Index

Symbols

--add colrev-data command line option colrev-dedupe command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-screen command line option colrev-search command line option --add_abstracts_from_tei colrev-screen command line option --add_criterion colrev-screen command line option --all colrev-push command line option --apply colrev-pdf-prep-man command line option --batch_size colrev-pdf-prep command line option --copy-to-repo colrev-pdf-get command line option --cpu colrev-prep command line option --create_split colrev-prescreen command line option colrev-screen command line option --debug colrev-dedupe command line option colrev-prep command line option --delete_criterion colrev-screen command line option --delete_first_page colrev-pdf-prep-man command line option --dir colrev-pdfs command line option --discard colrev-pdf-get-man command line option colrev-pdf-prep-man command line option colrev-pdfs command line option --example colrev-init command line option --exclude colrev-prescreen command line option --export colrev-pdf-get-man command line option --export_format colrev-prescreen command line option --extract colrev-pdf-prep-man command line option --filter colrev-validate command line option --fix_errors colrev-dedupe command line option --force colrev-data command line option colrev-dedupe command line option colrev-distribute command line option colrev-init command line option colrev-load command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-pdfs command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-pull command line option colrev-push command line option colrev-retrieve command line option colrev-screen command line option colrev-search command line option colrev-validate command line option --id colrev-trace command line option --import_table colrev-prescreen command line option --include colrev-prescreen command line option --include_all colrev-prescreen command line option colrev-screen command line option --include_all_always colrev-prescreen command line option colrev-screen command line option --index colrev-env command line option --install colrev-env command line option --keep_ids colrev-load command line option colrev-prep command line option --languages colrev-prep-man command line option --light colrev-init command line option --merge colrev-dedupe command line option --params colrev-data command line option colrev-dedupe command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-screen command line option colrev-search command line option --path colrev-distribute command line option --polish colrev-prep command line option --project_only colrev-push command line option --properties colrev-validate command line option --pull colrev-env command line option --reading_heuristics colrev-data command line option --records_only colrev-push command line option --register colrev-env command line option --relink_pdfs colrev-pdf-get command line option --rename colrev-pdf-get command line option --reprocess colrev-pdf-prep command line option --rerun colrev-search command line option --selected colrev-search command line option --setup_custom_script colrev-data command line option colrev-pdf-get command line option colrev-pdf-prep command line option colrev-prep command line option colrev-prescreen command line option colrev-screen command line option colrev-search command line option --skip colrev-search command line option --skip_query colrev-load command line option --split colrev-prescreen command line option colrev-screen command line option --stats colrev-pdf-prep-man command line option colrev-prep-man command line option --status colrev-env command line option --tei colrev-pdf-prep command line option

--threshold colrev-validate command line option --type colrev-init command line option --unmerge colrev-dedupe command line option --unregister colrev-env command line option --update_colrev_pdf_ids colrev-pdf-prep command line option --update_package_list colrev-env command line option --verbose colrev-data command line option colrev-dedupe command line option colrev-distribute command line option colrev-env command line option colrev-load command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-pdfs command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-pull command line option colrev-push command line option colrev-retrieve command line option colrev-screen command line option colrev-search command line option colrev-status command line option colrev-validate command line option --view colrev-dedupe command line option colrev-search command line option -a colrev-data command line option colrev-dedupe command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-push command line option colrev-screen command line option colrev-search command line option -abstracts colrev-screen command line option -ac colrev-screen command line option -b colrev-pdf-prep command line option -bws colrev-search command line option -c colrev-pdf-get command line option -d colrev-dedupe command line option colrev-pdfs command line option colrev-prep command line option -dc colrev-screen command line option -dfp colrev-pdf-prep-man command line option -e colrev-pdf-get-man command line option colrev-prescreen command line option -f colrev-data command line option colrev-dedupe command line option, [1] colrev-distribute command line option colrev-init command line option colrev-load command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-pdfs command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-pull command line option colrev-push command line option colrev-retrieve command line option colrev-screen command line option colrev-search command line option colrev-validate command line option -gid colrev-dedupe command line option -i colrev-env command line option colrev-prescreen command line option -k colrev-load command line option colrev-prep command line option -l colrev-prep-man command line option -m colrev-dedupe command line option -p colrev-data command line option colrev-dedupe command line option colrev-distribute command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-push command line option colrev-screen command line option colrev-search command line option -r colrev-env command line option colrev-pdf-get command line option colrev-push command line option colrev-search command line option -s colrev-env command line option colrev-search command line option -scs colrev-data command line option colrev-pdf-get command line option colrev-pdf-prep command line option colrev-prep command line option colrev-prescreen command line option colrev-screen command line option colrev-search command line option -sq colrev-load command line option -u colrev-dedupe command line option -ur colrev-env command line option -v colrev-data command line option colrev-dedupe command line option colrev-distribute command line option colrev-env command line option colrev-load command line option colrev-pdf-get command line option colrev-pdf-get-man command line option colrev-pdf-prep command line option colrev-pdf-prep-man command line option colrev-pdfs command line option colrev-prep command line option colrev-prep-man command line option colrev-prescreen command line option colrev-pull command line option colrev-push command line option colrev-retrieve command line option colrev-screen command line option colrev-search command line option colrev-status command line option colrev-validate command line option

A

add() (SQLiteIndexTOC method) add_abstracts_from_tei() (Screen method) add_changes() (Dataset method) add_command() (SpecialHelpOrder method) add_criterion() (Screen method) add_endpoint() (SearchSourceInterface method) add_field_provenance() (PDFRecord method) (PrepRecord method) (Record method) add_field_provenance_note() (PDFRecord method) (PrepRecord method) (Record method) add_from_tei() (in module colrev.ops.colrev_pandas) add_most_likely_sources() (Search method) add_new_sources() (CLISourceAdder method) add_package_to_settings() (in module colrev.ui_cli.add_package_to_settings) add_provenance_all() (PDFRecord method) (PrepRecord method) (Record method)

add_record_to_feed() (SearchAPIFeed method) add_setting_changes() (Dataset method) add_source_and_search() (Search method) add_to_type_identifier_endpoint_dict() (Package method) add_update_record() (SearchAPIFeed method) Advisor (class in colrev.ops.advisor) align_provenance() (PDFRecord method) (PrepRecord method) (Record method) allow_extra_args (SpecialHelpOrder attribute) allow_interspersed_args (SpecialHelpOrder attribute) always_apply_changes (PrepInterface attribute) AppendOnlyViolation apply_merges() (Dedupe method) apply_pdf_prep_man() (PDFPrepMan method) Author (class in colrev.settings) AuthorNotInPDFChecker (class in colrev.record.qm.pdf_checkers.author_not_in_pdf)

B

behind_remote() (Dataset method)

BIBLoader (class in colrev.loader.bib) build_docker_image() (DockerManager class method)

