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), [1] add_abstracts_from_tei() (Screen method), [1] add_changes() (Dataset method), [1] add_command() (SpecialHelpOrder method), [1] add_criterion() (Screen method), [1] add_endpoint() (SearchSourcePackageBaseClass class method), [1], [2] add_field_provenance() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] add_field_provenance_note() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] add_from_tei() (in module colrev.ops.colrev_pandas), [1] add_most_likely_sources() (Search method), [1] add_new_sources() (CLISourceAdder method), [1] add_package_to_settings() (in module colrev.ui_cli.add_package_to_settings), [1] add_provenance_all() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1]

add_record_to_feed() (SearchAPIFeed method), [1] add_setting_changes() (Dataset method), [1] add_source_and_search() (Search method), [1] add_to_type_identifier_endpoint_dict() (Package method), [1] add_update_record() (SearchAPIFeed method), [1] Advisor (class in colrev.ops.advisor), [1] align_provenance() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] allow_extra_args (SpecialHelpOrder attribute), [1] allow_interspersed_args (SpecialHelpOrder attribute), [1] AppendOnlyViolation, [1] apply_merges() (Dedupe method), [1] apply_pdf_prep_man() (PDFPrepMan method), [1] Author (class in colrev.settings), [1] AuthorNotInPDFChecker (class in colrev.record.qm.pdf_checkers.author_not_in_pdf), [1]

B

behind_remote() (Dataset method), [1] bib_entrytype_setter() (in module colrev.loader.load_utils), [1]

BIBLoader (class in colrev.loader.bib), [1] build_docker_image() (DockerManager class method), [1]

C

callback (SpecialHelpOrder attribute), [1] capitalize_entities() (in module colrev.record.record_prep), [1] catch_exception() (in module colrev.ui_cli.cli), [1] change_entrytype() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] check_change_in_propagated_id() (Checker method), [1] check_corrections_of_records() (Corrections method), [1] check_docker_installed() (DockerManager class method), [1] check_existing_unlinked_pdfs() (PDFGet method), [1] check_fields() (Checker method), [1] check_git_installed() (EnvironmentManager method), [1] check_grobid_availability() (GrobidService method), [1] check_operation_precondition() (ProcessModel class method), [1] check_precondition() (CheckOperation method), [1] (Data method), [1] (Dedupe method), [1] (Distribute method), [1] (Load method), [1] (Merge method), [1] (Operation method), [1] (PDFGet method), [1] (PDFGetMan method), [1] (PDFPrep method), [1] (PDFPrepMan method), [1] (Prep method), [1] (PrepDebug method), [1] (PrepMan method), [1] (Prescreen method), [1] (Pull method), [1] (Push method), [1] (Remove method), [1] (Repare method), [1] (Screen method), [1] (Search method), [1] (Status method), [1] (Trace method), [1] (Upgrade method), [1] (Validate method), [1] check_repo() (Checker method), [1] (ReviewManager method), [1] check_repo_basics() (Checker method), [1] check_repo_extended() (Checker method), [1] check_repository_setup() (Checker method), [1] (ReviewManager method), [1] check_sources() (Checker method), [1] check_status_transitions() (Checker method), [1] check_valid_bib() (in module colrev.loader.bib), [1] Checker (class in colrev.ops.checker), [1] CheckOperation (class in colrev.ops.check), [1] CleanRepoRequiredError, [1] CLISourceAdder (class in colrev.ui_cli.detect_and_add_source), [1] Clone (class in colrev.ops.clone), [1] clone_git_repo() (Clone method), [1] collect_usage_pieces() (SpecialHelpOrder method), [1] Colors (class in colrev.constants), [1] 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, [1] colrev.dataset module, [1] colrev.env module, [1] colrev.env.docker_manager module, [1] colrev.env.environment_manager module, [1] colrev.env.grobid_service module, [1]

