chore: batch commit remaining changes
Includes search engine improvements, Alembic migrations, new services (pubmed_daily_update, query_expansion), frontend updates, and documentation sync.
This commit is contained in:
34047007@qq.com
@@ -22,22 +22,58 @@ import re
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from dataclasses import dataclass, field
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from enum import Enum, auto
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# ─── 查询复杂度限制 ───
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MAX_TERMS = 50 # 与 API 层 check_query_complexity 的 50 词限制对齐
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MAX_PAREN_DEPTH = 10 # 括号嵌套最深层数
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# ─── 字段标签映射 ───
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_FIELD_TAG_MAP: dict[str, str] = {
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"TI": "title",
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"AB": "abstract",
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"TIAB": "all", # 映射到 field=all（title+abstract covered）
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"TIAB": "all",
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"AU": "author",
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"TA": "journal",
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"JT": "journal", # P1-2: Journal Title (同 TA)
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"AD": "affiliation",
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"CN": "author",
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"FAU": "author",
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"LAU": "author",
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"TW": "all",
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"OT": "all",
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# 新增标量字段
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"LA": "language",
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"VI": "volume",
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"IP": "issue",
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"PG": "pages",
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"LID": "lid",
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}
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# MeSH/PT/DP/PMID/DOI 需要特殊处理，不直接映射到 field 参数
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_SPECIAL_FIELDS = {"MH", "MAJR", "PT", "DP", "PMID", "DOI"}
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# 需要特殊处理的字段（不直接映射到 field 参数）
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_SPECIAL_FIELDS = {
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"MH", "MAJR", "PT", "DP", "PMID", "DOI",
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# 日期字段
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"EDAT", "CRDT", "MHDA", "LR", "DCOM",
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# JSONB 字段
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"GR", "SH", "RN", "NM", "SI", "PA",
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# 待补充抽取的字段（标记为特殊以便未来实现）
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"AUID", "COIS", "ED", "IR", "PS", "PUBN", "TT",
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}
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# 所有合法字段标签
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_ALL_FIELD_TAGS = set(_FIELD_TAG_MAP.keys()) | _SPECIAL_FIELDS
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# 支持日期范围语法的字段
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_DATE_RANGE_FIELDS = {"DP", "EDAT", "CRDT", "MHDA", "LR", "DCOM"}
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# 所有合法字段标签（PubMed 全量字段）
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# P1-1: 移除了 BOOK/FILTER/ISBN（未实现，降级为 plain text 不如报错透明）
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_ALL_FIELD_TAGS = {
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"AB", "AD", "AU", "CN", "FAU", "AUID", "LAU", "COIS",
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"DCOM", "CRDT", "EDAT", "MHDA", "LR", "DP", "DOI",
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"RN", "ED", "GR", "IR", "IP",
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"TA", "JT", "LA", "LID", "MAJR", "SH", "MH", "MH:NOEXP", "OT", "PG",
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"PA", "PT", "PMID", "PUBN", "SI", "PS", "NM", "TW",
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"TI", "TIAB", "TT", "VI",
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}
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# ─── Token Types ───
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@@ -53,6 +89,8 @@ class TokenType(Enum):
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COLON = auto() # :
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WORD = auto() # unquoted text
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NUMBER = auto() # digits (for PMID, year)
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DATE = auto() # YYYY-MM-DD (normalized from YYYY/MM/DD)
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UNKNOWN_FIELD = auto() # [...] 但内容不是已知字段标签
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EOF = auto() # end of input
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@@ -67,12 +105,14 @@ class Token:
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_TOKEN_PATTERNS: list[tuple[TokenType, str]] = [
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(TokenType.QUOTED, r'"(?:[^"\\]|\\.)*"'),
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(TokenType.FIELD, r'\[(?:' + '|'.join(_ALL_FIELD_TAGS) + r')\]'),
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(TokenType.UNKNOWN_FIELD, r'\[[^\]]*\]'), # 未识别的字段标签 → 触发降级
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(TokenType.AND, r'\bAND\b'),
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(TokenType.OR, r'\bOR\b'),
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(TokenType.NOT, r'\bNOT\b'),
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(TokenType.LPAREN, r'\('),
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(TokenType.RPAREN, r'\)'),
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(TokenType.COLON, r':'),
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(TokenType.DATE, r'\d{4}-\d{2}-\d{2}'),
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(TokenType.NUMBER, r'\d+'),
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(TokenType.WORD, r'[^\s"\[\]():]+'),
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]
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@@ -90,7 +130,12 @@ def tokenise(query: str) -> list[Token]:
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for name, value in m.groupdict().items():
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if value is not None:
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ttype = TokenType[name]
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if ttype == TokenType.UNKNOWN_FIELD:
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fname = value.strip('[]').upper()
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raise ParseError(f"不认识的字段标签 [{fname}]，降级为简单文本搜索")
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tokens.append(Token(ttype, value))
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if len(tokens) > MAX_TERMS:
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raise ParseError(f"查询词过多（超过 {MAX_TERMS} 个），降级为简单文本搜索")
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tokens.append(Token(TokenType.EOF))
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return tokens
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@@ -104,6 +149,8 @@ class Term:
