODE

TASK_DEFINITION_NODE = SyntaxKind.TASK_DEFINITION_NODE

TASK_HINTS_ITEM_NODE = SyntaxKind.TASK_HINTS_ITEM_NODE

TASK_HINTS_SECTION_NODE = SyntaxKind.TASK_HINTS_SECTION_NODE

TASK_KEYWORD = SyntaxKind.TASK_KEYWORD

THEN_KEYWORD = SyntaxKind.THEN_KEYWORD

TRUE_KEYWORD = SyntaxKind.TRUE_KEYWORD

TYPE_REF_NODE = SyntaxKind.TYPE_REF_NODE

UNBOUND_DECL_NODE = SyntaxKind.UNBOUND_DECL_NODE

UNKNOWN = SyntaxKind.UNKNOWN

UNPARSED = SyntaxKind.UNPARSED

VERSION = SyntaxKind.VERSION

VERSION_KEYWORD = SyntaxKind.VERSION_KEYWORD

VERSION_STATEMENT_NODE = SyntaxKind.VERSION_STATEMENT_NODE

WHITESPACE = SyntaxKind.WHITESPACE

WORKFLOW_DEFINITION_NODE = SyntaxKind.WORKFLOW_DEFINITION_NODE

WORKFLOW_HINTS_ARRAY_NODE = SyntaxKind.WORKFLOW_HINTS_ARRAY_NODE

WORKFLOW_HINTS_ITEM_NODE = SyntaxKind.WORKFLOW_HINTS_ITEM_NODE

WORKFLOW_HINTS_OBJECT_ITEM_NODE = SyntaxKind.WORKFLOW_HINTS_OBJECT_ITEM_NODE

WORKFLOW_HINTS_OBJECT_NODE = SyntaxKind.WORKFLOW_HINTS_OBJECT_NODE

WORKFLOW_HINTS_SECTION_NODE = SyntaxKind.WORKFLOW_HINTS_SECTION_NODE

WORKFLOW_KEYWORD = SyntaxKind.WORKFLOW_KEYWORD