colrev.env.language_service module, [1] colrev.env.local_index module, [1] colrev.env.local_index_builder module, [1] colrev.env.local_index_prep module, [1] colrev.env.local_index_sqlite module, [1] colrev.env.resources module, [1] colrev.env.tei_parser module, [1] colrev.env.utils module, [1] colrev.exceptions module, [1] colrev.hooks module, [1] colrev.hooks.check module, [1] colrev.hooks.format module, [1] colrev.hooks.report module, [1] colrev.hooks.share module, [1] colrev.loader module, [1] colrev.loader.bib module, [1] colrev.loader.enl module, [1] colrev.loader.json module, [1] colrev.loader.load_utils module, [1] colrev.loader.load_utils_formatter module, [1] colrev.loader.load_utils_name_formatter module, [1] colrev.loader.loader module, [1] colrev.loader.md module, [1] colrev.loader.nbib module, [1] colrev.loader.ris module, [1] colrev.loader.table module, [1] colrev.logger module, [1] colrev.ops module, [1] colrev.ops.advisor module, [1] colrev.ops.check module, [1] colrev.ops.checker module, [1] colrev.ops.clone module, [1] colrev.ops.colrev_pandas module, [1] colrev.ops.commit module, [1] colrev.ops.correct module, [1] colrev.ops.data module, [1] colrev.ops.dedupe module, [1] colrev.ops.distribute module, [1] colrev.ops.init module, [1] colrev.ops.load module, [1] colrev.ops.merge module, [1] colrev.ops.pdf_get module, [1] colrev.ops.pdf_get_man module, [1] colrev.ops.pdf_prep module, [1] colrev.ops.pdf_prep_man module, [1] colrev.ops.prep module, [1] colrev.ops.prep_debug module, [1] colrev.ops.prep_man module, [1] colrev.ops.prescreen module, [1] colrev.ops.pull module, [1] colrev.ops.push module, [1] colrev.ops.remove module, [1] colrev.ops.repare module, [1] colrev.ops.screen module, [1] colrev.ops.search module, [1] colrev.ops.search_api_feed module, [1] colrev.ops.status module, [1] colrev.ops.trace module, [1] colrev.ops.upgrade module, [1] colrev.ops.validate module, [1] colrev.package_manager module, [1] colrev.package_manager.check module, [1] colrev.package_manager.colrev_internal_packages module, [1] colrev.package_manager.doc_registry_manager module, [1] colrev.package_manager.init module, [1] colrev.package_manager.package module, [1] colrev.package_manager.package_base_classes module, [1] colrev.package_manager.package_manager module, [1] colrev.package_manager.package_settings module, [1] colrev.packages module, [1] colrev.packages.screen_utils module, [1] colrev.paths module, [1] colrev.process module, [1] colrev.process.model module, [1] colrev.process.operation module, [1] colrev.process.status module, [1] colrev.record module, [1] colrev.record.qm module, [1] colrev.record.qm.checkers module, [1] colrev.record.qm.checkers.container_title_abbreviated module, [1] colrev.record.qm.checkers.doi_not_matching_pattern module, [1] colrev.record.qm.checkers.erroneous_symbol_in_field module, [1] colrev.record.qm.checkers.erroneous_term_in_field module, [1] colrev.record.qm.checkers.erroneous_title_field module, [1] colrev.record.qm.checkers.html_tags module, [1] colrev.record.qm.checkers.identical_values_between_title_and_container module, [1] colrev.record.qm.checkers.incomplete_field module, [1] colrev.record.qm.checkers.inconsistent_content module, [1] colrev.record.qm.checkers.inconsistent_with_doi_metadata module, [1] colrev.record.qm.checkers.inconsistent_with_entrytype module, [1] colrev.record.qm.checkers.isbn_not_matching_pattern module, [1] colrev.record.qm.checkers.language_format_error module, [1] colrev.record.qm.checkers.language_unknown module, [1] colrev.record.qm.checkers.missing_field module, [1] colrev.record.qm.checkers.mostly_all_caps module, [1] colrev.record.qm.checkers.name_abbreviated module, [1] colrev.record.qm.checkers.name_format_separators module, [1] colrev.record.qm.checkers.name_format_titles module, [1] colrev.record.qm.checkers.name_particles module, [1] colrev.record.qm.checkers.page_range module, [1] colrev.record.qm.checkers.pubmedid_not_matching_pattern module, [1] colrev.record.qm.checkers.record_not_in_toc module, [1] colrev.record.qm.checkers.thesis_with_multiple_authors module, [1] colrev.record.qm.checkers.year_format module, [1] colrev.record.qm.pdf_checkers module, [1] colrev.record.qm.pdf_checkers.author_not_in_pdf module, [1] colrev.record.qm.pdf_checkers.no_text_in_pdf module, [1] colrev.record.qm.pdf_checkers.pdf_incomplete module, [1] colrev.record.qm.pdf_checkers.title_not_in_pdf module, [1] colrev.record.qm.quality_model module, [1] colrev.record.record module, [1] colrev.record.record_id_setter module, [1] colrev.record.record_identifier module, [1] colrev.record.record_merger module, [1] colrev.record.record_pdf module, [1] colrev.record.record_prep module, [1] colrev.record.record_similarity module, [1] colrev.review_manager module, [1] colrev.settings module, [1] colrev.ui_cli module, [1] colrev.ui_cli.add_package_to_settings module, [1] colrev.ui_cli.cli module, [1] colrev.ui_cli.cli_status_printer module, [1] colrev.ui_cli.cli_validation module, [1] colrev.ui_cli.dedupe_errors module, [1] colrev.ui_cli.detect_and_add_source module, [1] colrev.ui_cli.search_backward_selective module, [1] colrev.ui_cli.setup_custom_scripts module, [1] colrev.ui_cli.show_printer module, [1] colrev.writer module, [1] colrev.writer.bib module, [1] colrev.writer.csv module, [1] colrev.writer.excel module, [1] colrev.writer.ris module, [1] colrev.writer.write_utils module, [1] CoLRevException, [1] CoLRevUpgradeError, [1] CoLRevVersion (class in colrev.ops.upgrade), [1] command() (SpecialHelpOrder method), [1] command_class (SpecialHelpOrder attribute), [1] commands (SpecialHelpOrder attribute), [1] Commit (class in colrev.ops.commit), [1] commit() (SQLiteIndex method), [1] (SQLiteIndexRankings method), [1] (SQLiteIndexRecord method), [1] (SQLiteIndexTOC method), [1] complete_provenance() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] compute_language() (LanguageService method), [1] compute_language_confidence_values() (LanguageService method), [1] conclude() (CheckOperation method), [1] (Data method), [1] (Dedupe method), [1] (Distribute method), [1] (Load method), [1] (Merge method), [1] (Operation method), [1] (PDFGet method), [1] (PDFGetMan method), [1] (PDFPrep method), [1] (PDFPrepMan method), [1] (Prep method), [1] (PrepDebug method), [1] (PrepMan method), [1] (Prescreen method), [1] (Pull method), [1] (Push method), [1] (Remove method), [1] (Repare method), [1] (Screen method), [1] (Search method), [1] (Status method), [1] (Trace method), [1] (Upgrade method), [1] (Validate method), [1] connected_components() (Dedupe class method), [1] container_is_abbreviated() (in module colrev.record.record_similarity), [1] ContainerTitleAbbreviatedChecker (class in colrev.record.qm.checkers.container_title_abbreviated), [1] context_class (SpecialHelpOrder attribute), [1] context_settings (SpecialHelpOrder attribute), [1] copy_pdfs_to_repo() (PDFGet method), [1] copy_prep_rec() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] CorrectionPreconditionException, [1] Corrections (class in colrev.ops.correct), [1] create() (Commit method), [1] create_api_source() (Search method), [1] create_commit() (Dataset method), [1] create_db_source() (Search method), [1] create_prescreen_split() (Prescreen method), [1] create_screen_split() (Screen method), [1] CuratedOutletNotUnique, [1] custom_asdict_factory() (in module colrev.env.utils), [1]

D

Data (class in colrev.ops.data), [1] data (EndpointType attribute), [1] (PDFRecord attribute), [1] (PrepRecord attribute), [1] (Record attribute), [1] DataException, [1] DataPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] Dataset (class in colrev.dataset), [1] dataset (ReviewManager attribute), [1] DataSettings (class in colrev.settings), [1] decorate() (CheckOperation class method), [1] (Data class method), [1] (Dedupe class method), [1] (Distribute class method), [1] (Load class method), [1] (Merge class method), [1] (Operation class method), [1] (PDFGet class method), [1] (PDFGetMan class method), [1] (PDFPrep class method), [1] (PDFPrepMan class method), [1] (Prep class method), [1] (PrepDebug class method), [1] (PrepMan class method), [1] (Prescreen class method), [1] (Pull class method), [1] (Push class method), [1] (Remove class method), [1] (Repare class method), [1] (Screen class method), [1] (Search class method), [1] (Status class method), [1] (Trace class method), [1] (Upgrade class method), [1] (Validate class method), [1]

Dedupe (class in colrev.ops.dedupe), [1] dedupe (EndpointType attribute), [1] DedupeError, [1] DedupePackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] DedupeSettings (class in colrev.settings), [1] DefaultSettings (class in colrev.package_manager.package_settings), [1] DefaultSourceSettings (class in colrev.package_manager.package_settings), [1] DefectCodes (class in colrev.constants), [1] defects() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] delete_criterion() (Screen method), [1] DependencyConfigurationError, [1] dict_set_nested() (in module colrev.env.utils), [1] DirtyRepoAfterProcessingError, [1] discard() (PDFGetMan method), [1] (PDFPrepMan method), [1] discover_installed_packages() (PackageManager method), [1] discover_packages() (PackageManager method), [1] Distribute (class in colrev.ops.distribute), [1] DockerManager (class in colrev.env.docker_manager), [1] DocRegistryManager (class in colrev.package_manager.doc_registry_manager), [1] DOIPatternChecker (class in colrev.record.qm.checkers.doi_not_matching_pattern), [1] DuplicateIDsError, [1]

