search_query.pubmed package

Submodules

search_query.pubmed.constants module

Constants for PubMed.

search_query.pubmed.constants.generic_field_to_syntax_field(generic_field: str) → str: Convert a set of generic search fields to a set of syntax strings.

search_query.pubmed.constants.map_to_standard(syntax_str: str) → str: Map a syntax string to a standard syntax string.

search_query.pubmed.constants.syntax_str_to_generic_field_set(field_value: str) → set: Translate a search field

search_query.pubmed.linter module

Pubmed query linter.

class search_query.pubmed.linter.PubmedQueryListLinter(parser: PubmedListParser, string_parser_class: Type[QueryStringParser])

Bases: QueryListLinter

Linter for PubMed Query Strings

OPERATOR_NODE_REGEX = re.compile('#?\\d+|AND|OR|NOT')

last_read_index: Dict[int, int]

messages: dict

parser: PubmedListParser

validate_tokens() → None: Validate token list

class search_query.pubmed.linter.PubmedQueryStringLinter(query_str: str = '', *, original_str: str | None = None, silent: bool = False)

Bases: QueryStringLinter

Linter for PubMed Query Strings

PLATFORM: PLATFORM = 'pubmed'

PROXIMITY_REGEX = re.compile('^\\[(.+):~(.*)\\]$')

VALID_TOKEN_SEQUENCES: Dict[TokenTypes, List[TokenTypes]] = {TokenTypes.FIELD: [TokenTypes.LOGIC_OPERATOR, TokenTypes.PARENTHESIS_CLOSED, TokenTypes.RANGE_OPERATOR], TokenTypes.LOGIC_OPERATOR: [TokenTypes.TERM, TokenTypes.PARENTHESIS_OPEN], TokenTypes.PARENTHESIS_CLOSED: [TokenTypes.LOGIC_OPERATOR, TokenTypes.PARENTHESIS_CLOSED], TokenTypes.PARENTHESIS_OPEN: [TokenTypes.TERM, TokenTypes.PARENTHESIS_OPEN], TokenTypes.RANGE_OPERATOR: [TokenTypes.TERM], TokenTypes.TERM: [TokenTypes.FIELD, TokenTypes.LOGIC_OPERATOR, TokenTypes.PARENTHESIS_CLOSED]}

VALID_fieldS_REGEX: re.Pattern

YEAR_VALUE_REGEX = re.compile('^"?(?P<year>\\d{4})(?P<month>\\/(0[1-9]|1[0-2]))?(?P<day>\\/(0[1-9]|[12]\\d|3[01]))?(\\:(?P<year2>(\\d{4})(?P<month2>\\/(0[1-9]|1[0-2]))?(?P<day2>\\/(0[1-9]|[12]\\d|3[01]))?))?"?$', re.VERBOSE)

add_artificial_parentheses_for_operator_precedence(index: int = 0, output: list | None = None) → tuple[int, list[Token]]: Adds artificial parentheses with position (-1, -1) to enforce PubMed operator precedence.

check_character_replacement_in_term(query: Query) → None: Check a search term for invalid characters

check_implicit_fields() → None: Check the general search field

check_invalid_proximity_operator() → None: Check search field for invalid proximity operator

check_invalid_syntax() → None: Check for invalid syntax in the query string.

check_invalid_token_sequences() → None: Check token list for invalid token sequences.

check_invalid_wildcard(query: Query) → None: Check search term for invalid wildcard *

check_unsupported_pubmed_fields() → None: Check for the correct format of fields.

check_year_format(query: Query) → None: Check for the correct format of year.

messages: List[dict]

query: Optional[Query]

syntax_str_to_generic_field_set(field_value: str) → set: Translate a search field

tokens: List[Token]

validate_platform_query(query: Query) → None: Validate the query for the PubMed platform

validate_query_tree(query: Query) → None: Validate the query tree

validate_tokens(*, tokens: List[Token], query_str: str, field_general: str = '') → List[Token]: Validate token list

search_query.pubmed.parser module

Pubmed query parser.

class search_query.pubmed.parser.PubmedListParser(query_list: str, *, field_general: str = '')

Bases: QueryListParser

Parser for Pubmed (list format) queries.

parse() → Query: Parse the query in list format.

class search_query.pubmed.parser.PubmedParser(query_str: str, *, field_general: str = '', offset: dict | None = None, original_str: str | None = None, silent: bool = False)

Bases: QueryStringParser

Parser for Pubmed queries.

FIELD_REGEX = re.compile('\\[[^\\[]*?\\]')

LOGIC_OPERATOR_REGEX = re.compile('(\\||&|\\b(?:AND|OR|NOT|:)\\b)(?!\\s?\\[[^\\[]*?\\])')

PARENTHESIS_REGEX = re.compile('[\$\$]')

PROXIMITY_REGEX = re.compile('^\\[(.+):~(.*)\\]$')

SEARCH_PHRASE_REGEX = re.compile('\\".*?\\"')

TERM_REGEX = re.compile('[^\\s\\[\\]()\\|&]+')

linter: QueryStringLinter

parse() → Query: Parse a query string

parse_query_tree(tokens: list) → Query: Parse a query from a list of tokens

pattern = re.compile('\\[[^\\[]*?\\]|(\\||&|\\b(?:AND|OR|NOT|:)\\b)(?!\\s?\\[[^\\[]*?\\])|[\$\$]|\\".*?\\"|[^\\s\\[\\]()\\|&]+', re.IGNORECASE)

tokenize() → None: Tokenize the query_str

tokens: list

search_query.pubmed.serializer module

Pubmed serializer.

search_query.pubmed.serializer.to_string_pubmed(query: Query) → str: Serialize the Query tree into a PubMed search string.

search_query.pubmed.translator module

Pubmed query translator.

class search_query.pubmed.translator.PubmedTranslator

Bases: QueryTranslator

Translator for Pubmed queries.

classmethod to_generic_syntax(query: Query) → Query: Convert the query to a generic syntax.

classmethod to_specific_syntax(query: Query) → Query: Convert the query to a specific syntax.

classmethod translate_fields_to_generic(query: Query) → Query: Translate search fields

Module contents

Top-level package for PubMed.