Index

_

__version__ module

A

age_cap_label (scripts.security.phi_scrub.PHIScrubConfig attribute) age_cap_threshold (scripts.security.phi_scrub.PHIScrubConfig attribute) allowed (scripts.ai_assistant.ui.model_policy.ModelGateResult attribute) ampm (scripts.extraction.io.clinical_dates.ParsedDate attribute) AnalysisResult (class in scripts.ai_assistant.analytical_engine) apply_llm_config() (in module scripts.ai_assistant.ui.wizard) ArtifactVersionError as_log_block() (scripts.utils.errors.RePORTError method) as_user_message() (scripts.utils.errors.RePORTError method) assert_clean_zone() (in module scripts.security.secure_env)

assert_not_raw() (in module scripts.security.secure_env) assert_output_not_in_data() (in module scripts.security.secure_env) assert_output_zone() (in module scripts.security.secure_env) assert_trio_bundle_zone() (in module scripts.security.secure_env) assert_write_zone() (in module scripts.security.secure_env) atomic_write_dataframe_jsonl() (in module scripts.extraction.io.file_io) atomic_write_json() (in module scripts.extraction.io.file_io) atomic_write_jsonl() (in module scripts.extraction.io.file_io) ATOMIC_WRITE_SUFFIX (in module scripts.extraction.io.file_io) attach_to_logger() (in module scripts.utils.log_hygiene) audit files

B

birthdate_pattern (scripts.security.phi_scrub.PHIScrubConfig attribute) blocked (scripts.security.kanon_gate.KAnonResult attribute) (scripts.security.kanon_gate.LDiversityResult attribute) (scripts.security.phi_gate.PHIGateResult attribute)

BLOCKING_PATTERNS (in module scripts.security.phi_patterns) bootstrap_key() (in module scripts.security.phi_scrub) build() (scripts.ai_assistant.analytical_engine.CohortBuilder method) build_variables_reference() (in module scripts.extraction.build_variables_reference)

C

cache_hit (scripts.extraction.pdf_pipeline.ExtractionResult attribute) cap_numeric() (in module scripts.security.phi_scrub) cap_rule_for() (scripts.security.phi_scrub.PHIScrubConfig method) cap_rules (scripts.security.phi_scrub.PHIScrubConfig attribute) CapRule (class in scripts.security.phi_scrub) cause (scripts.utils.errors.RePORTError attribute) caveats (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) clean_cross_form_duplicates() (in module scripts.extraction.dedup) clean_duplicate_columns() (in module scripts.extraction.dedup) clean_existing_jsons() (in module scripts.extraction.extract_pdf_data) clean_record_for_json() (in module scripts.extraction.dataset_pipeline) clean_trio_datasets() (in module scripts.extraction.dataset_cleanup) cleanup_old_logs() (in module scripts.utils.logging_system) clear() (scripts.ai_assistant.keystore.KeyStore method) (scripts.ai_assistant.tool_cache.ToolCache method)

CLINICAL_PHRASES (in module scripts.security.phi_allowlist) CLINICAL_SINGLE_WORDS (in module scripts.security.phi_allowlist) code_succeeded (scripts.extraction.pdf_pipeline.ExtractionResult attribute) cohort_name (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) CohortBuilder (class in scripts.ai_assistant.analytical_engine) COMMON_FIRST_NAMES (in module scripts.security.phi_allowlist) COMMON_LAST_NAMES (in module scripts.security.phi_allowlist) compliance_posture (scripts.security.phi_scrub.PHIScrubConfig attribute) composer() (in module scripts.ai_assistant.ui.chat) compute_propagation_set() (in module scripts.extraction.cleanup_propagation) config module create_snapshot() (in module scripts.utils.snapshots) critical() (in module scripts.utils.logging_system) CustomFormatter (class in scripts.utils.logging_system)