E

EndpointType (class in colrev.constants), [1] ENLLoader (class in colrev.loader.enl), [1] ensure_append_only() (Load method), [1] (SearchSourcePackageBaseClass class method), [1], [2] ENTRYTYPES (class in colrev.constants), [1] EnvironmentManager (class in colrev.env.environment_manager), [1] ErroneousSymbolInFieldChecker (class in colrev.record.qm.checkers.erroneous_symbol_in_field), [1] ErroneousTermInFieldChecker (class in colrev.record.qm.checkers.erroneous_term_in_field), [1] ErroneousTitleFieldChecker (class in colrev.record.qm.checkers.erroneous_title_field), [1] exclude_records() (Prescreen method), [1] exists() (SQLiteIndexRecord method), [1] (SQLiteIndexTOC method), [1]

ExitCodes (class in colrev.constants), [1] export_retrieval_table() (PDFGetMan method), [1] export_table() (Prescreen method), [1] extract_content() (in module colrev.loader.bib), [1] extract_coverpage() (PDFPrepMan method), [1] extract_lastpage() (PDFPrepMan method), [1] extract_needs_pdf_prep_man() (PDFPrepMan method), [1] extract_pages() (PDFPrepMan method), [1] (PDFRecord method), [1] extract_pages_from_pdf() (PDFRecord class method), [1] extract_pdfs_for_data_extraction() (in module colrev.ops.colrev_pandas), [1] extract_text_by_page() (PDFRecord method), [1]

F

Fields (class in colrev.constants), [1] FieldSet (class in colrev.constants), [1] FieldValueError, [1] FieldValues (class in colrev.constants), [1] file_in_history() (Dataset method), [1] Filepaths (class in colrev.constants), [1] FileSets (class in colrev.constants), [1] fix_errors() (Dedupe method), [1] force_mode (ReviewManager attribute), [1] format_author_field() (PrepRecord class method), [1] format_bib_style() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1]

format_commands() (SpecialHelpOrder method), [1] format_epilog() (SpecialHelpOrder method), [1] format_help() (SpecialHelpOrder method), [1] format_help_text() (SpecialHelpOrder method), [1] format_if_mostly_upper() (PrepRecord method), [1] format_name() (NameParser method), [1] format_options() (SpecialHelpOrder method), [1] format_records_file() (Dataset method), [1] format_usage() (SpecialHelpOrder method), [1] fuse_fields() (in module colrev.record.record_merger), [1]

G

generate_module_content() (in module colrev.package_manager.init), [1] generate_tei() (PDFPrep method), [1] get() (SQLiteIndexRecord method), [1] get_abstract() (TEIParser method), [1] get_active_metadata_operation_info() (StatusStats method), [1] get_active_operations() (StatusStats method), [1] get_active_pdf_operation_info() (StatusStats method), [1] get_advice() (DataPackageBaseClass method), [1], [2] get_advisor() (ReviewManager method), [1] get_all() (ENTRYTYPES class method), [1] get_analytics() (Status method), [1] get_api_feed() (DefaultSourceSettings method), [1] (SearchSource method), [1] get_author_details() (TEIParser method), [1] get_by_path() (in module colrev.env.utils), [1] get_cached_session() (ReviewManager class method), [1] get_checker() (ReviewManager method), [1] get_citation_format() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_citations_per_section() (TEIParser method), [1] get_colrev_id() (in module colrev.record.record_identifier), [1] (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_colrev_pdf_id() (in module colrev.record.record_identifier), [1] (PDFRecord class method), [1] (PrepRecord class method), [1] (Record class method), [1] get_colrev_versions() (Checker method), [1] (ReviewManager method), [1] get_command() (SpecialHelpOrder method), [1] get_commit_message() (Dataset method), [1] get_committed_origin_state_dict() (Dataset method), [1] get_committer() (ReviewManager method), [1] get_completeness_condition() (ReviewManager method), [1] get_connecting_review_manager() (ReviewManager method), [1] get_container_title() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_curated_outlets() (EnvironmentManager method), [1] get_data() (PDFGetMan method), [1] (PDFPrepMan method), [1] (PDFRecord method), [1] (PrepMan method), [1] (PrepRecord method), [1] (Prescreen method), [1] (Record method), [1] (Screen method), [1] get_data_operation() (ReviewManager method), [1] get_dedupe_operation() (ReviewManager method), [1] get_diff() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_distribute_operation() (ReviewManager method), [1] get_docs_item() (PackageDoc method), [1] get_endpoint() (Package method), [1] get_endpoint_class() (Package method), [1] get_endpoint_item() (PackageDoc method), [1] get_environment_details() (EnvironmentManager method), [1] get_environment_manager() (ReviewManager class method), [1] get_environment_registry() (Distribute method), [1] get_field_provenance() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_field_provenance_notes() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_field_provenance_source() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_fields_to_remove() (LocalIndex method), [1] get_grobid_service() (ReviewManager class method), [1] get_grobid_version() (TEIParser method), [1] get_help() (SpecialHelpOrder method), [1] get_help_option() (SpecialHelpOrder method), [1] get_help_option_names() (SpecialHelpOrder method), [1] get_info() (Dedupe method), [1] get_instructions() (Advisor method), [1] get_internal_packages_dict() (in module colrev.package_manager.colrev_internal_packages), [1] get_journal_rankings() (LocalIndex method), [1] get_last_commit_date() (Dataset method), [1] get_last_commit_sha() (Dataset method), [1] get_last_updated() (SearchAPIFeed method), [1] get_load_operation() (ReviewManager method), [1] get_loggers() (ReviewManager method), [1] get_manual_extra_operations() (OperationsType class method), [1] get_merge_operation() (ReviewManager method), [1] get_metadata() (TEIParser method), [1] get_name_mail_from_git() (EnvironmentManager class method), [1] get_new_search_files() (Search method), [1] get_new_source_heuristic() (Search method), [1] get_next_id() (Distribute method), [1] get_non_processed_states() (RecordState class method), [1] get_nr_records() (BIBLoader class method), [1] (ENLLoader class method), [1] (in module colrev.loader.load_utils), [1] (JSONLoader class method), [1] (MarkdownLoader class method), [1] (NBIBLoader class method), [1] (RISLoader class method), [1] (TableLoader class method), [1]

