dae.query_variants package

Subpackages

• dae.query_variants.sql package
  • Subpackages
    • dae.query_variants.sql.schema1 package
      • Submodules
      • dae.query_variants.sql.schema1.base_query_builder module
      • dae.query_variants.sql.schema1.family_variants_query_builder module
      • dae.query_variants.sql.schema1.schema1_query_director module
      • dae.query_variants.sql.schema1.summary_variants_query_builder module
      • Module contents
    • dae.query_variants.sql.schema2 package
      • Subpackages
      • Submodules
      • dae.query_variants.sql.schema2.base_query_builder module
      • dae.query_variants.sql.schema2.family_builder module
      • dae.query_variants.sql.schema2.summary_builder module
      • Module contents
  • Module contents

Submodules

dae.query_variants.attributes_query module

class dae.query_variants.attributes_query.AndNode(children: Iterable[LeafNode | TreeNode])

Bases: TreeNode

class dae.query_variants.attributes_query.BaseQueryTransformerMatcher(parser: ~lark.lark.Lark = Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter: ~typing.Callable[[~typing.Any], ~typing.Any] | None = None)

Bases: object

Base class for query transformer matchers.

transform_query_string_to_tree(expression: str) → LeafNode | TreeNode

class dae.query_variants.attributes_query.BaseTreeTransformer

Bases: object

transform(node: LeafNode | TreeNode) → Any

class dae.query_variants.attributes_query.BitwiseTreeTransformer(token_converter: Callable[[Any], LeafNode | TreeNode])

Bases: Interpreter

Transform bitwise expressions.

arg(*args: LeafNode | TreeNode) → LeafNode | TreeNode

logical_and(*args: LeafNode | TreeNode) → LeafNode | TreeNode

logical_or(*args: LeafNode | TreeNode) → LeafNode | TreeNode

negation(*args: LeafNode | TreeNode) → LeafNode | TreeNode

simple_arg(*args: LeafNode | TreeNode) → LeafNode | TreeNode

class dae.query_variants.attributes_query.ContainsNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.ElementOfNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.EqualsNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.GreaterThanEqNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.GreaterThanNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.LeafNode(arg: LeafNode | TreeNode)

Bases: object

class dae.query_variants.attributes_query.LessThanEqNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.LessThanNode(arg: LeafNode | TreeNode)

Bases: LeafNode

class dae.query_variants.attributes_query.Matcher(tree: LeafNode | TreeNode, parser: Lark, matcher: Callable[[Any], bool])

Bases: object

No idea what this class is supposed to do. If you know please edit.

match(array: Iterable[Any]) → bool

query_str() → None

class dae.query_variants.attributes_query.NotNode(children)

Bases: TreeNode

class dae.query_variants.attributes_query.OrNode(children: Iterable[LeafNode | TreeNode])

Bases: TreeNode

class dae.query_variants.attributes_query.QueryTransformerMatcher(parser: ~lark.lark.Lark = Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter: ~typing.Callable[[~typing.Any], ~typing.Any] | None = None, transformer2: ~dae.query_variants.attributes_query.BaseTreeTransformer = <dae.query_variants.attributes_query.QueryTreeToLambdaTransformer object>)

Bases: BaseQueryTransformerMatcher

No idea what this is supposed to do. Please edit.

transform_tree_to_matcher(tree: LeafNode | TreeNode) → Matcher

class dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer

Bases: BaseTreeTransformer

No idea what this is supposed to do. Please edit.

AndNode(children: list[Callable[[Any], bool]]) → Callable[[Any], bool]

ContainsNode(arg: Any) → Callable[[Any], bool]

OrNode(children: list[Callable[[Any], bool]]) → Callable[[Any], bool]

class dae.query_variants.attributes_query.QueryTreeToLambdaTransformer

Bases: BaseTreeTransformer

Transforma all nodes to python lambda functions.