D

data (scripts.extraction.pdf_pipeline.ExtractionResult attribute) data dictionary date_offset_days() (in module scripts.security.phi_scrub) date_patterns (scripts.security.phi_scrub.PHIScrubConfig attribute) debug() (in module scripts.utils.logging_system) DEFAULT_CHUNK_SIZE (in module scripts.utils.integrity) DEFAULT_JUNK_FILENAMES (in module scripts.extraction.io.file_discovery) describe_allowlist() (in module scripts.ai_assistant.ui.model_policy) descriptive (scripts.ai_assistant.analytical_engine.AnalysisResult attribute)

DescriptiveAnalyzer (class in scripts.ai_assistant.analytical_engine) detail() (scripts.utils.logging_system.VerboseLogger method) detect_study_name() (in module config) discover_dataset_files() (in module scripts.extraction.dataset_pipeline) discover_dictionary_files() (in module scripts.extraction.load_dictionary) discover_files() (in module scripts.extraction.io.file_discovery) DMY_VARIABLES (in module scripts.extraction.io.clinical_dates) drop_patterns (scripts.security.phi_scrub.PHIScrubConfig attribute) dropped_events (scripts.extraction.dataset_pipeline.ExtractionResult attribute) dt (scripts.extraction.io.clinical_dates.ParsedDate attribute)

E

emit_lineage_manifest() (in module scripts.utils.lineage) ensure_directories() (in module config) ensure_llm_config() (in module scripts.ai_assistant.ui.wizard) env_for_subprocess() (scripts.ai_assistant.keystore.KeyStore method) error() (in module scripts.utils.logging_system) errors (scripts.extraction.dataset_pipeline.ExtractionResult attribute) events (scripts.ai_assistant.analytical_engine.AnalysisResult attribute)

exception() (in module scripts.utils.logging_system) extract_datasets() (in module scripts.extraction.dataset_pipeline) extract_pdf() (in module scripts.extraction.pdf_pipeline) extract_pdfs_to_jsonl() (in module scripts.extraction.extract_pdf_data) extract_single_dataset() (in module scripts.extraction.dataset_pipeline) ExtractionResult (class in scripts.extraction.dataset_pipeline) (class in scripts.extraction.pdf_pipeline)

F

field_is_birthdate() (scripts.security.phi_scrub.PHIScrubConfig method) field_is_date() (scripts.security.phi_scrub.PHIScrubConfig method) field_is_drop() (scripts.security.phi_scrub.PHIScrubConfig method) field_is_id() (scripts.security.phi_scrub.PHIScrubConfig method) field_is_keep() (scripts.security.phi_scrub.PHIScrubConfig method) field_is_suppress_small_cell() (scripts.security.phi_scrub.PHIScrubConfig method) figures (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) FILE_ENCODING (in module scripts.extraction.io.file_io) file_processing() (scripts.utils.logging_system.VerboseLogger method) files_created (scripts.extraction.dataset_pipeline.ExtractionResult attribute)

files_found (scripts.extraction.dataset_pipeline.ExtractionResult attribute) filter() (scripts.utils.log_hygiene.PHIRedactingFilter method) Finding (class in scripts.lint_doc_freshness) findings (scripts.ai_assistant.phi_safe.UserPromptGuardResult attribute) (scripts.security.phi_gate.PHIGateResult attribute) format (scripts.extraction.io.clinical_dates.ParsedDate attribute) format() (scripts.utils.logging_system.CustomFormatter method) (scripts.utils.logging_system.JSONFormatter method) format_for_log() (in module scripts.utils.errors) format_for_user() (in module scripts.utils.errors)