get_operation_in_progress() (StatusStats method), [1] get_options() (IDPattern class method), [1] (PDFPathType class method), [1] (ScreenCriterionType class method), [1] (SearchType class method), [1] (ShareStatReq class method), [1] get_origin_prefix() (DefaultSourceSettings method), [1] (SearchSource method), [1] get_origin_state_dict() (Dataset method), [1] get_package_endpoint_class() (PackageManager method), [1] get_package_file_content() (in module colrev.env.utils), [1] get_package_manager() (ReviewManager class method), [1] get_packages() (Settings method), [1] get_paper_keywords() (TEIParser method), [1] get_pdf() (PDFGet method), [1] (PDFGetPackageBaseClass method), [1], [2] get_pdf_get_man() (PDFGetMan method), [1] get_pdf_get_man_operation() (ReviewManager method), [1] get_pdf_get_operation() (ReviewManager method), [1] get_pdf_hash() (PDFRecord method), [1] get_pdf_prep_man_operation() (ReviewManager method), [1] get_pdf_prep_operation() (ReviewManager method), [1] get_pdf_qm() (ReviewManager method), [1] get_post_x_states() (RecordState class method), [1] get_preceding_states() (ProcessModel class method), [1] get_prep_man_operation() (ReviewManager method), [1] get_prep_operation() (ReviewManager method), [1] get_prescreen_operation() (ReviewManager method), [1] get_prev_feed_record() (SearchAPIFeed method), [1] get_priority_operations() (StatusStats method), [1] get_pull_operation() (ReviewManager method), [1] get_push_operation() (ReviewManager method), [1] get_qm() (ReviewManager method), [1] get_query() (DefaultSourceSettings method), [1] (SearchSource method), [1] get_query_filename() (Search method), [1] get_record_change_score() (in module colrev.record.record_similarity), [1] (PDFRecord class method), [1] (PrepRecord class method), [1] (Record class method), [1] get_record_header_items() (BIBLoader method), [1] get_record_ids_for_synthesis() (Data method), [1] get_record_similarity() (in module colrev.record.record_similarity), [1] (PDFRecord class method), [1] (PrepRecord class method), [1] (Record class method), [1] get_records_for_dedupe() (Dedupe class method), [1] get_references() (TEIParser method), [1] get_remote_url() (Dataset method), [1] get_remove_operation() (ReviewManager method), [1] get_repare() (ReviewManager method), [1] get_repo() (Dataset method), [1] get_resources() (ReviewManager class method), [1] get_review_instructions() (Advisor method), [1] get_review_manager() (in module colrev.ui_cli.cli), [1] get_review_status_report() (Status method), [1] get_screen_operation() (ReviewManager method), [1] get_screening_criteria() (Screen method), [1] get_screening_criteria_from_user_input() (in module colrev.packages.screen_utils), [1] get_search_files() (in module colrev.ui_cli.cli), [1] get_search_operation() (ReviewManager method), [1] get_settings_by_key() (EnvironmentManager method), [1] get_sharing_instructions() (Advisor method), [1] get_short_help_str() (SpecialHelpOrder method), [1] get_states_requiring_file() (RecordState class method), [1] get_status_operation() (ReviewManager method), [1] get_status_stats() (in module colrev.process.status), [1] (ReviewManager method), [1] get_target_filepath() (PDFGet method), [1] get_tei() (ReviewManager method), [1] get_tei_filename() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_tei_str() (TEIParser method), [1] get_template() (in module colrev.env.utils), [1] get_toc_items() (SQLiteIndexTOC method), [1] get_toc_key() (in module colrev.record.record_identifier), [1] (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_trace_operation() (ReviewManager method), [1] get_transitioned_records() (StatusStats method), [1] get_tree_hash() (Dataset method), [1] get_unique_filename() (Search method), [1] get_untracked_files() (Dataset method), [1] get_upgrade() (ReviewManager method), [1] get_usage() (SpecialHelpOrder method), [1] get_valid_transitions() (ProcessModel class method), [1] get_validate_operation() (ReviewManager method), [1] get_value() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] get_year_from_toc() (LocalIndex method), [1] GIT_URL colrev-clone command line option git_url (Clone attribute), [1] GitConflictError, [1] GitNotAvailableError, [1] GrobidService (class in colrev.env.grobid_service), [1] group() (SpecialHelpOrder method), [1] group_class (SpecialHelpOrder attribute), [1]

H

handle_new_entry() (in module colrev.loader.bib), [1] has_changes() (Dataset method), [1] has_endpoint() (Package method), [1] (PackageDoc method), [1] has_fatal_quality_defects() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] has_pdf_defects() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1]

has_quality_defects() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] has_record_changes() (Dataset method), [1] has_untracked_search_records() (Dataset method), [1] heuristic() (SearchSourcePackageBaseClass class method), [1], [2] high_level_operation (ReviewManager attribute), [1] HTMLTagChecker (class in colrev.record.qm.checkers.html_tags), [1]

I

IdenticalValuesChecker (class in colrev.record.qm.checkers.identical_values_between_title_and_container), [1] IDPattern (class in colrev.constants), [1] IDSetter (class in colrev.record.record_id_setter), [1] ignore_defect() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] ignore_unknown_options (SpecialHelpOrder attribute), [1] ignored_defect() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] import_package_docs() (PackageDoc method), [1] import_pdf() (PDFGet method), [1] import_table() (Prescreen method), [1] ImportException, [1] in_ci_environment() (ReviewManager class method), [1] in_test_environment() (ReviewManager class method), [1] in_virtualenv() (Checker class method), [1] (ReviewManager method), [1] include_all_in_screen() (Screen method), [1] include_records() (Prescreen method), [1] IncompleteFieldChecker (class in colrev.record.qm.checkers.incomplete_field), [1] InconsistentContentChecker (class in colrev.record.qm.checkers.inconsistent_content), [1] InconsistentWithDOIMetadataChecker (class in colrev.record.qm.checkers.inconsistent_with_doi_metadata), [1] InconsistentWithEntrytypeChecker (class in colrev.record.qm.checkers.inconsistent_with_entrytype), [1] index() (LocalIndexBuilder method), [1] index_colrev_project() (LocalIndexBuilder method), [1]

index_journal_rankings() (LocalIndexBuilder method), [1] index_records() (LocalIndexBuilder method), [1] initialize() (ReviewTypePackageBaseClass method), [1], [2] Initializer (class in colrev.ops.init), [1] inplace_change() (in module colrev.env.utils), [1] insert() (SQLiteIndexRecord method), [1] insert_df() (SQLiteIndexRankings method), [1] install() (PackageManager method), [1] install_curated_resource() (Resources method), [1] install_project() (PackageManager method), [1] InvalidLanguageCodeException, [1] InvalidPDFException, [1] InvalidQueryException, [1] InvalidSettingsError, [1] invoke() (SpecialHelpOrder method), [1] is_curated_masterdata_repo() (Settings method), [1] is_curated_repo() (Settings method), [1] is_curated_source() (DefaultSourceSettings method), [1] (SearchSource method), [1] is_installed() (PackageManager method), [1] is_md_source() (DefaultSourceSettings method), [1] (SearchSource method), [1] is_retracted() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] ISBNPatternChecker (class in colrev.record.qm.checkers.isbn_not_matching_pattern), [1]

J

JSONLoader (class in colrev.loader.json), [1]