C

callback (SpecialHelpOrder attribute) capitalize_entities() (in module colrev.record.record_prep) catch_exception() (in module colrev.ui_cli.cli) change_entrytype() (PDFRecord method) (PrepRecord method) (Record method) check_change_in_propagated_id() (Checker method) check_corrections_of_records() (Corrections method) check_docker_installed() (DockerManager class method) check_existing_unlinked_pdfs() (PDFGet method) check_fields() (Checker method) check_git_installed() (EnvironmentManager method) check_grobid_availability() (GrobidService method) check_operation_precondition() (ProcessModel class method) check_precondition() (CheckOperation method) (Data method) (Dedupe method) (Distribute method) (Load method) (Merge method) (Operation method) (PDFGet method) (PDFGetMan method) (PDFPrep method) (PDFPrepMan method) (Prep method) (PrepDebug method) (PrepMan method) (Prescreen method) (Pull method) (Push method) (Remove method) (Repare method) (Screen method) (Search method) (Status method) (Trace method) (Upgrade method) (Validate method) check_repo() (Checker method) (ReviewManager method) check_repo_basics() (Checker method) check_repo_extended() (Checker method) check_repository_setup() (Checker method) (ReviewManager method) check_sources() (Checker method) check_status_transitions() (Checker method) Checker (class in colrev.ops.checker) CheckOperation (class in colrev.ops.check) ci_supported (GeneralInterface attribute) CleanRepoRequiredError CLISourceAdder (class in colrev.ui_cli.detect_and_add_source) Clone (class in colrev.ops.clone) clone_git_repo() (Clone method) collect_usage_pieces() (SpecialHelpOrder method) Colors (class in colrev.constants) colrev module colrev-clone command line option GIT_URL colrev-data command line option --add --force --params --reading_heuristics --setup_custom_script --verbose -a -f -p -scs -v colrev-dedupe command line option --add --debug --fix_errors --force --merge --params --unmerge --verbose --view -a -d -f, [1] -gid -m -p -u -v colrev-distribute command line option --force --path --verbose -f -p -v colrev-env command line option --index --install --pull --register --status --unregister --update_package_list --verbose -i -r -s -ur -v colrev-init command line option --example --force --light --type -f colrev-load command line option --force --keep_ids --skip_query --verbose -f -k -sq -v colrev-pdf-get command line option --add --copy-to-repo --force --params --relink_pdfs --rename --setup_custom_script --verbose -a -c -f -p -r -scs -v colrev-pdf-get-man command line option --add --discard --export --force --params --verbose -a -e -f -p -v colrev-pdf-prep command line option --add --batch_size --force --params --reprocess --setup_custom_script --tei --update_colrev_pdf_ids --verbose -a -b -f -p -scs -v colrev-pdf-prep-man command line option --add --apply --delete_first_page --discard --extract --force --params --stats --verbose -a -dfp -f -p -v colrev-pdfs command line option --dir --discard --force --verbose -d -f -v colrev-prep command line option --add --cpu --debug --force --keep_ids --params --polish --setup_custom_script --verbose -a -d -f -k -p -scs -v colrev-prep-man command line option --add --force --languages --params --stats --verbose -a -f -l -p -v colrev-prescreen command line option --add --create_split --exclude --export_format --force --import_table --include --include_all --include_all_always --params --setup_custom_script --split --verbose -a -e -f -i -p -scs -v colrev-pull command line option --force --verbose -f -v colrev-push command line option --all --force --project_only --records_only --verbose -a -f -p -r -v colrev-retrieve command line option --force --verbose -f -v colrev-screen command line option --add --add_abstracts_from_tei --add_criterion --create_split --delete_criterion --force --include_all --include_all_always --params --setup_custom_script --split --verbose -a -abstracts -ac -dc -f -p -scs -v colrev-search command line option --add --force --params --rerun --selected --setup_custom_script --skip --verbose --view -a -bws -f -p -r -s -scs -v colrev-status command line option --verbose -v colrev-trace command line option --id colrev-validate command line option --filter --force --properties --threshold --verbose -f -v SCOPE colrev.constants module colrev.dataset module colrev.env module colrev.env.docker_manager module colrev.env.environment_manager module colrev.env.grobid_service module

colrev.env.language_service module colrev.env.local_index module colrev.env.local_index_builder module colrev.env.local_index_prep module colrev.env.local_index_sqlite module colrev.env.resources module colrev.env.tei_parser module colrev.env.utils module colrev.exceptions module colrev.hooks module colrev.hooks.check module colrev.hooks.format module colrev.hooks.report module colrev.hooks.share module colrev.hooks.update module colrev.loader module colrev.loader.bib module colrev.loader.enl module colrev.loader.json module colrev.loader.load_utils module colrev.loader.load_utils_formatter module colrev.loader.loader module colrev.loader.md module colrev.loader.nbib module colrev.loader.ris module colrev.loader.table module colrev.logger module colrev.ops module colrev.ops.advisor module colrev.ops.check module colrev.ops.checker module colrev.ops.clone module colrev.ops.colrev_pandas module colrev.ops.commit module colrev.ops.correct module colrev.ops.data module colrev.ops.dedupe module colrev.ops.distribute module colrev.ops.init module colrev.ops.load module colrev.ops.merge module colrev.ops.pdf_get module colrev.ops.pdf_get_man module colrev.ops.pdf_prep module colrev.ops.pdf_prep_man module colrev.ops.prep module colrev.ops.prep_debug module colrev.ops.prep_man module colrev.ops.prescreen module colrev.ops.pull module colrev.ops.push module colrev.ops.remove module colrev.ops.repare module colrev.ops.screen module colrev.ops.search module colrev.ops.search_api_feed module colrev.ops.status module colrev.ops.trace module colrev.ops.upgrade module colrev.ops.validate module colrev.package_manager module colrev.package_manager.check module colrev.package_manager.colrev_internal_packages module colrev.package_manager.doc_registry_manager module colrev.package_manager.init module colrev.package_manager.interfaces module colrev.package_manager.package module colrev.package_manager.package_manager module colrev.package_manager.package_settings module colrev.packages module colrev.packages.screen_utils module colrev.paths module colrev.process module colrev.process.model module colrev.process.operation module colrev.process.status module colrev.record module colrev.record.qm module colrev.record.qm.checkers module colrev.record.qm.checkers.container_title_abbreviated module colrev.record.qm.checkers.doi_not_matching_pattern module colrev.record.qm.checkers.erroneous_symbol_in_field module colrev.record.qm.checkers.erroneous_term_in_field module colrev.record.qm.checkers.erroneous_title_field module colrev.record.qm.checkers.html_tags module colrev.record.qm.checkers.identical_values_between_title_and_container module colrev.record.qm.checkers.incomplete_field module colrev.record.qm.checkers.inconsistent_content module colrev.record.qm.checkers.inconsistent_with_doi_metadata module colrev.record.qm.checkers.inconsistent_with_entrytype module colrev.record.qm.checkers.isbn_not_matching_pattern module colrev.record.qm.checkers.language_format_error module colrev.record.qm.checkers.language_unknown module colrev.record.qm.checkers.missing_field module colrev.record.qm.checkers.mostly_all_caps module colrev.record.qm.checkers.name_abbreviated module colrev.record.qm.checkers.name_format_separators module colrev.record.qm.checkers.name_format_titles module colrev.record.qm.checkers.name_particles module colrev.record.qm.checkers.page_range module colrev.record.qm.checkers.pubmedid_not_matching_pattern module colrev.record.qm.checkers.record_not_in_toc module colrev.record.qm.checkers.thesis_with_multiple_authors module colrev.record.qm.checkers.year_format module colrev.record.qm.pdf_checkers module colrev.record.qm.pdf_checkers.author_not_in_pdf module colrev.record.qm.pdf_checkers.no_text_in_pdf module colrev.record.qm.pdf_checkers.pdf_incomplete module colrev.record.qm.pdf_checkers.title_not_in_pdf module colrev.record.qm.quality_model module colrev.record.record module colrev.record.record_id_setter module colrev.record.record_identifier module colrev.record.record_merger module colrev.record.record_pdf module colrev.record.record_prep module colrev.record.record_similarity module colrev.review_manager module colrev.settings module colrev.ui_cli module colrev.ui_cli.add_package_to_settings module colrev.ui_cli.cli module colrev.ui_cli.cli_status_printer module colrev.ui_cli.cli_validation module colrev.ui_cli.dedupe_errors module colrev.ui_cli.detect_and_add_source module colrev.ui_cli.search_backward_selective module colrev.ui_cli.setup_custom_scripts module colrev.ui_cli.show_printer module colrev.writer module colrev.writer.bib module colrev.writer.csv module colrev.writer.excel module colrev.writer.ris module colrev.writer.write_utils module CoLRevException CoLRevUpgradeError CoLRevVersion (class in colrev.ops.upgrade) command() (SpecialHelpOrder method) command_class (SpecialHelpOrder attribute) commands (SpecialHelpOrder attribute) Commit (class in colrev.ops.commit) commit() (SQLiteIndex method) (SQLiteIndexRankings method) (SQLiteIndexRecord method) (SQLiteIndexTOC method) complete_provenance() (PDFRecord method) (PrepRecord method) (Record method) compute_language() (LanguageService method) compute_language_confidence_values() (LanguageService method) conclude() (CheckOperation method) (Data method) (Dedupe method) (Distribute method) (Load method) (Merge method) (Operation method) (PDFGet method) (PDFGetMan method) (PDFPrep method) (PDFPrepMan method) (Prep method) (PrepDebug method) (PrepMan method) (Prescreen method) (Pull method) (Push method) (Remove method) (Repare method) (Screen method) (Search method) (Status method) (Trace method) (Upgrade method) (Validate method) connected_components() (Dedupe class method) container_is_abbreviated() (in module colrev.record.record_similarity) ContainerTitleAbbreviatedChecker (class in colrev.record.qm.checkers.container_title_abbreviated) context_class (SpecialHelpOrder attribute) context_settings (SpecialHelpOrder attribute) copy_pdfs_to_repo() (PDFGet method) copy_prep_rec() (PDFRecord method) (PrepRecord method) (Record method) CorrectionPreconditionException Corrections (class in colrev.ops.correct) create() (Commit method) create_api_source() (Search method) create_commit() (Dataset method) create_db_source() (Search method) create_prescreen_split() (Prescreen method) create_screen_split() (Screen method) CuratedOutletNotUnique custom_asdict_factory() (in module colrev.env.utils)