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exact: bool = False # True if quoted phrase
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field: str | None = None # None = plain (no field tag); "title"/"abstract"/etc for mapped; "MH"/"PT"/etc for special
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is_not: bool = False # True if preceded by NOT
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group_id: int = -1 # -1 = top-level, >= 0 = parenthesized group index
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_noexp: bool = False # P1-4: [MH:noexp] 抑制树展开
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@dataclass
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@@ -119,14 +166,54 @@ class ParsedPubmedQuery:
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pub_types: list[str] = field(default_factory=list) # [PT]
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doi_terms: list[str] = field(default_factory=list) # [DOI]
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pmid_terms: list[int] = field(default_factory=list) # [PMID]
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affiliation_terms: list[Term] = field(default_factory=list) # [AD]
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language_terms: list[Term] = field(default_factory=list) # [LA]
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volume_terms: list[Term] = field(default_factory=list) # [VI]
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issue_terms: list[Term] = field(default_factory=list) # [IP]
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pages_terms: list[Term] = field(default_factory=list) # [PG]
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lid_terms: list[Term] = field(default_factory=list) # [LID]
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date_from: str | None = None # [DP] lower bound (YYYY-MM-DD)
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date_to: str | None = None # [DP] upper bound (YYYY-MM-DD)
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year_from: int | None = None # [DP] year lower
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year_to: int | None = None # [DP] year upper
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# 更多日期字段
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edat_from: str | None = None # [EDAT]
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edat_to: str | None = None
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crdt_from: str | None = None # [CRDT]
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crdt_to: str | None = None
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mhda_from: str | None = None # [MHDA]
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mhda_to: str | None = None
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lr_from: str | None = None # [LR]
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lr_to: str | None = None
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dcom_from: str | None = None # [DCOM]
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dcom_to: str | None = None
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# 特殊字段（存储 Term 以保留 is_not 标志）
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mesh_terms: list[Term] = field(default_factory=list) # [MH] (was list[str])
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majr_terms: list[Term] = field(default_factory=list) # [MAJR] (was list[str])
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pub_types: list[Term] = field(default_factory=list) # [PT] (was list[str])
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doi_terms: list[Term] = field(default_factory=list) # [DOI] (was list[str])
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pmid_terms: list[Term] = field(default_factory=list) # [PMID] (was list[int])
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# JSONB 字段
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grant_terms: list[Term] = field(default_factory=list) # [GR]
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subheading_terms: list[Term] = field(default_factory=list) # [SH]
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registry_terms: list[Term] = field(default_factory=list) # [RN]
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substance_terms: list[Term] = field(default_factory=list) # [NM]
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databank_terms: list[Term] = field(default_factory=list) # [SI]
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pharmaco_terms: list[Term] = field(default_factory=list) # [PA]
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ed_terms: list[Term] = field(default_factory=list) # [ED]
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investigator_terms: list[Term] = field(default_factory=list) # [IR]
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personal_name_terms: list[Term] = field(default_factory=list) # [PS]
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pubnote_terms: list[Term] = field(default_factory=list) # [PUBN]
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auid_terms: list[Term] = field(default_factory=list) # [AUID]
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cois_terms: list[Term] = field(default_factory=list) # [COIS]
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tt_terms: list[Term] = field(default_factory=list) # [TT]
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plain_terms: list[Term] = field(default_factory=list) # no field tag
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boolean_operator: str = "and" # "and" | "or" | "mixed"
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has_not: bool = False # contains NOT
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not_terms: list[Term] = field(default_factory=list) # terms under NOT
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groups: list[list[Term]] = field(default_factory=list) # parenthesized sub-groups
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group_operators: list[str] = field(default_factory=list) # "and"/"or" per group (P2-2)
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negated_date_ranges: set[str] = field(default_factory=set) # date fields negated by NOT
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# ─── Parser ───
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@@ -174,6 +261,7 @@ class PubmedQueryParser:
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def parse(self) -> ParsedPubmedQuery:
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"""入口：解析完整的查询字符串。"""
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result = ParsedPubmedQuery()
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self._depth = 0 # 括号嵌套深度计数器
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try:
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terms = self._parse_or_expr(result)
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except ParseError:
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@@ -187,12 +275,12 @@ class PubmedQueryParser:
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elif has_or and not has_and:
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result.boolean_operator = "or"
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result.has_not = any(t.is_not for t in terms if not getattr(t, '_is_range_end', False))
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result.not_terms = [t for t in terms if t.is_not and not getattr(t, '_is_range_end', False)]
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for t in terms:
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if getattr(t, '_is_range_end', False):