G

generalize_rule_for() (scripts.security.phi_scrub.PHIScrubConfig method) generalize_rules (scripts.security.phi_scrub.PHIScrubConfig attribute) generalize_value() (in module scripts.security.phi_scrub) GeneralizeRule (class in scripts.security.phi_scrub) generate() (scripts.ai_assistant.analytical_engine.PlotGenerator method) generate_caveats() (scripts.ai_assistant.analytical_engine.ResultInterpreter method) get() (scripts.ai_assistant.keystore.KeyStore method) (scripts.ai_assistant.tool_cache.ToolCache method) get_agent() (in module scripts.ai_assistant.agent_graph) get_checkpointer() (in module scripts.ai_assistant.agent_graph) get_cohort() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) get_default_outcome() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) get_derived_variable() (scripts.ai_assistant.study_knowledge.StudyKnowledge method)

get_join_plan() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) get_keystore() (in module scripts.ai_assistant.keystore) get_log_file_path() (in module scripts.utils.logging_system) get_logger() (in module scripts.utils.logging_system) get_meta() (in module scripts.ai_assistant.ui.state) get_outcome() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) get_value_encoding() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) get_verbose_logger() (in module scripts.utils.logging_system) get_version() (in module scripts.artifact_versions) guard_rows_with_kanon() (in module scripts.ai_assistant.phi_safe) guard_rows_with_kanon_and_ldiv() (in module scripts.ai_assistant.phi_safe) guard_text() (in module scripts.ai_assistant.phi_safe) guard_user_prompt() (in module scripts.ai_assistant.phi_safe)

H

has() (scripts.ai_assistant.keystore.KeyStore method) has_time (scripts.extraction.io.clinical_dates.ParsedDate attribute) hash_bytes() (in module scripts.utils.integrity) hash_directory() (in module scripts.utils.step_cache) hash_file() (in module scripts.utils.integrity) (in module scripts.utils.step_cache)

hash_path() (in module scripts.utils.lineage) hero() (in module scripts.ai_assistant.ui.chat) hint (scripts.utils.errors.RePORTError attribute) hosted LLM

I

id_label_for() (scripts.security.phi_scrub.PHIScrubConfig method) id_patterns (scripts.security.phi_scrub.PHIScrubConfig attribute) IdRule (class in scripts.security.phi_scrub) info() (in module scripts.utils.logging_system) init_state() (in module scripts.ai_assistant.ui.state) inject_css() (in module scripts.ai_assistant.ui.shell) inject_wizard_css() (in module scripts.ai_assistant.ui.wizard) install_bridge() (in module scripts.ai_assistant.ui.shell) install_phi_redactor() (in module scripts.utils.log_hygiene) interaction (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) InteractionAnalyzer (class in scripts.ai_assistant.analytical_engine) interactive (scripts.ai_assistant.analytical_engine.PlotArtifacts attribute) interactive_figures (scripts.ai_assistant.analytical_engine.AnalysisResult attribute)

interpret_descriptive() (scripts.ai_assistant.analytical_engine.ResultInterpreter method) interpret_interaction() (scripts.ai_assistant.analytical_engine.ResultInterpreter method) interpret_multivariate() (scripts.ai_assistant.analytical_engine.ResultInterpreter method) interpret_univariate() (scripts.ai_assistant.analytical_engine.ResultInterpreter method) invoke_query() (in module scripts.ai_assistant.agent_graph) is_agent_readable() (in module scripts.ai_assistant.file_access) is_capable_model() (in module scripts.utils.llm_capabilities) is_clinical_free_text() (in module scripts.security.phi_allowlist) is_clinical_phrase() (in module scripts.security.phi_allowlist) is_dataframe_empty() (in module scripts.extraction.dataset_pipeline) is_dmy_variable() (in module scripts.extraction.io.clinical_dates) is_model_allowed_for_study_load() (in module scripts.ai_assistant.ui.model_policy) is_step_fresh() (in module scripts.utils.step_cache) items_list() (scripts.utils.logging_system.VerboseLogger method)

J

JSONFormatter (class in scripts.utils.logging_system)

JSONL_EXT (in module scripts.extraction.io.file_io) JSONLParseError

K

kanon_check() (in module scripts.security.kanon_gate) KAnonResult (class in scripts.security.kanon_gate)

keep_patterns (scripts.security.phi_scrub.PHIScrubConfig attribute) KeyStore (class in scripts.ai_assistant.keystore)