L

LanguageChecker (class in colrev.record.qm.checkers.language_unknown), [1] LanguageFormatChecker (class in colrev.record.qm.checkers.language_format_error), [1] LanguageService (class in colrev.env.language_service), [1] link_pdf() (PDFGet method), [1] list_commands() (SpecialHelpOrder method), [1] list_commands_for_help() (SpecialHelpOrder method), [1] Load (class in colrev.ops.load), [1] load() (BIBLoader method), [1] (ENLLoader method), [1] (in module colrev.loader.load_utils), [1] (JSONLoader method), [1] (Loader method), [1] (MarkdownLoader method), [1] (NBIBLoader method), [1] (RISLoader method), [1] (SearchSourcePackageBaseClass class method), [1], [2] (TableLoader method), [1] load_active_sources() (Load method), [1] load_complementary_material_keywords() (in module colrev.env.utils), [1] load_complementary_material_prefixes() (in module colrev.env.utils), [1] load_complementary_material_strings() (in module colrev.env.utils), [1] load_dedupe_false_negatives() (in module colrev.ui_cli.dedupe_errors), [1] load_dedupe_false_positives() (in module colrev.ui_cli.dedupe_errors), [1] load_df() (in module colrev.loader.load_utils), [1] (in module colrev.ops.colrev_pandas), [1]

load_environment_registry() (EnvironmentManager method), [1] load_records_dict() (Dataset method), [1] (Upgrade method), [1] load_records_from_history() (Dataset method), [1] load_records_list() (BIBLoader method), [1] (ENLLoader method), [1] (JSONLoader method), [1] (Loader method), [1] (MarkdownLoader method), [1] (NBIBLoader method), [1] (RISLoader method), [1] (TableLoader method), [1] load_resolved_papers() (in module colrev.ops.colrev_pandas), [1] load_settings() (in module colrev.settings), [1] (ReviewManager method), [1] load_source_records() (Load method), [1] Loader (class in colrev.loader.loader), [1] LoadFormatter (class in colrev.loader.load_utils_formatter), [1] loads() (in module colrev.loader.load_utils), [1] local_repos() (EnvironmentManager method), [1] LocalIndex (class in colrev.env.local_index), [1] LocalIndexBuilder (class in colrev.env.local_index_builder), [1] LocalIndexFields (class in colrev.constants), [1]

M

main() (in module colrev.hooks.check), [1] (in module colrev.hooks.format), [1] (in module colrev.hooks.report), [1] (in module colrev.hooks.share), [1] (in module colrev.package_manager.check), [1] (in module colrev.package_manager.init), [1] (in module colrev.ui_cli.search_backward_selective), [1] (SpecialHelpOrder method), [1] (Upgrade method), [1] make_context() (SpecialHelpOrder method), [1] make_parser() (SpecialHelpOrder method), [1] mark_references() (TEIParser method), [1] MarkdownLoader (class in colrev.loader.md), [1] masterdata_is_curated() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] matches() (in module colrev.record.record_similarity), [1] md_imported (RecordState attribute), [1] md_needs_manual_preparation (RecordState attribute), [1] md_prepared (RecordState attribute), [1] md_processed (RecordState attribute), [1] md_retrieved (RecordState attribute), [1] Merge (class in colrev.ops.merge), [1] merge() (in module colrev.record.record_merger), [1] (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] merge_based_on_global_ids() (Dedupe method), [1] merge_records() (Dedupe method), [1] MissingDependencyError, [1] MissingFieldChecker (class in colrev.record.qm.checkers.missing_field), [1] MissingRecordQualityRuleSpecification, [1] module colrev colrev.constants, [1] colrev.dataset, [1] colrev.env, [1] colrev.env.docker_manager, [1] colrev.env.environment_manager, [1] colrev.env.grobid_service, [1] colrev.env.language_service, [1] colrev.env.local_index, [1] colrev.env.local_index_builder, [1] colrev.env.local_index_prep, [1] colrev.env.local_index_sqlite, [1] colrev.env.resources, [1] colrev.env.tei_parser, [1] colrev.env.utils, [1] colrev.exceptions, [1] colrev.hooks, [1] colrev.hooks.check, [1] colrev.hooks.format, [1] colrev.hooks.report, [1] colrev.hooks.share, [1] colrev.loader, [1] colrev.loader.bib, [1] colrev.loader.enl, [1] colrev.loader.json, [1] colrev.loader.load_utils, [1] colrev.loader.load_utils_formatter, [1] colrev.loader.load_utils_name_formatter, [1] colrev.loader.loader, [1] colrev.loader.md, [1] colrev.loader.nbib, [1] colrev.loader.ris, [1] colrev.loader.table, [1] colrev.logger, [1] colrev.ops, [1] colrev.ops.advisor, [1] colrev.ops.check, [1] colrev.ops.checker, [1] colrev.ops.clone, [1] colrev.ops.colrev_pandas, [1] colrev.ops.commit, [1] colrev.ops.correct, [1] colrev.ops.data, [1] colrev.ops.dedupe, [1] colrev.ops.distribute, [1] colrev.ops.init, [1] colrev.ops.load, [1] colrev.ops.merge, [1] colrev.ops.pdf_get, [1] colrev.ops.pdf_get_man, [1] colrev.ops.pdf_prep, [1] colrev.ops.pdf_prep_man, [1] colrev.ops.prep, [1] colrev.ops.prep_debug, [1] colrev.ops.prep_man, [1] colrev.ops.prescreen, [1] colrev.ops.pull, [1] colrev.ops.push, [1] colrev.ops.remove, [1] colrev.ops.repare, [1] colrev.ops.screen, [1] colrev.ops.search, [1] colrev.ops.search_api_feed, [1] colrev.ops.status, [1] colrev.ops.trace, [1] colrev.ops.upgrade, [1] colrev.ops.validate, [1] colrev.package_manager, [1] colrev.package_manager.check, [1] colrev.package_manager.colrev_internal_packages, [1] colrev.package_manager.doc_registry_manager, [1] colrev.package_manager.init, [1] colrev.package_manager.package, [1] colrev.package_manager.package_base_classes, [1] colrev.package_manager.package_manager, [1] colrev.package_manager.package_settings, [1] colrev.packages, [1] colrev.packages.screen_utils, [1] colrev.paths, [1] colrev.process, [1] colrev.process.model, [1] colrev.process.operation, [1] colrev.process.status, [1] colrev.record, [1] colrev.record.qm, [1] colrev.record.qm.checkers, [1] colrev.record.qm.checkers.container_title_abbreviated, [1] colrev.record.qm.checkers.doi_not_matching_pattern, [1] colrev.record.qm.checkers.erroneous_symbol_in_field, [1] colrev.record.qm.checkers.erroneous_term_in_field, [1] colrev.record.qm.checkers.erroneous_title_field, [1] colrev.record.qm.checkers.html_tags, [1] colrev.record.qm.checkers.identical_values_between_title_and_container, [1] colrev.record.qm.checkers.incomplete_field, [1] colrev.record.qm.checkers.inconsistent_content, [1] colrev.record.qm.checkers.inconsistent_with_doi_metadata, [1] colrev.record.qm.checkers.inconsistent_with_entrytype, [1] colrev.record.qm.checkers.isbn_not_matching_pattern, [1] colrev.record.qm.checkers.language_format_error, [1] colrev.record.qm.checkers.language_unknown, [1] colrev.record.qm.checkers.missing_field, [1] colrev.record.qm.checkers.mostly_all_caps, [1] colrev.record.qm.checkers.name_abbreviated, [1] colrev.record.qm.checkers.name_format_separators, [1] colrev.record.qm.checkers.name_format_titles, [1] colrev.record.qm.checkers.name_particles, [1] colrev.record.qm.checkers.page_range, [1] colrev.record.qm.checkers.pubmedid_not_matching_pattern, [1] colrev.record.qm.checkers.record_not_in_toc, [1] colrev.record.qm.checkers.thesis_with_multiple_authors, [1] colrev.record.qm.checkers.year_format, [1] colrev.record.qm.pdf_checkers, [1] colrev.record.qm.pdf_checkers.author_not_in_pdf, [1] colrev.record.qm.pdf_checkers.no_text_in_pdf, [1] colrev.record.qm.pdf_checkers.pdf_incomplete, [1] colrev.record.qm.pdf_checkers.title_not_in_pdf, [1] colrev.record.qm.quality_model, [1] colrev.record.record, [1] colrev.record.record_id_setter, [1] colrev.record.record_identifier, [1] colrev.record.record_merger, [1] colrev.record.record_pdf, [1] colrev.record.record_prep, [1] colrev.record.record_similarity, [1] colrev.review_manager, [1] colrev.settings, [1] colrev.ui_cli, [1] colrev.ui_cli.add_package_to_settings, [1] colrev.ui_cli.cli, [1] colrev.ui_cli.cli_status_printer, [1] colrev.ui_cli.cli_validation, [1] colrev.ui_cli.dedupe_errors, [1] colrev.ui_cli.detect_and_add_source, [1] colrev.ui_cli.search_backward_selective, [1] colrev.ui_cli.setup_custom_scripts, [1] colrev.ui_cli.show_printer, [1] colrev.writer, [1] colrev.writer.bib, [1] colrev.writer.csv, [1] colrev.writer.excel, [1] colrev.writer.ris, [1] colrev.writer.write_utils, [1]