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continue
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# 分组词不从 flat lists 走，避免括号内外的词被一起 AND/OR
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# 同时 has_not/not_terms 也只考虑非分组词
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_ungrouped = [t for t in terms if not getattr(t, '_is_range_end', False) and t.group_id < 0]
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result.has_not = any(t.is_not for t in _ungrouped)
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result.not_terms = [t for t in _ungrouped if t.is_not]
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for t in _ungrouped:
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self._dispatch_term(result, t)
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return result
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@@ -206,26 +294,75 @@ class PubmedQueryParser:
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result.tiab_terms.append(term)
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elif term.field == "author":
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result.author_terms.append(term)
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elif term.field == "affiliation":
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result.affiliation_terms.append(term)
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elif term.field == "journal":
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result.journal_terms.append(term)
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elif term.field == "language":
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result.language_terms.append(term)
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elif term.field == "volume":
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result.volume_terms.append(term)
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elif term.field == "issue":
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result.issue_terms.append(term)
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elif term.field == "pages":
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result.pages_terms.append(term)
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elif term.field == "lid":
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result.lid_terms.append(term)
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elif term.field == "MH":
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result.mesh_terms.append(term.text)
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result.mesh_terms.append(term)
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elif term.field == "MAJR":
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result.majr_terms.append(term.text)
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result.majr_terms.append(term)
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elif term.field == "PT":
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result.pub_types.append(term.text)
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result.pub_types.append(term)
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elif term.field == "PMID":
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try:
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result.pmid_terms.append(int(term.text))
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int(term.text) # validate
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except ValueError:
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result.plain_terms.append(term)
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return
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result.pmid_terms.append(term)
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elif term.field == "DOI":
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result.doi_terms.append(term.text)
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result.doi_terms.append(term)
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elif term.field == "GR":
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result.grant_terms.append(term)
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elif term.field == "SH":
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result.subheading_terms.append(term)
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elif term.field == "RN":
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result.registry_terms.append(term)
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elif term.field == "NM":
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result.substance_terms.append(term)
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elif term.field == "SI":
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result.databank_terms.append(term)
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elif term.field == "PA":
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result.pharmaco_terms.append(term)
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elif term.field is None:
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result.plain_terms.append(term)
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elif term.field == "__RANGE_DP__":
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# Already handled inline during parse; skip.
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pass
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elif term.field == "__RANGE_EDAT__":
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pass
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elif term.field == "__RANGE_CRDT__":
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pass
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elif term.field == "__RANGE_MHDA__":
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pass
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elif term.field == "__RANGE_LR__":
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pass
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elif term.field == "__RANGE_DCOM__":
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pass
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elif term.field == "ED":
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result.ed_terms.append(term)
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elif term.field == "IR":
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result.investigator_terms.append(term)
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elif term.field == "PS":
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result.personal_name_terms.append(term)
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elif term.field == "PUBN":
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result.pubnote_terms.append(term)
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elif term.field == "AUID":
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result.auid_terms.append(term)
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elif term.field == "COIS":
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result.cois_terms.append(term)
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elif term.field == "TT":
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result.tt_terms.append(term)
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else:
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result.plain_terms.append(term)
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@@ -240,7 +377,7 @@ class PubmedQueryParser:
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def _is_primary_start(self, token: Token) -> bool:
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"""Check if token could start a primary expression."""
