Index

A

abs_url (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) ACTIVE (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute) add_task_to_queue() (in module shared.database.operations.queue) (in module shared.db) agent.browsing.manual.manual module, [1] agent.browsing.manual.sources.base module, [1] agent.browsing.manual.sources.github module, [1] agent.browsing.manual.sources.google_scholar module, [1] agent.browsing.manual.sources.pubmed module, [1] agent.manager module agent.pipeline.analyze module, [1] agent.pipeline.decision module, [1] agent.pipeline.formatting module, [1] agent.pipeline.models module, [1] agent.pipeline.pipeline module, [1]

agent.pipeline.ranking module, [1] agent.pipeline.search module, [1] agent.pipeline.strategy module agent.pipeline.utils module, [1] agent_id (agent.manager.RuntimeConfig attribute) AgentStatus (class in shared.database.models) (class in shared.db) AnalysisAgentOutput (class in agent.pipeline.models), [1] AnalysisInput (class in agent.pipeline.models), [1] AnalysisResult (class in agent.pipeline.models), [1] analyze_candidates() (in module agent.pipeline.analyze), [1] analyzed (agent.pipeline.models.PipelineOutput attribute), [1] (api.app.RunResponse attribute) api.app module api_url (agent.browsing.manual.sources.github.GitHubRepoBrowser attribute), [1] arxiv_id (agent.pipeline.models.PaperCandidate attribute), [1] (api.app.PaperSummary attribute) arxiv_search() (in module agent.pipeline.search), [1] ArxivBrowser (class in agent.browsing.manual.manual), [1] ArxivPaper (class in shared.arxiv_parser) (class in shared.database.models) (class in shared.db) ArxivParser (class in shared.arxiv_parser) authors (shared.arxiv_parser.ArxivPaper attribute)

B

Base (class in shared.database.models) (class in shared.db) bm25_score (agent.pipeline.models.PaperCandidate attribute), [1] bot.handlers.general module bot.handlers.notifications.handlers module

bot.handlers.notifications.service module bot.handlers.task module bot.main module bot.utils module

C

cancel_task_creation() (in module bot.handlers.task) CANCELLED (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute) candidate (agent.pipeline.models.AnalysisInput attribute), [1] (agent.pipeline.models.AnalysisResult attribute), [1] categories (agent.pipeline.models.GeneratedQuery attribute), [1] (agent.pipeline.models.PipelineTask attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) check_new_analyses() (in module bot.handlers.notifications.service) check_rate_limit() (in module shared.database.operations.rate_limit) (in module shared.db) check_user_can_create_task() (in module shared.database.operations.user) (in module shared.db) collect_candidates() (in module agent.pipeline.search), [1] command_create_task() (in module bot.handlers.task) command_help_handler() (in module bot.handlers.general) command_history_handler() (in module bot.handlers.task) command_set_group_handler() (in module bot.handlers.notifications.handlers) command_set_notification_handler() (in module bot.handlers.notifications.handlers) command_start_handler() (in module bot.handlers.general) command_status_handler() (in module bot.handlers.task) command_unset_group_handler() (in module bot.handlers.notifications.handlers) comment (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) complete_task_processing() (in module shared.database.operations.integration) (in module shared.db)

COMPLETED (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute) contextual_reasoning (agent.pipeline.models.AnalysisAgentOutput attribute), [1] (agent.pipeline.models.AnalysisResult attribute), [1] count_analyses_for_user() (in module shared.database.operations.agent) (in module shared.db) count_relevant_analyses_for_user() (in module shared.database.operations.agent) (in module shared.db) create_arxiv_paper() (in module shared.database.operations.paper) (in module shared.db) create_paper_analysis() (in module shared.database.operations.paper) (in module shared.db) create_research_topic() (in module shared.database.operations.legacy) (in module shared.db) create_research_topic_for_user_task() (in module shared.database.operations.integration) (in module shared.db) create_search_query() (in module shared.database.operations.search) (in module shared.db) create_task() (in module shared.database.operations.generic_task) (in module shared.db) create_task_for_user() (in module bot.handlers.task) create_user_task() (in module shared.database.operations.integration) (in module shared.db) create_user_task_with_queue() (in module shared.database.operations.task) (in module shared.db) created_at (shared.event_system.Event attribute) cut_text() (in module bot.utils)