MostlyAllCapsFieldChecker (class in colrev.record.qm.checkers.mostly_all_caps), [1] mro() (SortedEnumMeta method), [1]

N

na (EndpointType attribute), [1] name (SpecialHelpOrder attribute), [1] NameAbbreviatedChecker (class in colrev.record.qm.checkers.name_abbreviated), [1] NameFormatSeparatorsChecker (class in colrev.record.qm.checkers.name_format_separators), [1] NameFormatTitleChecker (class in colrev.record.qm.checkers.name_format_titles), [1] NameParser (class in colrev.loader.load_utils_name_formatter), [1] NameParticlesChecker (class in colrev.record.qm.checkers.name_particles), [1] NBIBLoader (class in colrev.loader.nbib), [1] NextLine, [1], [2], [3], [4], [5] NonEmptyDirectoryError, [1] NoRecordsError, [1] NoRecordsToImport, [1] NotEnoughDataToIdentifyException, [1] NotFeedIdentifiableException, [1] notified_next_operation (ReviewManager attribute), [1] notify() (CheckOperation method), [1] (Data method), [1] (Dedupe method), [1] (Distribute method), [1] (Load method), [1] (Merge method), [1] (Operation method), [1] (PDFGet method), [1] (PDFGetMan method), [1] (PDFPrep method), [1] (PDFPrepMan method), [1] (Prep method), [1] (PrepDebug method), [1] (PrepMan method), [1] (Prescreen method), [1] (Pull method), [1] (Push method), [1] (Remove method), [1] (Repare method), [1] (Screen method), [1] (Search method), [1] (Status method), [1] (Trace method), [1] (Upgrade method), [1] (Validate method), [1]

NotTOCIdentifiableException, [1]

O

Operation (class in colrev.process.operation), [1]

OperationsType (class in colrev.constants), [1] OriginError, [1]

P

Package (class in colrev.package_manager.package), [1] PackageDoc (class in colrev.package_manager.doc_registry_manager), [1] PackageManager (class in colrev.package_manager.package_manager), [1] PackageParameterError, [1] PackageSettingMustStartWithPackagesException, [1] PageRangeChecker (class in colrev.record.qm.checkers.page_range), [1] ParameterError, [1] params (SpecialHelpOrder attribute), [1] parse_args() (SpecialHelpOrder method), [1] parse_names() (in module colrev.loader.load_utils_name_formatter), [1] parse_names_in_records() (in module colrev.loader.load_utils_name_formatter), [1] parse_provenance() (in module colrev.loader.bib), [1] parse_string() (NameParser method), [1] ParseError, [1], [2], [3], [4], [5] path (PDFRecord attribute), [1] (ReviewManager attribute), [1] PathManager (class in colrev.paths), [1] pdf_get (EndpointType attribute), [1] pdf_get_man (EndpointType attribute), [1] pdf_get_man() (PDFGetManPackageBaseClass method), [1], [2] pdf_get_man_record() (PDFGetMan method), [1] pdf_imported (RecordState attribute), [1] pdf_needs_manual_preparation (RecordState attribute), [1] pdf_needs_manual_retrieval (RecordState attribute), [1] pdf_not_available (RecordState attribute), [1] pdf_prep (EndpointType attribute), [1] pdf_prep_man (EndpointType attribute), [1] pdf_prep_man() (PDFPrepManPackageBaseClass method), [1], [2] pdf_prep_man_stats() (PDFPrepMan method), [1] pdf_prepared (RecordState attribute), [1] pdf_required_for_screen_and_synthesis (PDFGetSettings attribute), [1] PDFDefectCodes (class in colrev.constants), [1] PDFGet (class in colrev.ops.pdf_get), [1] PDFGetMan (class in colrev.ops.pdf_get_man), [1] PDFGetManPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PDFGetPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PDFGetSettings (class in colrev.settings), [1] PDFHashError, [1] PDFIncompletenessChecker (class in colrev.record.qm.pdf_checkers.pdf_incomplete), [1] PDFPathType (class in colrev.constants), [1] PDFPrep (class in colrev.ops.pdf_prep), [1] PDFPrepMan (class in colrev.ops.pdf_prep_man), [1] PDFPrepManPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PDFPrepPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PDFPrepSettings (class in colrev.settings), [1] PDFRecord (class in colrev.record.record_pdf), [1] pdfs_prepared_manually() (PDFPrepMan method), [1] pdfs_retrieved_manually() (PDFGetMan method), [1] percent_upper_chars() (in module colrev.env.utils), [1] PortAlreadyRegisteredException, [1] Prep (class in colrev.ops.prep), [1] prep (EndpointType attribute), [1] prep_link_md() (SearchSourcePackageBaseClass method), [1], [2]