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return token.type in (TokenType.WORD, TokenType.QUOTED, TokenType.NUMBER,
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return token.type in (TokenType.WORD, TokenType.QUOTED, TokenType.NUMBER, TokenType.DATE,
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TokenType.LPAREN, TokenType.NOT)
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def _parse_and_expr(self, result: ParsedPubmedQuery) -> list[Term]:
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@@ -272,9 +409,23 @@ class PubmedQueryParser:
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def _parse_primary(self, result: ParsedPubmedQuery, negated: bool = False) -> list[Term]:
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"""primary → atom FIELD? | LPAREN query RPAREN"""
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if self.peek().type == TokenType.LPAREN:
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self._depth += 1
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if self._depth > MAX_PAREN_DEPTH:
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raise ParseError(f"括号嵌套过深（超过 {MAX_PAREN_DEPTH} 层），降级为简单文本搜索")
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self.advance()
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start_pos = self.pos # P2-2: 记录组起始标记位置
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terms = self._parse_or_expr(result)
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end_pos = self.pos # P2-2: 记录组结束标记位置
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self.expect(TokenType.RPAREN)
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self._depth -= 1
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# 标记为子组，不放入 flat lists，保留括号分组结构
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group_id = len(result.groups)
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for t in terms:
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t.group_id = group_id
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result.groups.append(terms)
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# P2-2: 检测组内是否有显式 OR
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_has_or = any(t.type == TokenType.OR for t in self.tokens[start_pos:end_pos])
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result.group_operators.append("or" if _has_or else "and")
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if negated:
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for t in terms:
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t.is_not = True
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@@ -289,17 +440,19 @@ class PubmedQueryParser:
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- "quoted phrase"[FIELD]
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- word[FIELD]
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- NUMBER:NUMBER[DP] (year/date range)
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- DATE:DATE[DP] (full date range like 2024-01-01:2024-12-31)
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- NUMBER (bare number)
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- word (bare word)
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"""
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# Look ahead for NUMBER:NUMBER pattern
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# Look ahead for range pattern (NUMBER:NUMBER or DATE:DATE)
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t0 = self.peek()
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t1 = self.peek_n(1)
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t2 = self.peek_n(2)
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if (t0.type == TokenType.NUMBER
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and t1 is not None and t1.type == TokenType.COLON
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and t2 is not None and t2.type == TokenType.NUMBER):
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if (t1 is not None and t1.type == TokenType.COLON
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and t2 is not None
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and t0.type in (TokenType.NUMBER, TokenType.DATE, TokenType.WORD)
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and t2.type in (TokenType.NUMBER, TokenType.DATE, TokenType.WORD)):
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return self._parse_range(result, negated)
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# Normal atom
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@@ -307,16 +460,23 @@ class PubmedQueryParser:
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text = token.value.strip('"') if token.type == TokenType.QUOTED else token.value
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is_exact = (token.type == TokenType.QUOTED)
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field = None
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_noexp = False # P1-4
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if self.peek().type == TokenType.FIELD:
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ft = self.advance()
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field = ft.value[1:-1].upper()
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if field in _FIELD_TAG_MAP:
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field = _FIELD_TAG_MAP[field]
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raw = ft.value[1:-1].upper()
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# P1-4: [MH:noexp] → 抑制树展开
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if raw == "MH:NOEXP":
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field = "MH"
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_noexp = True
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else:
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field = raw
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if field in _FIELD_TAG_MAP:
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field = _FIELD_TAG_MAP[field]
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return [Term(text, exact=is_exact, field=field, is_not=negated)]
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return [Term(text, exact=is_exact, field=field, is_not=negated, _noexp=_noexp)]
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def _parse_range(self, result: ParsedPubmedQuery, negated: bool = False) -> list[Term]:
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"""Parse NUMBER:NUMBER[FIELD] — handles DP (year) ranges specially."""
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"""Parse NUMBER:NUMBER[FIELD] — handles date ranges specially."""