D

data (shared.event_system.Event attribute) deactivate_user_tasks() (in module shared.database.operations.task) (in module shared.db) deactivate_user_topics() (in module shared.database.operations.legacy) (in module shared.db)

DecisionReport (class in agent.pipeline.models), [1] doi (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) download_paper() (in module shared.arxiv_parser) download_pdf() (shared.arxiv_parser.ArxivParser method) dry_run (agent.manager.RuntimeConfig attribute)

E

ensure_connection() (in module shared.database.connection) (in module shared.db) escape_html() (in module bot.utils) Event (class in shared.event_system)

event_type (shared.event_system.Event attribute) EventType (class in shared.event_system) extra (agent.browsing.manual.sources.base.SearchItem attribute), [1] extract_text_from_pdf() (shared.arxiv_parser.ArxivParser method)

F

FAILED (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute) Finding (class in shared.database.models) (class in shared.db)

format_time_estimate() (in module bot.handlers.task) FREE (shared.database.enums.UserPlan attribute) (shared.db.UserPlan attribute)

G

generate_query_plan() (in module agent.pipeline.strategy) generated_queries (agent.pipeline.models.PipelineOutput attribute), [1] (api.app.RunResponse attribute) GeneratedQuery (class in agent.pipeline.models), [1] get() (agent.browsing.manual.manual.ArxivBrowser method), [1] get_active_topic_by_user() (in module shared.database.operations.legacy) (in module shared.db) get_agent_model() (in module shared.llm) get_agent_status() (in module shared.database.operations.agent) (in module shared.db) get_analysis_with_entities() (in module shared.database.operations.paper) (in module shared.db) get_arxiv_paper_by_arxiv_id() (in module shared.database.operations.paper) (in module shared.db) get_logger() (in module shared.logging) get_most_recent_active_user_task() (in module shared.database.operations.task) (in module shared.db) get_multimodal_model() (in module shared.llm) get_next_queued_task() (in module shared.database.operations.integration) (in module shared.db) get_next_task_from_queue() (in module shared.database.operations.queue) (in module shared.db) get_or_create_task_statistics() (in module shared.database.operations.task_statistics) (in module shared.db)

get_or_create_user() (in module shared.database.operations.user) (in module shared.db) get_or_create_user_settings() (in module shared.database.operations.legacy) (in module shared.db) get_paper() (in module shared.arxiv_parser) get_paper_by_id() (shared.arxiv_parser.ArxivParser method) get_paper_text_online() (shared.arxiv_parser.ArxivParser method) get_plan_display_name() (in module bot.handlers.task) get_recent_papers() (shared.arxiv_parser.ArxivParser method) get_status_emoji() (in module bot.handlers.task) get_target_chat_id() (in module bot.handlers.notifications.service) get_task() (in module shared.database.operations.generic_task) (in module shared.db) get_topic_by_user_and_text() (in module shared.database.operations.legacy) (in module shared.db) get_user_settings() (in module shared.database.operations.legacy) (in module shared.db) get_user_task_results() (in module shared.database.operations.integration) (in module shared.db) get_user_tasks() (in module shared.database.operations.task) (in module shared.db) github_search() (in module agent.pipeline.search), [1] GitHubRepoBrowser (class in agent.browsing.manual.sources.github), [1] GoogleScholarBrowser (class in agent.browsing.manual.sources.google_scholar), [1]