L

l_diversity_check() (in module scripts.security.kanon_gate) label (scripts.security.phi_scrub.CapRule attribute) (scripts.security.phi_scrub.IdRule attribute) latest_snapshot_name() (in module scripts.utils.snapshots) LDiversityResult (class in scripts.security.kanon_gate) line (scripts.lint_doc_freshness.Finding attribute) line_no (scripts.lint_doc_freshness.Finding attribute) LineageManifestError list_cohorts() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) list_concepts() (scripts.ai_assistant.study_knowledge.StudyKnowledge method) list_snapshots() (in module scripts.utils.snapshots)

llm_skipped_reason (scripts.extraction.pdf_pipeline.ExtractionResult attribute) llm_succeeded (scripts.extraction.pdf_pipeline.ExtractionResult attribute) load_json_object_line() (in module scripts.extraction.io.jsonl_reader) load_key() (in module scripts.security.phi_scrub) load_scrub_config() (in module scripts.security.phi_scrub) load_study_dictionary() (in module scripts.extraction.load_dictionary) local LLM log_errors() (in module scripts.utils.logging_system) log_execution_time() (in module scripts.utils.logging_system) log_time() (in module scripts.utils.logging_system) looks_like_real_name() (in module scripts.security.phi_allowlist)

M

main module main() (in module main) (in module scripts.ai_assistant.cli) (in module scripts.ai_assistant.sandbox.replicate) (in module scripts.ai_assistant.sandbox.runner) (in module scripts.ai_assistant.web_ui) (in module scripts.lint_doc_freshness) (in module scripts.utils.snapshots) make_preexec_fn() (in module scripts.ai_assistant.sandbox.limits) MANIFEST_VERSION (in module scripts.utils.step_cache) mapping (scripts.security.phi_scrub.GeneralizeRule attribute) mapping_name (scripts.security.phi_scrub.GeneralizeRule attribute) mask_small_cell() (in module scripts.security.kanon_gate) matches() (scripts.security.phi_scrub.CapRule method) (scripts.security.phi_scrub.GeneralizeRule method) (scripts.security.phi_scrub.IdRule method) max_jitter_days (scripts.security.phi_scrub.PHIScrubConfig attribute) message (scripts.utils.errors.RePORTError attribute) metric() (scripts.utils.logging_system.VerboseLogger method) ModelGateResult (class in scripts.ai_assistant.ui.model_policy) module __version__ config main scripts.ai_assistant.agent_graph scripts.ai_assistant.agent_prompts scripts.ai_assistant.agent_tools scripts.ai_assistant.analytical_engine scripts.ai_assistant.cli scripts.ai_assistant.file_access scripts.ai_assistant.keystore scripts.ai_assistant.phi_safe scripts.ai_assistant.sandbox.limits scripts.ai_assistant.sandbox.replicate scripts.ai_assistant.sandbox.runner scripts.ai_assistant.study_knowledge scripts.ai_assistant.tool_cache scripts.ai_assistant.ui.chat scripts.ai_assistant.ui.conversations scripts.ai_assistant.ui.model_policy scripts.ai_assistant.ui.providers scripts.ai_assistant.ui.shell scripts.ai_assistant.ui.state scripts.ai_assistant.ui.streaming scripts.ai_assistant.ui.wizard scripts.ai_assistant.web_ui scripts.artifact_versions scripts.extraction.build_variables_reference scripts.extraction.cleanup_propagation scripts.extraction.dataset_cleanup scripts.extraction.dataset_pipeline scripts.extraction.dedup scripts.extraction.extract_pdf_data scripts.extraction.io.clinical_dates scripts.extraction.io.file_discovery scripts.extraction.io.file_io scripts.extraction.io.jsonl_reader scripts.extraction.load_dictionary scripts.extraction.pdf_pipeline scripts.lint_doc_freshness scripts.security.kanon_gate scripts.security.phi_allowlist scripts.security.phi_gate scripts.security.phi_patterns scripts.security.phi_scrub scripts.security.secure_env scripts.utils.errors scripts.utils.integrity scripts.utils.lineage scripts.utils.llm_capabilities scripts.utils.log_hygiene scripts.utils.logging_system scripts.utils.secure_staging scripts.utils.snapshots scripts.utils.step_cache scripts.utils.telemetry

multivariate (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) MultivariateAnalyzer (class in scripts.ai_assistant.analytical_engine)

