Index

A

abstracts() (in module paper_firehose) AbstractSource (class in paper_firehose.core.abstract_source)

add_topic() (in module paper_firehose.commands.topic_cmd) apply_filters() (paper_firehose.processors.feed_processor.FeedProcessor method) available() (paper_firehose.processors.st_ranker.STRanker method)

B

backup_important_databases() (paper_firehose.core.database.DatabaseManager method)

C

check_unknown_keys() (paper_firehose.core.config.ConfigManager method) clean_abstract_for_db() (in module paper_firehose.core.text_utils) clear_current_db() (paper_firehose.core.database.DatabaseManager method) close() (paper_firehose.core.http_client.RetryableHTTPClient method) close_all_connections() (paper_firehose.core.database.DatabaseManager method)

CommandContext (class in paper_firehose.core.command_context) compute_entry_id() (paper_firehose.core.database.DatabaseManager method) ConfigManager (class in paper_firehose.core.config) crossref_pass() (in module paper_firehose.processors.abstract_fetcher) CrossrefSource (class in paper_firehose.core.abstract_source)

D

DatabaseManager (class in paper_firehose.core.database)

E

email() (in module paper_firehose) EmailRenderer (class in paper_firehose.processors.emailer) ensure_data_dir() (in module paper_firehose.core.paths)

ensure_local_model() (in module paper_firehose.core.model_manager) export_recent() (in module paper_firehose) extract_doi_from_entry() (in module paper_firehose.core.doi_utils) extract_doi_from_json() (in module paper_firehose.core.doi_utils)

F

fallback_pass() (in module paper_firehose.processors.abstract_fetcher) FeedProcessor (class in paper_firehose.processors.feed_processor) fetch_abstract() (paper_firehose.core.abstract_source.AbstractSource method) (paper_firehose.core.abstract_source.CrossrefSource method) (paper_firehose.core.abstract_source.OpenAlexSource method) (paper_firehose.core.abstract_source.PubMedSource method) (paper_firehose.core.abstract_source.SemanticScholarSource method)

fetch_feeds() (paper_firehose.processors.feed_processor.FeedProcessor method) fill_arxiv_summaries() (in module paper_firehose.processors.abstract_fetcher) filter() (in module paper_firehose) find_doi_in_text() (in module paper_firehose.core.doi_utils)

G

generate_html() (in module paper_firehose) generate_html_for_topic_from_database() (paper_firehose.processors.html_generator.HTMLGenerator method) generate_html_from_database() (paper_firehose.processors.html_generator.HTMLGenerator method) generate_pqa_summarized_html_from_database() (paper_firehose.processors.html_generator.HTMLGenerator method) generate_ranked_html_from_database() (paper_firehose.processors.html_generator.HTMLGenerator method) get_available_topics() (paper_firehose.core.config.ConfigManager method) get_biomedical_sources() (in module paper_firehose.core.abstract_source) get_connection() (paper_firehose.core.database.DatabaseManager method) get_crossref_abstract() (in module paper_firehose.core.apis) (in module paper_firehose.core.apis.crossref_client) get_current_entries() (paper_firehose.core.database.DatabaseManager method) get_data_dir() (in module paper_firehose.core.paths) get_default() (paper_firehose.core.command_context.CommandContext method) get_default_sources() (in module paper_firehose.core.abstract_source)

get_enabled_feeds() (paper_firehose.core.config.ConfigManager method) get_entries_by_criteria() (paper_firehose.core.database.DatabaseManager method) get_nested_default() (paper_firehose.core.command_context.CommandContext method) get_openalex_abstract() (in module paper_firehose.core.apis) (in module paper_firehose.core.apis.openalex_client) get_priority_journals() (paper_firehose.core.config.ConfigManager method) get_pubmed_abstract_by_doi() (in module paper_firehose.core.apis) (in module paper_firehose.core.apis.pubmed_client) get_semantic_scholar_abstract() (in module paper_firehose.core.apis) (in module paper_firehose.core.apis.semantic_scholar_client) get_system_dir() (in module paper_firehose.core.paths) get_system_path() (in module paper_firehose.core.paths) get_topics() (paper_firehose.core.command_context.CommandContext method) get_value() (in module paper_firehose.commands.config_cmd) get_with_retry() (paper_firehose.core.http_client.RetryableHTTPClient method)

H

has_model_files() (in module paper_firehose.core.model_manager)

html() (in module paper_firehose) HTMLGenerator (class in paper_firehose.processors.html_generator)

I

is_new_entry() (paper_firehose.core.database.DatabaseManager method) iter_history_entries() (paper_firehose.core.database.DatabaseManager method)

iter_targets() (in module paper_firehose.processors.abstract_fetcher) (paper_firehose.core.database.DatabaseManager method)

L

list_topics() (in module paper_firehose.commands.topic_cmd) load_config() (paper_firehose.core.config.ConfigManager method)

load_topic_config() (paper_firehose.core.command_context.CommandContext method) (paper_firehose.core.config.ConfigManager method)