H

has_paper_analysis() (in module shared.database.operations.paper) (in module shared.db)

health() (in module api.app) history_back_to_list() (in module bot.handlers.task) html (agent.pipeline.models.TelegramSummary attribute), [1]

I

id (shared.arxiv_parser.ArxivPaper attribute) init_db() (in module shared.database.connection) (in module shared.db) initialize_database() (in module shared.db) item_id (agent.browsing.manual.sources.base.SearchItem attribute), [1]

iter_all() (agent.browsing.manual.manual.ArxivBrowser method), [1] (agent.browsing.manual.sources.base.ManualSource method), [1] (agent.browsing.manual.sources.github.GitHubRepoBrowser method), [1] (agent.browsing.manual.sources.google_scholar.GoogleScholarBrowser method), [1] (agent.browsing.manual.sources.pubmed.PubMedBrowser method), [1]

J

journal_ref (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute)

K

key_fragments (agent.pipeline.models.AnalysisAgentOutput attribute), [1] (agent.pipeline.models.AnalysisResult attribute), [1]

L

link (api.app.PaperSummary attribute) link_analysis_to_user_task() (in module shared.database.operations.integration) (in module shared.db) list_active_queries_for_task() (in module shared.database.operations.search) (in module shared.db) list_active_topics() (in module shared.database.operations.legacy) (in module shared.db) list_active_user_tasks() (in module shared.database.operations.task) (in module shared.db)

list_completed_tasks_since() (in module shared.database.operations.generic_task) (in module shared.db) list_new_analyses_since() (in module shared.database.operations.paper) (in module shared.db) list_pending_tasks() (in module shared.database.operations.generic_task) (in module shared.db) list_recent_analyses_for_user() (in module shared.database.operations.agent) (in module shared.db) list_user_tasks() (in module shared.database.operations.task) (in module shared.db)

M

main() (in module agent.manager) (in module bot.main) make_decision_and_report() (in module agent.pipeline.decision), [1] ManualSource (class in agent.browsing.manual.sources.base), [1] mark_analysis_notified() (in module shared.database.operations.paper) (in module shared.db) mark_analysis_queued() (in module shared.database.operations.paper) (in module shared.db) mark_task_completed() (in module shared.database.operations.generic_task) (in module shared.db) mark_task_failed() (in module shared.database.operations.generic_task) (in module shared.db) mark_task_sent() (in module shared.database.operations.generic_task) (in module shared.db) Message (class in shared.database.models) MESSAGE_RECEIVED (shared.event_system.EventType attribute) module agent.browsing.manual.manual, [1] agent.browsing.manual.sources.base, [1] agent.browsing.manual.sources.github, [1] agent.browsing.manual.sources.google_scholar, [1] agent.browsing.manual.sources.pubmed, [1] agent.manager agent.pipeline.analyze, [1] agent.pipeline.decision, [1] agent.pipeline.formatting, [1] agent.pipeline.models, [1] agent.pipeline.pipeline, [1] agent.pipeline.ranking, [1] agent.pipeline.search, [1] agent.pipeline.strategy agent.pipeline.utils, [1] api.app bot.handlers.general bot.handlers.notifications.handlers bot.handlers.notifications.service bot.handlers.task bot.main bot.utils shared.arxiv_parser shared.database.connection shared.database.enums shared.database.models shared.database.operations.agent shared.database.operations.generic_task shared.database.operations.integration shared.database.operations.legacy shared.database.operations.paper shared.database.operations.queue shared.database.operations.rate_limit shared.database.operations.search shared.database.operations.task shared.database.operations.task_statistics shared.database.operations.user shared.db shared.event_system shared.llm shared.logging

N

notes (agent.pipeline.models.QueryPlan attribute), [1]

O

overall_score (agent.pipeline.models.ScoredAnalysis attribute), [1]