N

n (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) name (scripts.utils.telemetry.TelemetryLogger attribute)

NAMED_TEMP_PREFIX (in module scripts.extraction.io.file_io) narrative (scripts.ai_assistant.analytical_engine.AnalysisResult attribute)

O

ok (scripts.ai_assistant.phi_safe.UserPromptGuardResult attribute) on_custom_event() (scripts.utils.telemetry.TelemetryLogger method) on_llm_end() (scripts.utils.telemetry.TelemetryLogger method) on_tool_start() (scripts.utils.telemetry.TelemetryLogger method)

operation (scripts.utils.errors.RePORTError attribute) original (scripts.extraction.io.clinical_dates.ParsedDate attribute) orphan_quarantine_threshold (scripts.security.phi_scrub.PHIScrubConfig attribute) outcome (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) output_dir (scripts.extraction.dataset_pipeline.ExtractionResult attribute)

P

parse_date() (in module scripts.extraction.io.clinical_dates) ParsedDate (class in scripts.extraction.io.clinical_dates) path (scripts.lint_doc_freshness.Finding attribute) (scripts.utils.errors.RePORTError attribute) pattern (scripts.security.phi_scrub.CapRule attribute) (scripts.security.phi_scrub.GeneralizeRule attribute) (scripts.security.phi_scrub.IdRule attribute) pdf_name (scripts.extraction.pdf_pipeline.ExtractionResult attribute) PHI PHI key phi_gate_check() (in module scripts.security.phi_gate) phi_safe_return() (in module scripts.ai_assistant.phi_safe) PHIGateConfigError PHIGateResult (class in scripts.security.phi_gate) PHIKeyMissingError PHIKeyPermissionError PHIQuarantineOverflowError PHIRedactingFilter (class in scripts.utils.log_hygiene) PHISafetyError

PHIScrubConfig (class in scripts.security.phi_scrub) PHIScrubError PLOT_TYPES (scripts.ai_assistant.analytical_engine.PlotGenerator attribute) PlotArtifacts (class in scripts.ai_assistant.analytical_engine) PlotGenerator (class in scripts.ai_assistant.analytical_engine) preferred_or_installed_downgrade() (in module config) (in module scripts.ai_assistant.ui.providers) prepare_staging() (in module scripts.utils.secure_staging) process_csv_file() (in module scripts.extraction.load_dictionary) process_datasets() (in module scripts.extraction.dataset_pipeline) process_excel_file() (in module scripts.extraction.load_dictionary) process_single_pdf() (in module scripts.extraction.extract_pdf_data) processing_time (scripts.extraction.dataset_pipeline.ExtractionResult attribute) production_mode_enabled() (in module config) provider_slug_for() (in module scripts.ai_assistant.keystore) prune_dictionary() (in module scripts.extraction.cleanup_propagation) prune_pdfs() (in module scripts.extraction.cleanup_propagation) pseudo_id() (in module scripts.security.phi_scrub) published bundle put() (scripts.ai_assistant.tool_cache.ToolCache method)