prep_man (EndpointType attribute), [1] prep_man_langs() (PrepMan method), [1] prep_man_stats() (PrepMan method), [1] prep_pdf() (PDFPrepPackageBaseClass method), [1], [2] PreparationBreak, [1] prepare() (Prep method), [1] (PrepDebug method), [1] (PrepPackageBaseClass method), [1], [2] (SearchSourcePackageBaseClass method), [1], [2] prepare_manual() (PrepManPackageBaseClass method), [1], [2] prepare_pdf() (PDFPrep method), [1] prepare_record_for_indexing() (in module colrev.env.local_index_prep), [1] prepare_record_for_return() (in module colrev.env.local_index_prep), [1] PrepDebug (class in colrev.ops.prep_debug), [1] PrepMan (class in colrev.ops.prep_man), [1] PrepManPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PrepPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PrepRecord (class in colrev.record.record_prep), [1] PrepRound (class in colrev.settings), [1] PrepSettings (class in colrev.settings), [1] Prescreen (class in colrev.ops.prescreen), [1] prescreen (EndpointType attribute), [1] prescreen() (Prescreen method), [1] prescreen_exclude() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] PrescreenPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] PrescreenSettings (class in colrev.settings), [1] print_citation_format() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] print_collaboration_instructions() (in module colrev.ui_cli.cli_status_printer), [1] print_diff() (in module colrev.ui_cli.cli_validation), [1] print_diff_pair() (in module colrev.ui_cli.cli_validation), [1] print_environment_instructions() (in module colrev.ui_cli.cli_status_printer), [1] print_progress() (in module colrev.ui_cli.cli_status_printer), [1] print_project_status() (in module colrev.ui_cli.cli_status_printer), [1] print_review_instructions() (in module colrev.ui_cli.cli_status_printer), [1] print_sample() (in module colrev.ui_cli.show_printer), [1] print_string_diff() (in module colrev.ui_cli.cli_validation), [1] print_venv_notes() (in module colrev.ui_cli.show_printer), [1] process_key_value() (in module colrev.loader.bib), [1] process_lines() (in module colrev.loader.bib), [1] ProcessModel (class in colrev.process.model), [1] ProcessOrderViolation, [1] ProjectSettings (class in colrev.settings), [1] propagated_id() (Dataset method), [1] PropagatedIDChange, [1] Protocol (class in colrev.settings), [1] PubmedIDPatternChecker (class in colrev.record.qm.checkers.pubmedid_not_matching_pattern), [1] Pull (class in colrev.ops.pull), [1] pull_if_repo_clean() (Dataset method), [1] Push (class in colrev.ops.push), [1]

Q

QualityModel (class in colrev.record.qm.quality_model), [1]

R

read_next_record() (Dataset method), [1] reading_heuristics() (Data method), [1] Record (class in colrev.record.record), [1] record_field_inconsistencies (InconsistentWithEntrytypeChecker attribute), [1] record_field_requirements (MissingFieldChecker attribute), [1] RecordNotFoundException, [1] RecordNotFoundInPrepSourceException, [1] RecordNotIndexableException, [1] RecordNotInIndexException, [1] RecordNotInRepoException, [1] RecordNotInTOCChecker (class in colrev.record.qm.checkers.record_not_in_toc), [1] RecordNotInTOCException, [1] RecordNotParsableException, [1] records_changed() (Dataset method), [1] RecordState (class in colrev.constants), [1] register() (in module colrev.record.qm.checkers.container_title_abbreviated), [1] (in module colrev.record.qm.checkers.doi_not_matching_pattern), [1] (in module colrev.record.qm.checkers.erroneous_symbol_in_field), [1] (in module colrev.record.qm.checkers.erroneous_term_in_field), [1] (in module colrev.record.qm.checkers.erroneous_title_field), [1] (in module colrev.record.qm.checkers.html_tags), [1] (in module colrev.record.qm.checkers.identical_values_between_title_and_container), [1] (in module colrev.record.qm.checkers.incomplete_field), [1] (in module colrev.record.qm.checkers.inconsistent_content), [1] (in module colrev.record.qm.checkers.inconsistent_with_doi_metadata), [1] (in module colrev.record.qm.checkers.inconsistent_with_entrytype), [1] (in module colrev.record.qm.checkers.isbn_not_matching_pattern), [1] (in module colrev.record.qm.checkers.language_format_error), [1] (in module colrev.record.qm.checkers.language_unknown), [1] (in module colrev.record.qm.checkers.missing_field), [1] (in module colrev.record.qm.checkers.mostly_all_caps), [1] (in module colrev.record.qm.checkers.name_abbreviated), [1] (in module colrev.record.qm.checkers.name_format_separators), [1] (in module colrev.record.qm.checkers.name_format_titles), [1] (in module colrev.record.qm.checkers.name_particles), [1] (in module colrev.record.qm.checkers.page_range), [1] (in module colrev.record.qm.checkers.pubmedid_not_matching_pattern), [1] (in module colrev.record.qm.checkers.record_not_in_toc), [1] (in module colrev.record.qm.checkers.thesis_with_multiple_authors), [1] (in module colrev.record.qm.checkers.year_format), [1] (in module colrev.record.qm.pdf_checkers.author_not_in_pdf), [1] (in module colrev.record.qm.pdf_checkers.no_text_in_pdf), [1] (in module colrev.record.qm.pdf_checkers.pdf_incomplete), [1] (in module colrev.record.qm.pdf_checkers.title_not_in_pdf), [1] register_checker() (QualityModel method), [1] register_ports() (EnvironmentManager method), [1] register_repo() (EnvironmentManager method), [1] reinitialize_sqlite_db() (LocalIndexBuilder method), [1] relink_pdfs() (PDFGet method), [1] remote_ahead() (Dataset method), [1] Remove (class in colrev.ops.remove), [1] remove_accents() (in module colrev.env.utils), [1] remove_field() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] remove_field_provenance_note() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] remove_md_origins() (Validate method), [1] rename_field() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] rename_pdfs() (PDFGet method), [1] Repare (class in colrev.ops.repare), [1] repo_initialized() (Dataset method), [1] RepoInitError, [1] RepoSetupError, [1]

require_prov() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] reset_log_if_no_changes() (Dataset method), [1] reset_pdf_provenance_notes() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] reset_report_logger() (in module colrev.logger), [1] (ReviewManager method), [1] Resources (class in colrev.env.resources), [1] result_callback() (SpecialHelpOrder method), [1] retrieve() (LocalIndex method), [1] retrieve_based_on_colrev_pdf_id() (LocalIndex method), [1] retrieve_from_toc() (LocalIndex method), [1] retrieve_package_file() (in module colrev.env.utils), [1] rev_excluded (RecordState attribute), [1] rev_included (RecordState attribute), [1] rev_prescreen_excluded (RecordState attribute), [1] rev_prescreen_included (RecordState attribute), [1] rev_synthesized (RecordState attribute), [1] review_type (EndpointType attribute), [1] ReviewManager (class in colrev.review_manager), [1] ReviewManagerNotNotifiedError, [1] ReviewTypePackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] RISLoader (class in colrev.loader.ris), [1] run() (AuthorNotInPDFChecker method), [1] (ContainerTitleAbbreviatedChecker method), [1] (DOIPatternChecker method), [1] (ErroneousSymbolInFieldChecker method), [1] (ErroneousTermInFieldChecker method), [1] (ErroneousTitleFieldChecker method), [1] (HTMLTagChecker method), [1] (IdenticalValuesChecker method), [1] (IncompleteFieldChecker method), [1] (InconsistentContentChecker method), [1] (InconsistentWithDOIMetadataChecker method), [1] (InconsistentWithEntrytypeChecker method), [1] (ISBNPatternChecker method), [1] (LanguageChecker method), [1] (LanguageFormatChecker method), [1] (LoadFormatter method), [1] (MissingFieldChecker method), [1] (MostlyAllCapsFieldChecker method), [1] (NameAbbreviatedChecker method), [1] (NameFormatSeparatorsChecker method), [1] (NameFormatTitleChecker method), [1] (NameParticlesChecker method), [1] (PageRangeChecker method), [1] (PDFIncompletenessChecker method), [1] (PubmedIDPatternChecker method), [1] (QualityModel method), [1] (RecordNotInTOCChecker method), [1] (TextInPDFChecker method), [1] (ThesisWithMultipleAuthorsChecker method), [1] (TitleNotInPDFChecker method), [1] (YearFormatChecker method), [1] run_db_search() (Search method), [1] run_dedupe() (DedupePackageBaseClass method), [1], [2] run_fix_bib_file() (in module colrev.loader.bib), [1] run_pdf_quality_model() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] run_prescreen() (PrescreenPackageBaseClass method), [1], [2] run_quality_model() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] run_resolve_crossref() (in module colrev.loader.bib), [1] run_screen() (ScreenPackageBaseClass method), [1], [2]