P

paginate_results() (in module agent.browsing.manual.sources.base), [1] PaperAnalysis (class in shared.database.models) (class in shared.db) PaperCandidate (class in agent.pipeline.models), [1] PaperSummary (class in api.app) PAUSED (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute) pdf_url (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) PipelineOutput (class in agent.pipeline.models), [1] PipelineTask (class in agent.pipeline.models), [1] PipelineTaskRequest (class in api.app)

poll_seconds (agent.manager.RuntimeConfig attribute) PREMIUM (shared.database.enums.UserPlan attribute) (shared.db.UserPlan attribute) primary_category (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) process_completed_task() (in module bot.handlers.notifications.service) process_task_description() (in module bot.handlers.task) PROCESSING (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute) published (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) pubmed_search() (in module agent.pipeline.search), [1] PubMedBrowser (class in agent.browsing.manual.sources.pubmed), [1]

Q

query (agent.pipeline.models.PipelineTask attribute), [1] query_must_not_be_empty() (agent.pipeline.models.PipelineTask method), [1] query_text (agent.pipeline.models.GeneratedQuery attribute), [1]

QueryPlan (class in agent.pipeline.models), [1] QUEUED (shared.database.enums.TaskStatus attribute) (shared.db.TaskStatus attribute)

R

rank_candidates() (in module agent.pipeline.ranking), [1] rate_limit_check() (in module bot.handlers.task) RateLimitRecord (class in shared.database.models) (class in shared.db) rationale (agent.pipeline.models.GeneratedQuery attribute), [1] reasoning (agent.pipeline.models.ScoredAnalysis attribute), [1] record_finding() (in module shared.database.operations.search) (in module shared.db) relevance (agent.pipeline.models.AnalysisAgentOutput attribute), [1] (agent.pipeline.models.AnalysisResult attribute), [1] (api.app.PaperSummary attribute) remove_html_tags() (in module bot.utils) report_text (agent.pipeline.models.DecisionReport attribute), [1] (agent.pipeline.models.PipelineOutput attribute), [1] (api.app.RunResponse attribute)

ResearchTopic (class in shared.database.models) (class in shared.db) reset_daily_counters_if_needed() (in module shared.database.operations.user) (in module shared.db) RESPONSE_READY (shared.event_system.EventType attribute) result (agent.pipeline.models.ScoredAnalysis attribute), [1] retry_async() (in module agent.pipeline.utils), [1] run() (in module api.app) run_pipeline() (in module agent.pipeline.pipeline), [1] run_pipeline_sync() (in module agent.pipeline.pipeline), [1] RunResponse (class in api.app) RuntimeConfig (class in agent.manager)

S

scholar_search() (in module agent.pipeline.search), [1] score_result() (in module agent.pipeline.decision), [1] ScoredAnalysis (class in agent.pipeline.models), [1] search() (agent.browsing.manual.manual.ArxivBrowser method), [1] (agent.browsing.manual.sources.base.ManualSource method), [1] (agent.browsing.manual.sources.github.GitHubRepoBrowser method), [1] (agent.browsing.manual.sources.google_scholar.GoogleScholarBrowser method), [1] (agent.browsing.manual.sources.pubmed.PubMedBrowser method), [1] search_all() (agent.browsing.manual.manual.ArxivBrowser method), [1] (agent.browsing.manual.sources.base.ManualSource method), [1] (agent.browsing.manual.sources.github.GitHubRepoBrowser method), [1] (agent.browsing.manual.sources.google_scholar.GoogleScholarBrowser method), [1] (agent.browsing.manual.sources.pubmed.PubMedBrowser method), [1] search_by_author() (shared.arxiv_parser.ArxivParser method) search_by_category() (shared.arxiv_parser.ArxivParser method) search_papers() (in module shared.arxiv_parser) (shared.arxiv_parser.ArxivParser method) SearchItem (class in agent.browsing.manual.sources.base), [1] SearchQuery (class in shared.database.models) (class in shared.db) select_top() (in module agent.pipeline.decision), [1] selected (api.app.RunResponse attribute) send_analysis_report() (in module bot.handlers.notifications.service) send_message_to_target_chat() (in module bot.handlers.notifications.service) setup_logger() (in module shared.logging) shared.arxiv_parser module shared.database.connection module shared.database.enums module shared.database.models module shared.database.operations.agent module shared.database.operations.generic_task module shared.database.operations.integration module shared.database.operations.legacy module