D

Data (class in colrev.ops.data) data (EndpointType attribute) (PDFRecord attribute) (PrepRecord attribute) (Record attribute) DataException DataInterface (interface in colrev.package_manager.interfaces) Dataset (class in colrev.dataset) dataset (ReviewManager attribute) DataSettings (class in colrev.settings) decorate() (CheckOperation class method) (Data class method) (Dedupe class method) (Distribute class method) (Load class method) (Merge class method) (Operation class method) (PDFGet class method) (PDFGetMan class method) (PDFPrep class method) (PDFPrepMan class method) (Prep class method) (PrepDebug class method) (PrepMan class method) (Prescreen class method) (Pull class method) (Push class method) (Remove class method) (Repare class method) (Screen class method) (Search class method) (Status class method) (Trace class method) (Upgrade class method) (Validate class method)

Dedupe (class in colrev.ops.dedupe) dedupe (EndpointType attribute) DedupeError DedupeInterface (interface in colrev.package_manager.interfaces) DedupeSettings (class in colrev.settings) DefaultSettings (class in colrev.package_manager.package_settings) DefaultSourceSettings (class in colrev.package_manager.package_settings) DefectCodes (class in colrev.constants) defects() (PDFRecord method) (PrepRecord method) (Record method) delete_criterion() (Screen method) DependencyConfigurationError dict_set_nested() (in module colrev.env.utils) DirtyRepoAfterProcessingError discard() (PDFGetMan method) (PDFPrepMan method) discover_installed_packages() (PackageManager method) discover_packages() (PackageManager method) Distribute (class in colrev.ops.distribute) DockerManager (class in colrev.env.docker_manager) DocRegistryManager (class in colrev.package_manager.doc_registry_manager) DOIPatternChecker (class in colrev.record.qm.checkers.doi_not_matching_pattern) DuplicateIDsError

E

EndpointType (class in colrev.constants) ENLLoader (class in colrev.loader.enl) ensure_append_only() (Load method) ENTRYTYPES (class in colrev.constants) EnvironmentManager (class in colrev.env.environment_manager) ErroneousSymbolInFieldChecker (class in colrev.record.qm.checkers.erroneous_symbol_in_field) ErroneousTermInFieldChecker (class in colrev.record.qm.checkers.erroneous_term_in_field) ErroneousTitleFieldChecker (class in colrev.record.qm.checkers.erroneous_title_field) exclude_records() (Prescreen method) exists() (SQLiteIndexRecord method) (SQLiteIndexTOC method)

ExitCodes (class in colrev.constants) export_retrieval_table() (PDFGetMan method) export_table() (Prescreen method) extract_coverpage() (PDFPrepMan method) extract_lastpage() (PDFPrepMan method) extract_needs_pdf_prep_man() (PDFPrepMan method) extract_pages() (PDFPrepMan method) (PDFRecord method) extract_pages_from_pdf() (PDFRecord class method) extract_pdfs_for_data_extraction() (in module colrev.ops.colrev_pandas) extract_text_by_page() (PDFRecord method)

F

Fields (class in colrev.constants) FieldSet (class in colrev.constants) FieldValueError FieldValues (class in colrev.constants) file_in_history() (Dataset method) Filepaths (class in colrev.constants) FileSets (class in colrev.constants) fix_errors() (Dedupe method) force_mode (ReviewManager attribute) format_author_field() (PrepRecord class method) format_bib_style() (PDFRecord method) (PrepRecord method) (Record method)

format_commands() (SpecialHelpOrder method) format_epilog() (SpecialHelpOrder method) format_help() (SpecialHelpOrder method) format_help_text() (SpecialHelpOrder method) format_if_mostly_upper() (PrepRecord method) format_options() (SpecialHelpOrder method) format_records_file() (Dataset method) format_usage() (SpecialHelpOrder method) fuse_fields() (in module colrev.record.record_merger)