R

raw study files reason (scripts.ai_assistant.ui.model_policy.ModelGateResult attribute) (scripts.lint_doc_freshness.Finding attribute) redact_phi_in_text() (in module scripts.ai_assistant.phi_safe) refusal_message (scripts.ai_assistant.phi_safe.UserPromptGuardResult attribute) remove_within_file_duplicates() (in module scripts.extraction.dedup) render() (scripts.lint_doc_freshness.Finding method) render_setup_page() (in module scripts.ai_assistant.ui.wizard) render_thread() (in module scripts.ai_assistant.ui.chat) RePORTError (class in scripts.utils.errors) reset_agent() (in module scripts.ai_assistant.agent_graph) reset_logging() (in module scripts.utils.logging_system) resolve_concept() (scripts.ai_assistant.study_knowledge.StudyKnowledge method)

resolve_snapshot_name() (in module scripts.utils.snapshots) resolve_staging_root() (in module scripts.utils.secure_staging) restore_snapshot() (in module scripts.utils.snapshots) ResultInterpreter (class in scripts.ai_assistant.analytical_engine) run() (scripts.ai_assistant.analytical_engine.DescriptiveAnalyzer method) (scripts.ai_assistant.analytical_engine.InteractionAnalyzer method) (scripts.ai_assistant.analytical_engine.MultivariateAnalyzer method) (scripts.ai_assistant.analytical_engine.UnivariateAnalyzer method) run_full_analysis() (in module scripts.ai_assistant.analytical_engine) run_pipeline() (in module scripts.ai_assistant.ui.wizard) run_propagation() (in module scripts.extraction.cleanup_propagation) run_repl() (in module scripts.ai_assistant.cli) run_scrub() (in module scripts.security.phi_scrub) run_step() (in module main)

S

SandboxRejectionError sanitise_traceback() (in module scripts.ai_assistant.phi_safe) sanitise_untrusted_snippet() (in module scripts.ai_assistant.phi_safe) save_step_manifest() (in module scripts.utils.step_cache) scoped_umask() (in module scripts.utils.secure_staging) scripts.ai_assistant.agent_graph module scripts.ai_assistant.agent_prompts module scripts.ai_assistant.agent_tools module scripts.ai_assistant.analytical_engine module scripts.ai_assistant.cli module scripts.ai_assistant.file_access module scripts.ai_assistant.keystore module scripts.ai_assistant.phi_safe module scripts.ai_assistant.sandbox.limits module scripts.ai_assistant.sandbox.replicate module scripts.ai_assistant.sandbox.runner module scripts.ai_assistant.study_knowledge module scripts.ai_assistant.tool_cache module scripts.ai_assistant.ui.chat module scripts.ai_assistant.ui.conversations module scripts.ai_assistant.ui.model_policy module scripts.ai_assistant.ui.providers module scripts.ai_assistant.ui.shell module scripts.ai_assistant.ui.state module scripts.ai_assistant.ui.streaming module scripts.ai_assistant.ui.wizard module scripts.ai_assistant.web_ui module scripts.artifact_versions module scripts.extraction.build_variables_reference module scripts.extraction.cleanup_propagation module scripts.extraction.dataset_cleanup module scripts.extraction.dataset_pipeline module scripts.extraction.dedup module scripts.extraction.extract_pdf_data module scripts.extraction.io.clinical_dates module scripts.extraction.io.file_discovery module scripts.extraction.io.file_io module scripts.extraction.io.jsonl_reader module