shared.database.operations.paper module shared.database.operations.queue module shared.database.operations.rate_limit module shared.database.operations.search module shared.database.operations.task module shared.database.operations.task_statistics module shared.database.operations.user module shared.db module shared.event_system module shared.llm module shared.logging module should_notify (agent.pipeline.models.DecisionReport attribute), [1] (agent.pipeline.models.PipelineOutput attribute), [1] (api.app.RunResponse attribute) show_recent_analyses_all() (in module bot.handlers.task) show_task_history() (in module bot.handlers.task) simplify_for_layperson() (in module bot.handlers.notifications.service) snippet (agent.browsing.manual.sources.base.SearchItem attribute), [1] source (agent.pipeline.models.GeneratedQuery attribute), [1] start_interactive_task_creation() (in module bot.handlers.task) start_task_processing() (in module shared.database.operations.integration) (in module shared.db) summary (agent.pipeline.models.AnalysisAgentOutput attribute), [1] (agent.pipeline.models.AnalysisResult attribute), [1] (agent.pipeline.models.PaperCandidate attribute), [1] (api.app.PaperSummary attribute) (shared.arxiv_parser.ArxivPaper attribute) swap_user_active_topics() (in module shared.database.operations.agent) (in module shared.db)

T

task (agent.pipeline.models.PipelineOutput attribute), [1] (api.app.RunResponse attribute) Task (class in shared.database.models) TASK_COMPLETED (shared.event_system.EventType attribute) TASK_CREATED (shared.event_system.EventType attribute) TASK_FAILED (shared.event_system.EventType attribute) TaskCreationStates (class in bot.handlers.task) TaskQueue (class in shared.database.models) (class in shared.db) TaskStatistics (class in shared.database.models) (class in shared.db)

TaskStatus (class in shared.database.enums) (class in shared.db) TelegramSummary (class in agent.pipeline.models), [1] test_user_id (agent.manager.RuntimeConfig attribute) time_from (agent.pipeline.models.GeneratedQuery attribute), [1] time_to (agent.pipeline.models.GeneratedQuery attribute), [1] title (agent.browsing.manual.sources.base.SearchItem attribute), [1] (agent.pipeline.models.PaperCandidate attribute), [1] (api.app.PaperSummary attribute) (shared.arxiv_parser.ArxivPaper attribute) to_telegram_html() (in module agent.pipeline.formatting), [1] to_telegram_html_agent() (in module agent.pipeline.formatting), [1]

U

update_agent_status() (in module shared.database.operations.agent) (in module shared.db) update_queue_positions() (in module shared.database.operations.queue) (in module shared.db) update_search_query_stats() (in module shared.database.operations.search) (in module shared.db) update_task_statistics() (in module shared.database.operations.task_statistics) (in module shared.db) update_user_settings() (in module shared.database.operations.legacy) (in module shared.db) update_user_task_status() (in module shared.database.operations.task) (in module shared.db) update_user_task_status_for_user() (in module shared.database.operations.task) (in module shared.db)

updated (agent.pipeline.models.PaperCandidate attribute), [1] (shared.arxiv_parser.ArxivPaper attribute) upgrade_user_plan() (in module shared.database.operations.user) (in module shared.db) url (agent.browsing.manual.sources.base.SearchItem attribute), [1] User (class in shared.database.models) (class in shared.db) UserPlan (class in shared.database.enums) (class in shared.db) UserSettings (class in shared.database.models) (class in shared.db) UserTask (class in shared.database.models) (class in shared.db)