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Functions1,438 in github.com/Jennyee1/AcademicAgent

⨍ Functions 1,438◇ Types & classes 133↳ Endpoints 6

↓ 1,112 callersMethodget

(self, key: str, default: Any = None)

src/runtime/workflow.py:68

↓ 92 callersMethodon

lib/tom-select/tom-select.complete.min.js:6

↓ 90 callersFunctionKd

lib/vis-9.1.2/vis-network.min.js:26

↓ 90 callersFunctionYd

lib/vis-9.1.2/vis-network.min.js:26

↓ 69 callersMethodadd

(self, step: WorkflowStep)

src/runtime/workflow.py:141

↓ 62 callersFunctionAk

lib/vis-9.1.2/vis-network.min.js:26

↓ 47 callersFunctiono

lib/vis-9.1.2/vis-network.min.js:26

↓ 43 callersFunctiont

lib/vis-9.1.2/vis-network.min.js:26

↓ 39 callersFunctionQc

lib/vis-9.1.2/vis-network.min.js:26

↓ 38 callersFunction$d

lib/vis-9.1.2/vis-network.min.js:26

↓ 38 callersFunctionhm

lib/vis-9.1.2/vis-network.min.js:26

↓ 37 callersFunctionFu

lib/vis-9.1.2/vis-network.min.js:26

↓ 37 callersMethodf

lib/tom-select/tom-select.complete.min.js:146

↓ 36 callersFunctionKc

lib/vis-9.1.2/vis-network.min.js:26

↓ 34 callersFunctionr

lib/vis-9.1.2/vis-network.min.js:26

↓ 33 callersFunctionzk

lib/vis-9.1.2/vis-network.min.js:26

↓ 30 callersFunctionNk

lib/vis-9.1.2/vis-network.min.js:26

↓ 27 callersFunctionH

lib/tom-select/tom-select.complete.min.js:99

↓ 26 callersFunctionIS

lib/vis-9.1.2/vis-network.min.js:26

↓ 26 callersFunction_i

lib/vis-9.1.2/vis-network.min.js:26

↓ 26 callersFunctione

lib/vis-9.1.2/vis-network.min.js:26

↓ 26 callersFunctionpb

lib/vis-9.1.2/vis-network.min.js:26

↓ 26 callersMethodrun

执行整条 workflow。 reflector: 可选的 Reflector 实例； - reflector.should_retry(step_result_dict, attempt_count) -> bool - reflector

src/runtime/workflow.py:145

↓ 25 callersFunctionJc

lib/vis-9.1.2/vis-network.min.js:26

↓ 25 callersMethodfailure

( cls, tool: str, error: str, error_category: str = "tool_exception",

src/evaluation/adapters/base.py:38

↓ 24 callersFunctionP

lib/tom-select/tom-select.complete.min.js:83

↓ 24 callersFunctionh

lib/vis-9.1.2/vis-network.min.js:26

↓ 24 callersFunctionnm

lib/vis-9.1.2/vis-network.min.js:26

↓ 23 callersFunctionB

lib/tom-select/tom-select.complete.min.js:99

↓ 22 callersMethodexecute

( self, code: str, timeout: Optional[int] = None, skip_safety_check: bool = Fa

src/execution/sandbox.py:318

↓ 22 callersMethodlog_validation

记录一次验证 run。status: ok | warn | fail

src/recorder/refactor_recorder.py:208

↓ 22 callersMethodoff

lib/tom-select/tom-select.complete.min.js:6

↓ 21 callersFunctionP

lib/vis-9.1.2/vis-network.min.js:26

↓ 21 callersFunctionTn

lib/vis-9.1.2/vis-network.min.js:26

↓ 21 callersFunction_esc

scripts/build_spot_check_v2_html.py:21

↓ 21 callersMethodfrom_dict

从字典反序列化（容错：未知 node_type 不抛 ValueError，落到 OTHER 并 warn）

src/knowledge/schema.py:352

↓ 20 callersFunctionCh

lib/vis-9.1.2/vis-network.min.js:26

↓ 20 callersMethodset

(self, key: str, value: Any)