M

module paper_firehose paper_firehose.cli paper_firehose.commands paper_firehose.commands.abstracts paper_firehose.commands.config_cmd paper_firehose.commands.email_list paper_firehose.commands.export_recent paper_firehose.commands.filter paper_firehose.commands.generate_html paper_firehose.commands.migrate_db paper_firehose.commands.pqa_summary paper_firehose.commands.query paper_firehose.commands.rank paper_firehose.commands.status paper_firehose.commands.topic_cmd paper_firehose.core paper_firehose.core.abstract_source paper_firehose.core.apis paper_firehose.core.apis.crossref_client paper_firehose.core.apis.openalex_client paper_firehose.core.apis.pubmed_client paper_firehose.core.apis.semantic_scholar_client paper_firehose.core.command_context paper_firehose.core.command_utils paper_firehose.core.config paper_firehose.core.database paper_firehose.core.doi_utils paper_firehose.core.exit_codes paper_firehose.core.http_client paper_firehose.core.model_manager paper_firehose.core.paths paper_firehose.core.text_utils paper_firehose.processors paper_firehose.processors.abstract_fetcher paper_firehose.processors.emailer paper_firehose.processors.feed_processor paper_firehose.processors.html_generator paper_firehose.processors.st_ranker

N

names_match() (in module paper_firehose.core.text_utils)

normalize_name() (in module paper_firehose.core.text_utils)

O

OpenAlexSource (class in paper_firehose.core.abstract_source)

P

paper_firehose module paper_firehose.cli module paper_firehose.commands module paper_firehose.commands.abstracts module paper_firehose.commands.config_cmd module paper_firehose.commands.email_list module paper_firehose.commands.export_recent module paper_firehose.commands.filter module paper_firehose.commands.generate_html module paper_firehose.commands.migrate_db module paper_firehose.commands.pqa_summary module paper_firehose.commands.query module paper_firehose.commands.rank module paper_firehose.commands.status module paper_firehose.commands.topic_cmd module paper_firehose.core module paper_firehose.core.abstract_source module paper_firehose.core.apis module paper_firehose.core.apis.crossref_client module paper_firehose.core.apis.openalex_client module paper_firehose.core.apis.pubmed_client module

paper_firehose.core.apis.semantic_scholar_client module paper_firehose.core.command_context module paper_firehose.core.command_utils module paper_firehose.core.config module paper_firehose.core.database module paper_firehose.core.doi_utils module paper_firehose.core.exit_codes module paper_firehose.core.http_client module paper_firehose.core.model_manager module paper_firehose.core.paths module paper_firehose.core.text_utils module paper_firehose.processors module paper_firehose.processors.abstract_fetcher module paper_firehose.processors.emailer module paper_firehose.processors.feed_processor module paper_firehose.processors.html_generator module paper_firehose.processors.st_ranker module paperqa_summary() (in module paper_firehose) PaperQASession (class in paper_firehose.commands.pqa_summary) parse_name_parts() (in module paper_firehose.core.text_utils) pqa_summary() (in module paper_firehose) process_text() (paper_firehose.processors.html_generator.HTMLGenerator method) PubMedSource (class in paper_firehose.core.abstract_source) purge() (in module paper_firehose) (in module paper_firehose.commands.filter) purge_old_entries() (paper_firehose.core.database.DatabaseManager method)

Q

query() (in module paper_firehose)

query_entries() (paper_firehose.core.database.DatabaseManager method)

R

rank() (in module paper_firehose) render_full_email() (paper_firehose.processors.emailer.EmailRenderer method) render_ranked_entries() (paper_firehose.processors.emailer.EmailRenderer method) render_topic_digest() (paper_firehose.processors.emailer.EmailRenderer method) resolve_data_dir() (in module paper_firehose.core.paths) resolve_data_file() (in module paper_firehose.core.paths) resolve_data_path() (in module paper_firehose.core.paths) resolve_topics() (in module paper_firehose.core.command_utils) RetryableHTTPClient (class in paper_firehose.core.http_client)

run() (in module paper_firehose.commands.abstracts) (in module paper_firehose.commands.email_list) (in module paper_firehose.commands.export_recent) (in module paper_firehose.commands.filter) (in module paper_firehose.commands.generate_html) (in module paper_firehose.commands.migrate_db) (in module paper_firehose.commands.pqa_summary) (in module paper_firehose.commands.query) (in module paper_firehose.commands.rank) (in module paper_firehose.commands.status)

S

save_all_entries_to_dedup_db() (paper_firehose.processors.feed_processor.FeedProcessor method) save_current_entry() (paper_firehose.core.database.DatabaseManager method) save_feed_entry() (paper_firehose.core.database.DatabaseManager method) save_matched_entry() (paper_firehose.core.database.DatabaseManager method) score_entries() (paper_firehose.processors.st_ranker.STRanker method) search_crossref_abstract_by_title() (in module paper_firehose.core.apis) (in module paper_firehose.core.apis.crossref_client) SemanticScholarSource (class in paper_firehose.core.abstract_source) send() (paper_firehose.processors.emailer.SMTPSender method)

set_value() (in module paper_firehose.commands.config_cmd) show() (in module paper_firehose.commands.config_cmd) show_topic() (in module paper_firehose.commands.topic_cmd) SMTPSender (class in paper_firehose.processors.emailer) status() (in module paper_firehose) STRanker (class in paper_firehose.processors.st_ranker) strip_accents() (in module paper_firehose.core.text_utils) strip_jats() (in module paper_firehose.core.text_utils) summarize_pdf() (paper_firehose.commands.pqa_summary.PaperQASession method)

T

try_abstract_sources() (in module paper_firehose.processors.abstract_fetcher)

try_publisher_apis() (in module paper_firehose.processors.abstract_fetcher)

U

update_abstracts_batch() (paper_firehose.core.database.DatabaseManager method) update_entry_rank() (paper_firehose.core.database.DatabaseManager method)

update_history_abstracts_batch() (paper_firehose.core.database.DatabaseManager method) update_history_rank() (paper_firehose.core.database.DatabaseManager method)

V

validate() (in module paper_firehose.commands.config_cmd)

validate_config() (paper_firehose.core.config.ConfigManager method)