S

save() (in module colrev.ops.colrev_pandas), [1] (SearchAPIFeed method), [1] save_environment_registry() (EnvironmentManager method), [1] save_records_dict() (Dataset method), [1] (Upgrade method), [1] save_records_dict_to_file() (Dataset method), [1] save_settings() (in module colrev.settings), [1] (ReviewManager method), [1] SCOPE colrev-validate command line option Screen (class in colrev.ops.screen), [1] screen (EndpointType attribute), [1] screen() (Screen method), [1] ScreenCriterion (class in colrev.settings), [1] ScreenCriterionType (class in colrev.constants), [1] ScreenPackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] ScreenSettings (class in colrev.settings), [1] Search (class in colrev.ops.search), [1] search() (LocalIndex method), [1] (SearchSourcePackageBaseClass method), [1], [2] (SQLiteIndexRecord method), [1] search_source (EndpointType attribute), [1] SearchAPIFeed (class in colrev.ops.search_api_feed), [1] SearchNotAutomated, [1] SearchSettings (class in colrev.settings), [1] SearchSource (class in colrev.settings), [1] SearchSourceException, [1] SearchSourceHeuristicStatus (class in colrev.constants), [1] SearchSourcePackageBaseClass (class in colrev.package_manager.package_base_classes), [1], [2] SearchType (class in colrev.constants), [1] select() (SQLiteIndexRankings method), [1] select_format() (in module colrev.ui_cli.cli), [1] select_search_type() (Search method), [1] ServiceNotAvailableException, [1] set_data() (PrepMan method), [1] set_ids() (Dataset method), [1] (IDSetter method), [1] (Prep method), [1] (PrepDebug method), [1] set_masterdata_complete() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] set_masterdata_consistent() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1]

set_masterdata_curated() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] set_nr_pages_in_pdf() (PDFRecord method), [1] set_pdf_man_prepared() (PDFPrepMan method), [1] set_screening_criteria() (Screen method), [1] set_status() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] set_text_from_pdf() (PDFRecord method), [1] Settings (class in colrev.settings), [1] setup_custom_script() (Data method), [1] (PDFGet method), [1] (PDFPrep method), [1] (Prep method), [1] (PrepDebug method), [1] (Prescreen method), [1] (Screen method), [1] setup_custom_search_script() (in module colrev.ui_cli.setup_custom_scripts), [1] setup_for_load() (DefaultSourceSettings method), [1] (SearchSource method), [1] setup_logger() (in module colrev.logger), [1] setup_report_logger() (in module colrev.logger), [1] setup_source_for_load() (Load method), [1] ShareStatReq (class in colrev.constants), [1] shell_complete() (SpecialHelpOrder method), [1] SortedEnumMeta (class in colrev.constants), [1] source_identifier (SearchAPIFeed property), [1] SpecialHelpOrder (class in colrev.ui_cli.cli), [1] split_tex_string() (in module colrev.loader.load_utils_name_formatter), [1] SQLiteIndex (class in colrev.env.local_index_sqlite), [1] SQLiteIndexRankings (class in colrev.env.local_index_sqlite), [1] SQLiteIndexRecord (class in colrev.env.local_index_sqlite), [1] SQLiteIndexTOC (class in colrev.env.local_index_sqlite), [1] STANDARDIZED_FIELD_KEYS (FieldSet attribute), [1] start() (GrobidService method), [1] stash_unstaged_changes() (Dataset method), [1] Status (class in colrev.ops.status), [1] StatusFieldValueError, [1] StatusStats (class in colrev.process.status), [1] StatusStatsCurrently (class in colrev.process.status), [1] StatusStatsOverall (class in colrev.process.status), [1] StatusTransitionError, [1] store_current_key_value() (in module colrev.loader.bib), [1]

T

TableLoader (class in colrev.loader.table), [1] TEIException, [1] TEIParser (class in colrev.env.tei_parser), [1] TEITimeoutException, [1] TemplateNotAvailableError, [1] TextInPDFChecker (class in colrev.record.qm.pdf_checkers.no_text_in_pdf), [1] ThesisWithMultipleAuthorsChecker (class in colrev.record.qm.checkers.thesis_with_multiple_authors), [1] TitleNotInPDFChecker (class in colrev.record.qm.pdf_checkers.title_not_in_pdf), [1]

to_dataframe() (in module colrev.writer.csv), [1] (in module colrev.writer.excel), [1] to_info_dict() (SpecialHelpOrder method), [1] to_screen() (Screen method), [1] to_string() (in module colrev.writer.bib), [1] (in module colrev.writer.ris), [1] (in module colrev.writer.write_utils), [1] TOCNotAvailableException, [1] Trace (class in colrev.ops.trace), [1]

U

unify_pages_field() (PrepRecord method), [1] unify_to_iso_639_3_language_codes() (LanguageService method), [1] unmerge_records() (Dedupe method), [1] UnstagedGitChangesError, [1] UnsupportedImportFormatError, [1] update() (DocRegistryManager method), [1] (SQLiteIndexRecord method), [1] update_by_record() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] update_colrev_pdf_ids() (PDFPrep method), [1]

update_config() (ReviewManager method), [1] update_data() (DataPackageBaseClass method), [1], [2] update_field() (PDFRecord method), [1] (PrepRecord method), [1] (Record method), [1] update_gitignore() (Dataset method), [1] update_record_status_matrix() (DataPackageBaseClass method), [1], [2] update_registry() (EnvironmentManager method), [1] update_report() (Commit method), [1] update_status_yaml() (ReviewManager method), [1] Upgrade (class in colrev.ops.upgrade), [1]

V

Validate (class in colrev.ops.validate), [1] validate_filename() (DefaultSourceSettings class method), [1] (SearchSource class method), [1] validate_iso_639_3_language_codes() (LanguageService method), [1]

validate_merge_prescreen_screen() (Validate method), [1] validate_module_name() (in module colrev.package_manager.init), [1] validate_version() (in module colrev.package_manager.init), [1] verbose_mode (ReviewManager attribute), [1]

W

write_file() (in module colrev.writer.bib), [1] (in module colrev.writer.csv), [1] (in module colrev.writer.excel), [1] (in module colrev.writer.ris), [1] (in module colrev.writer.write_utils), [1]

Y

YearFormatChecker (class in colrev.record.qm.checkers.year_format), [1]