src/runtime/workflow.py:71

↓ 20 callersFunctiony

lib/tom-select/tom-select.complete.min.js:34

↓ 19 callersFunctioni

lib/vis-9.1.2/vis-network.min.js:26

↓ 19 callersFunctions

lib/vis-9.1.2/vis-network.min.js:26

↓ 19 callersMethodtrigger

lib/tom-select/tom-select.complete.min.js:8

↓ 18 callersMethodhook

lib/tom-select/tom-select.complete.min.js:298

↓ 18 callersFunctionsb

lib/vis-9.1.2/vis-network.min.js:26

↓ 18 callersFunctionw

lib/tom-select/tom-select.complete.min.js:74

↓ 17 callersMethodencode

(self, texts: list[str])

src/knowledge/semantic_index.py:83

↓ 17 callersFunctiong

lib/vis-9.1.2/vis-network.min.js:26

↓ 17 callersFunctionregister_tool

注册一个可被 WorkflowStep.tool 引用的 async callable。

src/runtime/workflow.py:41

↓ 17 callersMethodsearch

语义检索 top-k。

src/knowledge/semantic_index.py:190

↓ 16 callersFunctionC

lib/tom-select/tom-select.complete.min.js:78

↓ 16 callersFunctiona

lib/vis-9.1.2/vis-network.min.js:26

↓ 16 callersMethodadd_node

添加节点（自动去重合并）如果同 ID 节点已存在，合并其属性。返回节点 ID。

src/knowledge/graph_store.py:102

↓ 15 callersFunction_g

(gold: dict | None, key: str, default=None)

src/evaluation/metrics/__init__.py:64

↓ 15 callersMethodcheck_duplicate

三级去重检查，返回匹配的已有记录（如果存在）优先级：arXiv ID > DOI > 文件哈希 > 标题模糊匹配

src/core/paper_registry.py:225

↓ 15 callersMethoddestroy

lib/tom-select/tom-select.complete.min.js:294

↓ 15 callersFunctionn

lib/vis-9.1.2/vis-network.min.js:26

↓ 15 callersMethodnormalize

返回标准化标签。无命中则返回原 label（去首尾空白）。

src/knowledge/entity_linker.py:114

↓ 15 callersFunctionoe

lib/vis-9.1.2/vis-network.min.js:26

↓ 15 callersMethodsave

保存报告为 JSON + HTML 双格式 Returns: (json_path, html_path)

src/report/generator.py:208

↓ 15 callersFunctionwb

lib/vis-9.1.2/vis-network.min.js:26

↓ 14 callersFunctionHx

lib/vis-9.1.2/vis-network.min.js:26

↓ 14 callersMethodadd_edge

添加边（证据累积 + 冲突标记，Phase 2.3）合并语义： - 同 edge_id 已存在 → 把新 edge 的来源作为一条新 Evidence 追加， confidence 重算为 max(local) + 0

src/knowledge/graph_store.py:151

↓ 14 callersMethodclose

lib/tom-select/tom-select.complete.min.js:275

↓ 14 callersMethoddefine

lib/tom-select/tom-select.complete.min.js:116

↓ 14 callersMethodextract_full_text

提取全文文本。 Phase 3.1 (2026-05-20): fix_columns=True 时默认走 _extract_page_text_columned，自动按 bbox 列序重组，解决 IEEE/ACM 双栏论

src/core/pdf_parser.py:158

↓ 13 callersFunctionPk

lib/vis-9.1.2/vis-network.min.js:26

↓ 13 callersMethodadd_node

增量加一条；调用方负责后续 save_cache()。

src/knowledge/semantic_index.py:183

↓ 13 callersMethodclear

lib/tom-select/tom-select.complete.min.js:277

↓ 13 callersMethodget_node

根据 ID 获取节点

src/knowledge/graph_store.py:248

↓ 13 callersFunctionrich_text

构造 Notion rich_text 数组。超长自动分段（≤1900 char/段）。 color: Notion 支持 "default" / "red" / "blue" / ... / "red_background" / ...