AndNode(children: list[Callable[[Any], bool]]) → Callable[[Any], bool]

ContainsNode(arg: Any) → Callable[[Any], bool]

ElementOfNode(arg: Any) → Callable[[Any], bool]

EqualsNode(arg: Any) → Callable[[Any], bool]

NotNode(children: list[Callable[[Any], bool]]) → Callable[[Any], bool]

OrNode(children: list[Callable[[Any], bool]]) → Callable[[Any], bool]

class dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer(column_name: str, use_bit_and_function: bool = True)

Bases: QueryTreeToSQLTransformer

I don’t know what this class does. Please edit if you do.

static AndNode(children: list[str]) → str

ContainsNode(arg: Any) → str

static NotNode(children: list[str]) → str

static OrNode(children: list[str]) → str

class dae.query_variants.attributes_query.QueryTreeToSQLTransformer(column_name: str)

Bases: BaseTreeTransformer

I don’t know what this class does. Please edit if you do.

static token_converter(arg: Any) → str

class dae.query_variants.attributes_query.StringQueryToTreeTransformer(_parser: ~lark.lark.Lark = Lark(open('<string>'), parser='earley', lexer='dynamic', ...), token_converter: ~typing.Callable[[~typing.Any], ~typing.Any] | None = None)

Bases: InlineTransformer

Convert tokens using a token converter.

all(*args: LeafNode | TreeNode) → LeafNode | TreeNode

any(*args: LeafNode | TreeNode) → LeafNode | TreeNode

arg(*args: Any) → LeafNode | TreeNode

logical_and(*args: LeafNode | TreeNode) → LeafNode | TreeNode

logical_or(*args: LeafNode | TreeNode) → LeafNode | TreeNode

negation(*args: Any) → LeafNode | TreeNode

simple_arg(*args: Any) → Any

start(*args: Any) → Any

class dae.query_variants.attributes_query.TreeNode(children: Iterable[LeafNode | TreeNode])

Bases: object

dae.query_variants.attributes_query.get_bit_and_str(arg1: Any, arg2: Any, use_bit_and_function: bool) → str

dae.query_variants.attributes_query.inheritance_converter(arg: str | Inheritance) → Inheritance | None

dae.query_variants.attributes_query.roles_converter(arg: str | Role) → Role | None

dae.query_variants.attributes_query.sex_converter(arg: str | Sex) → Sex | None

dae.query_variants.attributes_query.variant_type_converter(arg: str | Type) → Type

dae.query_variants.attributes_query_inheritance module

class dae.query_variants.attributes_query_inheritance.Expression(expression: str)

Bases: object

class dae.query_variants.attributes_query_inheritance.InheritanceTransformer(attr_name: str, *args: Any, use_bit_and_function: bool = True, **kwargs: Any)

Bases: Transformer

No idea what this class is supposed to do. If you know please edit.

all(items: list) → Expression

any(items: list) → Expression

atom(items: list) → Primitive | NegPrimitive

atomlist(items: list) → Primitive

denovo(_items: list) → Primitive

expression(items: list) → Expression

Construct an Expression from items.

logical_and(items: list) → Expression

logical_or(items: list) → Expression

mendelian(_items: list) → Primitive

missing(_items: list) → Primitive

negative_primitive(items: list) → Primitive | NegPrimitive

omission(_items: list) → Primitive

other(_items: list) → Primitive

possible_denovo(_items: list) → Primitive

possible_omission(_items: list) → Primitive

primitive(items: list) → Primitive

reference(_items: list) → Primitive

unknown(_items: list) → Primitive

class dae.query_variants.attributes_query_inheritance.NegPrimitive(value: Any)

Bases: object

class dae.query_variants.attributes_query_inheritance.Primitive(value: Any)

Bases: object

dae.query_variants.query_runners module

class dae.query_variants.query_runners.QueryResult(runners: list[dae.query_variants.query_runners.QueryRunner], limit: int | None = -1)

Bases: object

Run a list of queries in the background.

The result of the queries is enqueued on result_queue

CHECK_VERBOSITY = 20

close() → None

Gracefully close and dispose of resources.

get(timeout: float = 0.0) → Any

Pop the next entry from the queue.

Return None if the queue is still empty after timeout seconds.

is_done() → bool

Check if the query result is done.

start() → None

class dae.query_variants.query_runners.QueryRunner(**kwargs: Any)

Bases: ABC

Run a query in the backround using the provided executor.

adapt(adapter_func: Callable[[Any], Any]) → None

close() → None

Close query runner.

is_closed() → bool

is_done() → bool

is_started() → bool

abstract run() → None

start(executor: Executor) → None

Module contents