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start_val = self.advance().value # NUMBER
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self.advance() # COLON
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end_val = self.advance().value # NUMBER
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@@ -326,25 +486,39 @@ class PubmedQueryParser:
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ft = self.advance()
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field = ft.value[1:-1].upper()
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if field == "DP":
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try:
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sy, ey = int(start_val), int(end_val)
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except ValueError:
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sy = ey = None
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||||
# Year-only range (e.g., 2024:2026[DP])
|
||||
if field in _DATE_RANGE_FIELDS:
|
||||
attr_map = {
|
||||
"DP": ("date_from", "date_to", "year_from", "year_to", "__RANGE_DP__"),
|
||||
"EDAT": ("edat_from", "edat_to", None, None, "__RANGE_EDAT__"),
|
||||
"CRDT": ("crdt_from", "crdt_to", None, None, "__RANGE_CRDT__"),
|
||||
"MHDA": ("mhda_from", "mhda_to", None, None, "__RANGE_MHDA__"),
|
||||
"LR": ("lr_from", "lr_to", None, None, "__RANGE_LR__"),
|
||||
"DCOM": ("dcom_from", "dcom_to", None, None, "__RANGE_DCOM__"),
|
||||
}
|
||||
date_attr, date_attr_to, yr_from_attr, yr_to_attr, marker_field = attr_map[field]
|
||||
# 反向范围自动交换（如 2026:2024[DP] → 2024:2026[DP]）
|
||||
if start_val.isdigit() and end_val.isdigit() and int(start_val) > int(end_val):
|
||||
start_val, end_val = end_val, start_val
|
||||
# Year-only range (e.g., 2024:2026[EDAT])
|
||||
if start_val.isdigit() and len(start_val) == 4:
|
||||
result.year_from = sy
|
||||
result.year_to = ey
|
||||
if yr_from_attr:
|
||||
setattr(result, yr_from_attr, int(start_val))
|
||||
setattr(result, yr_to_attr, int(end_val))
|
||||
else:
|
||||
# For non-DP date fields: convert year to full date for consistency
|
||||
setattr(result, date_attr, f"{start_val}-01-01")
|
||||
setattr(result, date_attr_to, f"{end_val}-12-31")
|
||||
else:
|
||||
# Full date range (e.g., 2024/01/01:2024/12/31[DP])
|
||||
result.date_from = start_val
|
||||
result.date_to = end_val
|
||||
# Return a marker term so not-terms tracking knows about it, but _dispatch skips.
|
||||
marker = Term(f"{start_val}:{end_val}", field="__RANGE_DP__", is_not=negated)
|
||||
# Full date range (e.g., 2024-01-01:2024-12-31[EDAT])
|
||||
setattr(result, date_attr, start_val)
|
||||
setattr(result, date_attr_to, end_val)
|
||||
marker = Term(f"{start_val}:{end_val}", field=marker_field, is_not=negated)
|
||||
marker._is_range_end = True
|
||||
if negated:
|
||||
result.negated_date_ranges.add(field)
|
||||
return [marker]
|
||||
|
||||
# Non-DP range or no field → plain text
|
||||
# Non-date range or no field → plain text
|
||||
txt = f"{start_val}:{end_val}"
|
||||
if field:
|
||||
txt = f"{txt}[{field}]"
|
||||
@@ -364,7 +538,7 @@ def is_pubmed_syntax(query: str) -> bool:
|
||||
return False
|
||||
if re.search(r'\[(' + '|'.join(_ALL_FIELD_TAGS) + r')\]', query, re.IGNORECASE):
|
||||
return True
|
||||
if re.search(r'\b(AND|OR|NOT)\b', query):
|
||||
if re.search(r'\b(AND|OR|NOT)\b', query, re.IGNORECASE):
|
||||
return True
|
||||
return False
|
||||
|
||||
@@ -378,6 +552,9 @@ def parse_pubmed_query(query: str) -> ParsedPubmedQuery:
|
||||
return ParsedPubmedQuery()
|
||||
|
||||
try:
|
||||
# 将 YYYY/MM/DD 格式的日期分隔符统一为 YYYY-MM-DD，使 tokeniser 正确识别为 DATE
|
||||
import re as _re
|
||||
query = _re.sub(r'(\d{4})/(\d{2})/(\d{2})', r'\1-\2-\3', query)
|
||||
tokens = tokenise(query)
|
||||
parser = PubmedQueryParser(tokens)
|
||||
return parser.parse()
|
||||
@@ -392,7 +569,9 @@ def extract_pubmed_query_for_prisma(query: str) -> tuple[str, list[str]]:
|
||||
(normalized_query, mesh_terms_used)
|
||||
"""
|
||||
parsed = parse_pubmed_query(query)
|
||||
mesh_used = list(set(parsed.mesh_terms + parsed.majr_terms))
|
||||
mesh_used = list(set(
|
||||
[t.text for t in parsed.mesh_terms] + [t.text for t in parsed.majr_terms]
|
||||
))
|
||||
mesh_used.sort()
|
||||
|
||||
# 标准化：统一字段大写
|
||||
|
||||
Reference in New Issue
Block a user