G

GeneralInterface (interface in colrev.package_manager.interfaces) generate_tei() (PDFPrep method) get() (SQLiteIndexRecord method) get_abstract() (TEIParser method) get_active_metadata_operation_info() (StatusStats method) get_active_operations() (StatusStats method) get_active_pdf_operation_info() (StatusStats method) get_advice() (DataInterface method) get_advisor() (ReviewManager method) get_all() (ENTRYTYPES class method) get_analytics() (Status method) get_api_feed() (DefaultSourceSettings method) (SearchSource method) get_author_details() (TEIParser method) get_by_path() (in module colrev.env.utils) get_cached_session() (ReviewManager class method) get_checker() (ReviewManager method) get_citation_format() (PDFRecord method) (PrepRecord method) (Record method) get_citations_per_section() (TEIParser method) get_colrev_id() (in module colrev.record.record_identifier) (PDFRecord method) (PrepRecord method) (Record method) get_colrev_pdf_id() (in module colrev.record.record_identifier) (PDFRecord class method) (PrepRecord class method) (Record class method) get_colrev_versions() (Checker method) (ReviewManager method) get_command() (SpecialHelpOrder method) get_commit_message() (Dataset method) get_committed_origin_state_dict() (Dataset method) get_committer() (ReviewManager method) get_completeness_condition() (ReviewManager method) get_connecting_review_manager() (ReviewManager method) get_container_title() (PDFRecord method) (PrepRecord method) (Record method) get_curated_outlets() (EnvironmentManager method) get_data() (PDFGetMan method) (PDFPrepMan method) (PDFRecord method) (PrepMan method) (PrepRecord method) (Prescreen method) (Record method) (Screen method) get_data_operation() (ReviewManager method) get_dedupe_operation() (ReviewManager method) get_diff() (PDFRecord method) (PrepRecord method) (Record method) get_distribute_operation() (ReviewManager method) get_docs_item() (PackageDoc method) get_endpoint() (Package method) get_endpoint_class() (Package method) get_endpoint_item() (PackageDoc method) get_environment_details() (EnvironmentManager method) get_environment_manager() (ReviewManager class method) get_environment_registry() (Distribute method) get_field_provenance() (PDFRecord method) (PrepRecord method) (Record method) get_field_provenance_notes() (PDFRecord method) (PrepRecord method) (Record method) get_field_provenance_source() (PDFRecord method) (PrepRecord method) (Record method) get_fields_to_remove() (LocalIndex method) get_grobid_service() (ReviewManager class method) get_grobid_version() (TEIParser method) get_help() (SpecialHelpOrder method) get_help_option() (SpecialHelpOrder method) get_help_option_names() (SpecialHelpOrder method) get_info() (Dedupe method) get_instructions() (Advisor method) get_internal_packages_dict() (in module colrev.package_manager.colrev_internal_packages) get_journal_rankings() (LocalIndex method) get_last_commit_date() (Dataset method) get_last_commit_sha() (Dataset method) get_last_updated() (SearchAPIFeed method) get_load_operation() (ReviewManager method) get_loggers() (ReviewManager method) get_manual_extra_operations() (OperationsType class method) get_merge_operation() (ReviewManager method) get_metadata() (TEIParser method) get_name_mail_from_git() (EnvironmentManager class method) get_new_search_files() (Search method) get_new_source_heuristic() (Search method) get_next_id() (Distribute method) get_non_processed_states() (RecordState class method) get_nr_records() (BIBLoader class method) (ENLLoader class method) (in module colrev.loader.load_utils) (JSONLoader class method) (MarkdownLoader class method) (NBIBLoader class method) (RISLoader class method) (TableLoader class method)

get_operation_in_progress() (StatusStats method) get_options() (IDPattern class method) (PDFPathType class method) (ScreenCriterionType class method) (SearchType class method) (ShareStatReq class method) get_origin_prefix() (DefaultSourceSettings method) (SearchSource method) get_origin_state_dict() (Dataset method) get_package_endpoint_class() (PackageManager method) get_package_file_content() (in module colrev.env.utils) get_package_manager() (ReviewManager class method) get_packages() (Settings method) get_paper_keywords() (TEIParser method) get_pdf() (PDFGet method) (PDFGetInterface method) get_pdf_get_man() (PDFGetMan method) get_pdf_get_man_operation() (ReviewManager method) get_pdf_get_operation() (ReviewManager method) get_pdf_hash() (PDFRecord method) get_pdf_prep_man_operation() (ReviewManager method) get_pdf_prep_operation() (ReviewManager method) get_pdf_qm() (ReviewManager method) get_post_x_states() (RecordState class method) get_preceding_states() (ProcessModel class method) get_prep_man_operation() (ReviewManager method) get_prep_operation() (ReviewManager method) get_prescreen_operation() (ReviewManager method) get_prev_feed_record() (SearchAPIFeed method) get_priority_operations() (StatusStats method) get_pull_operation() (ReviewManager method) get_push_operation() (ReviewManager method) get_qm() (ReviewManager method) get_query() (DefaultSourceSettings method) (SearchSource method) get_query_filename() (Search method) get_record_change_score() (in module colrev.record.record_similarity) (PDFRecord class method) (PrepRecord class method) (Record class method) get_record_header_items() (BIBLoader method) get_record_ids_for_synthesis() (Data method) get_record_similarity() (in module colrev.record.record_similarity) (PDFRecord class method) (PrepRecord class method) (Record class method) get_records_for_dedupe() (Dedupe class method) get_references() (TEIParser method) get_remote_url() (Dataset method) get_remove_operation() (ReviewManager method) get_repare() (ReviewManager method) get_repo() (Dataset method) get_resources() (ReviewManager class method) get_review_instructions() (Advisor method) get_review_manager() (in module colrev.ui_cli.cli) get_review_status_report() (Status method) get_screen_operation() (ReviewManager method) get_screening_criteria() (Screen method) get_screening_criteria_from_user_input() (in module colrev.packages.screen_utils) get_search_files() (in module colrev.ui_cli.cli) get_search_operation() (ReviewManager method) get_settings_by_key() (EnvironmentManager method) get_sharing_instructions() (Advisor method) get_short_help_str() (SpecialHelpOrder method) get_states_requiring_file() (RecordState class method) get_status_operation() (ReviewManager method) get_status_stats() (in module colrev.process.status) (ReviewManager method) get_target_filepath() (PDFGet method) get_tei() (ReviewManager method) get_tei_filename() (PDFRecord method) (PrepRecord method) (Record method) get_tei_str() (TEIParser method) get_template() (in module colrev.env.utils) get_toc_items() (SQLiteIndexTOC method) get_toc_key() (in module colrev.record.record_identifier) (PDFRecord method) (PrepRecord method) (Record method) get_trace_operation() (ReviewManager method) get_transitioned_records() (StatusStats method) get_tree_hash() (Dataset method) get_unique_filename() (Search method) get_untracked_files() (Dataset method) get_upgrade() (ReviewManager method) get_usage() (SpecialHelpOrder method) get_valid_transitions() (ProcessModel class method) get_validate_operation() (ReviewManager method) get_value() (PDFRecord method) (PrepRecord method) (Record method) get_year_from_toc() (LocalIndex method) GIT_URL colrev-clone command line option git_url (Clone attribute) GitConflictError GitNotAvailableError GrobidService (class in colrev.env.grobid_service) group() (SpecialHelpOrder method) group_class (SpecialHelpOrder attribute)