src/recorder/block_builders.py:28

↓ 12 callersFunctionLv

lib/vis-9.1.2/vis-network.min.js:26

↓ 12 callersFunctionSm

lib/vis-9.1.2/vis-network.min.js:26

↓ 12 callersFunction_esc

scripts/build_spot_check_html.py:18

↓ 12 callersFunction_norm_set

src/evaluation/metrics/capability.py:16

↓ 12 callersFunction_normalize_label

与 src/knowledge/schema.py KGNode._normalize_label 一致：小写 + 去特殊字符 + 空格转下划线。

src/evaluation/metrics/kg.py:16

↓ 12 callersMethodgenerate_learning_path

生成个性化学习路径 Args: focus_area: 可选，聚焦的领域关键词（如 "agent memory"） max_items: 最大推荐条目数 Returns: L

src/knowledge/graph_analyzer.py:623

↓ 12 callersFunctionpm

lib/vis-9.1.2/vis-network.min.js:26

↓ 12 callersFunctionq

lib/tom-select/tom-select.complete.min.js:94

↓ 11 callersFunctionload_preferences

读取偏好，缺失字段用默认值补齐（不写盘）。

src/runtime/preferences.py:46

↓ 10 callersFunction$y

lib/vis-9.1.2/vis-network.min.js:26

↓ 10 callersMethodcompute_importance

计算所有节点的重要性评分综合 4 个指标： 1. PageRank（全局重要性） 2. 度中心性（直接连接数） 3. 入度（被引用/使用次数） 4. 介数中心性（知识桥梁作用）【

src/knowledge/graph_analyzer.py:202

↓ 10 callersFunctioni

lib/tom-select/tom-select.complete.min.js:85

↓ 10 callersMethodparse_sections

将全文分割为标准化章节 Returns: dict: key = 章节名, value = 章节文本例如 {"abstract": "...", "method": "...", "experiments": ".

src/core/multimodal.py:443

↓ 10 callersMethodrefreshState

lib/tom-select/tom-select.complete.min.js:262

↓ 10 callersMethodto_dict

src/evaluation/schema.py:137

↓ 9 callersFunctionRv

lib/vis-9.1.2/vis-network.min.js:26

↓ 9 callersFunctioncheck_code_safety

静态扫描危险模式（黑名单，仅警告不拦截）。

src/execution/sandbox.py:168

↓ 9 callersFunctiond

lib/vis-9.1.2/vis-network.min.js:26

↓ 9 callersMethodload

lib/tom-select/tom-select.complete.min.js:184

↓ 9 callersMethodregister_paper

注册新论文如果检测到重复，返回已有记录而不是重复注册。注册后自动保存到 JSON。

src/core/paper_registry.py:305

↓ 8 callersFunctionCm

lib/vis-9.1.2/vis-network.min.js:26

↓ 8 callersFunctionHh

lib/vis-9.1.2/vis-network.min.js:26

↓ 8 callersFunctionMm

lib/vis-9.1.2/vis-network.min.js:26

↓ 8 callersFunctionS

lib/tom-select/tom-select.complete.min.js:78

↓ 8 callersFunction_norm

scripts/apply_gold_reviews.py:39

↓ 8 callersFunction_normalize

src/evaluation/metrics/retrieval_advanced.py:37

↓ 8 callersFunction_truncate

安全截断文本，处理 None

src/mcp_servers/paper_search.py:189

↓ 8 callersFunctionc

lib/tom-select/tom-select.complete.min.js:12

↓ 8 callersMethoddetect_knowledge_gaps

检测知识图谱中的盲区四种盲区类型： 1. foundation_gap (基础缺失): - PageRank 高（是核心概念）但属性稀疏（没有详细记录定义/描述） - 说明你知道这个概念存在，但没有深

src/knowledge/graph_analyzer.py:454

↓ 8 callersFunctionget_store

获取（或懒加载）指定 domain 的 store。路径策略： - 标准路径 data/kg_<domain>.json 存在 → 用它 - 否则若 domain=shared 且 legacy data/knowledge_graph.json 存在

src/mcp_servers/knowledge_graph.py:73

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