scripts.extraction.load_dictionary module scripts.extraction.pdf_pipeline module scripts.lint_doc_freshness module scripts.security.kanon_gate module scripts.security.phi_allowlist module scripts.security.phi_gate module scripts.security.phi_patterns module scripts.security.phi_scrub module scripts.security.secure_env module scripts.utils.errors module scripts.utils.integrity module scripts.utils.lineage module scripts.utils.llm_capabilities module scripts.utils.log_hygiene module scripts.utils.logging_system module scripts.utils.secure_staging module scripts.utils.snapshots module scripts.utils.step_cache module scripts.utils.telemetry module scrub secure_remove_tree() (in module scripts.utils.secure_staging) set() (scripts.ai_assistant.keystore.KeyStore method) setup_logger() (in module scripts.utils.logging_system) setup_logging() (in module scripts.utils.logging_system) shift_date() (in module scripts.security.phi_scrub) sidebar() (in module scripts.ai_assistant.ui.shell) small_cell_threshold (scripts.security.phi_scrub.PHIScrubConfig attribute) smallest_class_size (scripts.security.kanon_gate.KAnonResult attribute) smallest_diversity (scripts.security.kanon_gate.LDiversityResult attribute) snapshot baseline snapshot_exists() (in module scripts.utils.snapshots) snapshot_used (scripts.extraction.pdf_pipeline.ExtractionResult attribute) snapshot_versions() (in module scripts.artifact_versions) SnapshotError stage (scripts.utils.errors.RePORTError attribute) static (scripts.ai_assistant.analytical_engine.PlotArtifacts attribute) stats (scripts.ai_assistant.tool_cache.ToolCache property) step() (scripts.utils.logging_system.VerboseLogger method) step_progress() (in module scripts.utils.logging_system) stream_query() (in module scripts.ai_assistant.agent_graph) strict_study_detection_enabled() (in module config) study name study_description (scripts.ai_assistant.study_knowledge.StudyKnowledge property) study_name (scripts.ai_assistant.study_knowledge.StudyKnowledge property) StudyKnowledge (class in scripts.ai_assistant.study_knowledge) subject_id_fields (scripts.security.phi_scrub.PHIScrubConfig attribute) SUBJECT_ID_PATTERNS (in module scripts.security.phi_patterns) success() (in module scripts.utils.logging_system) SUPPORTED_TABULAR_EXTENSIONS (in module scripts.extraction.io.file_discovery) suppress_small_cell() (in module scripts.security.phi_scrub) suppress_small_cell_patterns (scripts.security.phi_scrub.PHIScrubConfig attribute) suppress_small_cells() (in module scripts.security.kanon_gate)

T

TelemetryLogger (class in scripts.utils.telemetry) threshold (scripts.security.phi_scrub.CapRule attribute) tier (scripts.extraction.pdf_pipeline.ExtractionResult attribute) timestamp (scripts.utils.errors.RePORTError attribute) timing() (scripts.utils.logging_system.VerboseLogger method) to_dict() (scripts.utils.errors.RePORTError method)

to_json() (scripts.utils.errors.RePORTError method) ToolCache (class in scripts.ai_assistant.tool_cache) topbar() (in module scripts.ai_assistant.ui.shell) total_records (scripts.extraction.dataset_pipeline.ExtractionResult attribute) traceback (scripts.utils.errors.RePORTError attribute) trio bundle

U

univariate (scripts.ai_assistant.analytical_engine.AnalysisResult attribute) UnivariateAnalyzer (class in scripts.ai_assistant.analytical_engine)

use_existing_study() (in module scripts.ai_assistant.ui.wizard) UserPromptGuardResult (class in scripts.ai_assistant.phi_safe)

V

validate_agent_read() (in module scripts.ai_assistant.file_access) validate_agent_write() (in module scripts.ai_assistant.file_access) validate_config() (in module config) validate_depends_on() (in module scripts.extraction.extract_pdf_data) validate_paths() (in module scripts.security.secure_env) validate_sandbox_write() (in module scripts.ai_assistant.file_access)

validate_versions() (in module scripts.artifact_versions) value_looks_like_date() (in module scripts.extraction.io.clinical_dates) variable_richness_score() (in module scripts.extraction.dedup) VerboseLogger (class in scripts.utils.logging_system) VERSIONS (in module scripts.artifact_versions) violating_classes (scripts.security.kanon_gate.LDiversityResult attribute) violating_keys (scripts.security.kanon_gate.KAnonResult attribute)

W

WARN_PATTERNS (in module scripts.security.phi_patterns) warning() (in module scripts.utils.logging_system)

warnings (scripts.extraction.pdf_pipeline.ExtractionResult attribute) wrap() (in module scripts.utils.errors)

Y

yaml_get() (in module config)

Z

ZoneViolationError