H

has_changes() (Dataset method) has_endpoint() (Package method) (PackageDoc method) has_fatal_quality_defects() (PDFRecord method) (PrepRecord method) (Record method) has_pdf_defects() (PDFRecord method) (PrepRecord method) (Record method)

has_quality_defects() (PDFRecord method) (PrepRecord method) (Record method) has_record_changes() (Dataset method) has_untracked_search_records() (Dataset method) heuristic() (SearchSourceInterface method) heuristic_status (SearchSourceInterface attribute) high_level_operation (ReviewManager attribute) HTMLTagChecker (class in colrev.record.qm.checkers.html_tags)

I

IdenticalValuesChecker (class in colrev.record.qm.checkers.identical_values_between_title_and_container) IDPattern (class in colrev.constants) IDSetter (class in colrev.record.record_id_setter) ignore_defect() (PDFRecord method) (PrepRecord method) (Record method) ignore_unknown_options (SpecialHelpOrder attribute) ignored_defect() (PDFRecord method) (PrepRecord method) (Record method) import_package_docs() (PackageDoc method) import_pdf() (PDFGet method) import_table() (Prescreen method) ImportException in_ci_environment() (ReviewManager class method) in_test_environment() (ReviewManager class method) in_virtualenv() (Checker class method) (ReviewManager method) include_all_in_screen() (Screen method) include_records() (Prescreen method) IncompleteFieldChecker (class in colrev.record.qm.checkers.incomplete_field) InconsistentContentChecker (class in colrev.record.qm.checkers.inconsistent_content) InconsistentWithDOIMetadataChecker (class in colrev.record.qm.checkers.inconsistent_with_doi_metadata) InconsistentWithEntrytypeChecker (class in colrev.record.qm.checkers.inconsistent_with_entrytype) index() (LocalIndexBuilder method) index_colrev_project() (LocalIndexBuilder method)

index_journal_rankings() (LocalIndexBuilder method) index_records() (LocalIndexBuilder method) initialize() (ReviewTypeInterface method) Initializer (class in colrev.ops.init) inplace_change() (in module colrev.env.utils) insert() (SQLiteIndexRecord method) insert_df() (SQLiteIndexRankings method) install() (PackageManager method) install_curated_resource() (Resources method) install_project() (PackageManager method) InvalidLanguageCodeException InvalidPDFException InvalidQueryException InvalidSettingsError invoke() (SpecialHelpOrder method) is_curated_masterdata_repo() (Settings method) is_curated_repo() (Settings method) is_curated_source() (DefaultSourceSettings method) (SearchSource method) is_installed() (PackageManager method) is_md_source() (DefaultSourceSettings method) (SearchSource method) is_retracted() (PDFRecord method) (PrepRecord method) (Record method) ISBNPatternChecker (class in colrev.record.qm.checkers.isbn_not_matching_pattern)

J

JSONLoader (class in colrev.loader.json)

L

LanguageChecker (class in colrev.record.qm.checkers.language_unknown) LanguageFormatChecker (class in colrev.record.qm.checkers.language_format_error) LanguageService (class in colrev.env.language_service) link_pdf() (PDFGet method) list_commands() (SpecialHelpOrder method) list_commands_for_help() (SpecialHelpOrder method) Load (class in colrev.ops.load) load() (BIBLoader method) (ENLLoader method) (in module colrev.loader.load_utils) (JSONLoader method) (Loader method) (MarkdownLoader method) (NBIBLoader method) (RISLoader method) (SearchSourceInterface method) (TableLoader method) load_active_sources() (Load method) load_complementary_material_keywords() (in module colrev.env.utils) load_complementary_material_prefixes() (in module colrev.env.utils) load_complementary_material_strings() (in module colrev.env.utils) load_dedupe_false_negatives() (in module colrev.ui_cli.dedupe_errors) load_dedupe_false_positives() (in module colrev.ui_cli.dedupe_errors)

load_df() (in module colrev.ops.colrev_pandas) load_environment_registry() (EnvironmentManager method) load_records_dict() (Dataset method) (Upgrade method) load_records_from_history() (Dataset method) load_records_list() (BIBLoader method) (ENLLoader method) (JSONLoader method) (Loader method) (MarkdownLoader method) (NBIBLoader method) (RISLoader method) (TableLoader method) load_resolved_papers() (in module colrev.ops.colrev_pandas) load_settings() (in module colrev.settings) (ReviewManager method) load_source_records() (Load method) Loader (class in colrev.loader.loader) LoadFormatter (class in colrev.loader.load_utils_formatter) loads() (in module colrev.loader.load_utils) local_repos() (EnvironmentManager method) LocalIndex (class in colrev.env.local_index) LocalIndexBuilder (class in colrev.env.local_index_builder) LocalIndexFields (class in colrev.constants)

M

main() (in module colrev.hooks.check) (in module colrev.hooks.format) (in module colrev.hooks.report) (in module colrev.hooks.share) (in module colrev.hooks.update) (in module colrev.package_manager.check) (in module colrev.package_manager.init) (in module colrev.ui_cli.search_backward_selective) (SpecialHelpOrder method) (Upgrade method) make_context() (SpecialHelpOrder method) make_parser() (SpecialHelpOrder method) mark_references() (TEIParser method) MarkdownLoader (class in colrev.loader.md) masterdata_is_curated() (PDFRecord method) (PrepRecord method) (Record method) matches() (in module colrev.record.record_similarity) md_imported (RecordState attribute) md_needs_manual_preparation (RecordState attribute) md_prepared (RecordState attribute) md_processed (RecordState attribute) md_retrieved (RecordState attribute) Merge (class in colrev.ops.merge) merge() (in module colrev.record.record_merger) (PDFRecord method) (PrepRecord method) (Record method) merge_based_on_global_ids() (Dedupe method) merge_records() (Dedupe method) MissingDependencyError MissingFieldChecker (class in colrev.record.qm.checkers.missing_field) MissingRecordQualityRuleSpecification module colrev colrev.constants colrev.dataset colrev.env colrev.env.docker_manager colrev.env.environment_manager colrev.env.grobid_service colrev.env.language_service colrev.env.local_index colrev.env.local_index_builder colrev.env.local_index_prep colrev.env.local_index_sqlite colrev.env.resources colrev.env.tei_parser colrev.env.utils colrev.exceptions colrev.hooks colrev.hooks.check colrev.hooks.format colrev.hooks.report colrev.hooks.share colrev.hooks.update colrev.loader colrev.loader.bib colrev.loader.enl colrev.loader.json colrev.loader.load_utils colrev.loader.load_utils_formatter colrev.loader.loader colrev.loader.md colrev.loader.nbib colrev.loader.ris colrev.loader.table colrev.logger colrev.ops colrev.ops.advisor colrev.ops.check colrev.ops.checker colrev.ops.clone colrev.ops.colrev_pandas colrev.ops.commit colrev.ops.correct colrev.ops.data colrev.ops.dedupe colrev.ops.distribute colrev.ops.init colrev.ops.load colrev.ops.merge colrev.ops.pdf_get colrev.ops.pdf_get_man colrev.ops.pdf_prep colrev.ops.pdf_prep_man colrev.ops.prep colrev.ops.prep_debug colrev.ops.prep_man colrev.ops.prescreen colrev.ops.pull colrev.ops.push colrev.ops.remove colrev.ops.repare colrev.ops.screen colrev.ops.search colrev.ops.search_api_feed colrev.ops.status colrev.ops.trace colrev.ops.upgrade colrev.ops.validate colrev.package_manager colrev.package_manager.check colrev.package_manager.colrev_internal_packages colrev.package_manager.doc_registry_manager colrev.package_manager.init colrev.package_manager.interfaces colrev.package_manager.package colrev.package_manager.package_manager colrev.package_manager.package_settings colrev.packages colrev.packages.screen_utils colrev.paths colrev.process colrev.process.model colrev.process.operation colrev.process.status colrev.record colrev.record.qm colrev.record.qm.checkers colrev.record.qm.checkers.container_title_abbreviated colrev.record.qm.checkers.doi_not_matching_pattern colrev.record.qm.checkers.erroneous_symbol_in_field colrev.record.qm.checkers.erroneous_term_in_field colrev.record.qm.checkers.erroneous_title_field colrev.record.qm.checkers.html_tags colrev.record.qm.checkers.identical_values_between_title_and_container colrev.record.qm.checkers.incomplete_field colrev.record.qm.checkers.inconsistent_content colrev.record.qm.checkers.inconsistent_with_doi_metadata colrev.record.qm.checkers.inconsistent_with_entrytype colrev.record.qm.checkers.isbn_not_matching_pattern colrev.record.qm.checkers.language_format_error colrev.record.qm.checkers.language_unknown colrev.record.qm.checkers.missing_field colrev.record.qm.checkers.mostly_all_caps colrev.record.qm.checkers.name_abbreviated colrev.record.qm.checkers.name_format_separators colrev.record.qm.checkers.name_format_titles colrev.record.qm.checkers.name_particles colrev.record.qm.checkers.page_range colrev.record.qm.checkers.pubmedid_not_matching_pattern colrev.record.qm.checkers.record_not_in_toc colrev.record.qm.checkers.thesis_with_multiple_authors colrev.record.qm.checkers.year_format colrev.record.qm.pdf_checkers colrev.record.qm.pdf_checkers.author_not_in_pdf colrev.record.qm.pdf_checkers.no_text_in_pdf colrev.record.qm.pdf_checkers.pdf_incomplete colrev.record.qm.pdf_checkers.title_not_in_pdf colrev.record.qm.quality_model colrev.record.record colrev.record.record_id_setter colrev.record.record_identifier colrev.record.record_merger colrev.record.record_pdf colrev.record.record_prep colrev.record.record_similarity colrev.review_manager colrev.settings colrev.ui_cli colrev.ui_cli.add_package_to_settings colrev.ui_cli.cli colrev.ui_cli.cli_status_printer colrev.ui_cli.cli_validation colrev.ui_cli.dedupe_errors colrev.ui_cli.detect_and_add_source colrev.ui_cli.search_backward_selective colrev.ui_cli.setup_custom_scripts colrev.ui_cli.show_printer colrev.writer colrev.writer.bib colrev.writer.csv colrev.writer.excel colrev.writer.ris colrev.writer.write_utils

MostlyAllCapsFieldChecker (class in colrev.record.qm.checkers.mostly_all_caps) mro() (SortedEnumMeta method)

N

na (EndpointType attribute) name (SpecialHelpOrder attribute) NameAbbreviatedChecker (class in colrev.record.qm.checkers.name_abbreviated) NameFormatSeparatorsChecker (class in colrev.record.qm.checkers.name_format_separators) NameFormatTitleChecker (class in colrev.record.qm.checkers.name_format_titles) NameParticlesChecker (class in colrev.record.qm.checkers.name_particles) NBIBLoader (class in colrev.loader.nbib) NextLine, [1], [2] NonEmptyDirectoryError NoRecordsError NoRecordsToImport NotEnoughDataToIdentifyException NotFeedIdentifiableException notified_next_operation (ReviewManager attribute) notify() (CheckOperation method) (Data method) (Dedupe method) (Distribute method) (Load method) (Merge method) (Operation method) (PDFGet method) (PDFGetMan method) (PDFPrep method) (PDFPrepMan method) (Prep method) (PrepDebug method) (PrepMan method) (Prescreen method) (Pull method) (Push method) (Remove method) (Repare method) (Screen method) (Search method) (Status method) (Trace method) (Upgrade method) (Validate method)

NotTOCIdentifiableException

O

Operation (class in colrev.process.operation)

OperationsType (class in colrev.constants) OriginError

P

Package (class in colrev.package_manager.package) PackageDoc (class in colrev.package_manager.doc_registry_manager) PackageManager (class in colrev.package_manager.package_manager) PackageParameterError PackageSettingMustStartWithPackagesException PageRangeChecker (class in colrev.record.qm.checkers.page_range) ParameterError params (SpecialHelpOrder attribute) parse_args() (SpecialHelpOrder method) ParseError, [1], [2] path (PDFRecord attribute) (ReviewManager attribute) PathManager (class in colrev.paths) pdf_get (EndpointType attribute) pdf_get_man (EndpointType attribute) pdf_get_man() (PDFGetManInterface method) pdf_get_man_record() (PDFGetMan method) pdf_imported (RecordState attribute) pdf_needs_manual_preparation (RecordState attribute) pdf_needs_manual_retrieval (RecordState attribute) pdf_not_available (RecordState attribute) pdf_prep (EndpointType attribute) pdf_prep_man (EndpointType attribute) pdf_prep_man() (PDFPrepManInterface method) pdf_prep_man_stats() (PDFPrepMan method) pdf_prepared (RecordState attribute) pdf_required_for_screen_and_synthesis (PDFGetSettings attribute) PDFDefectCodes (class in colrev.constants) PDFGet (class in colrev.ops.pdf_get) PDFGetInterface (interface in colrev.package_manager.interfaces) PDFGetMan (class in colrev.ops.pdf_get_man) PDFGetManInterface (interface in colrev.package_manager.interfaces) PDFGetSettings (class in colrev.settings) PDFHashError PDFIncompletenessChecker (class in colrev.record.qm.pdf_checkers.pdf_incomplete) PDFPathType (class in colrev.constants) PDFPrep (class in colrev.ops.pdf_prep) PDFPrepInterface (interface in colrev.package_manager.interfaces) PDFPrepMan (class in colrev.ops.pdf_prep_man) PDFPrepManInterface (interface in colrev.package_manager.interfaces) PDFPrepSettings (class in colrev.settings) PDFRecord (class in colrev.record.record_pdf) pdfs_prepared_manually() (PDFPrepMan method) pdfs_retrieved_manually() (PDFGetMan method) percent_upper_chars() (in module colrev.env.utils) PortAlreadyRegisteredException Prep (class in colrev.ops.prep) prep (EndpointType attribute) prep_link_md() (SearchSourceInterface method) prep_man (EndpointType attribute)

prep_man_langs() (PrepMan method) prep_man_stats() (PrepMan method) prep_pdf() (PDFPrepInterface method) PreparationBreak prepare() (Prep method) (PrepDebug method) (PrepInterface method) (SearchSourceInterface method) prepare_manual() (PrepManInterface method) prepare_pdf() (PDFPrep method) prepare_record_for_indexing() (in module colrev.env.local_index_prep) prepare_record_for_return() (in module colrev.env.local_index_prep) PrepDebug (class in colrev.ops.prep_debug) PrepInterface (interface in colrev.package_manager.interfaces) PrepMan (class in colrev.ops.prep_man) PrepManInterface (interface in colrev.package_manager.interfaces) PrepRecord (class in colrev.record.record_prep) PrepRound (class in colrev.settings) PrepSettings (class in colrev.settings) Prescreen (class in colrev.ops.prescreen) prescreen (EndpointType attribute) prescreen() (Prescreen method) prescreen_exclude() (PDFRecord method) (PrepRecord method) (Record method) PrescreenInterface (interface in colrev.package_manager.interfaces) PrescreenSettings (class in colrev.settings) print_citation_format() (PDFRecord method) (PrepRecord method) (Record method) print_collaboration_instructions() (in module colrev.ui_cli.cli_status_printer) print_diff() (in module colrev.ui_cli.cli_validation) print_diff_pair() (in module colrev.ui_cli.cli_validation) print_environment_instructions() (in module colrev.ui_cli.cli_status_printer) print_progress() (in module colrev.ui_cli.cli_status_printer) print_project_status() (in module colrev.ui_cli.cli_status_printer) print_review_instructions() (in module colrev.ui_cli.cli_status_printer) print_sample() (in module colrev.ui_cli.show_printer) print_string_diff() (in module colrev.ui_cli.cli_validation) print_venv_notes() (in module colrev.ui_cli.show_printer) ProcessModel (class in colrev.process.model) ProcessOrderViolation ProjectSettings (class in colrev.settings) propagated_id() (Dataset method) PropagatedIDChange Protocol (class in colrev.settings) PubmedIDPatternChecker (class in colrev.record.qm.checkers.pubmedid_not_matching_pattern) Pull (class in colrev.ops.pull) pull_if_repo_clean() (Dataset method) Push (class in colrev.ops.push)

Q

QualityModel (class in colrev.record.qm.quality_model)

R

read_next_record() (Dataset method) reading_heuristics() (Data method) Record (class in colrev.record.record) record_field_inconsistencies (InconsistentWithEntrytypeChecker attribute) record_field_requirements (MissingFieldChecker attribute) RecordNotFoundException RecordNotFoundInPrepSourceException RecordNotIndexableException RecordNotInIndexException RecordNotInRepoException RecordNotInTOCChecker (class in colrev.record.qm.checkers.record_not_in_toc) RecordNotInTOCException RecordNotParsableException records_changed() (Dataset method) RecordState (class in colrev.constants) register() (in module colrev.record.qm.checkers.container_title_abbreviated) (in module colrev.record.qm.checkers.doi_not_matching_pattern) (in module colrev.record.qm.checkers.erroneous_symbol_in_field) (in module colrev.record.qm.checkers.erroneous_term_in_field) (in module colrev.record.qm.checkers.erroneous_title_field) (in module colrev.record.qm.checkers.html_tags) (in module colrev.record.qm.checkers.identical_values_between_title_and_container) (in module colrev.record.qm.checkers.incomplete_field) (in module colrev.record.qm.checkers.inconsistent_content) (in module colrev.record.qm.checkers.inconsistent_with_doi_metadata) (in module colrev.record.qm.checkers.inconsistent_with_entrytype) (in module colrev.record.qm.checkers.isbn_not_matching_pattern) (in module colrev.record.qm.checkers.language_format_error) (in module colrev.record.qm.checkers.language_unknown) (in module colrev.record.qm.checkers.missing_field) (in module colrev.record.qm.checkers.mostly_all_caps) (in module colrev.record.qm.checkers.name_abbreviated) (in module colrev.record.qm.checkers.name_format_separators) (in module colrev.record.qm.checkers.name_format_titles) (in module colrev.record.qm.checkers.name_particles) (in module colrev.record.qm.checkers.page_range) (in module colrev.record.qm.checkers.pubmedid_not_matching_pattern) (in module colrev.record.qm.checkers.record_not_in_toc) (in module colrev.record.qm.checkers.thesis_with_multiple_authors) (in module colrev.record.qm.checkers.year_format) (in module colrev.record.qm.pdf_checkers.author_not_in_pdf) (in module colrev.record.qm.pdf_checkers.no_text_in_pdf) (in module colrev.record.qm.pdf_checkers.pdf_incomplete) (in module colrev.record.qm.pdf_checkers.title_not_in_pdf) register_checker() (QualityModel method) register_ports() (EnvironmentManager method) register_repo() (EnvironmentManager method) reinitialize_sqlite_db() (LocalIndexBuilder method) relink_pdfs() (PDFGet method) remote_ahead() (Dataset method) Remove (class in colrev.ops.remove) remove_accents() (in module colrev.env.utils) remove_field() (PDFRecord method) (PrepRecord method) (Record method) remove_field_provenance_note() (PDFRecord method) (PrepRecord method) (Record method) remove_md_origins() (Validate method) rename_field() (PDFRecord method) (PrepRecord method) (Record method) rename_pdfs() (PDFGet method) Repare (class in colrev.ops.repare) repo_initialized() (Dataset method) RepoInitError report() (ReviewManager method)

RepoSetupError require_prov() (PDFRecord method) (PrepRecord method) (Record method) reset_log_if_no_changes() (Dataset method) reset_pdf_provenance_notes() (PDFRecord method) (PrepRecord method) (Record method) reset_report_logger() (in module colrev.logger) (ReviewManager method) Resources (class in colrev.env.resources) result_callback() (SpecialHelpOrder method) retrieve() (LocalIndex method) retrieve_based_on_colrev_pdf_id() (LocalIndex method) retrieve_from_toc() (LocalIndex method) retrieve_package_file() (in module colrev.env.utils) rev_excluded (RecordState attribute) rev_included (RecordState attribute) rev_prescreen_excluded (RecordState attribute) rev_prescreen_included (RecordState attribute) rev_synthesized (RecordState attribute) review_type (EndpointType attribute) ReviewManager (class in colrev.review_manager) ReviewManagerNotNotifiedError ReviewTypeInterface (interface in colrev.package_manager.interfaces) RISLoader (class in colrev.loader.ris) run() (AuthorNotInPDFChecker method) (ContainerTitleAbbreviatedChecker method) (DOIPatternChecker method) (ErroneousSymbolInFieldChecker method) (ErroneousTermInFieldChecker method) (ErroneousTitleFieldChecker method) (HTMLTagChecker method) (IdenticalValuesChecker method) (IncompleteFieldChecker method) (InconsistentContentChecker method) (InconsistentWithDOIMetadataChecker method) (InconsistentWithEntrytypeChecker method) (ISBNPatternChecker method) (LanguageChecker method) (LanguageFormatChecker method) (LoadFormatter method) (MissingFieldChecker method) (MostlyAllCapsFieldChecker method) (NameAbbreviatedChecker method) (NameFormatSeparatorsChecker method) (NameFormatTitleChecker method) (NameParticlesChecker method) (PageRangeChecker method) (PDFIncompletenessChecker method) (PubmedIDPatternChecker method) (QualityModel method) (RecordNotInTOCChecker method) (TextInPDFChecker method) (ThesisWithMultipleAuthorsChecker method) (TitleNotInPDFChecker method) (YearFormatChecker method) run_db_search() (Search method) run_dedupe() (DedupeInterface method) run_pdf_quality_model() (PDFRecord method) (PrepRecord method) (Record method) run_prescreen() (PrescreenInterface method) run_quality_model() (PDFRecord method) (PrepRecord method) (Record method) run_screen() (ScreenInterface method)

S

save() (in module colrev.ops.colrev_pandas) (SearchAPIFeed method) save_environment_registry() (EnvironmentManager method) save_records_dict() (Dataset method) (Upgrade method) save_records_dict_to_file() (Dataset method) save_settings() (in module colrev.settings) (ReviewManager method) SCOPE colrev-validate command line option Screen (class in colrev.ops.screen) screen (EndpointType attribute) screen() (Screen method) ScreenCriterion (class in colrev.settings) ScreenCriterionType (class in colrev.constants) ScreenInterface (interface in colrev.package_manager.interfaces) ScreenSettings (class in colrev.settings) Search (class in colrev.ops.search) search() (LocalIndex method) (SearchSourceInterface method) (SQLiteIndexRecord method) search_source (EndpointType attribute) search_types (SearchSourceInterface attribute) SearchAPIFeed (class in colrev.ops.search_api_feed) SearchNotAutomated SearchSettings (class in colrev.settings) SearchSource (class in colrev.settings) SearchSourceException SearchSourceHeuristicStatus (class in colrev.constants) SearchSourceInterface (interface in colrev.package_manager.interfaces) SearchType (class in colrev.constants) select() (SQLiteIndexRankings method) select_search_type() (Search method) ServiceNotAvailableException set_data() (PrepMan method) set_ids() (Dataset method) (IDSetter method) (Prep method) (PrepDebug method) set_masterdata_complete() (PDFRecord method) (PrepRecord method) (Record method) set_masterdata_consistent() (PDFRecord method) (PrepRecord method) (Record method) set_masterdata_curated() (PDFRecord method) (PrepRecord method) (Record method) set_nr_pages_in_pdf() (PDFRecord method) set_pdf_man_prepared() (PDFPrepMan method)

set_screening_criteria() (Screen method) set_status() (PDFRecord method) (PrepRecord method) (Record method) set_text_from_pdf() (PDFRecord method) Settings (class in colrev.settings) settings_class (DataInterface attribute) (DedupeInterface attribute) (PDFGetInterface attribute) (PDFGetManInterface attribute) (PDFPrepInterface attribute) (PDFPrepManInterface attribute) (PrepInterface attribute) (PrepManInterface attribute) (PrescreenInterface attribute) (ScreenInterface attribute) (SearchSourceInterface attribute) setup_custom_script() (Data method) (PDFGet method) (PDFPrep method) (Prep method) (PrepDebug method) (Prescreen method) (Screen method) setup_custom_search_script() (in module colrev.ui_cli.setup_custom_scripts) setup_for_load() (DefaultSourceSettings method) (SearchSource method) setup_logger() (in module colrev.logger) setup_report_logger() (in module colrev.logger) setup_source_for_load() (Load method) ShareStatReq (class in colrev.constants) sharing() (ReviewManager method) shell_complete() (SpecialHelpOrder method) SortedEnumMeta (class in colrev.constants) source_correction_hint (PrepInterface attribute) source_identifier (SearchSourceInterface attribute) SpecialHelpOrder (class in colrev.ui_cli.cli) SQLiteIndex (class in colrev.env.local_index_sqlite) SQLiteIndexRankings (class in colrev.env.local_index_sqlite) SQLiteIndexRecord (class in colrev.env.local_index_sqlite) SQLiteIndexTOC (class in colrev.env.local_index_sqlite) STANDARDIZED_FIELD_KEYS (FieldSet attribute) start() (GrobidService method) stash_unstaged_changes() (Dataset method) Status (class in colrev.ops.status) StatusFieldValueError StatusStats (class in colrev.process.status) StatusStatsCurrently (class in colrev.process.status) StatusStatsOverall (class in colrev.process.status) StatusTransitionError stop_logger() (in module colrev.logger)

T

TableLoader (class in colrev.loader.table) TEIException TEIParser (class in colrev.env.tei_parser) TEITimeoutException TemplateNotAvailableError TextInPDFChecker (class in colrev.record.qm.pdf_checkers.no_text_in_pdf) ThesisWithMultipleAuthorsChecker (class in colrev.record.qm.checkers.thesis_with_multiple_authors) TitleNotInPDFChecker (class in colrev.record.qm.pdf_checkers.title_not_in_pdf)

to_dataframe() (in module colrev.writer.csv) (in module colrev.writer.excel) to_info_dict() (SpecialHelpOrder method) to_screen() (Screen method) to_string() (in module colrev.writer.bib) (in module colrev.writer.ris) (in module colrev.writer.write_utils) TOCNotAvailableException Trace (class in colrev.ops.trace)

U

unify_pages_field() (PrepRecord method) unify_to_iso_639_3_language_codes() (LanguageService method) unmerge_records() (Dedupe method) UnstagedGitChangesError UnsupportedImportFormatError update() (DocRegistryManager method) (SQLiteIndexRecord method) update_by_record() (PDFRecord method) (PrepRecord method) (Record method) update_colrev_pdf_ids() (PDFPrep method)

update_config() (ReviewManager method) update_data() (DataInterface method) update_field() (PDFRecord method) (PrepRecord method) (Record method) update_gitignore() (Dataset method) update_record_status_matrix() (DataInterface method) update_registry() (EnvironmentManager method) update_report() (Commit method) update_status_yaml() (ReviewManager method) Upgrade (class in colrev.ops.upgrade)

V

Validate (class in colrev.ops.validate) validate_filename() (DefaultSourceSettings class method) (SearchSource class method) validate_iso_639_3_language_codes() (LanguageService method)

validate_merge_prescreen_screen() (Validate method) validate_module_name() (in module colrev.package_manager.init) validate_version() (in module colrev.package_manager.init) verbose_mode (ReviewManager attribute)

W

write_file() (in module colrev.writer.bib) (in module colrev.writer.csv) (in module colrev.writer.excel) (in module colrev.writer.ris) (in module colrev.writer.write_utils)

Y

YearFormatChecker (class in colrev.record.qm.checkers.year_format)